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Zika virus ( ZIKV ) has gained worldwide attention since it emerged , and a global effort is underway to understand the correlates of protection and develop diagnostics to identify rates of infection . As new therapeutics and vaccine approaches are evaluated in clinical trials , additional effort is focused on identify...	Since the detection of ZIKV in the Americas in 2015 , urgent efforts have been made to develop ZIKV-specific methods of diagnosis and novel vaccines . However , a full understanding of the natural history of infection , interactions with other arboviruses , and the protection mediated by therapeutics or vaccination is ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "nervous", "system", "pathogens", "animal", "models", "of", "disease", "immunology", "microbiology", "animal", "models", "viruses", "model", "...	2018	CD4+T cells mediate protection against Zika associated severe disease in a mouse model of infection
Eukaryotic cells integrate layers of gene regulation to coordinate complex cellular processes; however , mechanisms of post-transcriptional gene regulation remain poorly studied . The human fungal pathogen Histoplasma capsulatum ( Hc ) responds to environmental or host temperature by initiating unique transcriptional p...	Eukaryotic cells alter their developmental programs in response to environmental signals . Histoplasma capsulatum ( Hc ) , a ubiquitous fungal pathogen of humans , establishes unique transcriptional programs to specify growth in either a multicellular hyphal form or unicellular yeast form in response to temperature . S...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma
Conformational polymorphism of DNA is a major causative factor behind several incurable trinucleotide repeat expansion disorders that arise from overexpansion of trinucleotide repeats located in coding/non-coding regions of specific genes . Hairpin DNA structures that are formed due to overexpansion of CAG repeat lead ...	When a set of 3 nucleotides in a DNA sequence repeats beyond a certain number , it leads to incurable neurological or neuromuscular disorders . Such DNA sequences tend to form unusual DNA structures comprising of base pairing schemes different from the canonical A…T/G…C base pairs . Influence of such unusual base pairi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Twisting Right to Left: A…A Mismatch in a CAG Trinucleotide Repeat Overexpansion Provokes Left-Handed Z-DNA Conformation
The recent success of genome-wide association studies ( GWAS ) is now followed by the challenge to determine how the reported susceptibility variants mediate complex traits and diseases . Expression quantitative trait loci ( eQTLs ) have been implicated in disease associations through overlaps between eQTLs and GWAS si...	Genome-wide association studies have led to the identification of susceptibility loci for a variety of human complex traits . What is still largely missing , however , is the understanding of the biological context in which these candidate variants act and of how they determine each trait . Given the localization of ma...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/gene", "expression" ]	2010	Candidate Causal Regulatory Effects by Integration of Expression QTLs with Complex Trait Genetic Associations
Ixodid ticks are notorious blood-sucking ectoparasites and are completely dependent on blood-meals from hosts . In addition to the direct severe effects on health and productivity , ixodid ticks transmit various deadly diseases to humans and animals . Unlike rapidly feeding vessel-feeder hematophagous insects , the har...	Ixodid ticks are serious blood-sucking ectoparasites that are essentially dependent on blood-meals from hosts for survival . The feeding mechanism of hard ticks , however , is very complex and is quite different from that of blood-sucking insects that suck blood rapidly and directly from blood vessels . Hard ticks suck...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/parasitology", "infectious", "diseases/protozoal", "infections", "microbiology/cellular", "microbiology", "and", "pathogenesis", "microbiology/medical", "microbiology" ]	2011	Longistatin, a Plasminogen Activator, Is Key to the Availability of Blood-Meals for Ixodid Ticks
Receptive fields acquired through unsupervised learning of sparse representations of natural scenes have similar properties to primary visual cortex ( V1 ) simple cell receptive fields . However , what drives in vivo development of receptive fields remains controversial . The strongest evidence for the importance of se...	The responses of neurons in the primary visual cortex ( V1 ) , a region of the brain involved in encoding visual input , are modified by the visual experience of the animal during development . For example , most neurons in animals reared viewing stripes of a particular orientation only respond to the orientation that ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental", "neuroscience", "computational", "neuroscience", "sensory", "systems", "biology", "neuroscience", "coding", "mechanisms" ]	2013	Sparse Coding Can Predict Primary Visual Cortex Receptive Field Changes Induced by Abnormal Visual Input
Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina , ( Basidiomycota , fungi ) that otherwise consists almost exclusively of plant pathogens . Malassezia are typically isolated from warm-blooded animals , are dominant members of the human skin mycobiome and are associated with comm...	Malassezia are the dominant eukaryotic residents of human skin and are associated with the most common skin disorders , including dandruff , atopic dermatitis , eczema , and others . Despite significant effort , the role of Malassezia in skin disease and homeostasis remains unclear . Malassezia are also unique among fu...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin
