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Human T-lymphotropic Virus-1 ( HTLV-1 ) is a retrovirus that persists lifelong by driving clonal proliferation of infected T-cells . HTLV-1 causes a neuroinflammatory disease and adult T-cell leukemia/lymphoma . Strongyloidiasis , a gastrointestinal infection by the helminth Strongyloides stercoralis , and Infective De...	HTLV-1 is a human retrovirus estimated to infect 20 million people world-wide and is causing in a small proportion of the infected individuals an inflammatory disease or a leukemia/lymphoma . HTLV-1 persists lifelong by driving clonal proliferation of infected T-cells . Strongyloidiasis , a gastrointestinal infection b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "leukemias", "viruses", "and", "cancer", "microbiology", "parasitic", "diseases", "helminth", "infection", "hematologic", "cancers", "and", "related", "disorders", "skin", "infections", "neglected", "tropical", "diseases", "lymphomas", "infectious", "diseases"...	2013	Strongyloidiasis and Infective Dermatitis Alter Human T Lymphotropic Virus-1 Clonality in vivo
Evolution of complex multicellular life began from the emergence of a life cycle involving the formation of cell clusters . The opportunity for cells to interact within clusters provided them with an advantage over unicellular life forms . However , what kind of interactions may lead to the evolution of multicellular l...	Multicellular organisms are ubiquitous . But how did the first multicellular organisms arise ? It is typically argued that this occurred due to benefits coming from interactions between cells . One example of such interactions is the division of labour . For instance , colonial cyanobacteria delegate photosynthesis and...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "organismal", "evolution", "medicine", "and", "health", "sciences", "immune", "cells", "applied", "mathematics", "cell", "cycle", "and", "cell", "division", "cell", "processes", "immunology", "microbiology", "evolutionary", "developmental", "biology", ...	2019	Interacting cells driving the evolution of multicellular life cycles
A decade ago , a team of biochemists including two of us , modeled yeast glycolysis and showed that one of the most studied biochemical pathways could not be quite understood in terms of the kinetic properties of the constituent enzymes as measured in cell extract . Moreover , when the same model was later applied to d...	Baker's yeast is widely applied in modern biotechnology , for instance for production of heterologous protein or biofuel . For such applications a thorough understanding of the central energy metabolism of the bug is crucial . Nevertheless , even for this well-known organism , attempts to build models ab initio , based...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "biochemistry", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2012	Testing Biochemistry Revisited: How In Vivo Metabolism Can Be Understood from In Vitro Enzyme Kinetics
Most individuals throughout the Americas are admixed descendants of Native American , European , and African ancestors . Complex historical factors have resulted in varying proportions of ancestral contributions between individuals within and among ethnic groups . We developed a panel of 446 ancestry informative marker...	Individuals from Latin America are descendants of multiple ancestral populations , primarily Native American , European , and African ancestors . The relative proportions of these ancestries can be estimated using genetic markers , known as ancestry informative markers ( AIMs ) , whose allele frequency varies between t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "population", "genetics", "biology", "human", "genetics", "genetics", "and", "genomics" ]	2012	Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas
Sparse coding algorithms trained on natural images can accurately predict the features that excite visual cortical neurons , but it is not known whether such codes can be learned using biologically realistic plasticity rules . We have developed a biophysically motivated spiking network , relying solely on synaptically ...	In a sparse coding model , individual input stimuli are represented by the activities of model neurons , the majority of which are inactive in response to any particular stimulus . For a given class of stimuli , the neurons are optimized so that the stimuli can be faithfully represented with the minimum number of co-ac...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "systems", "biology", "visual", "system", "theoretical", "biology", "computational", "neuroscience", "biophysics", "theory", "biology", "sensory", "systems", "biophysics", "neuroscience", "genetics", "and", "genomics", "coding", "mechanisms" ]	2011	A Sparse Coding Model with Synaptically Local Plasticity and Spiking Neurons Can Account for the Diverse Shapes of V1 Simple Cell Receptive Fields
The human Y chromosome exhibits surprisingly low levels of genetic diversity . This could result from neutral processes if the effective population size of males is reduced relative to females due to a higher variance in the number of offspring from males than from females . Alternatively , selection acting on new muta...	The human Y chromosome is found only in males , and exhibits surprisingly low levels of genetic diversity . This low diversity could result from neutral processes , for example , if there are fewer males successfully mating ( and thus fewer Y chromosomes being inherited ) relative to the number of females who successfu...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "population", "modeling", "evolutionary", "modeling", "molecular", "genetics", "population", "genetics", "biology", "genomics", "evolutionary", "biology", "population", "biology", "computational", "biology", "evolutionary", "genetics" ]	2014	Natural Selection Reduced Diversity on Human Y Chromosomes
Pseudomonas taiwanensis is a broad-host-range entomopathogenic bacterium that exhibits insecticidal activity toward agricultural pests Plutella xylostella , Spodoptera exigua , Spodoptera litura , Trichoplusia ni and Drosophila melanogaster . Oral infection with different concentrations ( OD = 0 . 5 to 2 ) of wild-type...	Most entomopathogenic bacteria can produce toxin proteins and proliferate in the intestines of insects after natural oral ingestion . These bacteria can evade the systemic and local immune responses of insects . Here , we used insect larva of the diamond back moth ( Plutella xylostella ) , a cruciferous crop pest to st...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "pest", "control", "biology", "and", "life", "sciences", "microbiology", "molecular", "cell", "biology", "agricultural", "biotechnology", "agriculture" ]	2014	Characterization of an Insecticidal Toxin and Pathogenicity of Pseudomonas taiwanensis against Insects
Retroduplications come from reverse transcription of mRNAs and their insertion back into the genome . Here , we performed comprehensive discovery and analysis of retroduplications in a large cohort of 2 , 535 individuals from 26 human populations , as part of 1000 Genomes Phase 3 . We developed an integrated approach t...	We developed an approach and performed comprehensive discovery of retroduplications from 26 human populations , utilizing whole-exome and whole-genome sequencing data . Our high-resolution landscape of retroduplications reveals that variable retroduplications are effective markers of human populations and can track pop...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "taxonomy", "pseudogenes", "functional", "genomics", "genome", "evolution", "phylogenetics", "data", "management", "phylogenetic", "analysis", "genome", "analysis", "gene", "types", "epigenetics", "chromatin", "genomic", "libraries", "computer", "and", "information", "sci...	2017	Landscape and variation of novel retroduplications in 26 human populations
The patterns of genomic divergence during ecological speciation are shaped by a combination of evolutionary forces . Processes such as genetic drift , local reduction of gene flow around genes causing reproductive isolation , hitchhiking around selected variants , variation in recombination and mutation rates are all f...	A variety of evolutionary forces influence the genomic landscape of divergence during ecological speciation . Here we characterize the evolution of genomic divergence patterns based on 60 fully sequenced three-spined stickleback genomes , contrasting lake and river populations that differ in parasite abundance . Our co...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Genomics of Divergence along a Continuum of Parapatric Population Differentiation
Transcriptional regulation is one of the most important processes for modulating gene expression . Though much of this control is attributed to transcription factors , histones , and associated enzymes , it is increasingly apparent that the spatial organization of chromosomes within the nucleus has a profound effect on...	The eukaryotic genome is spatially distributed in a highly organized manner , with chromosomal regions localizing to well-defined sub-nuclear positions . This organization could have a profound effect on chromatin accessibility and transcriptional activity on a genome-wide level . Using high-resolution , genome-wide , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "molecular", "biology/chromatin", "structure", "molecular", "biology/histone", "modification", "molecular", "biology/transcription", "initiation", "and", "activation", "cell", "biology/nuclear", "structure", "and", "function", "genetics",...	2010	Nuclear Pore Proteins Nup153 and Megator Define Transcriptionally Active Regions in the Drosophila Genome
The question whether metacylic trypomastigote ( MT ) forms of different T . cruzi strains differentially release surface molecules , and how they affect host cell invasion , remains to be fully clarified . We addressed that question using T . cruzi strains that differ widely in the ability to invade cells . Metacyclic ...	The molecular basis of wide differences in the ability of metacylic trypomastigote ( MT ) forms of different T . cruzi strains to invade host cells is not fully understood . We investigated the possibility that surface molecules gp82 and gp90 , which function as mediator and down regulator of cell invasion respectively...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "lysosomes", "medicine", "and", "health", "sciences", "vesicles", "immune", "physiology", "viral", "transmission", "and", "infection", "hela", "cells", "biological", "cultures", "immunology", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "protozoans"...	2016	Surface Molecules Released by Trypanosoma cruzi Metacyclic Forms Downregulate Host Cell Invasion
Assessing brain activity during complex voluntary motor behaviors that require the recruitment of multiple neural sites is a field of active research . Our current knowledge is primarily based on human brain imaging studies that have clear limitations in terms of temporal and spatial resolution . We developed a physiol...	Our knowledge of brain activity and network organization during complex motor behaviors in humans relies mainly on neuroimaging studies . However , the majority of available brain imaging methods are not feasible for quantifying the neural processes that occur on very short time-scales at the microscopic level . To add...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "simulation", "and", "modeling", "computational", "neuroscience", "neurotransmission", "biology", "and", "life", "sciences", "computational", "biology", "neuroscience", "neuroimaging", "research", "and", "analysis", "methods" ]	2014	A Neural Population Model Incorporating Dopaminergic Neurotransmission during Complex Voluntary Behaviors
