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Hepadnaviridae are double-stranded DNA viruses that infect some species of birds and mammals . This includes humans , where hepatitis B viruses ( HBVs ) are prevalent pathogens in considerable parts of the global population . Recently , endogenized sequences of HBVs ( eHBVs ) have been discovered in bird genomes where ...	Viruses are not known to leave physical fossil traces , which makes our understanding of their evolutionary prehistory crucially dependent on the detection of endogenous viruses . Ancient endogenous viruses , also known as paleoviruses , are relics of viral genomes or fragments thereof that once infiltrated their host'...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "cancer", "genetics", "genome", "evolution", "evolutionary", "biology", "microbiology", "oncogenes", "hepatitis", "b", "virus", "liver", "diseases", "infectious", "hepatitis", "hepatitis", "gastroenterology", "and", "hepatology", ...	2014	Early Mesozoic Coexistence of Amniotes and Hepadnaviridae
The murine parasite Heligmosomoides polygyrus is a convenient experimental model to study immune responses and pathology associated with gastrointestinal nematode infections . The excretory-secretory products ( ESP ) produced by this parasite have potent immunomodulatory activity , but the protein ( s ) responsible has...	Gastrointestinal ( GI ) nematode infections are major causes of human and animal disease . Much of their morbidity is associated with establishment of chronic infections in the host , reflecting the deployment of mechanisms to evade and modulate the immune response . The molecules responsible for these activities are p...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biotechnology", "medicine", "biochemistry", "infectious", "diseases", "model", "organisms", "global", "health", "immunology", "biology", "proteomics" ]	2011	Proteomic Analysis of Excretory-Secretory Products of Heligmosomoides polygyrus Assessed with Next-Generation Sequencing Transcriptomic Information
The proteins responsible for the key molecular events leading to the structural changes between the developmental stages of Echinococcus granulosus remain unknown . In this work , azidohomoalanine ( AHA ) -specific labeling was used to identify proteins expressed by E . granulosus protoscoleces ( PSCs ) upon the induct...	In the life cycle of the parasite Echinococcus granulosus , hydatid cysts produce the pre-adult form , which has the ability to either differentiate into an adult worm ( strobilation ) or dedifferentiate into a secondary hydatid cyst . We used different protein tags that allowed for the visualization and purification o...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Identification of Newly Synthesized Proteins by Echinococcus granulosus Protoscoleces upon Induction of Strobilation
Recent studies have demonstrated that the topography of thalamocortical ( TC ) axon projections is initiated before they reach the cortex , in the ventral telencephalon ( VTel ) . However , at this point , the molecular mechanisms patterning the topography of TC projections in the VTel remains poorly understood . Here ...	The functional properties of each structure in the central nervous system are critically dependent on the precision of neuronal connectivity . The cerebral cortex in particular is a highly organized structure divided into many distinct cortical areas underlying important sensory , motor , and cognitive functions in the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience" ]	2008	Topography of Thalamic Projections Requires Attractive and Repulsive Functions of Netrin-1 in the Ventral Telencephalon
Over the last decades , researchers have characterized a set of “clock genes” that drive daily rhythms in physiology and behavior . This arduous work has yielded results with far-reaching consequences in metabolic , psychiatric , and neoplastic disorders . Recent attempts to expand our understanding of circadian regula...	Daily rhythms are ever-present in the living world , driving the sleep–wake cycle and many other physiological changes . In the last two decades , several labs have identified “clock genes” that interact to generate underlying molecular oscillations . However , many aspects of circadian molecular physiology remain unex...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "molecular", "neuroscience", "behavioral", "neuroscience", "genomics", "gene", "expression", "genetics", "gene", "regulation", "biology", "and", "life", "sciences", "molecular", "genetics", "computational", "biology", "neuroscience" ]	2014	Machine Learning Helps Identify CHRONO as a Circadian Clock Component
Light is an important environmental cue that affects physiology and development of Neurospora crassa . The light-sensing transcription factor ( TF ) WCC , which consists of the GATA-family TFs WC1 and WC2 , is required for light-dependent transcription . SUB1 , another GATA-family TF , is not a photoreceptor but has al...	In this study we have investigated the roles of the Neurospora transcription factors ( TFs ) WCC and SUB1 in light-activation of transcription . In principle TFs could exert identical functions for transcriptional activation and the extent of transcription will be determined by the sum of activity of the TFs . In this ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Combinatorial Control of Light Induced Chromatin Remodeling and Gene Activation in Neurospora
Mitochondria form a dynamic tubular reticulum within eukaryotic cells . Currently , quantitative understanding of its morphological characteristics is largely absent , despite major progress in deciphering the molecular fission and fusion machineries shaping its structure . Here we address the principles of formation a...	Mitochondria control energy production , initiation of cell death and several other critical cellular processes . Most often , they form a constantly reshaping tubular reticulum spread over the cytosol . Despite extensive knowledge of mitochondrial physiology , accurate description of their large-scale architecture is ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "cellular", "structures", "subcellular", "organelles", "cellular", "stress", "responses", "synthetic", "biology", "biophysics", "simulations", "theoretical", "biology", "biology", "biophysics", "systems", "biology", "cell", "biology", "biophysic", "al", ...	2012	Emergence of the Mitochondrial Reticulum from Fission and Fusion Dynamics
Soil-transmitted helminths ( STH ) – a class of parasites that affect billions of people – can be mitigated using mass drug administration , though reinfection following treatment occurs within a few months . Improvements to water , sanitation and hygiene ( WASH ) likely provide sustained benefit , but few rigorous stu...	Soil-transmitted helminths ( STH ) are pervasive enteric parasites that lead to cognitive , nutritional and educational sequelae . Mass drug administration is employed to reduce morbidity , but reinfection occurs rapidly in the absence of changes to other environmental conditions , such as improvements to water , sanit...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "infectious", "diseases", "helminth", "infections", "environmental", "health", "medicine", "and", "health", "sciences", "environmental", "epidemiology", "epidemiology", "global", "health", "neglected", "tropical", "diseases", "ho...	2014	Exploring the Relationship between Access to Water, Sanitation and Hygiene and Soil-Transmitted Helminth Infection: A Demonstration of Two Recursive Partitioning Tools
Group B Streptococcus ( GBS ) is a common agent of bacterial sepsis and meningitis in newborns . The GBS surface capsule contains sialic acids ( Sia ) that engage Sia-binding immunoglobulin-like lectins ( Siglecs ) on leukocytes . Here we use mice lacking Siglec-E , an inhibitory Siglec of myelomonocytic cells , to stu...	The bacterium Group B Streptococcus ( GBS ) causes serious infections such as meningitis in human newborn babies . The surface of GBS is coated with a capsule made of sugar molecules . Prominent among these is sialic acid ( Sia ) , a human-like sugar that interacts with protein receptors called Siglecs on the surface o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2014	Group B Streptococcus Engages an Inhibitory Siglec through Sialic Acid Mimicry to Blunt Innate Immune and Inflammatory Responses In Vivo
Regeneration in adult chordates is confined to a few model cases and terminates in restoration of restricted tissues and organs . Here , we study the unique phenomenon of whole body regeneration ( WBR ) in the colonial urochordate Botrylloides leachi in which an entire adult zooid is restored from a miniscule blood ves...	Whole body regeneration ( WBR ) in Animalia is rare , confined to morphologically less complex taxa such as sponges , cnidarians , and flatworms . In the chordate phylum , only colonial ascidians ( invertebrate chordates also known as sea squirts ) have the documented ability to wholly regenerate . Once separated from ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "developmental", "biology", "cell", "biology", "vertebrates", "evolutionary", "biology" ]	2007	Systemic Bud Induction and Retinoic Acid Signaling Underlie Whole Body Regeneration in the Urochordate Botrylloides leachi
Clincialtrials . gov , NCT01119521 Almost a quarter of the global population is infected with Mycobacterium tuberculosis ( M . tb ) [1] , placing millions at risk for tuberculosis ( TB ) disease . Five to 15% of infected individuals progress to active TB disease within their lifetimes . A spectrum of clinical disease s...	To define biological mechanisms that underlie progression of Mycobacterium tuberculosis infection to active tuberculosis , we followed M . tuberculosis-infected adolescents longitudinally . Those who ultimately developed tuberculosis disease ( “progressors” ) were compared with matched controls , who remained healthy ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "inflammatory", "diseases", "medicine", "and", "health", "sciences", "body", "fluids", "immune", "cells", "immunology", "tropical", "diseases", "bacterial", "diseases", "infectious", "diseases", "white", "blood", "cells", "animal", "cells", "tubercul...	2017	Sequential inflammatory processes define human progression from M. tuberculosis infection to tuberculosis disease
Insecticide resistance ( IR ) can undermine efforts to control vectors of public health importance . Aedes aegypti is the main vector of resurging diseases in the Americas such as yellow fever and dengue , and recently emerging chikungunya and Zika fever , which have caused unprecedented epidemics in the region . Vecto...	Mosquito control is the primary method of managing the spread of many diseases transmitted by the yellow fever mosquito ( Aedes aegypti ) . Throughout much of Latin America the transmission of diseases like dengue fever and Zika fever pose a serious risk to public health . The rise of insecticide resistance ( IR ) is a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "invertebrates", "medicine", "and", "health", "sciences", "ecuador", "chemical", "compounds", "variant", "genotypes", "geographical", "locations", "malathion", "organic", "compounds", "animals", "genetic", "mapping", "organophosphates", "population", "bi...	2019	Seasonal and geographic variation in insecticide resistance in Aedes aegypti in southern Ecuador
Axons require a constant supply of the labile axon survival factor Nmnat2 from their cell bodies to avoid spontaneous axon degeneration . Here we investigate the mechanism of fast axonal transport of Nmnat2 and its site of action for axon maintenance . Using dual-colour live-cell imaging of axonal transport in SCG prim...	Neurons are polarized cells that rely on bidirectional transport to deliver thousands of cargos between the cell body and the most distal ends of their axons . One cargo that is of particular importance is the NAD-synthesising enzyme Nmnat2 . This surprisingly unstable protein is produced in the cell body and its const...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "neuroscience", "neurobiology", "of", "disease", "and", "regeneration", "cell", "biology", "membranes", "and", "sorting", "biology", "molecular", "cell", "biology", "neuroscience" ]	2013	Subcellular Localization Determines the Stability and Axon Protective Capacity of Axon Survival Factor Nmnat2