Environmental signals that trigger bacterial pathogenesis and biofilm formation are mediated by changes in the level of cyclic dimeric guanosine monophosphate ( c-di-GMP ) , a unique eubacterial second messenger . Tight regulation of cellular c-di-GMP concentration is governed by diguanylate cyclases and phosphodiester...	Bacteria can switch from a single-cell , free-floating behavioral mode to a community life-form via colonization of surfaces and the secretion of an extracellular matrix . This process , called biofilm formation , has been attributed to a majority of chronic infections , including the lungs , as occurs in patients with...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "biochemistry", "infectious", "diseases", "cell", "biology", "microbiology", "biophysics" ]	2008	Phosphorylation-Independent Regulation of the Diguanylate Cyclase WspR
Schistosoma mansoni tetraspanin 2 ( Sm-TSP-2 ) has been shown to be strongly recognized by IgG1 and IgG3 antibodies from individuals putatively resistant to schistosome infection , but not chronically infected people , and to induce high levels of protection against challenge infection in the murine model of schistosom...	Schistosoma mansoni tetraspanin 2 ( Sm-TSP-2 ) is considered a lead target for vaccine development against schistosomiasis mansoni because: ( 1 ) It is located in the schistosome tegument and is involved in tegument formation; ( 2 ) It is strongly recognized by IgG1 and IgG3 antibodies from individuals putatively resis...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "schistosomiasis", "neglected", "tropical", "diseases" ]	2011	Inconsistent Protective Efficacy and Marked Polymorphism Limits the Value of Schistosoma japonicum Tetraspanin-2 as a Vaccine Target
The human parvovirus Adeno-Associated Virus ( AAV ) type 2 can only replicate in cells co-infected with a helper virus , such as Adenovirus or Herpes Simplex Virus type 1 ( HSV-1 ) ; whereas , in the absence of a helper virus , it establishes a latent infection . Previous studies demonstrated that the ternary HSV-1 hel...	The Adeno-Associated Virus ( AAV ) is a human parvovirus that is widely used as a recombinant vector for gene transfer in animal studies and clinical trials designed to treat acquired or inherited genetic diseases . Wild type AAV is defined as a defective virus because it requires the presence of a helper virus to effi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/persistence", "and", "latency", "virology/viral", "replication", "and", "gene", "regulation", "virology" ]	2009	Definition of Herpes Simplex Virus Type 1 Helper Activities for Adeno-Associated Virus Early Replication Events
In mating fission yeast cells , sensing and response to extracellular pheromone concentrations occurs through an exploratory Cdc42 patch that stochastically samples the cell cortex before stabilizing towards a mating partner . Active Ras1 ( Ras1-GTP ) , an upstream regulator of Cdc42 , and Gap1 , the GTPase-activating ...	Unicellular fission yeasts mate by fusing with partners of the opposite mating type . Each pair member grows towards its selected partner that signals its presence through secreted pheromone . The process of partner selection occurs through an exploratory patch ( containing activated signaling protein Cdc42 and upstrea...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "mechanisms", "of", "signal", "transduction", "light", "microscopy", "guanine", "nucleotide", "exchange", "factors", "fungi", "model", "organisms", "microscopy", "experimental", "organism", "systems", "cellular", "structures", "and", "organelles", "schizosaccharomyces", "...	2018	Exploration and stabilization of Ras1 mating zone: A mechanism with positive and negative feedbacks
The Drosophila melanogaster photoreceptor cell has long served as a model system for researchers focusing on how animal sensory neurons receive information from their surroundings and translate this information into chemical and electrical messages . Electroretinograph ( ERG ) analysis of Drosophila mutants has helped ...	During signaling in the nervous system , individual nerve cells transfer information to one another by a complex process called synaptic transmission . This communication involves the release of a specific neurotransmitter into the synaptic cleft , which then triggers signaling in the downstream neuron by binding to an...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Supporting", "Information" ]	[ "drosophila", "cell", "biology" ]	2007	The Role of Carcinine in Signaling at the Drosophila Photoreceptor Synapse
The previously identified LRS ( Loss of rDNA Silencing ) domain of the nucleosome is critically important for silencing at both ribosomal DNA and telomeres . To understand the function of the LRS surface in silencing , we performed an EMS mutagenesis screen to identify suppressors of the H3 A75V LRS allele . We identif...	The chromatin in which eukaryotic DNA is wrapped is organized in nucleosome units , consisting of eight core histone molecules . We study gene silencing , thought to be associated with chromatin compaction in Saccharomyces cerevisiae , which has most of its genome in the form of open chromatin , i . e . , the genes are...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "molecular", "biology/histone", "modification", "genetics", "and", "genomics", "molecular", "biology/chromatin", "structure" ]	2008	Compensatory Interactions between Sir3p and the Nucleosomal LRS Surface Imply Their Direct Interaction