The many subcomponents of the human cortex are known to follow an anatomical pattern and functional relationship that appears to be highly conserved between individuals . This suggests that this pattern and the relationship among cortical regions are important for cortical function and likely shaped by genetic factors ...	Although functional and anatomical connections among cortical regions have been intensively explored , genetically-mediated relationships between cortical regions have not been pursued to the same degree . Identifying genetic factors that mediate these relationships among different brain subcomponents can provide insig...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "population", "genetics", "brain", "neuroscience", "twins", "genome", "analysis", "population", "biology", "neuroimaging", "research", "and", "analysis", "methods", "frontal", "lobe", "imaging", "techniques", "genetic", "polymorp...	2016	Conservation of Distinct Genetically-Mediated Human Cortical Pattern
Paramyxovirus spread generally involves assembly of individual viral particles which then infect target cells . We show that infection of human bronchial airway cells with human metapneumovirus ( HMPV ) , a recently identified paramyxovirus which causes significant respiratory disease , results in formation of intercel...	Human metapneumovirus ( HMPV ) is an important human respiratory pathogen that affects all age groups worldwide . There are currently no vaccines or treatments available for HMPV , and key aspects of its life cycle remain unknown . We examined the late events of the HMPV infection cycle in human bronchial epithelial ce...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "respiratory", "infections", "immunology", "cell", "processes", "microbiology", "viral", "structure", "pulmonology", "membrane", "proteins", "antibodies", "cellular", "structures", "and", "organelles", "rese...	2016	Human metapneumovirus Induces Reorganization of the Actin Cytoskeleton for Direct Cell-to-Cell Spread
Rabies is a fatal zoonotic disease that has been known in Ethiopia for centuries in society as “Mad Dog Disease” . It is an important disease with veterinary and public health significance in the North western zone of Tigray where previous studies have not been conducted . Frequent occurrence of outbreaks in the area l...	Rabies is a deadly disease of human and animals . The disease has been recognized in Ethiopia for centuries , but its impact remained underestimated . This limitation masks the true magnitude of rabies incidence and has been a stumbling block for its prevention and control . The aim of the study was to determine the in...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "geographical", "locations", "vertebrates", "microbiology", "dogs", "animals", "mammals", "veterinary", "hospitals", "viruses", "preve...	2017	High Incidence of Human Rabies Exposure in Northwestern Tigray, Ethiopia: A Four-Year Retrospective Study
ciRS-7 is an intensely studied , highly expressed and conserved circRNA . Essentially nothing is known about its biogenesis , including the location of its promoter . A prevailing assumption has been that ciRS-7 is an exceptional circRNA because it is transcribed from a locus lacking any mature linear RNA transcripts o...	circRNAs were recently discovered to be a significant product of ‘host’ gene expression programs but little is known about their transcriptional regulation . Here , we have studied the expression of a functional and highly expressed circRNA named ciRS-7 . ciRS-7 has an unusual function for a circRNA; it is believed to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "hela", "cells", "gene", "regulation", "rna", "analysis", "biological", "cultures", "cell", "cultures", "mammalian", "genomics", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "...	2017	ciRS-7 exonic sequence is embedded in a long non-coding RNA locus
Recent and classical work has revealed biologically and medically significant subtypes in complex diseases and traits . However , relevant subtypes are often unknown , unmeasured , or actively debated , making automated statistical approaches to subtype definition valuable . We propose reverse GWAS ( RGWAS ) to identif...	Complex diseases depend on interactions between many known and unknown genetic and environmental factors . However , most studies aggregate these strata and test for associations on average across samples , though biological factors and medical interventions can have dramatically different effects on different people ....	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "carbohydrate", "metabolism", "medicine", "and", "health", "sciences", "drugs", "quantitative", "traits", "glucose", "metabolism", "simulation", "and", "modeling", "genome", "analysis", "pharmacology", "research", "and", "analysis"...	2019	Reverse GWAS: Using genetics to identify and model phenotypic subtypes
miR-263a/b are members of a conserved family of microRNAs that are expressed in peripheral sense organs across the animal kingdom . Here we present evidence that miR-263a and miR-263b play a role in protecting Drosophila mechanosensory bristles from apoptosis by down-regulating the pro-apoptotic gene head involution de...	In spite of continuous challenges from the ever-changing environment , biological systems exhibit incredible stability in their developmental and physiological processes . In addition to extrinsic variability caused by environmental fluctuations , cells face intrinsic variability arising from the inherent noise of gene...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental", "biology" ]	2010	Drosophila microRNAs 263a/b Confer Robustness during Development by Protecting Nascent Sense Organs from Apoptosis
The synaptonemal complex ( SC ) is a widely conserved structure that mediates the intimate alignment of homologous chromosomes during meiotic prophase and is required for proper homolog segregation at meiosis I . However , fundamental details of SC architecture and assembly remain poorly understood . The coiled-coil pr...	The meiotic cell cycle enables sexually reproducing organisms to generate reproductive cells with half their chromosome complement . Chromosome ploidy is reduced during meiosis by virtue of prior associations established between homologous chromosomes ( homologs ) . Such associations , which are ultimately secured by c...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	SUMO Localizes to the Central Element of Synaptonemal Complex and Is Required for the Full Synapsis of Meiotic Chromosomes in Budding Yeast
Experimental NMR relaxation studies have shown that peptide binding induces dynamical changes at the side-chain level throughout the second PDZ domain of PTP1e , identifying as such the collection of residues involved in long-range communication . Even though different computational approaches have identified subsets o...	Intra-protein communication has recently attracted an increasing interest from the scientific community , because of its important functional consequences: allostery and signalling . Unravelling how information is processed and transferred within a protein structure requires the study of the dynamical effects of , for ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "protein", "structure", "biology", "computational", "biology", "macromolecular", "structure", "analysis" ]	2012	Accurate Prediction of the Dynamical Changes within the Second PDZ Domain of PTP1e
Deciphering gene regulatory mechanisms through the analysis of high-throughput expression data is a challenging computational problem . Previous computational studies have used large expression datasets in order to resolve fine patterns of coexpression , producing clusters or modules of potentially coregulated genes . ...	The cell uses complex regulatory networks to modulate the expression of genes in response to changes in cellular and environmental conditions . The transcript level of a gene is directly affected by the binding of transcriptional regulators to DNA motifs in its promoter sequence . Therefore , both expression levels of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/transcriptional", "regulation", "computational", "biology/systems", "biology", "computational", "biology/genomics", "computational", "biology" ]	2008	A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast
Despite the importance of vaccinia virus in basic and applied immunology , our knowledge of the human immune response directed against this virus is very limited . CD4+ T cell responses are an important component of immunity induced by current vaccinia-based vaccines , and likely will be required for new subunit vaccin...	Although the routine use of vaccinia virus for vaccination against smallpox was stopped after eradication of this disease , there is a possibility for an accidental or intentional release of this virus . In response to this challenge , vaccination of at least emergency personnel has been suggested . However , adverse r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "viruses", "virology", "immunology", "computational", "biology", "homo", "(human)" ]	2007	Human CD4+ T Cell Epitopes from Vaccinia Virus Induced by Vaccination or Infection
Dengue is a major cause of morbidity in Puerto Rico and is well-known to its physicians . Early case identification and timely initiation of treatment for patients with severe dengue can reduce medical complications and mortality . To determine clinical management and reporting practices , and assess knowledge of dengu...	Dengue is a major cause of morbidity in Puerto Rico and is well-known to its physicians . Early case identification and timely initiation of treatment for patients with severe dengue can reduce medical complications and mortality . We conducted a survey among physicians who practice in Puerto Rico to determine clinical...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "dengue", "virus", "infectious", "diseases", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "flaviviruses", "medical", "microbiology", "dengue", "fever", "viral", "pathogens", "microbial", "pathogens", "pathogens", "biology", "and...	2014	Physician Survey to Determine How Dengue Is Diagnosed, Treated and Reported in Puerto Rico
Most bacterial infections induce the activation of polymorphonuclear neutrophils ( PMNs ) , enhance their microbicidal function , and promote the survival of these leukocytes for protracted periods of time . Brucella abortus is a stealthy pathogen that evades innate immunity , barely activates PMNs , and resists the ki...	The absence of obvious clinical symptoms during the early stages of brucellosis is linked to the Brucella stealthy strategy and its non-canonical PAMPs , which are low PRRs agonists . Still , there are clinical profiles that require explanation . For instance ‒despite the fact that neutrophils readily ingest Brucella d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Brucella abortus Induces the Premature Death of Human Neutrophils through the Action of Its Lipopolysaccharide
The glideosome is an actomyosin-based machinery that powers motility in Apicomplexa and participates in host cell invasion and egress from infected cells . The central component of the glideosome , myosin A ( MyoA ) , is a motor recruited at the pellicle by the acylated gliding-associated protein GAP45 . In Toxoplasma ...	Toxoplasma gondii can infect most warm-blooded animals , and is an important opportunistic pathogen for humans . This obligate intracellular parasite is able to invade virtually all nucleated cells , and as with most parasites of the Apicomplexa phylum , relies on a substrate-dependent gliding motility to actively pene...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "parasitology", "microbiology" ]	2014	Plasticity between MyoC- and MyoA-Glideosomes: An Example of Functional Compensation in Toxoplasma gondii Invasion
Rift Valley fever phlebovirus ( RVFV; Phenuiviridae , Phlebovirus ) is an important mosquito-borne pathogen of both humans and ruminants . The RVFV genome is composed of tripartite , single stranded , negative or ambisense RNAs . The small ( S ) segment encodes both the nucleocapsid protein ( N ) and the non-structural...	Rift Valley fever phlebovirus ( RVFV ) remains an ongoing serious socio-economic threat , and with a lack of widely available licensed vaccines and treatments it is increasingly important to understand the underlying biology behind RVFV viral replication . Re-analysis of RVFV nucleocapsid , a key protein within the RVF...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "transfection", "rna-binding", "proteins", "medicine", "and", "health", "sciences", "rift", "valley", "fever", "virus", "protein", "interactions", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "nucleocapsids", "viral", "structure", "viruses", ...	2017	Mutational analysis of Rift Valley fever phlebovirus nucleocapsid protein indicates novel conserved, functional amino acids