Ocular herpes simplex virus infection can cause a blinding CD4+ T cell orchestrated immuno-inflammatory lesion in the cornea called Stromal Keratitis ( SK ) . A key to controlling the severity of SK lesions is to suppress the activity of T cells that orchestrate lesions and enhance the representation of regulatory cell...	This report describes a novel approach to control a blinding immuno-inflammatory reaction in the eye caused by herpes simplex virus . We showed that a single administration of TCDD , a stable agonist of the aryl hydrocarbon receptor , significantly reduced the severity of herpes keratitis lesions . The outcome of the t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunopathology", "medicine", "infectious", "diseases", "inflammation", "immunity", "virology", "immunology", "biology", "microbiology", "viral", "diseases", "immunomodulation", "immune", "response" ]	2011	Controlling Viral Immuno-Inflammatory Lesions by Modulating Aryl Hydrocarbon Receptor Signaling
The insulin/IGF-1 signaling pathway plays a critical role in stress resistance and longevity , but the mechanisms are not fully characterized . To identify genes that mediate stress resistance , we screened for C . elegans mutants that can tolerate high levels of dietary zinc . We identified natc-1 , which encodes an e...	What are the mechanisms used by animals to cope with stressful environments that inflict damage or restrict essential processes such as growth , development , and reproduction ? One strategy is changes in physiology that increase stress resistance , and an extreme version of this strategy is diapause , an alternative d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "animal", "genetics", "caenorhabditis", "gene", "regulation", "animals", "dna", "transcription", "gene", "function", "animal", "models", "mutation", "caenorhabditis", "elegans", "model", "organisms", "molecular", "genetics", "research", "and", "analysis",...	2014	The DAF-16 FOXO Transcription Factor Regulates natc-1 to Modulate Stress Resistance in Caenorhabditis elegans, Linking Insulin/IGF-1 Signaling to Protein N-Terminal Acetylation
Phage-encoded serine integrases mediate directionally regulated site-specific recombination between short attP and attB DNA sites without host factor requirements . These features make them attractive for genome engineering and synthetic genetics , although the basis for DNA site selection is poorly understood . Here w...	Site-specific recombinases catalyze recombination between two specific DNA sites to generate the products of recombination . The Integrase encoded by mycobacteriophage Bxb1 is a member of the serine-recombinase family and catalyzes strand exchange between attP and attB , the attachment sites for the phage and bacterial...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "genetic", "mutation", "mutation", "types", "nucleic", "acids", "genetics", "biology" ]	2013	Attachment Site Selection and Identity in Bxb1 Serine Integrase-Mediated Site-Specific Recombination
Genome-scale metabolic models have proven useful for answering fundamental questions about metabolic capabilities of a variety of microorganisms , as well as informing their metabolic engineering . However , only a few models are available for oxygenic photosynthetic microorganisms , particularly in cyanobacteria in wh...	Cyanobacteria have been promoted as platforms for biofuel production due to their useful physiological properties such as photosynthesis , relatively rapid growth rates , ability to accumulate high amounts of intracellular compounds and tolerance to extreme environments . However , development of a computational model ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "biology", "computational", "biology" ]	2012	Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142
We investigate spatiotemporal dynamics of human interphase chromosomes by employing a heteropolymer model that incorporates the information of human chromosomes inferred from Hi-C data . Despite considerable heterogeneities in the chromosome structures generated from our model , chromatins are organized into crumpled g...	Chromosomes are giant chain molecules made of hundreds of megabase-long DNA intercalated with proteins . Structure and dynamics of interphase chromatin in space and time hold the key to understanding the cell type-dependent gene regulation . In this study , we establish that the crumpled and space-filling ( SF ) organi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "relaxation", "time", "chromosome", "structure", "and", "function", "monomers", "chromosome", "mapping", "materials", "science", "epigenetics", "molecular", "biology", "techniques", "macromolecules", "chromatin", "research", "and", "analysis", "methods", "polymers", "poly...	2018	Chain organization of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci
In mammalian cells , AU-rich elements ( AREs ) are well known regulatory sequences located in the 3′ untranslated region ( UTR ) of many short-lived mRNAs . AREs cause mRNAs to be degraded rapidly and thereby suppress gene expression at the posttranscriptional level . Based on the number of AUUUA pentamers , their prox...	Many genes are regulated at the posttranscriptional level by factors that influence the stability of the messenger RNA . In mammals , AU-rich elements are known to cause rapid degradation of messenger RNAs and thereby suppress gene expression . In order to identify such elements on a genome-wide scale , we developed a ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "gene", "regulation", "rna", "stability", "eukaryotic", "cells", "genome", "analysis", "tools", "molecular", "genetics", "gene", "expression", "biology", "molecular", "biology", "transcriptomes", "biochemistry", "rna", "cell", "biology", "nucleic", "acids", "genetic", ...	2012	Genome-Wide Assessment of AU-Rich Elements by the AREScore Algorithm
Francisella tularensis is a potent mammalian pathogen well adapted to intracellular habitats , whereas F . novicida and F . philomiragia are less virulent in mammals and appear to have less specialized lifecycles . We explored adaptations within the genus that may be linked to increased host association , as follows . ...	The intracellular bacterium Francisella tularensis causes the disease tularemia in various mammals , including humans , and is highly infectious ( so infectious that highly virulent forms of the pathogen were developed as biological aerosol weapons during the Cold War ) . Little is known about where F . tularensis resi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "public", "health", "and", "epidemiology/infectious", "diseases", "microbiology/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/population", "genetics" ]	2009	Molecular Evolutionary Consequences of Niche Restriction in Francisella tularensis, a Facultative Intracellular Pathogen
The gene mutated in Bloom's syndrome , BLM , is important in the repair of damaged replication forks , and it has both pro- and anti-recombinogenic roles in homologous recombination ( HR ) . At damaged forks , BLM interacts with RAD51 recombinase , the essential enzyme in HR that catalyzes homology-dependent strand inv...	Replication is the process in which cellular DNA is duplicated . DNA damage incurred during replication is detrimental to the cell . Homologous recombination , in which DNA sequences are exchanged between two similar or identical strands of DNA , plays a pivotal role in correcting replication processes that have failed...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/replication", "and", "repair", "genetics", "and", "genomics/cancer", "genetics", "cell", "biology/cellular", "death", "and", "stress", "responses" ]	2009	SUMO Modification Regulates BLM and RAD51 Interaction at Damaged Replication Forks
Reverse genetics in the mosquito Anopheles gambiae by RNAi mediated gene silencing has led in recent years to an advanced understanding of the mosquito immune response against infections with bacteria and malaria parasites . We developed RNAi screens in An . gambiae hemocyte-like cells using a library of double-strande...	The mosquito immune system relies on innate humoral and cellular reactions to fight infections , including those by malaria parasites that must pass through mosquitoes before they can infect humans . Therefore , a detailed molecular understanding of these reactions could assist the design of new ways to control the spr...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "complement", "system", "immune", "activation", "immunology", "microbiology", "host-pathogen", "interaction", "parasitology", "gene", "function", "anopheles", "immune", "defense", "gene", "expression", "biology", "immune", "system", "cell", "biology", "...	2013	Comprehensive Genetic Dissection of the Hemocyte Immune Response in the Malaria Mosquito Anopheles gambiae
The dissacharide trehalose is an important intracellular osmoprotectant and the OtsA/B pathway is the principal pathway for trehalose biosynthesis in a wide range of bacterial species . Scaffolding proteins and other cytoskeletal elements play an essential role in morphogenetic processes in bacteria . Here we describe ...	For free living bacteria , little is known about how environmental cues are perceived and translated into changes in cell morphology . Here we describe how a biosynthetic enzyme involved in synthesis of an important intracellular osmoprotectant doubles as an osmotic stress sensing morphogenetic protein . This protein i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fluorescence", "imaging", "urea", "chemical", "compounds", "disaccharides", "arthrobacter", "cell", "cycle", "and", "cell", "division", "cell", "processes", "carbohydrates", "organic", "compounds", "materials", "science", "macromolecules", "bacteria", "materials", "by", ...	2017	A trehalose biosynthetic enzyme doubles as an osmotic stress sensor to regulate bacterial morphogenesis
Severe fever with thrombocytopenia syndrome ( SFTS ) is a tick-borne infectious disease with a high case fatality rate , and is caused by the SFTS virus ( SFTSV ) . SFTS is endemic to China , South Korea , and Japan . The viral RNA level in sera of patients with SFTS is known to be strongly associated with outcomes . V...	Severe fever with thrombocytopenia syndrome ( SFTS ) is a tick-borne emerging infectious disease caused by a novel bunyavirus , SFTS virus ( SFTSV ) . Since first discovered in China in 2011 , SFTSV has been detected from SFTS patients and ticks with expanding geographic ranges from China to Japan and South Korea . The...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "rift", "valley", "fever", "virus", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "viruses", "rna", "viruses", "signs", "and", ...	2016	Severe Fever with Thrombocytopenia Syndrome Virus Antigen Detection Using Monoclonal Antibodies to the Nucleocapsid Protein
Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language . For native South Americans , however , such evidence has been lacking so far . Therefore , we examined the relationship between Y-ch...	In the largest population genetic study of South Americans to date , we analyzed the Y-chromosomal makeup of more than 1 , 000 male natives . We found that the male-specific genetic variation of Native Americans lacks any clear structure that could sensibly be related to their geographic and/or linguistic relationships...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetic", "mutation", "genetics", "molecular", "genetics", "population", "genetics", "biology", "population", "biology" ]	2013	Continent-Wide Decoupling of Y-Chromosomal Genetic Variation from Language and Geography in Native South Americans