Increasing clinical and biochemical evidence implicate mitochondrial dysfunction in the pathophysiology of Autism Spectrum Disorder ( ASD ) , but little is known about the biological basis for this connection . A possible cause of ASD is the genetic variation in the mitochondrial DNA ( mtDNA ) sequence , which has yet ...	Mitochondria contain their own genome , the mitochondrial DNA ( mtDNA ) , and are abundant in the brain where they produce energy and intracellular signals required for normal brain function and cognition . Mitochondrial dysfunction has been proposed as a cause of Autism Spectrum Disorder ( ASD ) , but the genetic basi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "mitochondrial", "dna", "autism", "social", "sciences", "developmental", "psychology", "neuroscience", "mutation", "drug", "design", "forms", "of", "dna", "heteroplasmy", "dna", "ph...	2016	Genetic Evidence for Elevated Pathogenicity of Mitochondrial DNA Heteroplasmy in Autism Spectrum Disorder
The timing of DNA synthesis , mitosis and cell division is regulated by a complex network of biochemical reactions that control the activities of a family of cyclin-dependent kinases . The temporal dynamics of this reaction network is typically modeled by nonlinear differential equations describing the rates of the com...	The physiological behaviors of cells ( growth and division , differentiation , movement , death , etc . ) are controlled by complex networks of interacting genes and proteins , and a fundamental goal of computational cell biology is to develop dynamical models of these regulatory networks that are realistic , accurate ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "biology/cell", "growth", "and", "division", "biophysics/theory", "and", "simulation", "computational", "biology/systems", "biology" ]	2011	A Hybrid Model of Mammalian Cell Cycle Regulation
Food deprivation is known to affect physiology and behavior . Changes that occur could be the result of the organism's monitoring of internal and external nutrient availability . In C . elegans , male mating is dependent on food availability; food-deprived males mate with lower efficiency compared to their well-fed cou...	We demonstrate that lack of sensation of food in the environment can alleviate spontaneous muscle seizures via an insulin-like mediated pathway . Food restriction is known to promote many adaptive physiological responses , including the mobilization of fat-stores , increases in life span , and suppression of seizures ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/behavioral", "neuroscience", "neuroscience/sensory", "systems", "cell", "biology/cell", "signaling", "neuroscience/neuronal", "signaling", "mechanisms", "neurological", "disorders/epilepsy" ]	2008	Sensory Perception of Food and Insulin-Like Signals Influence Seizure Susceptibility
Strains of Extraintestinal Pathogenic Escherichia coli ( ExPEC ) exhibit an array of virulence strategies and are a major cause of urinary tract infections , sepsis and meningitis . Efforts to understand ExPEC pathogenesis are challenged by the high degree of genetic and phenotypic variation that exists among isolates ...	Antibiotic resistance is an increasingly serious problem , especially among pathogenic strains of Escherichia coli that cause urinary tract infections , sepsis and meningitis . It is important to obtain a more comprehensive genome-wide understanding of bacterial virulence because it has the potential to uncover novel a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "escherichia", "coli", "medicine", "bacterial", "diseases", "infectious", "diseases", "gram", "negative", "genetic", "screens", "gene", "identification", "and", "analysis", "genetics", "microbial", "pathogens", "molecular", "genetics", "host-pathogen", "interaction", "bio...	2013	Combining Quantitative Genetic Footprinting and Trait Enrichment Analysis to Identify Fitness Determinants of a Bacterial Pathogen
Human whipworm ( Trichuris trichiura ) infects approximately 1 in 15 people worldwide , representing the leading infectious cause of colitis and subsequent , inflammatory bowel disease ( IBD ) . Current control measures focused on mass deworming have had limited success due to low drug efficacies . Vaccination would be...	Human whipworm ( Trichuris trichiura ) is pervasive intestinal parasite that causes malnutrition and inflammatory bowel disease ( IBD ) , predominately among the world’s most impoverished billion people . Available treatment strategies have had little impact on the disease prevalence or morbidity . A vaccine against hu...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "enzyme-linked", "immunoassays", "immunology", "tropical", "diseases", "parasitic", "diseases", "animal", "models", "preventive", "medicine", "developmental", "biol...	2018	Trichuris muris whey acidic protein induces type 2 protective immunity against whipworm
Mass treatment to trachoma endemic communities is a critical part of the World Health Organization SAFE strategy . However , non-participation may not be at random , affecting coverage surveys and effectiveness if infection is differential . As part of the Partnership for Rapid Elimination of Trachoma ( PRET ) , 32 com...	Trachoma , an infectious disease , continues to cause blindness . A great deal of the trachoma burden is concentrated in developing countries . The World Health Organization recommends mass treatment for entire communities in trachoma-endemic regions . In 32 Tanzanian and 48 Gambian communities with trachoma , mass tre...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/epidemiology", "public", "health", "and", "epidemiology/infectious", "diseases" ]	2010	Mass Treatment with Azithromycin for Trachoma Control: Participation Clusters in Households
Dendrite morphology , a neuron's anatomical fingerprint , is a neuroscientist's asset in unveiling organizational principles in the brain . However , the genetic program encoding the morphological identity of a single dendrite remains a mystery . In order to obtain a formal understanding of dendritic branching , we stu...	Neural computation has been shown to be heavily dependent not only on the connectivity of single neurons but also on their specific dendritic shape—often used as a key feature for their classification . Still , very little is known about the constraints determining a neuron's morphological identity . In particular , on...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/computational", "neuroscience", "neuroscience/neurodevelopment", "neuroscience/theoretical", "neuroscience" ]	2008	The Morphological Identity of Insect Dendrites