Ensuring the adequacy of response to rabies vaccination in dogs is important , particularly in the context of pet travel . Few studies have examined the factors associated with dogs’ failure to achieve an adequate antibody titer after vaccination ( 0 . 5 IU/ml ) . This study evaluated rabies antibody titers in dogs aft...	For rabies prevention and control it is important that pets and domestic animals be vaccinated , this is especially relevant for rabies-free areas of the world which tightly control dog and cat entry to ensure rabies is not imported . Adequate response to rabies must be proven by testing the pet’s serum for rabies anti...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "animal", "types", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "vertebrates", "pets", "and", "companion", "animals", "dogs", "animals", ...	2017	Risk factors for inadequate antibody response to primary rabies vaccination in dogs under one year of age
Defining endpoints for trachoma programs can be a challenge as clinical signs of infection may persist in the absence of detectable bacteria . Antibody-based tests may provide an alternative testing strategy for surveillance during terminal phases of the program . Antibody-based assays , in particular ELISAs , have bee...	Trachoma is an ocular disease caused by repeated infections with the bacteria Chlamydia trachomatis that is observed mostly in children and women . Scarring after repeated infections causes eyelashes to turn under the lid , possibly leading to corneal opacity and blindness . Efforts have increased by multiple organizat...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "clinical", "immunology", "neglected", "tropical", "diseases", "immunology", "biology", "trachoma" ]	2012	CT694 and pgp3 as Serological Tools for Monitoring Trachoma Programs
Friedreich ataxia ( FRDA ) and Fragile X syndrome ( FXS ) are among 40 diseases associated with expansion of repeated sequences ( TREDs ) . Although their molecular pathology is not well understood , formation of repressive chromatin and unusual DNA structures over repeat regions were proposed to play a role . Our stud...	Friedreich ataxia and Fragile X syndrome are among 40 human diseases associated with expansion of repeated sequences . In both disorders repeat expansion leads to gene silencing , the molecular mechanism of which is not well understood , impeding the development of specific therapies to treat these disorders . It is pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "rna", "medicine", "and", "health", "sciences", "rna", "processing", "cell", "biology", "chromosome", "biology", "neurology", "gene", "expression", "genetics", "gene", "regulation", "biology", "and", "life", "sciences", "epigenetics", "neurodegenerative"...	2014	R-loops Associated with Triplet Repeat Expansions Promote Gene Silencing in Friedreich Ataxia and Fragile X Syndrome
For efficient polarity and migration , cells need to regulate the magnitude and spatial distribution of actin assembly . This process is coordinated by reciprocal interactions between the actin cytoskeleton and mechanical forces . Actin polymerization-based protrusion increases tension in the plasma membrane , which in...	How cells regulate the size and number of their protrusions for efficient polarity and motility is a fundamental question in cell biology . We recently found that immune cells known as neutrophils use physical forces to regulate this process . Actin polymerization-based protrusion stretches the plasma membrane , and th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "built", "structures", "engineering", "and", "technology", "immunology", "cell", "processes", "condensed", "matter", "physics", "osmotic", "shock", "membrane", "structures", "cell", "nucleus...	2016	Membrane Tension Acts Through PLD2 and mTORC2 to Limit Actin Network Assembly During Neutrophil Migration
Long-lasting forms of long-term potentiation ( LTP ) represent one of the major cellular mechanisms underlying learning and memory . One of the fundamental questions in the field of LTP is why different molecules are critical for long-lasting forms of LTP induced by diverse experimental protocols . Further complexity s...	Long-term potentiation of the strength of synaptic connections is a mechanism of learning and memory storage . One of the most confusing aspects of hippocampal synaptic potentiation is that numerous experiments have revealed the requirement for a plethora of signaling molecules . Furthermore the degree to which molecul...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "neurochemistry", "chemical", "compounds", "enzymes", "enzymology", "neuroscience", "organic", "compounds", "surgical", "and", "invasive", "medical", "procedures", "hormones", "phosphatases", "synaptic", "plasticit...	2017	β-adrenergic signaling broadly contributes to LTP induction
To take advantage of emerging opportunities to reduce morbidity and mortality from diarrheal disease , we need to better understand the determinants of life-threatening severe dehydration ( SD ) in resource-poor settings . We analyzed records of patients admitted with acute diarrheal disease over twenty-two years at th...	To best help patients with diarrheal disease , we need to better understand what causes patients to tip from mild disease to severe disease . In this study , we analyzed records of patients presenting to one of the largest hospitals in the world dedicated to the management of diarrheal diseases . Patients with and with...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "dehydration", "(medicine)", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "vibrio", "microbiology", "reoviruses", "viruses", "age", "groups", "bacterial", "diseases", "adults", "vibrio", "cholerae", "signs", "and", ...	2017	Determinants of severe dehydration from diarrheal disease at hospital presentation: Evidence from 22 years of admissions in Bangladesh
Genome-wide association studies ( GWAS ) and subsequent dense-genotyping of associated loci identified over a hundred single-nucleotide polymorphism ( SNP ) variants associated with the risk of rheumatoid arthritis ( RA ) , type 1 diabetes ( T1D ) , and celiac disease ( CeD ) . Immunological and genetic studies suggest...	Genome-wide association studies have identified hundreds of genetic variants associated to autoimmune diseases . To understand the mechanisms and pathways affected by these variants , follow-up studies of molecular phenotypes and functions are required . Given the diversity of cell types and specialization of functions...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "genome-wide", "association", "studies", "genome", "expression", "analysis", "rheumatology", "medicine", "and", "health", "sciences", "functional", "genomics", "immune", "cells", "immunology", "genome", "analysis", "epigenomics", "autoimmunity", "white",...	2014	Regulation of Gene Expression in Autoimmune Disease Loci and the Genetic Basis of Proliferation in CD4+ Effector Memory T Cells
Congenital human cytomegalovirus ( HCMV ) occurs in 0 . 5–1% of live births and approximately 10% of infected infants develop hearing loss . The mechanism ( s ) of hearing loss remain unknown . We developed a murine model of CMV induced hearing loss in which murine cytomegalovirus ( MCMV ) infection of newborn mice lea...	Congenital infection with human cytomegalovirus ( HCMV ) is the most common viral infection of the fetus and occurs in 0 . 5–2 . 0% of all live births in most regions in the world . Infection of the fetus can result in a spectrum of end-organ disease , including long term damage to the central nervous system ( CNS ) . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Murine CMV-Induced Hearing Loss Is Associated with Inner Ear Inflammation and Loss of Spiral Ganglia Neurons
Polysaccharide capsules are important virulence factors for many microbial pathogens including the opportunistic fungus Cryptococcus neoformans . In the present study , we demonstrate an unusual role for a secreted lactonohydrolase of C . neoformans , LHC1 in capsular higher order structure . Analysis of extracted caps...	Polysaccharide capsules are important virulence factors in pathogenic microbes that provide a protective coat against host immunity . Cryptococcus neoformans is a pathogenic encapsulated yeast that is a major opportunistic infection , causing approximately 600 , 000 cases of meningitis per year in AIDS patients globall...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "biology", "and", "life", "sciences", "immunology", "microbiology" ]	2014	A Role for LHC1 in Higher Order Structure and Complement Binding of the Cryptococcus neoformans Capsule
Precise regulation of stem cell self-renewal and differentiation properties is essential for tissue homeostasis . Using the adult Drosophila intestine to study molecular mechanisms controlling stem cell properties , we identify the gene split-ends ( spen ) in a genetic screen as a novel regulator of intestinal stem cel...	A fundamental challenge is to identify genes that have essential functions in controlling adult stem cells . Here , we use the Drosophila intestinal stem cells as a model of adult stem cells . Through a genetic screen strategy designed to reveal important stem cell regulators in an unbiased manner , we uncovered the ge...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "cell", "cycle", "and", "cell", "division", "cell", "processes", "cloning", "notch", "signaling", "cell", "differentiation", "developmental", "biology", "stem", "cells", "molecular", "biology", "techniques", "digestive", "syste...	2018	Spen limits intestinal stem cell self-renewal
It is still challenging and difficult to treat patients with eumycetoma; the current treatment has many side effects and has proven to be expensive and characterized by high recurrence rate , hence the poor patients' treatment compliance . Most of the patients are of low socio-economic status , have many financial cons...	This work was conducted to determine the use of herbal treatment among a group of eumycetoma patients . As mycetoma is a good example of a badly neglected tropical disease across the world , many mycetoma patients tend to present late with advanced infection , one of the important reasons for which is the use of herbal...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "complementary", "and", "alternative", "medicine", "public", "health", "medicine" ]	2013	Mycetoma Herbal Treatment: The Mycetoma Research Centre, Sudan Experience
Epstein-Barr virus ( EBV ) causes infectious mononucleosis and is associated with multiple human malignancies . EBV drives B-cell proliferation , which contributes to the pathogenesis of multiple lymphomas . Yet , knowledge of how EBV subverts host biosynthetic pathways to transform resting lymphocytes into activated l...	EBV , the first human tumor virus identified , persistently infects >95% of adults worldwide . Upon infection of small , resting B-lymphocytes , EBV establishes a state of viral latency , where viral oncoproteins and non-coding RNAs activate host pathways to promote rapid B-cell proliferation . EBV’s growth-transformin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "gene", "regulation", "pathogens", "regulatory", "proteins", "immunology", "microbiology", "dna-binding", "pro...	2019	Epstein-Barr virus subverts mevalonate and fatty acid pathways to promote infected B-cell proliferation and survival