Recent advances in the identification of susceptibility genes and environmental exposures provide broad support for a post-infectious autoimmune basis for narcolepsy/hypocretin ( orexin ) deficiency . We genotyped loci associated with other autoimmune and inflammatory diseases in 1 , 886 individuals with hypocretin-def...	While there is now broad consensus that narcolepsy-hypocretin deficiency results from a highly specific autoimmune attack on hypocretin cells , little is understood regarding the initiation and progression of the underlying autoimmune process . We have taken advantage of a unique high-density genotyping platform ( the ...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "genetics", "immunology", "biology", "genetics", "and", "genomics" ]	2013	ImmunoChip Study Implicates Antigen Presentation to T Cells in Narcolepsy
The serotonin 2C receptor ( 5-HT2CR ) –a key regulator of diverse neurological processes–exhibits functional variability derived from editing of its pre-mRNA by site-specific adenosine deamination ( A-to-I pre-mRNA editing ) in five distinct sites . Here we describe a statistical technique that was developed for analys...	The serotonin receptor 2C is a key regulator of diverse neurological processes that affect feeding behavior , sleep , sexual behavior , anxiety and depression . The function of the receptor itself is regulated via so-called pre-mRNA editing , i . e . site-specific adenosine deamination in five distinct sites . The grea...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "molecular", "neuroscience", "biology", "neuroscience" ]	2012	Dependencies among Editing Sites in Serotonin 2C Receptor mRNA
The molecular clock and its phylogenetic applications to genomic data have changed how we study and understand one of the major human pathogens , Mycobacterium tuberculosis ( MTB ) , the etiologic agent of tuberculosis . Genome sequences of MTB strains sampled at different times are increasingly used to infer when a pa...	One of the major recent advancements in evolutionary biology is the development of statistical methods to infer the past evolutionary history of species and populations with genomic data . In the last five years , many researchers have used the molecular clock ( i . e . the observation that genomes accumulate mutations...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Methods" ]	[ "taxonomy", "medicine", "and", "health", "sciences", "tropical", "diseases", "bacterial", "diseases", "phylogenetics", "data", "management", "extensively", "drug-resistant", "tuberculosis", "phylogenetic", "analysis", "population", "biology", "bacteria", "infectious", "dise...	2019	The molecular clock of Mycobacterium tuberculosis
Epstein-Barr virus , a B-lymphotropic herpesvirus , is the cause of infectious mononucleosis , has strong aetiologic links with several malignancies and has been implicated in certain autoimmune diseases . Efforts to develop a prophylactic vaccine to prevent or reduce EBV-associated disease have , to date , focused on ...	Epstein-Barr virus infects the vast majority of the world’s population; in most individuals both primary infection and long-term virus carriage are asymptomatic . However , EBV is the major cause of glandular fever , is associated with multiple cancers and is implicated in various autoimmune conditions; thus there is a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "enzyme-linked", "immunoassays", "immunology", "microbiology", "cloning", "cytotoxic", "t", "cells", "molecular", "biology", "techniques", "immunologic", "techniques", "research", "and", "anal...	2016	Early T Cell Recognition of B Cells following Epstein-Barr Virus Infection: Identifying Potential Targets for Prophylactic Vaccination
Diet may be modified seasonally or by biogeographic , demographic or cultural shifts . It can differentially influence mitochondrial bioenergetics , retrograde signalling to the nuclear genome , and anterograde signalling to mitochondria . All these interactions have the potential to alter the frequencies of mtDNA hapl...	The detection and quantitation of mtDNA polymorphisms in populations and across whole habitats continues to be used as a central investigatory tool in evolutionary genetics . But , the approach is laden with assumptions about selection that are rarely examined . We present a series of studies that traverse the genotype...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "mitochondrial", "dna", "computational", "biology", "diet", "animals", "invertebrate", "genomics", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "nutrition", "e...	2018	Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness
Alphaviruses , such as chikungunya virus , and flaviviruses , such as dengue virus , are ( re ) -emerging arboviruses that are endemic in tropical environments . In Africa , arbovirus infections are often undiagnosed and unreported , with febrile illnesses often assumed to be malaria . This cross-sectional study aimed ...	There are many examples of recent emergence of mosquito-borne viruses , such as chikungunya virus outbreaks throughout the Caribbean in 2013 , Zika virus outbreaks throughout Southern and Central America in 2015 , and yellow fever virus in Brazil in 2017 . Each outbreak draws attention to the limits associated with pre...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "pathogens", "geographical", "locations", "microbiology", "alphaviruses", "viruses", "chikungunya", "virus", "rna", "viruses", "animal", "behavior", "flooding", "zoology"...	2017	Serological and spatial analysis of alphavirus and flavivirus prevalence and risk factors in a rural community in western Kenya
Several protein structure classification schemes exist that partition the protein universe into structural units called folds . Yet these schemes do not discuss how these units sit relative to each other in a global structure space . In this paper we construct networks that describe such global relationships between fo...	Folds are considered to be the structural units which make up the protein universe . Structural classification schemes focus on the assignment and organisation of protein domains into folds . However , they do not suggest how different folds might relate to one another in a global way . We introduce the concept of brid...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Structural Bridges through Fold Space
Molecular epidemiology at the community level has an important guiding role in zoonotic disease control programmes where genetic markers are suitably variable to unravel the dynamics of local transmission . We evaluated the molecular diversity of Trypanosoma cruzi , the etiological agent of Chagas disease , in southern...	Trypanosoma cruzi is transmitted by blood sucking insects known as triatomines . This protozoan parasite commonly infects wild and domestic mammals in South and Central America . However , triatomines also transmit the parasite to people , and human infection with T . cruzi is known as Chagas disease , a major public h...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/neglected", "tropical", "diseases" ]	2010	Sex, Subdivision, and Domestic Dispersal of Trypanosoma cruzi Lineage I in Southern Ecuador
Programs for control of soil-transmitted helminth ( STH ) infections are increasingly evaluating national mass drug administration ( MDA ) interventions . However , “unprogrammed deworming” ( receipt of deworming drugs outside of nationally-run STH control programs ) occurs frequently . Failure to account for these act...	In countries with endemic soil-transmitted helminth infections , deworming medications are widely available from multiple sources , including over the counter . However , in many countries , national programs already provide deworming medications in mass drug administrations to primary school students , as part of Worl...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Unprogrammed Deworming in the Kibera Slum, Nairobi: Implications for Control of Soil-Transmitted Helminthiases
Zoonotic Echinococcus spp . cestodes ( E . canadensis and E . multilocularis ) infect domestic animals , wildlife , and people in regions of Canada and the USA . We recovered and quantified Echinococcus spp . cestodes from 22 of 307 intestinal tracts of wild canids ( 23 wolves , 100 coyotes , 184 red and arctic foxes )...	Echinococcosis is a zoonosis caused by ingestion of tapeworm eggs in feces of wild or domestic canids ( e . g . foxes , wolves , coyotes , and dogs ) . In North America , the number of new human echinococcosis cases reported annually is low; however , recent reports of these parasites in unusual presentations , in new ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "united", "states", "invertebrates", "canada", "cestodes", "helminths", "geographical", "locations", "wolves", "vertebrates", "animals", "mammals", "echinococcus", "north", "america", "research", "and", "analysis", "methods", "sequence", "analysis", "foxes", "bioinformati...	2018	Echinococcus in wild canids in Québec (Canada) and Maine (USA)
Leishmaniasis remains a worldwide public health problem . The limited therapeutic options , drug toxicity and reports of resistance , reinforce the need for the development of new treatment options . Previously , we showed that 17- ( allylamino ) -17-demethoxygeldanamycin ( 17-AAG ) , a Heat Shock Protein 90 ( HSP90 ) ...	Antimony-containing compounds are the main drugs used to treat leishmaniasis but the severe associated side effects pose the need for alternative chemotherapeutic options . Herein , we evaluated the ability of 17-AAG ( a Heat Shock Protein 90 inhibitor ) to kill Leishmania ( Viannia ) braziliensis parasites , a species...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "leishmaniasis", "neglected", "tropical", "diseases", "biology", "and", "life", "sciences", "tropical", "diseases", "protozoan", "infections", "parasitic", "diseases",...	2014	Chemotherapeutic Potential of 17-AAG against Cutaneous Leishmaniasis Caused by Leishmania (Viannia) braziliensis
Identification of common mechanistic principles that shed light on the action of the many chemically diverse toxicants to which we are exposed is of central importance in understanding how toxicants disrupt normal cellular function and in developing more effective means of protecting against such effects . Of particula...	Discovering general principles underlying the effects of toxicant exposure on biological systems is one of the central challenges of toxicological research . We have discovered a previously unrecognized regulatory pathway on which chemically diverse toxicants converge , at environmentally relevant exposure levels , to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "public", "health", "and", "epidemiology", "cell", "biology", "in", "vitro", "mus", "(mouse)", "neuroscience", "molecular", "biology" ]	2007	Chemically Diverse Toxicants Converge on Fyn and c-Cbl to Disrupt Precursor Cell Function
Hepatitis C virus ( HCV ) is a single-stranded RNA virus that replicates on endoplasmic reticulum-derived membranes . HCV particle assembly is dependent on the association of core protein with cellular lipid droplets ( LDs ) . However , it remains uncertain whether HCV assembly occurs at the LD membrane itself or at cl...	Hepatitis C virus ( HCV ) chronically infects about 170 million people worldwide and can ultimately lead to liver failure and liver cancer . HCV , like other RNA viruses , exploits cellular proteins and membranes to promote their own replication and virion production . In particular , HCV replication occurs at membrane...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "hepatitis", "c", "medicine", "infectious", "diseases", "hepatitis", "host", "cells", "rna", "viruses", "viral", "transmission", "and", "infection", "viral", "classification", "virology", "host-pathogen", "interaction", "biology", "microbiology", "viral", "packaging", "...	2013	Rab18 Binds to Hepatitis C Virus NS5A and Promotes Interaction between Sites of Viral Replication and Lipid Droplets