Bacterial survival requires adaptation to different environmental perturbations such as exposure to antibiotics , changes in temperature or oxygen levels , DNA damage , and alternative nutrient sources . During adaptation , bacteria often develop beneficial mutations that confer increased fitness in the new environment...	Bacteria must constantly adapt to many different environmental challenges , but how do they adapt when they lose a key gene product ? We addressed this question using Escherichia coli lacking pgi , a major metabolic gene involved in sugar utilization , by serially passing replicates lacking the pgi gene for 50 days and...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "microbiology/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/comparative", "genomics" ]	2010	Genetic Basis of Growth Adaptation of Escherichia coli after Deletion of pgi, a Major Metabolic Gene
The fungus Fusarium fujikuroi causes “bakanae” disease of rice due to its ability to produce gibberellins ( GAs ) , but it is also known for producing harmful mycotoxins . However , the genetic capacity for the whole arsenal of natural compounds and their role in the fungus' interaction with rice remained unknown . Her...	Fungi produce numerous “secondary metabolites” ( SMs ) that are not essential for life but can provide an advantage under natural conditions , e . g . in fungal-host interactions . Here , we conducted the most comprehensive analysis to date of secondary metabolism in fungi using Fusarium fujikuroi . This fungus causes ...	[ "Abstract", "Introduction", "Results/Discussion", "Material", "and", "Methods" ]	[ "genome-wide", "association", "studies", "genome", "expression", "analysis", "microbial", "metabolism", "spectrometric", "identification", "of", "proteins", "functional", "genomics", "host-pathogen", "interaction", "microbiology", "protein", "abundance", "fungal", "physiology...	2013	Deciphering the Cryptic Genome: Genome-wide Analyses of the Rice Pathogen Fusarium fujikuroi Reveal Complex Regulation of Secondary Metabolism and Novel Metabolites
Dendritic cells ( DCs ) are specialized phagocytes that internalize exogenous antigens and microbes at peripheral sites , and then migrate to lymphatic organs to display foreign peptides to naïve T cells . There are several examples where DCs have been shown to be more efficient at restricting the intracellular replica...	The immune system is designed to identify microbes that enter the body and elicit responses that prevent the replication and dissemination of these organisms . Dendritic cells play an important role in regulating host immunity to pathogens . Their phagocytic capacity enables DCs to internalize and destroy most microbes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/cellular", "microbiology", "and", "pathogenesis", "microbiology/innate", "immunity", "cell", "biology/cellular", "death", "and", "stress", "responses" ]	2009	Rapid Pathogen-Induced Apoptosis: A Mechanism Used by Dendritic Cells to Limit Intracellular Replication of Legionella pneumophila
RNA-seq is a promising technology to re-sequence protein coding genes for the identification of single nucleotide variants ( SNV ) , while simultaneously obtaining information on structural variations and gene expression perturbations . We asked whether RNA-seq is suitable for the detection of driver mutations in T-cel...	The quest for somatic mutations underlying oncogenic processes is a central theme in today's cancer research . High-throughput genomics approaches including amplicon re-sequencing , exome re-sequencing , full genome re-sequencing , and SNP arrays have contributed to cataloguing driver genes across cancer types . Thus f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Comprehensive Analysis of Transcriptome Variation Uncovers Known and Novel Driver Events in T-Cell Acute Lymphoblastic Leukemia
We have accumulated a large amount of biological network data and expect even more to come . Soon , we anticipate being able to compare many different biological networks as we commonly do for molecular sequences . It has long been believed that many of these networks change , or “rewire” , at different rates . It is t...	Biological networks represent various types of molecular organizations in a cell . During evolution , molecules have been shown to change at varying rates . Therefore , it is important to investigate the evolution of biological networks in terms of network rewiring . Understanding how biological networks evolve could e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology" ]	2011	Measuring the Evolutionary Rewiring of Biological Networks
Nuclear RNAs are subject to a number of RNA decay pathways that serve quality control and regulatory functions . As a result , any virus that expresses its genes in the nucleus must have evolved mechanisms that avoid these pathways , but the how viruses evade nuclear RNA decay remains largely unknown . The multifunctio...	Eukaryotic cells contain numerous nuclear RNA quality control ( QC ) systems that ensure transcriptome fidelity by detecting and degrading aberrant RNAs . Some viral RNAs are also predicted to be degraded by these RNA QC systems , so viruses have evolved mechanisms that counter host RNA QC pathways . Previous studies s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "vesicles", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "messenger", "rna", "rna", "extraction", "microbiology", "small", "nuclear", "rna", "viruses", "dna", "viruses", "cellular", "structur...	2019	Kaposi’s sarcoma-associated herpesvirus ORF57 protein protects viral transcripts from specific nuclear RNA decay pathways by preventing hMTR4 recruitment