In Colombia , the cutaneous leishmaniasis ( CL ) is the most common manifestation across the army personnel . Hence , it is mandatory to determine the species associated with the disease as well as the association with the clinical traits . A total of 273 samples of male patients with CL were included in the study and ...	Colombia is one of the countries with the highest incidence of Cutaneous Leishmaniasis in the world and the army population is the most vulnerable population . Herein , we identified the infecting Leishmania species ( L . braziliensis , L . panamensis , L . guyanensis , L . mexicana and L . lainsoni ) . We also showed ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "biogeography", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "pathology", "and", "laboratory", "medicine", "population", "dynamics", "population", "genetics", "tropical", "diseases", "social", "sciences", "parasitic", "diseases",...	2017	Spatial distribution, Leishmania species and clinical traits of Cutaneous Leishmaniasis cases in the Colombian army
Spermatogenesis is a dynamic developmental process requiring precisely timed transitions between discrete stages . Specifically , the germline undergoes three transitions: from mitotic spermatogonia to spermatocytes , from meiotic spermatocytes to spermatids , and from morphogenetic spermatids to spermatozoa . The soma...	Sexual reproduction in animals requires the production of male and female gametes , spermatozoa and ova , respectively . Gametes are derived from specialized cells known as the germline through a process called gametogenesis . Gametogenesis typically takes place in a gonad and requires the germ cells to be surrounded b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "meiosis", "medicine", "and", "health", "sciences", "cell", "cycle", "and", "cell", "division", "cell", "processes", "cell", "differentiation", "reproductive", "physiology", "cell", "polarity", "germ", "cells", "developmental", "biology", "stem",...	2017	Identification of genetic networks that act in the somatic cells of the testis to mediate the developmental program of spermatogenesis
The development of high-throughput genome sequencing enables accurate measurements of levels of sub-consensus intra-host virus genetic diversity and analysis of the role played by natural selection during cross-species transmission . We analysed the natural and experimental evolution of rabies virus ( RABV ) , an impor...	Understanding the mechanisms that underpin the cross-species transmission and host adaptation of rabies virus ( RABV ) remains an important part of the ongoing goal to reduce and eliminate rabies . We utilized next-generation sequencing to perform a deep comparative analysis of the genomic evolution of RABV subpopulati...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "organismal", "evolution", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "vertebrates", "dogs", "animals", "mammals", "viruses", "rna", "viruses", "microbial", "evolution", "evolutionary", "adaptation",...	2019	Comparison of intra- and inter-host genetic diversity in rabies virus during experimental cross-species transmission
Much emphasis has been placed on the identification , functional characterization , and therapeutic potential of somatic variants in tumor genomes . However , the majority of somatic variants lie outside coding regions and their role in cancer progression remains to be determined . In order to establish a system to tes...	Here we investigate the relationship between somatic variants and non-coding regulatory regions . To do this , we develop a new algorithm for identifying single nucleotide somatic variants in whole-genome sequencing data and apply it to a metastatic melanoma sample and a cell culture derived from this sample . Our resu...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "medicine", "dermatology", "functional", "genomics", "genome", "sequencing", "skin", "neoplasms", "genome", "analysis", "tools", "malignant", "skin", "neoplasms", "personalized", "medicine", "melanomas", "comparative", "genomics", "biology", "genetics", "genomics", "genet...	2012	Mutational Signatures of De-Differentiation in Functional Non-Coding Regions of Melanoma Genomes
Group A Streptococcus ( Streptococcus pyogenes or GAS ) causes pharyngitis , severe invasive infections , and the post-infectious syndromes of glomerulonephritis and rheumatic fever . GAS can be internalized and killed by epithelial cells in vitro , a process that may contribute to local innate defense against pharynge...	Group A Streptococcus ( Streptococcus pyogenes or GAS ) is the agent of streptococcal pharyngitis ( strep throat ) , invasive infections such as necrotizing fasciitis and streptococcal toxic shock , and post-infectious complications including rheumatic heart disease . Epithelial cells internalize and kill GAS in vitro ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "streptococci", "immunity", "innate", "immunity", "host-pathogen", "interaction", "biology", "microbiology", "group", "a", "streptococcal", "infection", "bacterial", "pathogens" ]	2013	Streptolysin O and its Co-Toxin NAD-glycohydrolase Protect Group A Streptococcus from Xenophagic Killing
It is commonly accepted that the Inferior Olive ( IO ) provides a timing signal to the cerebellum . Stable subthreshold oscillations in the IO can facilitate accurate timing by phase-locking spikes to the peaks of the oscillation . Several theoretical models accounting for the synchronized subthreshold oscillations hav...	There is a profound interest in the dynamics of neuronal networks and the simulation of network models is a prevalent approach to study these dynamics . Generally , network models contain neurons that are connected mostly through chemical synapses to form either a completely regular topology ( such as nearest neighbor ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "circuit", "models", "computational", "neuroscience", "biology", "computational", "biology", "neuroscience" ]	2012	The Generation of Phase Differences and Frequency Changes in a Network Model of Inferior Olive Subthreshold Oscillations
The transmission dynamics of Schistosoma japonicum remain poorly understood , as over forty species of mammals are suspected of serving as reservoir hosts . However , knowledge of the population genetic structure and of the full-sibship structuring of parasites at two larval stages will be useful in defining and tracki...	Schistosoma japonicum involves two obligatory host stages , with asexual reproduction within a molluscan host and sexual reproduction within a mammalian host . Having over 40 species of mammals suspected of being potential reservoirs complicates the transmission patterns . Understanding the complex transmission pattern...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/epidemiology", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "infectious", "diseas...	2010	Transmission of Schistosoma japonicum in Marshland and Hilly Regions of China: Parasite Population Genetic and Sibship Structure
In order for a virus to persist , there must be a balance between viral replication and immune clearance . It is commonly believed that adaptive immunity drives clearance of viral infections and , thus , dysfunction or viral evasion of adaptive immunity is required for a virus to persist . Type I interferons ( IFNs ) p...	In vertebrates , innate immunity provides early control of viral infection and initiates adaptive immunity . It is generally thought that a virus must either avoid or evade an adaptive immune response to persist within a vertebrate host . The role of innate immunity in preventing viral persistence , apart from its role...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "spleen", "immunology", "microbiology", "cloning", "cytotoxic", "t", "cells", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "white",...	2016	Type I Interferon Receptor Deficiency in Dendritic Cells Facilitates Systemic Murine Norovirus Persistence Despite Enhanced Adaptive Immunity
Biomolecular function is realized by recognition , and increasing evidence shows that recognition is determined not only by structure but also by flexibility and dynamics . We explored a biomolecular recognition process that involves a major conformational change – protein folding . In particular , we explore the bindi...	The intrinsically disordered peptide IA3 is the endogenous inhibitor for the enzyme named yeast aspartic proteinase saccharopepsin ( YPrA ) . In the presence of YPrA , IA3 folds itself into an amphipathic helix that blocks the active site cleft of the enzyme . We developed a multi-scaled approach to explore the underly...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics/protein", "folding", "biophysics/theory", "and", "simulation", "biophysics/biomacromolecule-ligand", "interactions", "computational", "biology/molecular", "dynamics", "physics/interdisciplinary", "physics" ]	2011	Multi-Scaled Explorations of Binding-Induced Folding of Intrinsically Disordered Protein Inhibitor IA3 to its Target Enzyme
Phagocytosis is essential to maintain tissue homeostasis in a large number of inflammatory and autoimmune diseases , but its role in the diseased brain is poorly explored . Recent findings suggest that in the adult hippocampal neurogenic niche , where the excess of newborn cells undergo apoptosis in physiological condi...	Phagocytosis , the engulfment and digestion of cellular debris , is at the core of the regenerative response of the damaged tissue , because it prevents the spillover of toxic intracellular contents and is actively anti-inflammatory . In the brain , the professional phagocytes are microglia , whose dynamic processes ra...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "inflammatory", "diseases", "cell", "death", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "cell", "processes", "immunology", "brain", "microglial", "cells", "a...	2016	Neuronal Hyperactivity Disturbs ATP Microgradients, Impairs Microglial Motility, and Reduces Phagocytic Receptor Expression Triggering Apoptosis/Microglial Phagocytosis Uncoupling
To counter systemic risk of infection by parasitic wasps , Drosophila larvae activate humoral immunity in the fat body and mount a robust cellular response resulting in encapsulation of the wasp egg . Innate immune reactions are tightly regulated and are resolved within hours . To understand the mechanisms underlying a...	Parasitoid wasps are a large group of insects in which the female injects her eggs into the bodies of host caterpillars ( also called larvae ) . When the wasp egg hatches , the parasite larva gradually eats the host alive and takes over its body . Soon after the parasite egg is laid , an arms race between the parasite ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/transcription", "initiation", "and", "activation", "genetics", "and", "genomics/genetics", "of", "the", "immune", "system", "cell", "biology/cell", "signaling", "immunology/innate", "immunity", "genetics", "and", "genomics/disease", "models", "patholog...	2010	Role for Sumoylation in Systemic Inflammation and Immune Homeostasis in Drosophila Larvae
The ROP16 kinase of Toxoplasma gondii is injected into the host cell cytosol where it activates signal transducer and activator of transcription ( STAT ) -3 and STAT6 . Here , we generated a ROP16 deletion mutant on a Type I parasite strain background , as well as a control complementation mutant with restored ROP16 ex...	Toxoplasma gondii is an extremely widespread intracellular protozoan parasite that establishes long-lasting infection in humans and animals . Because Toxoplasma infection is most often asymptomatic , it is evident that this parasite has developed sophisticated ways to manipulate host immunity . Recently , the parasite ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immune", "cells", "immunity", "immunology", "biology", "microbiology", "host-pathogen", "interaction", "immunomodulation", "parasitology" ]	2011	Toxoplasma gondii Rhoptry Kinase ROP16 Activates STAT3 and STAT6 Resulting in Cytokine Inhibition and Arginase-1-Dependent Growth Control