Chagas disease remains one of the most neglected diseases in the world despite being the most important parasitic disease in Latin America . The characteristic chronic manifestation of chagasic cardiomyopathy is the region’s leading cause of heart-related illness , causing significant mortality and morbidity . Due to t...	Trypanosoma cruzi is a protozoan parasite belonging to the Kinetoplastida class responsible for Chagas disease , a neglected tropical illness that affects an estimated 6 to 8 million people in Latin America and some Southern regions of the USA , with another 25 million at risk of acquiring the disease and a death toll ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "alkaloids", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "enzymology", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "protozoan", "life", "cycles", "toxicology", "neuroscience", "dev...	2018	Inhibitors of Trypanosoma cruzi Sir2 related protein 1 as potential drugs against Chagas disease
Upstream events that trigger initiation of cell division , at a point called START in yeast , determine the overall rates of cell proliferation . The identity and complete sequence of those events remain unknown . Previous studies relied mainly on cell size changes to identify systematically genes required for the time...	What determines when cells begin a new round of cell division also dictates how fast cells multiply . Knowing which cellular pathways and how these pathways affect the machinery of cell division will allow modulations of cell proliferation . Baker's yeast is suited for genetic and biochemical studies of eukaryotic cell...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "model", "organisms", "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2012	A Systematic Analysis of Cell Cycle Regulators in Yeast Reveals That Most Factors Act Independently of Cell Size to Control Initiation of Division
Wastewater irrigation is associated with several benefits but can also lead to significant health risks . The health risk for contracting infections from Soil Transmitted Helminths ( STHs ) among farmers has mainly been assessed indirectly through measured quantities in the wastewater or on the crops alone and only on ...	Wastewater irrigation in agriculture is a common reality in many developing cities , linked to rapid urbanization . Approximately 50%-90% of urban dwellers in West Africa consume wastewater/ polluted surface water irrigated-vegetables within cities with 10% of the population involved in the practice . Viral , bacterial...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "agricultural", "irrigation", "medicine", "and", "health", "sciences", "helminths", "tropical", "diseases", "hookworms", "parasitic", "diseases", "animals", "seasons", "farms", "ascaris", "agricultural", "methods", "neglected", "tropical", "diseases", "ag...	2016	Contribution of Wastewater Irrigation to Soil Transmitted Helminths Infection among Vegetable Farmers in Kumasi, Ghana
The RFAM database defines families of ncRNAs by means of sequence similarities that are sufficient to establish homology . In some cases , such as microRNAs and box H/ACA snoRNAs , functional commonalities define classes of RNAs that are characterized by structural similarities , and typically consist of multiple RNA f...	For a long time , it was believed that the control of processes in living organisms is almost only performed by proteins . Only recently , scientists learned that a further class of molecules , namely special RNAs , plays an important role in cell control . In consequence , research on such RNAs enjoys increasing atten...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Supporting", "Information" ]	[ "ascidians", "(sea", "squirts)", "eukaryotes", "computational", "biology", "molecular", "biology", "animals" ]	2007	Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering
Elucidation of the biological role of linker histone ( H1 ) and heterochromatin protein 1 ( HP1 ) in mammals has been difficult owing to the existence of a least 11 distinct H1 and three HP1 subtypes in mice . Caenorhabditis elegans possesses two HP1 homologues ( HPL-1 and HPL-2 ) and eight H1 variants . Remarkably , o...	Linker histone ( H1 ) and heterochromatin protein 1 ( HP1 ) play central roles in the formation of higher-order chromatin structure and gene expression . Recent studies have shown a physical interaction between H1 and HP1; however , the biological role of histone H1 and HP1 is not well understood . Additionally , the f...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental", "biology", "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2012	Transcriptional Repression of Hox Genes by C. elegans HP1/HPL and H1/HIS-24
Mycobacterium tuberculosis ( Mtb ) , the causative agent of tuberculosis ( TB ) , infects one third of the world's population . Among these infections , clinical isolates belonging to the W-Beijing appear to be emerging , representing about 50% of Mtb isolates in East Asia , and about 13% of all Mtb isolates worldwide ...	Mycobacterium tuberculosis ( Mtb ) , the causative agent of tuberculosis ( TB ) , infects one third of the world's population . Among these infections , clinical isolates belonging to the W-Beijing are emerging , representing about 50% of Mtb isolates in East Asia , and about 13% of all Mtb isolates worldwide . In anim...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "bacterial", "diseases", "infectious", "diseases", "medicine", "and", "health", "sciences", "tuberculosis", "tropical", "diseases" ]	2014	Unexpected Role for IL-17 in Protective Immunity against Hypervirulent Mycobacterium tuberculosis HN878 Infection
Rickettsia ( R . ) helvetica is the most prevalent rickettsia found in Ixodes ricinus ticks in Germany . Several studies reported antibodies against R . helvetica up to 12 . 5% in humans investigated , however , fulminant clinical cases are rare indicating a rather low pathogenicity compared to other rickettsiae . We i...	The pathogenicity of Rickettsia helvetica has not been investigated in depth to date . In humans , seroprevalences up to 12 . 5% against R . helvetica have been demonstrated with forest workers being predisposed to infection . However , fulminant clinical cases are rare indicating a rather low pathogenicity compared to...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "nuclear", "staining", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "biological", "cultures", "microbiology", "light", "microscopy", "rickettsia", "eukaryotic", "cells", ...	2018	In vitro studies of Rickettsia-host cell interactions: Confocal laser scanning microscopy of Rickettsia helvetica-infected eukaryotic cell lines
Human cytomegalovirus ( CMV ) is a herpes virus with poorly understood transmission dynamics . Person-to-person transmission is thought to occur primarily through transfer of saliva or urine , but no quantitative estimates are available for the contribution of different infection routes . Using data from a large popula...	Human cytomegalovirus ( CMV ) is a herpes virus causing lifelong infection . In high-income countries , the probability of infection increases gradually with age such that at old age up to 100% of the population is infected . CMV is thought to be transmitted mainly by transfer of saliva or urine , but little quantitati...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "infectious", "disease", "epidemiology", "pathogens", "immunology", "microbiology", "cytomegalovirus", "infection", "viruses", "pr...	2017	Infectious reactivation of cytomegalovirus explaining age- and sex-specific patterns of seroprevalence
Mutagenic translesion DNA polymerase V ( UmuD′2C ) is induced as part of the DNA damage-induced SOS response in Escherichia coli , and is subjected to multiple levels of regulation . The UmuC subunit is sequestered on the cell membrane ( spatial regulation ) and enters the cytosol after forming a UmuD′2C complex , ~ 45...	Escherichia coli upregulates more than 40 genes as part of the DNA damage-induced SOS regulon , many of which are involved in DNA repair and cell division . However , three DNA polymerases , pols V , II , and IV , are also induced to rescue replication forks blocked at persisting template lesions . Pol V ( UmuD′2C ) , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical", "bonding", "nucleic", "acid", "synthesis", "condensed", "matter", "physics", "dna-binding", "proteins", "anisotropy", "fluorophotometry", "dna", "damage", "nucleoproteins", "polymerases", "materials", "science", "dna", "dna", "synthesis", "chemical", "synthesi...	2019	Conformational regulation of Escherichia coli DNA polymerase V by RecA and ATP
Despite the wide use of Caenorhabditis elegans as a model organism , the first virus naturally infecting this organism was not discovered until six years ago . The Orsay virus and its related nematode viruses have a positive-sense RNA genome , encoding three proteins: CP , RdRP , and a novel δ protein that shares no ho...	Orsay , the only virus known to naturally infect the nematode Caenorhabditis elegans , expresses a capsid-δ fusion protein . We have demonstrated that the Orsay fusion protein is incorporated into Orsay capsid and forms a ~420-Å long fiber protruding from the capsid surface . Crystal structure of an N-terminal fragment...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "crystal", "structure", "caenorhabditis", "condensed", "matter", "physics", "microbiology", "viral", "structure", "parasitic", "diseases", "animals", "nematode", "infections", "animal", "mode...	2017	Structure of a pentameric virion-associated fiber with a potential role in Orsay virus entry to host cells
Despite decades of research , the question of how the mRNA splicing machinery precisely identifies short exonic islands within the vast intronic oceans remains to a large extent obscure . In this study , we analyzed Alu exonization events , aiming to understand the requirements for correct selection of exons . Comparis...	A typical human gene consists of 9 exons around 150 nucleotides in length , separated by introns that are ∼3 , 000 nucleotides long . The challenge of the splicing machinery is to precisely identify and ligate the exons , while removing the introns . We aimed to understand how the splicing machinery meets this momentou...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/alternative", "splicing" ]	2009	Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery
Ribosomal proteins are essential to life . While the functions of ribosomal protein-encoding genes ( RPGs ) are highly conserved , the evolution of their regulatory mechanisms is remarkably dynamic . In Saccharomyces cerevisiae , RPGs are unusual in that they are commonly present as two highly similar gene copies and i...	Eukaryotic genes are littered with non-coding intervening sequences , or introns , that must be precisely excised from a messenger RNA before it can be properly translated into protein . Despite their ubiquity , the evolution and function of introns remain poorly understood . Consequently , we cannot accurately predict...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "animal", "models", "forms", "of", "evolution", "genomics", "model", "organisms", "gene", "expression", "genetics", "molecular", "genetics", "biology", "evolutionary", "biology", "yeast", "and", "fungal", "models", "microbiology", "evolutionary", "processes", "genetics"...	2012	Diverse Forms of RPS9 Splicing Are Part of an Evolving Autoregulatory Circuit
The acylphloroglucinol rhodomyrtone is a promising new antibiotic isolated from the rose myrtle Rhodomyrtus tomentosa , a plant used in Asian traditional medicine . While many studies have demonstrated its antibacterial potential in a variety of clinical applications , very little is known about the mechanism of action...	Bacterial antibiotic resistance constitutes a major public healthcare issue and deaths caused by antimicrobial resistance are expected to soon exceed the number of cancer-related fatalities . In order to fight resistance , new antibiotics have to be developed that are not affected by existing microbial resistance strat...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "membrane", "staining", "bacillus", "microbiology", "membrane", "proteins", "prokaryotic", "models", "antibiotics", "experimental", "organism", "...	2018	The novel antibiotic rhodomyrtone traps membrane proteins in vesicles with increased fluidity