Comparative studies suggest that at least some bird species have evolved mental skills similar to those found in humans and apes . This is indicated by feats such as tool use , episodic-like memory , and the ability to use one's own experience in predicting the behavior of conspecifics . It is , however , not yet clear...	A crucial step in the emergence of self-recognition is the understanding that one's own mirror reflection does not represent another individual but oneself . In nonhuman species and in children , the “mark test” has been used as an indicator of self-recognition . In these experiments , subjects are placed in front of a...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "neuroscience", "evolutionary", "biology" ]	2008	Mirror-Induced Behavior in the Magpie (Pica pica): Evidence of Self-Recognition
Facultative bacterial pathogens must adapt to multiple stimuli to persist in the environment or establish infection within a host . Temperature is often utilized as a signal to control expression of virulence genes necessary for infection or genes required for persistence in the environment . However , very little is k...	The ability to sense and respond to environmental changes is essential for the survival of all living organisms . Thermosensors are cellular components that can transform temperature changes into significant cellular responses necessary for adaptation and survival . In this study , we identify a protein thermosensor , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2011	A Protein Thermometer Controls Temperature-Dependent Transcription of Flagellar Motility Genes in Listeria monocytogenes
Stomata , valves on the plant epidermis , are critical for plant growth and survival , and the presence of stomata impacts the global water and carbon cycle . Although transcription factors and cell-cell signaling components regulating stomatal development have been identified , it remains unclear as to how their regul...	Generation of self-organized , functional tissue patterns is critical for development and regeneration in multicellular organisms . Small valves on the epidermis of land plants , called stomata , mediate gas-exchange while minimizing water loss . Density and spacing of stomata are regulated by transcription factors tha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Molecular Framework of a Regulatory Circuit Initiating Two-Dimensional Spatial Patterning of Stomatal Lineage
The engulfment of apoptotic cells is required for normal metazoan development and tissue remodeling . In Caenorhabditis elegans , two parallel and partially redundant conserved pathways act in cell-corpse engulfment . One pathway includes the adaptor protein CED-2 CrkII and the small GTPase CED-10 Rac , and acts to rea...	Cell death or apoptosis is a normal part of animal development , as is the engulfment and removal of dead cells by other cells . In the nematode Caenorhabditis elegans , ten highly conserved proteins have been characterized previously for their roles in engulfment and in cell migration , both of which involve the forma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "cell", "biology", "genetics", "and", "genomics" ]	2009	Abl Kinase Inhibits the Engulfment of Apopotic Cells in Caenorhabditis elegans
Metal acquisition is crucial for all cells and for the virulence of many bacterial pathogens . In particular , nickel is a virulence determinant for the human gastric pathogen Helicobacter pylori as it is the cofactor of two enzymes essential for in vivo colonization , urease and a [NiFe] hydrogenase . To import nickel...	Helicobacter pylori is a bacterium that persistently colonizes the stomach of half of the human population worldwide . Infection by H . pylori is associated with gastritis , peptic ulcer disease and adenocarcinoma . To resist gastric acidity and proliferate in the stomach , H . pylori possesses an urease , this enzyme ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "ureases", "enzymes", "pathogens", "microbiology", "enzymology", "animal", "models", "mutation", "model", "organisms", "helicobacter", "stomach", "bacteria", "nickel", "bacterial", "p...	2016	Characterization in Helicobacter pylori of a Nickel Transporter Essential for Colonization That Was Acquired during Evolution by Gastric Helicobacter Species
Spermine synthase ( SMS ) is an enzyme which function is to convert spermidine into spermine . It was shown that gene defects resulting in amino acid changes of the wild type SMS cause Snyder-Robinson syndrome , which is a mild-to-moderate mental disability associated with osteoporosis , facial asymmetry , thin habitus...	Proteins are constantly subjected to evolutionary pressure to assure the organism's survival and reproduction . At the same time , the proteins' amino acid sequence undergoes mutations , some of which may cause diseases while others may be reflecting natural differences within the population ( non-synonymous single nuc...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "biochemistry", "mutation", "evolutionary", "biology", "enzymes", "biology", "computational", "biology", "biophysics", "simulations", "biophysics", "evolutionary", "processes" ]	2013	Enhancing Human Spermine Synthase Activity by Engineered Mutations
Whole genome sequencing is a powerful tool in the discovery of single nucleotide polymorphisms ( SNPs ) and small insertions/deletions ( indels ) among mutant strains , which simplifies forward genetics approaches . However , identification of the causative mutation among a large number of non-causative SNPs in a mutan...	Whole genome sequencing is a powerful tool to detect changes in genomic DNA . However , how to identify a causative mutation from over 20 , 000 changes remains a big challenge . For the unicellular green alga Chlamydomonas , we built a library that consists of over 2 million changes from 16 strains . A comparison of ch...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Whole Genome Sequencing Identifies a Deletion in Protein Phosphatase 2A That Affects Its Stability and Localization in Chlamydomonas reinhardtii