During embryogenesis , the transcription factor , Sox10 , drives the survival and differentiation of the melanocyte lineage . However , the role that Sox10 plays in postnatal melanocytes is not established . We show in vivo that melanocyte stem cells ( McSCs ) and more differentiated melanocytes express SOX10 but that ...	The melanocyte stem cells ( McSCs ) that reside in the hair follicle are critical for generating the melanocytes that will differentiate and produce pigment for the hair during successive rounds of hair growth . The inappropriate maintenance of McSCs results in hair graying . Thus , our understanding of McSC biology is...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "function", "aging", "developmental", "biology", "animal", "genetics", "organism", "development", "stem", "cells", "gene", "regulation", "genetics", "organogenesis", "molecular", "genetics", "biology", "gene", "networks", "cell", "differentiation", "adult", "ste...	2013	A Dual Role for SOX10 in the Maintenance of the Postnatal Melanocyte Lineage and the Differentiation of Melanocyte Stem Cell Progenitors
Altered glucose and lipid metabolism fuel cystic growth in polycystic kidneys , but the cause of these perturbations is unclear . Renal cysts also associate with mutations in Bicaudal C1 ( Bicc1 ) or in its self-polymerizing sterile alpha motif ( SAM ) . Here , we found that Bicc1 maintains normoglycemia and the expres...	Polycystic kidney diseases ( PKD ) are incurable inherited chronic disorders marked by fluid-filled cysts that frequently cause renal failure . A glycolytic metabolism reminiscent of cancerous cells accelerates cystic growth , but the mechanism underlying such metabolic re-wiring is poorly understood . PKD-like cystic ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "affinity", "chromatography", "messenger", "rna", "fungi", "model", "organisms", "immunoprecipitation", "materials", "science", "experimental", "organism", "systems", "co-immunoprecipitation", "glutathione", "chromatography", "kidneys"...	2018	Role of Bicaudal C1 in renal gluconeogenesis and its novel interaction with the CTLH complex
Population structure can strongly affect evolutionary dynamics . The most general way to describe population structures are graphs . An important observable on evolutionary graphs is the probability that a novel mutation spreads through the entire population . But what drives this spread of a mutation towards fixation ...	Evolving populations , companies , social circles are networks in which genes , resources and ideas circulate . Imagine a useful novelty is introduced in the network: a favorable mutation , a new product concept or a smart idea . Will this novelty be retained and propagated through the network or rather lost ? Using to...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infographics", "deletion", "mutation", "mutation", "mathematics", "algebra", "directed", "graphs", "computer", "and", "information", "sciences", "evolutionary", "theory", "graph", "theory", "evolutionary", "genetics", "eigenvectors", "data", "visualization", "linear", "a...	2018	Invasion and effective size of graph-structured populations
Malaria threatens half the world's population and exacts a devastating human toll . The principal malaria vector in Africa , the mosquito Anopheles gambiae , encodes 24 members of a recently identified family of leucine-rich repeat proteins named LRIMs . Two members of this family , LRIM1 and APL1C , are crucial compon...	The malaria-transmitting mosquito , Anopheles gambiae , uses a complement-like pathway to defend against Plasmodium parasites . The complement C3-like protein , TEP1 , binds to the surface of invading parasites , triggering their destruction and clearance . LRIM1 and APL1C , two leucine-rich repeat proteins , form a di...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "immune", "system", "proteins", "complement", "system", "mosquitoes", "proteins", "immunity", "innate", "immunity", "vector", "biology", "anopheles", "immunology", "biology", "microbiology", "immune", "system" ]	2011	Structure-Function Analysis of the Anopheles gambiae LRIM1/APL1C Complex and its Interaction with Complement C3-Like Protein TEP1
Chikungunya virus ( CHIKV ) is an arthritogenic alphavirus causing epidemics of acute and chronic arthritic disease . Herein we describe a comprehensive RNA-Seq analysis of feet and lymph nodes at peak viraemia ( day 2 post infection ) , acute arthritis ( day 7 ) and chronic disease ( day 30 ) in the CHIKV adult wild-t...	The largest chikungunya virus ( CHIKV ) epidemic ever recorded began in 2004 in Africa and spread across Asia reaching Europe and recently the Americas , with millions of cases reported . We undertook a detailed analysis of the mRNA expression profile during acute and chronic arthritis in an adult wild-type mouse model...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "gene", "regulation", "pathogens", "regulatory", "proteins", "tropical", "diseases", "microbiology", "dna-binding", "proteins", "alphaviruses", ...	2017	RNA-Seq analysis of chikungunya virus infection and identification of granzyme A as a major promoter of arthritic inflammation
Hendra and Nipah viruses ( family Paramyxoviridae , genus Henipavirus ) are bat-borne viruses that cause fatal disease in humans and a range of other mammalian species . Gaining a deeper understanding of host pathways exploited by henipaviruses for infection may identify targets for new anti-viral therapies . Here we h...	The henipaviruses Hendra and Nipah are bat-borne paramyxoviruses that are highly pathogenic in humans . Until recently the constraints of working at biosafety level 4 had hindered the large scale study of host factors associated with henipavirus infection . MicroRNAs are a class of single-stranded non-coding RNAs that ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "respiratory", "infections", "hela", "cells", "gene", "regulation", "henipavirus", "pathogens", "biological", "cultures", "microbiology", "vertebrates", "animals",...	2016	Dual microRNA Screens Reveal That the Immune-Responsive miR-181 Promotes Henipavirus Entry and Cell-Cell Fusion
Intracellular Toll-like receptors ( TLRs ) expressed by dendritic cells recognize nucleic acids derived from pathogens and play an important role in the immune responses against the influenza virus ( IAV ) , a single-stranded RNA sensed by different receptors including TLR7 . However , the importance of TLR7 processing...	Influenza A virus , a negative stranded RNA , can cause severe illness in humans and animals and stimulates many receptors including Toll like receptors 7 ( TLR7 ) . TLR signaling induces maturation of dendritic cells and the production of a variety of inflammatory cytokines that are crucial for both innate and adaptiv...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "immune", "cells", "cytokines", "viral", "transmission", "and", "infection", "viral", "classification", "immune", "activation", "antigen-presenting", "cells", "immunity", "to", "infections", "immunology", "microbiology", "lymphoid", "organs", "adaptive", "immunity", "rna"...	2012	Asparagine Endopeptidase Controls Anti-Influenza Virus Immune Responses through TLR7 Activation
Hox mediated neuroblast apoptosis is a prevalent way to pattern larval central nervous system ( CNS ) by different Hox genes , but the mechanism of this apoptosis is not understood . Our studies with Abdominal-A ( Abd-A ) mediated larval neuroblast ( pNB ) apoptosis suggests that AbdA , its cofactor Extradenticle ( Exd...	Specification of the head to tail axis of the developing central nervous system is carried out by Hox genes . Hox mediated programmed cell death of the neural progenitor cells plays an important role in specification of this axis , but the molecular mechanism of this phenomenon is not well understood . We have studied ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "chemical", "characterization", "rna", "interference", "nervous", "system", "cell", "processes", "dna-binding", "proteins", "cloning", "notch", "signaling", "sequence", "motif", "analysis", "epigenetics", "molecu...	2017	Combinatorial action of Grainyhead, Extradenticle and Notch in regulating Hox mediated apoptosis in Drosophila larval CNS
Tularemia is a geographically widespread , severely debilitating , and occasionally lethal disease in humans . It is caused by infection by a gram-negative bacterium , Francisella tularensis . In order to better understand its potency as an etiological agent as well as its potential as a biological weapon , we have com...	Tularemia is a zoonotic disease that is widely disseminated throughout the Northern Hemisphere and is caused by different strain types of bacteria belonging to the genus Francisella . In general , Francisella tularensis subspecies are able to infect a wide range of mammals including humans and are often transmitted via...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/evolutionary", ...	2009	Comparative Genomic Characterization of Francisella tularensis Strains Belonging to Low and High Virulence Subspecies
Dengue control programs commonly employ reactive insecticide spraying around houses of reported cases , with the assumption that most dengue virus ( DENV ) transmission occurs in the home . Focal household transmission has been demonstrated in rural settings , but it is unclear whether this holds true in dense and mobi...	Dengue is a viral disease transmitted between humans by Aedes aegypti mosquitoes . It is an increasing health problem in tropical regions , with no vaccine or drug available . The main approach used for dengue prevention and control is reducing mosquito numbers , which is commonly done by spraying insecticide around th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Households as Foci for Dengue Transmission in Highly Urban Vietnam
The inference of gene regulatory networks ( GRNs ) from expression data can mine the direct regulations among genes and gain deep insights into biological processes at a network level . During past decades , numerous computational approaches have been introduced for inferring the GRNs . However , many of them still suf...	Gene regulatory network ( GRN ) represents how some genes encode regulatory molecules such as transcription factors or microRNAs for regulating the expression of other genes . Accurate inference of GRN is an important task to understand the biological activity from signal emulsion to metabolic dynamics , prioritize pot...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Methods" ]	[ "infographics", "genetic", "networks", "gene", "regulation", "applied", "mathematics", "simulation", "and", "modeling", "algorithms", "regulator", "genes", "probability", "distribution", "mathematics", "network", "analysis", "genome", "analysis", "gene", "types", "researc...	2016	Inference of Gene Regulatory Network Based on Local Bayesian Networks
Several arenaviruses cause hemorrhagic fever ( HF ) diseases that are associated with high morbidity and mortality in humans . Accordingly , HF arenaviruses have been listed as top-priority emerging diseases for which countermeasures are urgently needed . Because arenavirus nucleoprotein ( NP ) plays critical roles in ...	Arenaviruses include severe pathogens causing hemorrhagic fevers and have been recently incorporated by the World Health Organization in a list of critical emerging diseases for which additional research and identification of clinical targets is urgently required . A better understanding of how viral proteins interact ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "gene", "regulation", "pathogens", "microbiology", "dna-binding", "proteins", "immunoblotting", "plasmid", "construction", "viruses", "rna", "viruses...	2018	DDX3 suppresses type I interferons and favors viral replication during Arenavirus infection
Long-term potentiation ( LTP ) , a long-lasting enhancement in communication between neurons , is considered to be the major cellular mechanism underlying learning and memory . LTP triggers high-frequency calcium pulses that result in the activation of Calcium/Calmodulin ( CaM ) -dependent kinase II ( CaMKII ) . CaMKII...	CaMKII enzymes transmit calcium ion ( Ca2+ ) signals released inside the cell by regulating signal transduction pathways through phosphorylation: Ca2+ first binds to the small regulatory protein CaM; this Ca2+/CaM complex then binds to and activates the kinase , which phosphorylates other proteins in the cell . Since C...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "biochemistry/cell", "signaling", "and", "trafficking", "structures", "biochemistry/protein", "chemistry", "biochemistry/macromolecular", "assemblies", "and", "machines" ]	2010	Structure of the CaMKIIδ/Calmodulin Complex Reveals the Molecular Mechanism of CaMKII Kinase Activation