Marijuana and its main psychotropic ingredient Δ9-tetrahydrocannabinol ( THC ) exert a plethora of psychoactive effects through the activation of the neuronal cannabinoid receptor type 1 ( CB1 ) , which is expressed by different neuronal subpopulations in the central nervous system . The exact neuroanatomical substrate...	Marijuana and its main psychoactive component , THC , exert a plethora of behavioural and autonomic effects on humans and animals . Some of these effects are the cause of the widespread illicit use of marijuana , while others might be involved in the potential therapeutic use of this drug for the treatment of several n...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "anesthesiology", "and", "pain", "management", "pharmacology", "neuroscience" ]	2007	Genetic Dissection of Behavioural and Autonomic Effects of Δ9-Tetrahydrocannabinol in Mice
The pathogenic fungus Cryptococcus neoformans uses the Bwc1-Bwc2 photoreceptor complex to regulate mating in response to light , virulence and ultraviolet radiation tolerance . How the complex controls these functions is unclear . Here , we identify and characterize a gene in Cryptococcus , UVE1 , whose mutation leads ...	The majority of fungi sense light using the White Collar complex ( WCC ) , a two-protein combination of a photoreceptor and a transcription factor . The WCC regulates circadian rhythms , sexual development , sporulation , metabolism , and virulence . As such , the exposure to light controls properties of fungi that are...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The Uve1 Endonuclease Is Regulated by the White Collar Complex to Protect Cryptococcus neoformans from UV Damage
Correct repair of damaged DNA is critical for genomic integrity . Deficiencies in DNA repair are linked with human cancer . Here we report a novel mechanism by which a virus manipulates DNA damage responses . Infection with murine polyomavirus sensitizes cells to DNA damage by UV and etoposide . Polyomavirus large T an...	DNA repair protects genome integrity and unrepaired DNA damage can cause cancer . We have identified a new mechanism by which a tumor virus makes cells hypersensitive to DNA damage . The Large T Antigen ( LT ) of polyoma virus blocks DNA repair pathways , making cells 100 fold more sensitive to DNA damage . LT does thi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Viral Interference with DNA Repair by Targeting of the Single-Stranded DNA Binding Protein RPA
Somatic mutations affecting ETV6 often occur in acute lymphoblastic leukemia ( ALL ) , the most common childhood malignancy . The genetic factors that predispose to ALL remain poorly understood . Here we identify a novel germline ETV6 p . L349P mutation in a kindred affected by thrombocytopenia and ALL . A second ETV6 ...	Inherited mutations of transcription factors have recently been associated with susceptibility to acute leukemia . Here we report two unrelated kindreds with inherited mutations in ETV6 , the gene encoding the transcription factor ETS variant 6 . These families were characterized by a low platelet count ( thrombocytope...	[ "Abstract", "Introduction", "Results/Discussion", "Discussion", "Materials", "&", "Methods" ]	[]	2015	Germline ETV6 Mutations Confer Susceptibility to Acute Lymphoblastic Leukemia and Thrombocytopenia
Plasmode is a term coined several years ago to describe data sets that are derived from real data but for which some truth is known . Omic techniques , most especially microarray and genomewide association studies , have catalyzed a new zeitgeist of data sharing that is making data and data sets publicly available on a...	Plasmode is a term used to describe a data set that has been derived from real data but for which some truth is known . Statistical methods that analyze data from high dimensional experiments ( HDEs ) seek to estimate quantities that are of interest to scientists , such as mean differences in gene expression levels and...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "mathematics", "science", "policy", "computational", "biology", "molecular", "biology", "genetics", "and", "genomics" ]	2008	Evaluating Statistical Methods Using Plasmode Data Sets in the Age of Massive Public Databases: An Illustration Using False Discovery Rates
The intracellular pathogenic bacterium Brucella generates a replicative vacuole ( rBCV ) derived from the endoplasmic reticulum via subversion of the host cell secretory pathway . rBCV biogenesis requires the expression of the Type IV secretion system ( T4SS ) VirB , which is thought to translocate effector proteins th...	Many intracellular parasites ensure their survival and proliferation within host cells by secreting an array of effector molecules that modulate various cellular functions . Among these , Brucella abortus , the causative agent of the worldwide zoonosis brucellosis , controls the intracellular trafficking of its vacuole...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "analysis", "tools", "genomics", "molecular", "cell", "biology", "emerging", "infectious", "diseases", "microbial", "pathogens", "membranes", "and", "sorting", "host-pathogen", "interaction", "microbiology", "biology", "pathogenesis", "bacterial", "pathogens" ]	2013	Brucella Modulates Secretory Trafficking via Multiple Type IV Secretion Effector Proteins
The diagnosis of cystic echinococcosis ( CE ) is based primarily on imaging , in particular with ultrasound for abdominal CE , complemented by serology when imaging results are unclear . In rural endemic areas , where expertise in ultrasound may be scant and conventional serology techniques are unavailable due to lack ...	Cystic echinococcosis ( CE ) is a parasitic zoonosis prevalent worldwide , especially in economically poor livestock raising areas . Parasitic cysts develop most commonly in the liver and are diagnosed primarily by ultrasound . Serology helps with diagnosis , particularly when ultrasound features are unclear . Unfortun...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "diagnostic", "radiology", "pathology", "and", "laboratory", "medicine", "ultrasound", "imaging", "tropical", "diseases", "parasitic", "diseases", "animals", "echinococcus", "veterina...	2016	Comparison of the Diagnostic Accuracy of Three Rapid Tests for the Serodiagnosis of Hepatic Cystic Echinococcosis in Humans
The high level of functional diversity and plasticity in monocytes/macrophages has been defined within in vitro systems as M1 ( classically activated ) , M2 ( alternatively activated ) and deactivated macrophages , of which the latter two subtypes are associated with suppression of cell mediated immunity , that confers...	Monocyte/macrophage subsets following their polarization by the microenvironement serve as important immune sentinels that play a vital role in host defense and homeostasis . The polarization of macrophage function has been broadly classified as M1 ( classical ) and M2 ( alternate ) activation , wherein M1 polarised ce...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	M2 Polarization of Monocytes-Macrophages Is a Hallmark of Indian Post Kala-Azar Dermal Leishmaniasis
Necrotrophic plant pathogens acquire nutrients from dead plant cells , which requires the disintegration of the plant cell wall and tissue structures by the pathogen . Infected plants lose tissue integrity and functional immunity as a result , exposing the nutrient rich , decayed tissues to the environment . One challe...	Virulence and vegetative growth are two distinct lifestyles in pathogenic bacteria . Although virulence factors are critical for pathogens to successfully cause infections , producing these factors is costly and imposes growth penalty to the pathogen . Although each single bacterial cell exists in one lifestyle or the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "plant", "anatomy", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "dna-binding", "proteins", "cell", "metabolism", "plant", "science", "potato", "plants", "vegetables", "proteins", "gene", "ex...	2019	Cell-length heterogeneity: a population-level solution to growth/virulence trade-offs in the plant pathogen Dickeya dadantii
Optimality principles have been proposed as a general framework for understanding motor control in animals and humans largely based on their ability to predict general features movement in idealized motor tasks . However , generalizing these concepts past proof-of-principle to understand the neuromechanical transformat...	The nervous system has the ability to rapidly and flexibly coordinate many muscles and limbs to produce movements . This neuromechanical transformation must robustly achieve motor goals under the changing mechanics of the body and environment , and select one solution amongst many alternatives . What computational prin...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "anatomy", "and", "physiology", "neuroscience", "biomechanics", "motor", "systems", "control", "engineering", "computational", "neuroscience", "neurological", "system", "nervous", "system", "physiology", "musculoskeletal", "system", "biology", "control", "system...	2012	Optimization of Muscle Activity for Task-Level Goals Predicts Complex Changes in Limb Forces across Biomechanical Contexts
Heritable differences in gene expression between individuals are an important source of phenotypic variation . The question of how closely the effects of genetic variation on protein levels mirror those on mRNA levels remains open . Here , we addressed this question by using ribosome profiling to examine how genetic di...	Individuals in a species differ from each other in many ways . For many traits , a fraction of this variation is genetic—it is caused by DNA sequence variants in the genome of each individual . Some of these variants influence traits by altering how much certain genes are expressed , i . e . how many mRNA and protein m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "functional", "genomics", "quantitative", "trait", "loci", "variant", "genotypes", "quantitative", "traits", "genetic", "mapping", "next-generation", "sequencing", "genome", "analysis", "trait", "locus", "analysis", "gene", "expression", "evolutionary", "genetics", "genet...	2014	Genetic Influences on Translation in Yeast
Muller's ratchet is a paradigmatic model for the accumulation of deleterious mutations in a population of finite size . A click of the ratchet occurs when all individuals with the least number of deleterious mutations are lost irreversibly due to a stochastic fluctuation . In spite of the simplicity of the model , a qu...	Muller's ratchet is a paradigmatic model in population genetics which describes the fixation of a deleterious mutation in a population of finite size due to an unfortunate stochastic fluctuation . Obtaining quantitative predictions of the ratchet rate , i . e . the frequency with which such a mutation fixes , is believ...	[ "Abstract", "Introduction", "Models", "Results/Discussion" ]	[]	2013	Distribution of the Fittest Individuals and the Rate of Muller's Ratchet in a Model with Overlapping Generations
IL-10 is a critical regulatory cytokine involved in the pathogenesis of visceral leishmaniasis caused by Leishmania donovani and clinical and experimental data indicate that disease progression is associated with expanded numbers of CD4+ IFNγ+ T cells committed to IL-10 production . Here , combining conditional cell-sp...	Dendritic cells are well known as myeloid cells that bridge innate and adaptive immunity , and play an important role in the induction of cell-mediated immunity to a variety of pathogens . However , very little is known about the function of dendritic cells after infection has become established . In this study , we ha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "immune", "cells", "cytokines", "antigen-presenting", "cells", "immunology", "microbiology", "host-pathogen", "interaction", "parasitology", "parastic", "protozoans", "neglected", "tropical", "diseases", "immunomodulation", "infectious", "diseases", "t", "cells", ...	2012	IL-10-Producing Th1 Cells and Disease Progression Are Regulated by Distinct CD11c+ Cell Populations during Visceral Leishmaniasis