Reproductive division of labor is a hallmark of multicellular organisms . However , the evolutionary pressures that give rise to delineated germ and somatic cells remain unclear . Here we propose a hypothesis that the mutagenic consequences associated with performing metabolic work favor such differentiation . We prese...	Cells within an organism are categorized as “germ” if they are able to grow into a whole new offspring organism or as “soma” if they contribute to the body's functionality but cannot produce an offspring themselves . From an evolutionary perspective , it is important to ask why and how a multicellular organism would de...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "biology", "and", "life", "sciences", "evolutionary", "theory" ]	2014	The Evolutionary Origin of Somatic Cells under the Dirty Work Hypothesis
Xenografts -as simplified animal models of cancer- differ substantially in vasculature and stromal architecture when compared to clinical tumours . This makes mathematical model-based predictions of clinical outcome challenging . Our objective is to further understand differences in tumour progression and physiology be...	Tumour-bearing animal models of cancer are needed to discover new drugs to treat cancer . We aim in this article to capture—through mathematics- some underlying phenomena of tumour growth in animals . We propose a set of equations that , despite being very simple , describe tumour growth , hypoxia and necrosis . Cells ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Oxygen-Driven Tumour Growth Model: A Pathology-Relevant Mathematical Approach
Leprosy is a chronic infectious disease caused by Mycobacterium leprae and mainly affects skin , peripheral nerves . Vitamin D receptor ( VDR ) gene polymorphism has been found to be associated with leprosy . Vitamin D has been shown to control several host immunomodulating properties through VDR gene . Vitamin D defic...	Present study was carried out to find out the association of vitamin D receptor ( VDR ) gene polymorphism , mRNA gene expression of VDR gene and level of vitamin D with leprosy reactions and leprosy patients . Surprisingly , level of vitamin D in leprosy patients was not found to be associated with the disease and its ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "variant", "genotypes", "tropical", "diseases", "immunology", "organic", "compounds", "genetic", "mapping", "bacterial", "diseases", "neglected", "tropical", "diseases", "molecular", "biology", "techniques"...	2018	VDR polymorphism, gene expression and vitamin D levels in leprosy patients from North Indian population
Epidermolysis Bullosa ( EB ) encompasses a spectrum of mechanobullous disorders caused by rare mutations that result in structural weakening of the skin and mucous membranes . While gene mutated and types of mutations present are broadly predictive of the range of disease to be expected , a remarkable amount of phenoty...	Epidermolysis bullosa ( EB ) is a group of rare genetic Mendelian disorders that result in mechanical fragility of the skin and mucosal membranes . Junctional EB is a subset caused by mutations that result in cleavage of the dermal-epidermal junction . All forms of EB demonstrate substantial variability in their clinic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2014	Molecular Identification of Collagen 17a1 as a Major Genetic Modifier of Laminin Gamma 2 Mutation-Induced Junctional Epidermolysis Bullosa in Mice
It is known that genetic variants can affect gene expression , but it is not yet completely clear through what mechanisms genetic variation mediate this expression . We therefore compared the cis-effect of single nucleotide polymorphisms ( SNPs ) on gene expression between blood samples from 1 , 240 human subjects and ...	Gene expression can be affected by genetic variation , e . g . single nucleotide polymorphisms ( SNPs ) . These are called expression-affecting SNPs or eSNPs . Gene expression levels are known to vary across different tissues in the same individual , despite the fact that genetic variation is the same in these tissues ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genomics", "genetics", "biology", "human", "genetics", "genetics", "and", "genomics" ]	2012	Unraveling the Regulatory Mechanisms Underlying Tissue-Dependent Genetic Variation of Gene Expression
Kaposi’s sarcoma ( KS ) -associated herpesvirus ( KSHV ) is an oncogenic pathogen that displays latent and lytic life cycles . In KS lesions , infiltrated immune cells , secreted viral and/or cellular cytokines , and hypoxia orchestrate a chronic pro-lytic microenvironment that can promote KSHV reactivation . However ,...	KSHV infected cells display significant heterogeneity in viral lytic replication within the universal pro-lytic inflammatory milieu , suggesting that the balance between latency and reactivation is carefully regulated . This fine-tuned regulatory mechanism is essential for KSHV to persist in the host and drive cells to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "microbiology", "notch", "signaling", "plasmid", "construction", "viruses", "dna", "viruses", "dna", "construction", "molecular", "biology", "techni...	2016	Fine-Tuning of the Kaposi’s Sarcoma-Associated Herpesvirus Life Cycle in Neighboring Cells through the RTA-JAG1-Notch Pathway