During embryogenesis , multicellular animals are shaped via cell proliferation , cell rearrangement , and apoptosis . At the end of development , tissue architecture is then maintained through balanced rates of cell proliferation and loss . Here , we take an in silico approach to look for generic systems features of mo...	During development , multicellular animals are shaped by cell proliferation , cell rearrangement , and cell death to generate an adult whose form is maintained over time . Disruption of this finely balanced state can have devastating consequences , including aging , psoriasis , and cancer . Typically , however , develo...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental", "biology", "developmental", "biology/stem", "cells", "developmental", "biology/developmental", "evolution", "evolutionary", "biology/bioinformatics", "computational", "biology", "evolutionary", "biology", "evolutionary", "biology/developmental", "evolution" ]	2008	The Evolution of Robust Development and Homeostasis in Artificial Organisms
The involvement of ethylene in fruit ripening is well documented , though knowledge regarding the crosstalk between ethylene and other hormones in ripening is lacking . We discovered that AUXIN RESPONSE FACTOR 2A ( ARF2A ) , a recognized auxin signaling component , functions in the control of ripening . ARF2A expressio...	The hormone ethylene is known to be involved in fleshy fruit ripening , although the role of other hormones is less well studied . Here we investigated the role of AUXIN RESPONSE FACTOR 2A ( ARF2A ) in tomato fruit ripening and suggest that it may be involved in the crosstalk between ethylene and other hormones . We sh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chemical", "compounds", "ethylene", "signaling", "cascade", "ethylene", "organic", "compounds", "hormones", "plant", "science", "plant", "hormones", "crops", "plants", "cytokinins", "crop", "science", "gene", "expression", "chemistry", "tomatoes", "fruits", "agricultur...	2016	AUXIN RESPONSE FACTOR 2 Intersects Hormonal Signals in the Regulation of Tomato Fruit Ripening
Signaling output of bone morphogenetic proteins ( BMPs ) is determined by two sets of opposing interactions , one with heterotetrameric complexes of cell surface receptors , the other with secreted antagonists that act as ligand traps . We identified two mutations ( N445K , T ) in patients with multiple synostosis synd...	The development of the human skeleton is regulated by intricate signaling pathways involving secreted molecules that bind to cell surface receptors to elicit a response in the target cell . Bone morphogenetic proteins ( BMPs ) are an important part of this process . Their signaling capacity is regulated on several leve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "developmental", "biology/embryology", "genetics", "and", "genomics/gene", "function", "genetics", "and", "genomics/medical", "genetics" ]	2009	Mutations in GDF5 Reveal a Key Residue Mediating BMP Inhibition by NOGGIN
Cells employ active measures to restrict infection by pathogens , even prior to responses from the innate and humoral immune defenses . In this context selective autophagy is activated upon pathogen induced membrane rupture to sequester and deliver membrane fragments and their pathogen contents for lysosomal degradatio...	Cells have developed surveillance systems to detect invading pathogens , e . g . when they damage the membrane upon cell entry . Cells respond to membrane damage by activating selective autophagy to target pathogens for lysosomal degradation and pathogen removal . In this manuscript we show that endosome penetrating ad...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "innate", "immune", "system", "autophagic", "cell", "death", "medicine", "and", "health", "sciences", "antigen", "presentation", "immune", "physiology", "classical", "mechanics", "vesicles", "cell", "processes", "immunology", "microbiology", "in", "vi...	2017	Multi-layered control of Galectin-8 mediated autophagy during adenovirus cell entry through a conserved PPxY motif in the viral capsid
Anonymized electronic medical records are an increasingly popular source of research data . However , these datasets often lack race and ethnicity information . This creates problems for researchers modeling human disease , as race and ethnicity are powerful confounders for many health exposures and treatment outcomes;...	Race and ethnicity are typically unspecified in very large electronic medical claims datasets . Computationally estimating a patient’s missing race and ethnicity from their medical records is important on both an academic and practical basis . Academically , discriminative medical events tell us about racial and ethnic...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "neural", "networks", "hispanic", "people", "applied", "mathematics", "neuroscience", "ethnicities", "algorithms", "simulation", "and", "modeling", "mathematics", "artificial", "intelligence", "research", "and", "analysis", "method...	2018	RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning
National mapping of soil-transmitted helminth infections ( STH ) was conducted for the first time in all of the 77 districts of Benin ( West Africa ) from 2013 to 2015 . This mapping aimed to provide basic epidemiological data essential for the implementation of the national strategy against the neglected tropical dise...	Benin , like other low or moderate-income countries in the African continent , is endemic for several neglected tropical diseases , including soil-transmitted helminthiases . The National Program for Neglected Tropical Diseases of the Ministry of Health has conducted the national STH mapping using the Kato-Katz method ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "education", "helminths", "sociology", "tropical", "diseases", "hookworms", "social", "sciences", "geographical", "locations", "parasitic", "diseases", "animals", "ascaris", "ascaris", "lumbricoides", "benin", "neg...	2018	Results of the first mapping of soil-transmitted helminths in Benin: Evidence of countrywide hookworm predominance
Polycomb group proteins mediate transcriptional silencing in diverse developmental processes . Sex chromosomes undergo chromosome-wide transcription silencing during male meiosis . Here we report that mouse SCML2 ( Sex comb on midleg-like 2 ) , an X chromosome-encoded polycomb protein , is specifically expressed in ger...	Chromatin-modifying enzymes regulate the chromatin state during development and disease . Polycomb group proteins control the expression of homeotic genes in developmental patterning by catalyzing post-translational modifications of histones—core protein components of the chromatin . Most studies have focused on widely...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Polycomb Protein SCML2 Associates with USP7 and Counteracts Histone H2A Ubiquitination in the XY Chromatin during Male Meiosis
Disturbance of cellular functions results in the activation of stress-signaling pathways that aim at restoring homeostasis . We performed a genome-wide screen to identify components of the signal transduction of the mitochondrial unfolded protein response ( UPRmt ) to a nuclear chaperone promoter . We used the ROS gene...	Cellular respiration takes place in the mitochondria . Reactive oxygen species ( ROS ) are a damaging byproduct of cellular respiration . In adverse conditions , when the load of ROS becomes critical for mitochondrial function , a stress-response pathway , the unfolded protein response of the mitochondria ( UPRmt ) , i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "genetic", "screens", "genetics", "biology", "genetics", "and", "genomics" ]	2013	Surveillance-Activated Defenses Block the ROS–Induced Mitochondrial Unfolded Protein Response
Outbreaks of Rift Valley fever ( RVF ) , a mosquito-borne viral zoonosis , have previously been associated with unusually heavy rainfall and extensive flooding . The disease is a serious public health problem in Africa and the Middle East , and is a potential global health threat . In Kenya , outbreaks of the disease h...	In this study , we showed that , although pastoralist communities living in Ijara district of Kenya had a positive attitude towards RVF prevention , they had little knowledge regarding the vectors , transmission , and signs or symptoms of RVF . Community members were not aware that abortion of pregnant animals and high...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Knowledge, Attitudes and Practices (KAP) on Rift Valley Fever among Pastoralist Communities of Ijara District, North Eastern Kenya
The filoviruses , Marburg virus and Ebola virus , cause severe hemorrhagic fever with high mortality in humans and nonhuman primates . Among the most promising filovirus vaccines under development is a system based on recombinant vesicular stomatitis virus ( rVSV ) that expresses an individual filovirus glycoprotein ( ...	Ebola and Marburg viruses are categorized as Category A priority pathogens by several US Government agencies as a result of their high mortality rates and potential for use as agents of bioterrorism . There are currently no vaccines or therapeutics approved for human use . A replication-competent , recombinant vesicula...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "biology", "microbiology" ]	2012	Recombinant Vesicular Stomatitis Virus Vaccine Vectors Expressing Filovirus Glycoproteins Lack Neurovirulence in Nonhuman Primates
Mechanotransduction modulates cellular functions as diverse as migration , proliferation , differentiation , and apoptosis . It is crucial for organ development and homeostasis and leads to pathologies when defective . However , despite considerable efforts made in the past , the molecular basis of mechanotransduction ...	Cells sense mechanical forces and design an appropriate response crucial for cell and organ shape and differentiation during development , as well as for physiological adaptation . In particular , cardiac muscle continuously adapts to the mechanical constraints generated by its own rhythmic contractile activity . Conse...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/functional", "genomics", "cardiovascular", "disorders/arrhythmias,", "electrophysiology,", "and", "pacing", "physiology/cardiovascular", "physiology", "and", "circulation", "genetics", "and", "genomics/gene", "function", "physiology/integrative", "phy...	2010	Response to Mechanical Stress Is Mediated by the TRPA Channel Painless in the Drosophila Heart
Unlike their counterparts in bacterial and higher eukaryotic hosts , most fungal viruses are transmitted intracellularly and lack an extracellular phase . Here we determined the cryo-EM structure at 3 . 7 Å resolution of Rosellinia necatrix quadrivirus 1 ( RnQV1 ) , a fungal double-stranded ( ds ) RNA virus . RnQV1 , t...	Most fungal RNA viruses are transmitted by cytoplasmic interchange without leaving the host . We report the cryo-electron microscopy structure , at near-atomic resolution , of the double-stranded RNA Rosellinia necatrix quadrivirus 1 ( RnQV1 ) ; this virus infects the fungus Rosellinia necatrix , a pathogenic ascomycet...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "dimers", "(chemical", "physics)", "fungal", "genetics", "microbiology", "viral", "structure", "fungal", "structure", "electron", "cryo-microscopy", "viruses", "rna", "viruses", "microscopy", "research", "and", "analysis", "methods", "sequence", "analysis", "mycology", ...	2017	Acquisition of functions on the outer capsid surface during evolution of double-stranded RNA fungal viruses