To generate a cytopathic effect , the catalytic A1 subunit of cholera toxin ( CT ) must be separated from the rest of the toxin . Protein disulfide isomerase ( PDI ) is thought to mediate CT disassembly by acting as a redox-driven chaperone that actively unfolds the CTA1 subunit . Here , we show that PDI itself unfolds...	Protein disulfide isomerase ( PDI ) is a luminal endoplasmic reticulum ( ER ) protein with related but independent oxidoreductase and chaperone activities . The molecular mechanism of PDI chaperone function remains unidentified . Here , we report that PDI unfolds upon contact with the catalytic A1 subunit of cholera to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "protein", "folding", "host-pathogen", "interaction", "biology", "microbiology", "pathogenesis", "biophysics" ]	2014	Substrate-Induced Unfolding of Protein Disulfide Isomerase Displaces the Cholera Toxin A1 Subunit from Its Holotoxin
Recurrent and feedback networks are capable of holding dynamic memories . Nonetheless , training a network for that task is challenging . In order to do so , one should face non-linear propagation of errors in the system . Small deviations from the desired dynamics due to error or inherent noise might have a dramatic e...	The ability to learn and execute actions in fine temporal resolution is crucial , as many of our day to day actions require such temporal ordering ( e . g . limb movement and speech ) . Indeed , generating stable time-varying outputs , using neural networks has attracted a lot of attention over the last years . One of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "medicine", "and", "health", "sciences", "statistical", "noise", "neural", "networks", "nervous", "system", "social", "sciences", "electrophysiology", "neuroscience", "learning", "and", "memory", "simulation", "and", "modeling", "cognitive", "psychology", "m...	2017	Stabilizing patterns in time: Neural network approach
Two-component signal transduction systems ( TCS ) are used by bacteria to sense and respond to their environment . TCS are typically composed of a sensor histidine kinase ( HK ) and a response regulator ( RR ) . The Vibrio cholerae genome encodes 52 RR , but the role of these RRs in V . cholerae pathogenesis is largely...	Pathogenic bacteria experience varying conditions during infection of human hosts and often use two-component signal transduction systems ( TCSs ) to monitor their environment . TCS consists of a histidine kinase ( HK ) , which senses environmental signals , and a corresponding response regulator ( RR ) , which mediate...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Vibrio cholerae Response Regulator VxrB Controls Colonization and Regulates the Type VI Secretion System
During herpes simplex virus 1 ( HSV1 ) egress in neurons , viral particles travel from the neuronal cell body along the axon towards the synapse . Whether HSV1 particles are transported as enveloped virions as proposed by the ‘married’ model or as non-enveloped capsids suggested by the ‘separate’ model is controversial...	Herpes simplex virus 1 ( HSV1 ) establishes lifelong latent infections in the peripheral nervous system . After reactivation , progeny viral particles travel within sensory neurons towards sites of initial infection . There are conflicting reports what type of viral structures are transported: some studies observed non...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "motility", "cellular", "structures", "microtubules", "macromolecular", "assemblies", "microbiology", "host-pathogen", "interaction", "viral", "structure", "neuroscience", "motor", "systems", "protein", "structure", "cytoskeleton", "proteins", "biology", "biophysics",...	2011	Cryo Electron Tomography of Herpes Simplex Virus during Axonal Transport and Secondary Envelopment in Primary Neurons
Estimates of genetic diversity in helminth infections of humans often have to rely on genotyping ( immature ) parasite transmission stages instead of adult worms . Here we analyse the results of one such study investigating a single polymorphic locus ( a change at position 200 of the β-tubulin gene ) in microfilariae o...	During the last decade , there has been a substantial increase in the use of mass drug administration to reduce the disease caused by parasitic worms . With so many people regularly receiving treatment , there is a risk that drug resistance may develop . As a result , the number of studies looking for genetic markers o...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "helminths", "variant", "genotypes", "population", "genetics", "mathematical", "models", "parasitic", "diseases", "alleles", "animals", "genetic", "mapping", "infectious", "diseases/neglected", "tropical", "diseases"...	2008	An Analysis of Genetic Diversity and Inbreeding in Wuchereria bancrofti: Implications for the Spread and Detection of Drug Resistance
The mucosal immune system identifies and fights invading pathogens , while allowing non-pathogenic organisms to persist . Mechanisms of pathogen/non-pathogen discrimination are poorly understood , as is the contribution of human genetic variation in disease susceptibility . We describe here a new , IRF3-dependent signa...	The host immune system must identify pathogens and defeat them through TLR-dependent signaling pathway activation , while distinguishing them from commensal flora . Contrary to current dogma , the host cannot solely use “pattern recognition” since the microbial molecules involved in such recognition are present on path...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases/urological", "infections", "immunology/immune", "response", "microbiology/innate", "immunity" ]	2010	Pathogen Specific, IRF3-Dependent Signaling and Innate Resistance to Human Kidney Infection
The origin and evolution of new microRNAs ( miRNAs ) is important because they can impact the transcriptome broadly . As miRNAs can potentially emerge constantly and rapidly , their rates of birth and evolution have been extensively debated . However , most new miRNAs identified appear not to be biologically significan...	During Metazoan evolution , the architecture of the genome changed dramatically in size , gene number and regulatory elements . Genomic architecture is often assumed to be correlated with morphological complexity . However , it is still not known whether the gene repertoire , both for protein coding and non-coding gene...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "adaptation", "sexual", "selection", "genome", "evolution", "natural", "selection", "population", "genetics", "comparative", "genomics", "biology", "genomics", "evolutionary", "biology", "genomic", "evolution", "evolutionary", "processes", "evolutionary", "genetics" ]	2014	New MicroRNAs in Drosophila—Birth, Death and Cycles of Adaptive Evolution
Wolbachia are maternally inherited endosymbiotic bacteria , widespread among arthropods thanks to host reproductive manipulations that increase their prevalence into host populations . The most commonly observed manipulation is cytoplasmic incompatibility ( CI ) . CI leads to embryonic death in crosses between i ) infe...	In some crosses , mosquito males belonging to the species Culex pipiens prevent their females from having live progenies . This phenomenon called cytoplasmic incompatibility ( CI ) is caused by intracellular bacteria named Wolbachia . CI occurs when males infected with Wolbachia fertilize females infected with genetica...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "reproductive", "system", "condensation", "condensed", "matter", "physics", "dna-binding", "proteins", "animals", "wolbachia", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", ...	2018	The cellular phenotype of cytoplasmic incompatibility in Culex pipiens in the light of cidB diversity
In the recent 2014–2016 Ebola epidemic in West Africa , non-hospitalized cases were an important component of the chain of transmission . However , non-hospitalized cases are at increased risk of going unreported because of barriers to access to healthcare . Furthermore , underreporting rates may fluctuate over space a...	Epidemics are defined by a surge of cases of a disease , yet often a significant number of cases in an epidemic are never reported , for example because not all infected individuals have access to medical care . This underreporting can introduce bias into analyses of disease spread , by distorting patterns in where and...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "death", "rates", "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "geographical", "locations", "health", "care", "population", "biology", "infectious", "disease", "control", "africa", "public", "and", "occupational", "health", "infectio...	2018	Unreported cases in the 2014-2016 Ebola epidemic: Spatiotemporal variation, and implications for estimating transmission
p53 tumor suppressor has been identified as a protein interacting with the large T antigen produced by simian vacuolating virus 40 ( SV40 ) . Subsequent research on p53 inhibition by SV40 and other tumor viruses has not only helped to gain a better understanding of viral biology , but also shaped our knowledge of human...	This review focuses on a novel aspect of host–bacteria interactions: the direct interplay between bacterial pathogens and tumor suppression mechanisms that protect the host from cancer development . Recent studies revealed that various pathogenic bacteria actively inhibit the major tumor suppression pathway mediated by...	[ "Abstract", "Historical", "Perspective", "of", "Microbial", "Inhibition", "of", "p53", "If", "Viruses", "Can", "Do", "It,", "Why", "Can’t", "Other,", "More", "Complex", "Microorganisms?", "Summary" ]	[]	2015	Microbial Regulation of p53 Tumor Suppressor
Within the context of a field trial conducted by the Cuban vector control program ( AaCP ) , we assessed acceptability of insecticide-treated curtains ( ITCs ) and residual insecticide treatment ( RIT ) with deltamethrin by the community . We also assessed the potential influence of interviewees’ risk perceptions for g...	We aimed to understand what makes insecticide-treated curtains ( ITCs ) and residual insecticide treatment ( RIT ) with deltamethrin acceptable or not to users of these tools . In-depth interviews were conducted as part of a field trial conducted by the Cuban vector control program ( AaCP ) to test the effectiveness of...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "smell", "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "immunology", "geographical", "locations", "social", "sciences", "neuroscience", "animals", "toxicology", "north", "america", "research", "design", "toxicity",...	2018	Insecticide treated curtains and residual insecticide treatment to control Aedes aegypti: An acceptability study in Santiago de Cuba
To determine the spatial and temporal dynamics of influenza A virus during a single epidemic , we examined whole-genome sequences of 284 A/H1N1 and 69 A/H3N2 viruses collected across the continental United States during the 2006–2007 influenza season , representing the largest study of its kind undertaken to date . A p...	This study is the first of its kind to reconstruct the spread of an epidemic of influenza A virus across a single country , in this case the United States . In contrast to a single viral lineage spreading across this country , a phylogenetic analysis of the whole-genome sequences of more than 300 influenza A viruses of...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases/viral", "infections", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases", "genetics", "and", "genomics/population", "genetics" ]	2008	Molecular Epidemiology of A/H3N2 and A/H1N1 Influenza Virus during a Single Epidemic Season in the United States