Here we describe field trials designed to standardize tools for the control of Glossina tachinoides , G . palpalis gambiensis and G . morsitans submorsitans in West Africa based on existing trap/target/bait technology . Blue and black biconical and monoconical traps and 1 m2 targets were made in either phthalogen blue ...	Tsetse flies transmit trypanosomes that cause sleeping sickness in humans and ngana in animals in sub-Saharan Africa . These diseases remain an intractable burden on human health and livestock production on the continent . Visual devices made of fabrics and impregnated with insecticide have the potential for controllin...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "health", "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "zoology", "pest", "control", "vector", "biology", "neglected", "tropical", "diseases", "animal", "management", "biology", "microbiology", "vectors", "and", "hosts", "...	2012	Standardizing Visual Control Devices for Tsetse Flies: West African Species Glossina tachinoides, G. palpalis gambiensis and G. morsitans submorsitans
The somites of the vertebrate embryo are clocked out sequentially from the presomitic mesoderm ( PSM ) at the tail end of the embryo . Formation of each somite corresponds to one cycle of oscillation of the somite segmentation clock—a system of genes whose expression switches on and off periodically in the cells of the...	Somites—the embryonic segments of the vertebrate body—are formed sequentially , with a spacing determined by a gene expression oscillator , the segmentation clock , operating in the cells at the tail end of the embryo . This system provides a rare opportunity to analyse how the timing of at least one set of development...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "vertebrates", "developmental", "biology", "cell", "biology", "danio", "(zebrafish)", "computational", "biology" ]	2007	Setting the Tempo in Development: An Investigation of the Zebrafish Somite Clock Mechanism
We use reinforcement learning to train an agent for computational RNA design: given a target secondary structure , design a sequence that folds to that structure in silico . Our agent uses a novel graph convolutional architecture allowing a single model to be applied to arbitrary target structures of any length . After...	Designing RNA sequences that fold to desired structures is an important problem in bioengineering . We have applied recent advances in machine learning to address this problem . The computer learns without any human input , using only trial and error to figure out how to design RNA . It quickly discovers powerful strat...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "machine", "learning", "algorithms", "applied", "mathematics", "database", "searching", "simulation", "and", "modeling", "algorithms", "mathematics", "artificial", "intelligence", "sequence", "motif", "analysis", "thermodynamics", "sequence", "similarity", "searching", "res...	2018	Solving the RNA design problem with reinforcement learning
Various methods have been developed for identifying gene–gene interactions in genome-wide association studies ( GWAS ) . However , most methods focus on individual markers as the testing unit , and the large number of such tests drastically erodes statistical power . In this study , we propose novel interaction tests o...	Epistasis is likely to play a significant role in complex diseases or traits and is one of the many possible explanations for “missing heritability . ” However , epistatic interactions have been difficult to detect in genome-wide association studies ( GWAS ) due to the limited power caused by the multiple-testing corre...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "epistasis", "genome-wide", "association", "studies", "trait", "locus", "heredity", "genetic", "association", "studies", "genetics", "biology", "computational", "biology", "quantitative", "traits", "genetics", "and", "genomics", "complex", "traits", "human", "genetics" ]	2013	Gene-Based Testing of Interactions in Association Studies of Quantitative Traits
Two-component signal transduction systems , composed of histidine kinases ( HK ) and response regulators ( RR ) , allow bacteria to respond to diverse environmental stimuli . The HK can control both phosphorylation and subsequent dephosphorylation of its cognate RR . The majority of HKs utilize the HisKA subfamily of d...	Bacterial histidine kinases ( HK ) serve as bifunctional enzymes capable of both phosphorylation and dephosphorylation of their cognate response regulators ( RR ) . The majority of HKs ( 77% ) belong to the HisKA subfamily . While both kinase and phosphatase functions have been assayed for HisKA proteins , relatively f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "protein", "interactions", "enzymes", "regulatory", "proteins", "dna-binding", "proteins", "microbiology", "microbial", "growth", "and", "development", "enzyme", "kinetics", "microbial", "physiology", "proteins", "enzyme", "regulation", "biology", "recombina...	2012	Genetic and Biochemical Dissection of a HisKA Domain Identifies Residues Required Exclusively for Kinase and Phosphatase Activities
A study of the helminth infection status of primary-school children and the hygiene condition of schools in Ikenne Local Government Area of Ogun State , Nigeria was undertaken between November 2004 and February 2005 to help guide the development of a school-based health programme . Three primary schools were randomly s...	We studied intestinal helminth infection status in primary-school children and the hygiene conditions of primary schools in Ikenne Local Government Area of Ogun State , Nigeria in order to help guide the development of school-based health programmes . Two government-owned schools ( one urban and the other rural ) plus ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/helminth", "infections", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases", "infectious", "diseases/neglected", "tropical", "diseases" ]	2008	Helminthiasis and Hygiene Conditions of Schools in Ikenne, Ogun State, Nigeria