Studies have suggested that somatic events in tumors can depend on an individual's constitutional genotype . We used squamous cell carcinomas ( SCC ) of the skin , which arise in high multiplicity in organ transplant recipients , as a model to compare the pattern of somatic alterations within and across individuals . S...	Tumors exhibit DNA copy number gains and losses , many of which alter the dosage of genes that promote or suppress tumorigenesis . Evidence from familial cancer syndromes and animal models have shown that DNA copy number changes acquired somatically during tumor progression can be controlled by the constitutional genot...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/cancer", "genetics", "oncology/skin", "cancers" ]	2010	Germline Variation Controls the Architecture of Somatic Alterations in Tumors
The antibiotic treatment of people with trachoma helps to prevent transmission the disease in a community . Currently , Zithromax is the drug recommended for mass drug administration ( MDA ) . MDA should be carried out annually for three to five years in trachoma endemic areas . Coverage survey is essential to track pr...	Ethiopia has the world's highest burden of trachoma . The disease causes significant blindness and visual impairment , particularly in poorer communities . To prevent the transmission of active trachoma , mass administration of Zithromax is given every year , which is implemented for consecutive three to five years in ...	[ "Abstract", "Introduction", "Method", "Discussion" ]	[ "medicine", "and", "health", "sciences", "maternal", "health", "obstetrics", "and", "gynecology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "political", "science", "health", "care", "bacterial", "diseases", "women's", "health", "pharmace...	2018	Coverage, social mobilization and challenges of mass Zithromax administration campaign in South and South East zones of Tigray, Northern Ethiopia: A cross sectional study
Transcription factors act in concert to induce lineage commitment towards Th1 , Th2 , or T regulatory ( Treg ) cells , and their counter-regulatory mechanisms were shown to be critical for polarization between Th1 and Th2 phenotypes . FOXP3 is an essential transcription factor for natural , thymus-derived ( nTreg ) and...	Specific immune responses against foreign or autologous antigens are driven by specialized epitope-specific T cells , whose numbers expand upon recognition of antigen found on professional antigen-presenting cells . The subsequent maturation process involves the differentiation of certain T cell phenotypes such as pro-...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology" ]	2007	GATA3-Driven Th2 Responses Inhibit TGF-β1–Induced FOXP3 Expression and the Formation of Regulatory T Cells
X chromosome inactivation ( XCI ) is the phenomenon occurring in female mammals whereby dosage compensation of X-linked genes is obtained by transcriptional silencing of one of their two X chromosomes , randomly chosen during early embryo development . The earliest steps of random X-inactivation , involving counting of...	In mammals , female cells silence one of their two X chromosomes to equalize X products with respect to males . The mechanism whereby cells count their X's and randomly choose the one to inactivate is , though , one of the most mysterious aspects of X chromosome inactivation ( XCI ) . The longstanding hypothesis is tha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physics", "biophysics", "genetics", "and", "genomics", "mammals" ]	2007	Self-Assembly and DNA Binding of the Blocking Factor in X Chromosome Inactivation
Variation of an inherited trait across a population cannot be explained by additive contributions of relevant genes , due to epigenetic effects and biochemical interactions ( epistasis ) . Detecting epistasis in genomic data still represents a significant challenge that requires a better understanding of epistasis from...	Epistasis is a widespread and ubiquitous genetic property of biological networks that shape evolutionary trajectories . Detecting epistasis in genomic data still represents a great challenge that could be met with a better understanding of epistasis from a mechanistic , evolutionary point of view . Here , using a stand...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "organismal", "evolution", "deletion", "mutation", "microbiology", "genetic", "mapping", "epistasis", "mutation", "microbial", "evolution", "genome", "analysis", "thermodynamics", "fitness", "epistasis", "genomics", "entropy", "evolutionary", "genetics", "viral", "evolution...	2018	Evolutionary footprint of epistasis
The regulatory logic of time- and tissue-specific gene expression has mostly been dissected in the context of the smallest DNA fragments that , when isolated , recapitulate native expression in reporter assays . It is not known if the genomic sequences surrounding such fragments , often evolutionarily conserved , have ...	In this study we provide evidence that eukaryotic enhancers contain regulatory sequences that provide robustness of gene expression to genetic and environmental perturbation . The regulatory logic of tissue-specific gene expression is encoded by compact non-coding enhancer sequences . We hypothesized that enhancers fun...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "molecular", "development", "genetics", "gene", "expression", "molecular", "genetics", "biology", "pattern", "formation", "genetics", "and", "genomics", "cell", "fate", "determination", "evolutionary", "developmental", "biology" ]	2011	Consequences of Eukaryotic Enhancer Architecture for Gene Expression Dynamics, Development, and Fitness
Proteins of the Fanconi Anemia ( FA ) complementation group are required for crosslink ( CL ) repair in humans and their loss leads to severe pathological phenotypes . Here we characterize a homolog of the Fe-S cluster helicase FANCJ in the model plant Arabidopsis , AtFANCJB , and show that it is involved in interstran...	The Fanconi Anemia and Hoyeraal-Hreidarsson syndromes are severe human genetic diseases that are correlated with DNA repair deficiencies . Interestingly , plants harbour homologues of factors in their genome that are causative for the respective diseases upon mutation . Using the model plant Arabidopsis , we analysed i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "engineering", "and", "technology", "nucleases", "enzymes", "brassica", "enzymology", "dna-binding", "proteins", "dna", "damage", "plant", "science", "model", "organisms", "dna", "replication", "experimental", "organism", "systems", "plant", "genomics", ...	2019	An Arabidopsis FANCJ helicase homologue is required for DNA crosslink repair and rDNA repeat stability
Epistatic interactions between genes and individual mutations are major determinants of the evolutionary properties of genetic systems and have therefore been well documented , but few quantitative data exist on epistatic interactions between beneficial mutations , presumably because such mutations are so much rarer th...	Epistasis , the extent to which the effects of a mutation depend on its genetic context , can have profound effects on the evolutionary process and strongly affects our understanding of the prevalence of sexual reproduction . It has been investigated in a diverse array of organisms but almost exclusively for deleteriou...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "microbiology", "evolutionary", "biology", "genetics", "and", "genomics" ]	2011	Epistasis between Beneficial Mutations and the Phenotype-to-Fitness Map for a ssDNA Virus
Scrub typhus is a life-threatening disease , due to infection with O . tsutsugamushi , a Gram-negative bacterium that preferentially replicates in endothelial cells and professional phagocytes . Meningoencephalitis has been reported in scrub typhus patients and experimentally-infected animals; however , the neurologica...	Scrub typhus is a life-threatening disease , due to infection with O . tsutsugamushi , a Gram-negative bacterium that preferentially replicates in endothelial cells and professional phagocytes . Meningoencephalitis has been reported in scrub typhus patients and in experimentally infected animals; however , the neurolog...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "bacteriology", "typhus", "medicine", "and", "health", "sciences", "innate", "immune", "system", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "brain", "damage", "nervous", "system", "pathogens", "animal", "models", "of", "disease"...	2017	Type 1-skewed neuroinflammation and vascular damage associated with Orientia tsutsugamushi infection in mice
Sri Lanka’s Anti-Filariasis Campaign conducted 5 annual rounds of mass drug administration ( MDA ) with diethylcarbamazine ( DEC ) plus albendazole to eliminate lymphatic filariasis ( LF ) in all endemic districts between 2002 and 2006 . Post-MDA surveillance has consistently documented Wuchereria bancrofti microfilare...	Lymphatic filariasis ( LF , also commonly known as “elephantiasis ) is a leading cause of disability in the developing world . It is caused by parasitic worms that are transmitted by mosquitoes . The Sri Lankan Anti-Filariasis Campaign provided five annual rounds of MDA with diethylcarbamazine and albendazole in all in...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "and", "discussion", "Additional", "discussion", "and", "conclusions" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "european", "union", "education", "sociology", "geographical", "locations", "social", "sciences", "parasitic", "diseases", "animals", "filariasis", "insect", "vectors", "public", "and", "occupat...	2019	Systematic sampling of adults as a sensitive means of detecting persistence of lymphatic filariasis following mass drug administration in Sri Lanka
How cell shape is controlled is a fundamental question in developmental biology , but the genetic and molecular mechanisms that determine cell shape are largely unknown . Arabidopsis trichomes have been used as a good model system to investigate cell shape at the single-cell level . Here we describe the trichome cell s...	The particular shape of plant cells is not only crucial for their biological functions but also affects the overall shape of organs . How cell shape is controlled is a fundamental question in developmental biology , and the study of plant cell shape regulation is an interesting part of plant biology . Arabidopsis trich...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "anatomy", "trichomes", "microtubules", "plant", "growth", "and", "development", "plant", "embryo", "anatomy", "brassica", "developmental", "biology", "plant", "science", "model", "organisms", "seedlings", "tubulins", "plants", "cellular", "structures", "and", ...	2016	TCS1, a Microtubule-Binding Protein, Interacts with KCBP/ZWICHEL to Regulate Trichome Cell Shape in Arabidopsis thaliana
The Ross-Macdonald model has dominated theory for mosquito-borne pathogen transmission dynamics and control for over a century . The model , like many other basic population models , makes the mathematically convenient assumption that populations are well mixed; i . e . , that each mosquito is equally likely to bite an...	Pathogens transmitted by mosquitoes , such as malaria and dengue , are notorious for the biological complexity associated with how they are transmitted within local communities . Yet mathematical models for these pathogens , which are critical tools for making recommendations for control policy , are based around conce...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "metapopulation", "dynamics", "theoretical", "biology", "infectious", "disease", "epidemiology", "epidemiology", "disease", "dynamics", "population", "dynamics", "population", "biology", "biology", "epidemiological", "methods", "spatial", "epidemiology" ]	2013	Heterogeneity, Mixing, and the Spatial Scales of Mosquito-Borne Pathogen Transmission
Dosage compensation in male Drosophila relies on the X chromosome–specific recruitment of a chromatin-modifying machinery , the dosage compensation complex ( DCC ) . The principles that assure selective targeting of the DCC are unknown . According to a prevalent model , X chromosome targeting is initiated by recruitmen...	In sexually dimorphic species , unequal distribution of sex chromosomes requires adjustment of gene expression levels between the sexes . Male flies enhance transcription from the single X chromosome to meet the levels in females ( XX ) . The specific recognition of sex chromosomes is a crucial step in this dosage comp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "molecular", "biology/chromatin", "structure", "cell", "biology/nuclear", "structure", "and", "function", "molecular", "biology/chromosome", "structure", "genetics", "and", "genomics/chromosome", "biology", "genetics", "and", "genomics/...	2008	The Chromosomal High-Affinity Binding Sites for the Drosophila Dosage Compensation Complex