The antiparasitic agent niclosamide has been demonstrated to inhibit the arthropod-borne Zika virus . Here , we investigated the antiviral capacity of niclosamide against dengue virus ( DENV ) serotype 2 infection in vitro and in vivo . Niclosamide effectively retarded DENV-induced infection in vitro in human adenocarc...	Dengue and severe dengue cause global health concerns annually . Without antiviral drugs , supportive care is the only treatment option for patients with DENV infection . A current vaccine has been approved for protection against DENV infection; however , the potential risks and challenges associated with the immunopat...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "cell", "processes", "microbiology", "toxicology", "viruses", "protein", "expression", "rna", "viruses", ...	2018	The antiparasitic drug niclosamide inhibits dengue virus infection by interfering with endosomal acidification independent of mTOR
Treatment failure after therapy of pulmonary tuberculosis ( TB ) infections is an important challenge , especially when it coincides with de novo emergence of multi-drug-resistant TB ( MDR-TB ) . We seek to explore possible causes why MDR-TB has been found to occur much more often in patients with a history of previous...	Our ability to treat and control acute pulmonary tuberculosis ( TB ) is threatened by the increasing occurrence of multi-drug-resistant tuberculosis ( MDR-TB ) in many countries around the globe . It is not clear whether MDR-TB occurs predominantly due to transmission , or whether there is a substantial contribution du...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "antimicrobials", "medicine", "and", "health", "sciences", "immune", "cells", "granulomas", "drugs", "immunology", "tropical", "diseases", "microbiology", "bacterial", "diseases", "streptomycin", "pharmaceutics", "antibiotics", "drug", "administration", ...	2016	The Role of Adherence and Retreatment in De Novo Emergence of MDR-TB
Ribosome biogenesis is essential for cell growth and proliferation and is commonly elevated in cancer . Accordingly , numerous oncogene and tumor suppressor signaling pathways target rRNA synthesis . In breast cancer , non-canonical Wnt signaling by Wnt5a has been reported to antagonize tumor growth . Here , we show th...	Synthesis of the translation machinery , including the mega-Dalton , RNA-protein ribosome complex , serves as a key driver of cellular growth and proliferation . It is therefore unsurprising that ribosomal biogenesis is under intricate regulation . The process through which ribosomes are made entails the coordination o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "breast", "tumors", "cancers", "and", "neoplasms", "dna", "transcription", "oncology", "epigenetics", "immunologic", "techniques", "cellular", "structures", "and", "organelles", "chromatin", "research", "and", "analysis", "method...	2016	Wnt5a Signals through DVL1 to Repress Ribosomal DNA Transcription by RNA Polymerase I
Trypanosoma cruzi ( Tc ) infection causes chagasic cardiomyopathy; however , why 30–40% of the patients develop clinical disease is not known . To discover the pathomechanisms in disease progression , we obtained the proteome signature of peripheral blood mononuclear cells ( PBMCs ) of normal healthy controls ( N/H , n...	Chagasic cardiomyopathy is elicited by Trypanosoma cruzi infection . T . cruzi transmission is prevalent in Latin American countries , and its transmission is also noted in Mexico and Southern parts of the United States . In this manuscript , we have utilized blood samples from human subjects that were normal healthy o...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "tropical", "diseases", "dna-binding", "proteins", "parasitic", "diseases", "parasitic", "protozoans", "protozoans", "neglected", "tropical", "diseases", "infectious", "disease", "control", "contrac...	2016	Changes in Proteome Profile of Peripheral Blood Mononuclear Cells in Chronic Chagas Disease
N-Acetyl-L-Glutamate Kinase ( NAGK ) is the structural paradigm for examining the catalytic mechanisms and dynamics of amino acid kinase family members . Given that the slow conformational dynamics of the NAGK ( at the microseconds time scale or slower ) may be rate-limiting , it is of importance to assess the mechanis...	During the last 20 years both the experimental and computational communities have provided strong evidence that proteins cannot be regarded as static entities , but as intrinsically flexible molecules that exploit their fluctuation dynamics for catalytic and ligand-binding events , as well as for allosteric regulation ...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "computer", "science/numerical", "analysis", "and", "theoretical", "computing", "biophysics", "biochemistry", "computational", "biology" ]	2010	On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family: NAGK the Paradigm
Typhoid fever , caused by Salmonella enterica serovar Typhi ( S . Typhi ) , remains a serious global health concern . Since their emergence in the mid-1970s multi-drug resistant ( MDR ) S . Typhi now dominate drug sensitive equivalents in many regions . MDR in S . Typhi is almost exclusively conferred by self-transmiss...	Typhoid fever is caused by the bacterium Salmonella enterica serovar Typhi ( S . Typhi ) . Treatment relies on antimicrobial drugs , however many S . Typhi are multi-drug resistant ( MDR ) , severely compromising treatment options . MDR typhoid is associated with multiple drug resistance genes , which can be transferre...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "bacterial", "and", "foodborne", "illness", "gastroenterology", "and", "hepatology", "population", "genetics", "biology", "evolutionary", "biology" ]	2011	Emergence of a Globally Dominant IncHI1 Plasmid Type Associated with Multiple Drug Resistant Typhoid
Enteropathogenic Escherichia coli ( EPEC ) represents a major causative agent of infant diarrhea associated with significant morbidity and mortality in developing countries . Although studied extensively in vitro , the investigation of the host-pathogen interaction in vivo has been hampered by the lack of a suitable sm...	Enteropathogenic Escherichia coli ( EPEC ) is an important causative agent of infant diarrhea associated with significant morbidity and mortality particularly in the developing world . Current knowledge on EPEC pathogenesis has mainly emanated from in vitro studies as research is limited by the absence of a suitable sm...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "antimicrobials", "small", "intestine", "medicine", "and", "health", "sciences", "microbiome", "drugs", "microbiology", "animal", "models", "bacterial", "diseases", "model", "organisms", "antibiotics", "gastroenterology", "and", "hepatology", "pharmacology", "microbial", ...	2016	Age-Dependent Susceptibility to Enteropathogenic Escherichia coli (EPEC) Infection in Mice
How cells control the overall size and growth of membrane-bound organelles is an important unanswered question of cell biology . Fission yeast cells maintain a nuclear size proportional to cellular size , resulting in a constant ratio between nuclear and cellular volumes ( N/C ratio ) . We have conducted a genome-wide ...	Membrane-bound organelles are maintained at a size proportional to cell size during cell growth and division . How this is achieved is a little-understood area of cell biology . The nucleus is generally present in single copy within a cell and provides a useful model to study overall membrane-bound organelle growth and...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "deletion", "mutation", "messenger", "rna", "vertebrates", "animals", "xenopus", "animal", "models", "mutation", "fungi", "model", "organisms", "amphibians", "experimental", "organism", "systems", "cell", "nucleus", "cellular", "structures", "and", "organelles", "schizo...	2017	A systematic genomic screen implicates nucleocytoplasmic transport and membrane growth in nuclear size control
Sex hormone-binding globulin ( SHBG ) is a glycoprotein responsible for the transport and biologic availability of sex steroid hormones , primarily testosterone and estradiol . SHBG has been associated with chronic diseases including type 2 diabetes ( T2D ) and with hormone-sensitive cancers such as breast and prostate...	Sex hormone-binding globulin ( SHBG ) is the key protein responsible for binding and transporting the sex steroid hormones , testosterone and estradiol , in the circulatory system . SHBG regulates their bioavailability and therefore their effects in the body . SHBG has been linked to chronic diseases including type 2 d...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "public", "health", "and", "epidemiology", "epidemiology", "endocrinology", "reproductive", "endocrinology", "diabetes", "and", "endocrinology", "genetic", "epidemiology", "endocrine", "physiology" ]	2012	A Genome-Wide Association Meta-Analysis of Circulating Sex Hormone–Binding Globulin Reveals Multiple Loci Implicated in Sex Steroid Hormone Regulation
In a 1997 seminal paper , W . Maddison proposed minimizing deep coalescences , or MDC , as an optimization criterion for inferring the species tree from a set of incongruent gene trees , assuming the incongruence is exclusively due to lineage sorting . In a subsequent paper , Maddison and Knowles provided and implement...	Inferring the evolutionary history of a set of species , known as the species tree , is a task of utmost significance in biology and beyond . The traditional approach to accomplishing this task from molecular sequences entails sequencing a gene in the set of species under consideration , reconstructing the gene's evolu...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "computational", "biology/population", "genetics", "computer", "science/applications", "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "computational", "biology/comparative", "sequence", "analysis", ...	2009	Species Tree Inference by Minimizing Deep Coalescences
Leishmania braziliensis is the main causative agent of cutaneous leishmaniasis in Brazil . Protection against infection is related to development of Th1 responses , but the mechanisms that mediate susceptibility are still poorly understood . Murine models have been the most important tools in understanding the immunopa...	Leishmaniasis is a neglected disease that affects more than 12 million people worldwide . In Brazil , the cutaneous disease is more prevalent with about 28 , 000 new cases reported each year , and L . braziliensis is the main causative agent . The interesting data about the infection with this parasite is the wide vari...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "immunology", "infectious", "diseases/protozoal", "infections", "immunology/immunity", "to", "infections" ]	2011	BALB/c Mice Infected with Antimony Treatment Refractory Isolate of Leishmania braziliensis Present Severe Lesions due to IL-4 Production
Several studies highlighted the relevance of extrinsic noise in shaping cell decision making and differentiation in molecular networks . Bimodal distributions of gene expression levels provide experimental evidence of phenotypic differentiation , where the modes of the distribution often correspond to different physiol...	Phenotypic differentiation often relies on bimodal distributions of gene expression levels , which can normally be achieved by different molecular mechanisms . During the past decade microRNAs , small noncoding RNA molecules , were found to downregulate the expression of preferred mRNA targets by sequestering and succe...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "gene", "regulation", "cell", "cycle", "and", "cell", "division", "messenger", "rna", "cell", "processes", "micrornas", "probability", "distribution", "mathematics", "phase", "diagrams", "computer", "and", "information", "sciences", "gene", "expression", "probability", ...	2018	On the role of extrinsic noise in microRNA-mediated bimodal gene expression