Although retinoic acid ( RA ) has been implicated as an extrinsic signal regulating forebrain neurogenesis , the processes regulated by RA signaling remain unclear . Here , analysis of retinaldehyde dehydrogenase mutant mouse embryos lacking RA synthesis demonstrates that RA generated by Raldh3 in the subventricular zo...	The vitamin A metabolite retinoic acid is an important signaling molecule needed for development of the central nervous system . Previous studies have shown a role for retinoic acid in regulating genes involved in the generation of motor neurons both in the hindbrain and spinal cord , but the role of retinoic acid in t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/embryology", "developmental", "biology/stem", "cells", "cell", "biology/cell", "signaling", "cell", "biology/neuronal", "signaling", "mechanisms", "developmental", "biology/cell", "differentiation", "developmental", "biology/neurodevelopment", "development...	2011	Retinoic Acid Functions as a Key GABAergic Differentiation Signal in the Basal Ganglia
Latin Americans are highly heterogeneous regarding the type of Native American ancestry . Consideration of specific associations with common diseases may lead to substantial advances in unraveling of disease etiology and disease prevention . Here we investigate possible associations between the type of Native American ...	A lot of attention has been paid to Latino heterogeneity related to individual proportions of Native American , European and African ancestry . The importance of the type of Native American ancestry for health , however , has hardly been studied . Here we examined genetic data from 2 , 039 admixed Chileans to investiga...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "death", "rates", "dermatology", "medicine", "and", "health", "sciences", "chile", "(country)", "education", "demography", "sociology", "geographical", "locations", "cancers", "and", "neoplasms", "social", "sciences", "gastrointestinal", "tumors", "ethnicities", "oncology...	2017	Subtypes of Native American ancestry and leading causes of death: Mapuche ancestry-specific associations with gallbladder cancer risk in Chile
The role of the E6 oncoprotein from high-risk members of the α human papillomavirus genus in anogenital cancer has been well established . However , far less is known about the E6 protein from the β human papillomavirus genus ( β-HPVs ) . Some β-HPVs potentially play a role in non-melanoma skin cancer development , alt...	Human papillomaviruses are a large family of viruses that can cause ailments ranging from benign warts to anogenital cancer . Recently , interest has increased for a subgroup of these viruses , the β-HPVs , because of their potential involvement in squamous cell skin cancer . In this work , we show that the E6 protein ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology", "viruses", "and", "cancer", "biology", "microbiology" ]	2012	HPV 5 and 8 E6 Abrogate ATR Activity Resulting in Increased Persistence of UVB Induced DNA Damage
Accumulation of genome rearrangements is a characteristic of aged tissues . Since genome rearrangements result from faulty repair of DNA double strand breaks ( DSBs ) , we hypothesized that DNA DSB repair becomes less efficient with age . The Non-Homologous End Joining ( NHEJ ) pathway repairs a majority of DSBs in ver...	DNA damage disrupting both DNA strands , termed double strand breaks ( DSBs ) , poses a threat to cell survival . If repaired inappropriately , such DNA breaks lead to genomic rearrangements , mutations , and ultimately cancer . Nonhomologous end joining ( NHEJ ) is the major pathway for repairing double-stranded break...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "aging", "cell", "physiology", "biochemistry", "developmental", "biology", "animal", "models", "model", "organisms", "organism", "development", "cell", "biology", "biology", "and", "life", "sciences", "dna", "repair", "dna", "mouse", "models", "cell", "aging", "rese...	2014	Knock-In Reporter Mice Demonstrate that DNA Repair by Non-homologous End Joining Declines with Age
C-type lectins dectin-1 and dectin-2 on dendritic cells elicit protective immunity against fungal infections through induction of TH1 and TH-17 cellular responses . Fungal recognition by dectin-1 on human dendritic cells engages the CARD9-Bcl10-Malt1 module to activate NF-κB . Here we demonstrate that Malt1 recruitment...	Fungal infections are a major health threat and the incidence is growing worldwide . There is a need for efficient antifungal vaccines . Adaptive immune responses and in particular T helper cell type 17 ( TH-17 ) responses are crucial in the defence against fungal infections . Human dendritic cells ( DCs ) induce TH-17...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/immunomodulation", "infectious", "diseases/fungal", "infections", "immunology/innate", "immunity", "immunology/leukocyte", "signaling", "and", "gene", "expression", "immunology/immunity", "to", "infections" ]	2011	Selective C-Rel Activation via Malt1 Controls Anti-Fungal TH-17 Immunity by Dectin-1 and Dectin-2
Urinary Schistosomiasis is a neglected tropical disease endemic in many sub Saharan -African countries . Collectin Kidney 1 ( CL-K1 , encoded by COLEC11 on chromosome 2p25 . 3 ) , a member of the vertebrate C-type lectin super family , has recently been identified as pattern-recognition molecule ( PRR ) of the lectin c...	Collectin Kidney 1 ( CL-K1 ) was discovered in 2006 . It is a pattern-recognition molecule ( PRR ) of the lectin complement pathway and is mainly expressed in the kidneys . We investigated a possible functional role of CL-K1 during urinary schistosomiasis on the basis of the rationale: i ) . Schistosome teguments are f...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Lectin Complement Protein Collectin 11 (CL-K1) and Susceptibility to Urinary Schistosomiasis
Unlike other monoamine neurotransmitters , the mechanism by which the brain's histamine content is regulated remains unclear . In mammals , vesicular monoamine transporters ( VMATs ) are expressed exclusively in neurons and mediate the storage of histamine and other monoamines . We have studied the visual system of Dro...	Neurons , the cells in the brain responsible for carrying information , communicate with each other using a class of chemicals known as neurotransmitters . One family of neurotransmitters , the monoamines , includes dopamine , serotonin , and histamine , all of which play major physiological roles . However , unlike do...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/neuronal", "and", "glial", "cell", "biology", "neuroscience/sensory", "systems", "genetics", "and", "genomics/gene", "function", "neuroscience/neuronal", "and", "glial", "cell", "biology", "neuroscience" ]	2008	A Glial Variant of the Vesicular Monoamine Transporter Is Required To Store Histamine in the Drosophila Visual System
Insect fat body is the organ for intermediary metabolism , comparable to vertebrate liver and adipose tissue . Larval fat body is disintegrated to individual fat body cells and then adult fat body is remodeled at the pupal stage . However , little is known about the dissociation mechanism . We find that the moth Helico...	Insect fat body is the intermediary metabolism organ and the main source of hemolymph components , and it is crucial for insect development and metamorphosis . However , molecular mechanism for the fat body remodeling is almost unknown other than in Drosophila melanogaster . A pupal diapause species the cotton bollworm...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "pest", "control", "biology", "agriculture" ]	2013	A Regulatory Pathway, Ecdysone-Transcription Factor Relish-Cathepsin L, Is Involved in Insect Fat Body Dissociation
The clinical spectrum of ciliopathies affecting motile cilia spans impaired mucociliary clearance in the respiratory system , laterality defects including heart malformations , infertility and hydrocephalus . Using linkage analysis and whole exome sequencing , we identified two recessive loss-of-function MNS1 mutations...	Although no clear explanation is yet provided for the correct establishment of the left-right body asymmetry in human , animal studies have clearly shown that tiny-hair-like organelles in the ventral node of the embryo—called motile nodal monocilia—beat regularly and play an important role in this process . To date , d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "urology", "medicine", "and", "health", "sciences", "microtubules", "male", "infertility", "germ", "cells", "mutation", "developmental", "biology", "dyneins", "molecular", "motors", "nonsense", "mutation", "genome", "analysis", "embryos", "cellular", "structures", "and"...	2018	Homozygous loss-of-function mutations in MNS1 cause laterality defects and likely male infertility
The use of DNA microarray technology to study global Schistosoma gene expression has led to the rapid identification of novel biological processes , pathways or associations . Implementation of standardized DNA microarray protocols across laboratories would assist maximal interpretation of generated datasets and extend...	Infection with parasitic schistosome worms causes schistosomiasis , a major neglected tropical disease currently affecting millions of individuals living in the developing world . A virtually unique characteristic of the schistosome life style in comparison to other members of the Phylum Platyhelminthes is that schisto...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/helminth", "infections", "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "computational", "biology/genomics", "infectious", "diseases/neglected", "tropical", "diseases" ]	2008	Use of Genomic DNA as an Indirect Reference for Identifying Gender-Associated Transcripts in Morphologically Identical, but Chromosomally Distinct, Schistosoma mansoni Cercariae
Helminth parasites rely on fast-synaptic transmission in their neuromusculature to experience the outside world and respond to it . Acetylcholine plays a pivotal role in this and its receptors are targeted by a wide variety of both natural and synthetic compounds used in human health and for the control of parasitic di...	Parasitic nematodes pose a global threat to human health and severely impact livestock animals and crops . Most anthelmintic drugs paralyze worms , targeting pentameric neurotransmitter receptors in the neuromuscular synapse . A detailed understanding of this signaling allows the most effective use of existing drugs an...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "caenorhabditis", "vertebrates", "parasitic", "diseases", "animals", "xenopus", "nematode", "infections", "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "amphi...	2016	Recent Duplication and Functional Divergence in Parasitic Nematode Levamisole-Sensitive Acetylcholine Receptors
Schistosomiasis ( bilharzia ) is a tropical disease caused by trematode parasites ( Schistosoma ) that affects hundreds of millions of people in the developing world . Currently only a single drug ( praziquantel ) is available to treat this disease , highlighting the importance of developing new techniques to study Sch...	Schistosomes are parasitic flatworms that infect hundreds of millions of people worldwide . The development of genomic resources and recent application of functional genomic tools ( e . g . , global gene expression studies , inhibition of gene expression by RNA interference , and transgenesis ) hold the promise of revo...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology", "zoology", "parasitology", "helminthology" ]	2011	An Atlas for Schistosoma mansoni Organs and Life-Cycle Stages Using Cell Type-Specific Markers and Confocal Microscopy

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