The delta-retrovirus Human T-cell leukemia virus type 1 ( HTLV-1 ) preferentially infects CD4+ T-cells via cell-to-cell transmission . Viruses are transmitted by polarized budding and by transfer of viral biofilms at the virological synapse ( VS ) . Formation of the VS requires the viral Tax protein and polarization of...	Human T-cell leukemia virus type 1 ( HTLV-1 ) is the only human retrovirus causing cancer and is transmitted via breast feeding , sexual intercourse , and cell-containing blood products . Efficient infection of CD4+ T-cells occurs via polarized budding of virions or via cell surface transfer of viral biofilms at a tigh...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "293t", "cells", "pathogens", "immunology", "biological", "cultures", "microbiology", "plasmid", "construction", "retroviruse...	2016	The Tax-Inducible Actin-Bundling Protein Fascin Is Crucial for Release and Cell-to-Cell Transmission of Human T-Cell Leukemia Virus Type 1 (HTLV-1)
Transcription factor nuclear factor kappa B ( NF-κB ) regulates cellular responses to environmental cues . Many stimuli induce NF-κB transiently , making time-dependent transcriptional outputs a fundamental feature of NF-κB activation . Here we show that NF-κB target genes have distinct kinetic patterns in activated B ...	The nuclear factor kappa B ( NF-κB ) family of transcription factors regulates cellular responses to a wide variety of environmental cues . These could be extracellular stimuli that activate cell surface receptors , such as pathogens , or intracellular stress signals such as DNA damage or oxidative stress . In response...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "binding", "sequencing", "techniques", "cell", "physiology", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "cloning", "dna", "transcription", "transcription", "factors", "sequence", "motif", "analysis", "molecular", "biology", "techniq...	2018	Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation
A fundamental challenge in human health is the identification of disease-causing genes . Recently , several studies have tackled this challenge via a network-based approach , motivated by the observation that genes causing the same or similar diseases tend to lie close to one another in a network of protein-protein or ...	Understanding the genetic background of diseases is crucial to medical research , with implications in diagnosis , treatment and drug development . As molecular approaches to this challenge are time consuming and costly , computational approaches offer an efficient alternative . Such approaches aim at prioritizing gene...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "neurological", "disorders/alzheimer", "disease", "computational", "biology/systems", "biology", "oncology/prostate", "cancer", "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/genetics", "of", "disease", "computational", "biology/genomics", "geneti...	2010	Associating Genes and Protein Complexes with Disease via Network Propagation
Highly pathogenic avian influenza ( HPAI ) H5N1 was first encountered in 1996 in Guangdong province ( China ) and started spreading throughout Asia and the western Palearctic in 2004–2006 . Compared to several other countries where the HPAI H5N1 distribution has been studied in some detail , little is known about the e...	The geographical distribution of highly pathogenic avian influenza ( HPAI ) H5N1 and agro-ecological risk factors have been studied in a number of countries in Southeast Asia . However , little is know of its distribution in China where HPAI H5N1 first emerged in 1996 , evolved , and spread throughout Asia and the west...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/epidemiology", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases", "ecology/spatial", "and", "landscape", "ecology" ]	2011	Spatial Distribution and Risk Factors of Highly Pathogenic Avian Influenza (HPAI) H5N1 in China
Measuring the prevalence of transmissible Trypanosoma brucei rhodesiense in tsetse populations is essential for understanding transmission dynamics , assessing human disease risk and monitoring spatio-temporal trends and the impact of control interventions . Although an important epidemiological variable , identifying ...	Human African trypanosomiasis is a fatal disease that is carried by a tsetse vector . Assessing the proportion of tsetse which carries human-infective trypanosomes is important in assessing human disease risk and understanding disease transmission dynamics . However , identifying flies which carry transmissible infecti...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology", "epidemiology", "biology", "microbiology", "population", "biology" ]	2012	Using Molecular Data for Epidemiological Inference: Assessing the Prevalence of Trypanosoma brucei rhodesiense in Tsetse in Serengeti, Tanzania
The current Ebola virus outbreak has highlighted the uncertainties surrounding many aspects of Ebola virus virology , including routes of transmission . The scientific community played a leading role during the outbreak—potentially , the largest of its kind—as many of the questions surrounding ebolaviruses have only be...	Basic scientific research is now considered an integral component of the fight against emerging infectious diseases like Ebola virus . The recent Ebola outbreak , however , demonstrates how the ineffective communication of basic science can stoke public panic more than it provides helpful tools to responders; basic sci...	[ "Abstract", "Introduction", "“Airborne”", "Ebola:", "Potential", "Pandemic", "or", "Tempest", "in", "a", "Teacup?", "Managing", "Uncertainty", "Moving", "Forward" ]	[]	2015	Effectively Communicating the Uncertainties Surrounding Ebola Virus Transmission
Restoring natural speech in paralyzed and aphasic people could be achieved using a Brain-Computer Interface ( BCI ) controlling a speech synthesizer in real-time . To reach this goal , a prerequisite is to develop a speech synthesizer producing intelligible speech in real-time with a reasonable number of control parame...	Speech Brain-Computer-Interfaces may restore communication for people with severe paralysis by decoding cortical speech activity to control in real time a speech synthesizer . Recent data indicate that the speech motor cortex houses a detailed topographical representation of the different speech articulators of the voc...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "acoustics", "linguistics", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "audio", "signal", "processing", "signal", "processing", "social", "sciences", "signal", "filtering", "tongue", "audio", "equipment", "digestive", "system", "vowels"...	2016	Real-Time Control of an Articulatory-Based Speech Synthesizer for Brain Computer Interfaces
Intestinal schistosomiasis is widely distributed around Lake Victoria in Kenya where about 16 million people in 56 districts are at risk of the infection with over 9 . 1 million infected . Its existence in rural settings has been extensively studied compared to urban settings where there is limited information about th...	Bilharzia also known as schistosomiasis is one of the neglected tropical diseases found in western part of Kenya . The major source of infection is Lake Victoria; however , there is evidence of inland transmission especially within the informal settlements of Kisumu city . Schistosomiasis can be controlled using three ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "social", "sciences" ]	2014	Low Levels of Awareness Despite High Prevalence of Schistosomiasis among Communities in Nyalenda Informal Settlement, Kisumu City, Western Kenya
To understand the genetic mechanisms leading to phenotypic differentiation , it is important to identify genomic regions under selection . We scanned the genome of two chicken lines from a single trait selection experiment , where 50 generations of selection have resulted in a 9-fold difference in body weight . Analyse...	Evolution is the process of change in response to selection . Typically , this results in more or less obvious changes to the appearance and physical properties—the phenotype—of an organism . However , these changes reflect underlying changes to the genome of that organism—the genotype . We examine the genomes of two l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/population", "genetics", "genetics", "and", "genomics/animal", "genetics", "computational", "biology/molecular", "genetics", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/physiogenomics", "computational", "biology/genomics...	2010	Genome-Wide Effects of Long-Term Divergent Selection
Most current methods for detecting natural selection from DNA sequence data are limited in that they are either based on summary statistics or a composite likelihood , and as a consequence , do not make full use of the information available in DNA sequence data . We here present a new importance sampling approach for a...	Current methods to study natural selection using modern population genomic data are limited in their power and flexibility . Here , we present a new method to infer natural selection that builds on recent methodological advances in estimating genome-wide genealogies . By using importance sampling we are able to efficie...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "taxonomy", "markov", "models", "population", "dynamics", "geographical", "locations", "genetic", "mapping", "simulation", "and", "modeling", "phylogenetics", "data", "management", "mathematics", "phylogenetic", "analysis", "molecular", "genetics", "population", "biology", ...	2019	An approximate full-likelihood method for inferring selection and allele frequency trajectories from DNA sequence data
Descent of testes from a position near the kidneys into the lower abdomen or into the scrotum is an important developmental process that occurs in all placental mammals , with the exception of five afrotherian lineages . Since soft-tissue structures like testes are not preserved in the fossil record and since key parts...	While fossils of whales with legs demonstrate that these species evolved from legged ancestors , the ancestral state of nonfossilizing soft-tissue structures can only be indirectly inferred . This difficulty is also confounded by uncertainties in the phylogenetic relationships between the animals concerned . A prime ex...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taxonomy", "hyraxes", "vertebrates", "animals", "mammals", "animal", "phylogenetics", "phylogenetics", "data", "management", "mammalian", "genomics", "zoology", "research", "and", "analysis", "methods", "sequence", "analysis", "computer", "and", "information", "sciences"...	2018	Loss of RXFP2 and INSL3 genes in Afrotheria shows that testicular descent is the ancestral condition in placental mammals
Human α-defensins are potent anti-microbial peptides with the ability to neutralize bacterial and viral targets . Single alanine mutagenesis has been used to identify determinants of anti-bacterial activity and binding to bacterial proteins such as anthrax lethal factor . Similar analyses of α-defensin interactions wit...	Human α-defensins are an important component of the innate immune response and provide an initial block against a broad number of infectious agents , including viruses and bacteria . Characteristics of α-defensins that are necessary for their anti-bacterial activity have been identified , but our understanding of deter...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "immune", "system", "proteins", "viral", "entry", "defensins", "proteins", "viral", "transmission", "and", "infection", "virology", "biology", "and", "life", "sciences", "immunology", "microbiology" ]	2014	Delineation of Interfaces on Human Alpha-Defensins Critical for Human Adenovirus and Human Papillomavirus Inhibition

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