An active search for Mycobacterium leprae drug resistance was carried out , 243 multibacillary patients from endemic regions of Colombia were included from 2004 to 2013 in a surveillance program . This program was a World Health Organization initiative for drug resistance surveillance in leprosy , where Colombia is a s...	Mycobacterium leprae drug resistance is cause of surveillance due to the increase of leprosy relapsed cases . World Health Organization initiative for drug resistance surveillance in leprosy included Colombia , a country considered in post-elimination stage , as a sentinel country . During 10 years ( 2004–20013 ) an ac...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "mycobacterium", "leprae", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "geographical", "locations", "microbiology", "bacterial", "diseases", "mutation", "signs", "and", "symptoms", "pharmaceutics", "neglec...	2016	Leprosy Drug Resistance Surveillance in Colombia: The Experience of a Sentinel Country
Prolactin is a major hormone product of the pituitary gland , the central endocrine regulator . Despite its physiological importance , the cell-level mechanisms of prolactin production are not well understood . Having significantly improved the resolution of real-time-single-cell-GFP-imaging , the authors recently reve...	Prolactin is a major hormone product of the pituitary gland , the central endocrine regulator found underneath the brain . In mammals it is crucial for milk production and reproductive function . Production of such an important protein needs to be regulated tightly , and therefore one might imagine that its gene expres...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "nervous", "system", "paracrine", "signaling", "messenger", "rna", "geodesics", "geometry", "neuroscience", "hormones", "endocrine", "physiology", "dna", "transcription", "mathematics", "prolactin", "pituitary", "gland", "endocrino...	2019	Disentangling juxtacrine from paracrine signalling in dynamic tissue
Understanding how avian influenza viruses adapt to human hosts is critical for the monitoring and prevention of future pandemics . Host specificity is determined by multiple sites in different viral proteins , and mutation of only a limited number of these sites can lead to inter-species transmission . Several of these...	There is worldwide concern that currently circulating avian influenza viruses will cross the species barrier and become highly pathogenic , human transmissible strains with pandemic potential . This could result from residue changes in several influenza proteins , either by point mutations , or through shuffling of the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virulence", "factors", "and", "mechanisms", "virology/viral", "replication", "and", "gene", "regulation", "virology/diagnosis", "virology/mechanisms", "of", "resistance", "and", "susceptibility,", "including", "host", "genetics", "infectious", "diseases/viral", "inf...	2008	Host Determinant Residue Lysine 627 Lies on the Surface of a Discrete, Folded Domain of Influenza Virus Polymerase PB2 Subunit
HCV entry into cells is a multi-step and slow process . It is believed that the initial capture of HCV particles by glycosaminoglycans and/or lipoprotein receptors is followed by coordinated interactions with the scavenger receptor class B type I ( SR-BI ) , a major receptor of high-density lipoprotein ( HDL ) , the CD...	More than 180 million people are chronically infected by hepatitis C virus ( HCV ) , a leading cause of liver failure and cancer , stimulating the need to fully define the biology of HCV infection for developing novel and effective therapeutics . During the first steps of infection , the virus is taken up and penetrate...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/viral", "replication", "and", "gene", "regulation" ]	2009	Receptor Complementation and Mutagenesis Reveal SR-BI as an Essential HCV Entry Factor and Functionally Imply Its Intra- and Extra-Cellular Domains
Schistosomiasis japonica is a zoonotic parasitic disease and oral vaccine delivery system would be benefit for prevention of this disease . Although attenuated salmonella has been used as an antigen expression vector for oral vaccine development , the membrane-bound vacuoles in which bacteria reside hinders the present...	Schistosomiasis japonica is a zoonotic parasitic disease and occurs predominantly in Southeast Asia and China . Using a simple , cheap , yet efficient oral method to deliver the vaccine antigen would benefit to control its transmission in that the oral vaccine could be made into a preparation and mixed with feedstuffs ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "vaccines", "medicine", "vaccination", "infectious", "diseases", "schistosomiasis", "clinical", "immunology", "immunity", "neglected", "tropical", "diseases", "vaccine", "development", "immunology", "parasitic", "diseases" ]	2011	Oral Delivery of the Sj23LHD-GST Antigen by Salmonella typhimurium Type III Secretion System Protects against Schistosoma japonicum Infection in Mice
Neural signals are processed in nervous systems of animals responding to variable environmental stimuli . This study shows that a novel and highly conserved protein , macoilin ( MACO-1 ) , plays an essential role in diverse neural functions in Caenorhabditis elegans . maco-1 mutants showed abnormal behaviors , includin...	Any animals , including humans , have to be capable of properly sensing and responding to various environmental stimuli for survival and reproduction . Environmental stimuli are evaluated and , based on past experiences , converted to produce appropriate adaptive behaviors . Even the small , free-living soil nematode C...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/behavioral", "neuroscience", "genetics", "and", "genomics/gene", "function", "neuroscience/sensory", "systems" ]	2011	Novel and Conserved Protein Macoilin Is Required for Diverse Neuronal Functions in Caenorhabditis elegans
Epigenetic processes are the main conductors of phenotypic variation in eukaryotes . The malaria parasite Plasmodium falciparum employs antigenic variation of the major surface antigen PfEMP1 , encoded by 60 var genes , to evade acquired immune responses . Antigenic variation of PfEMP1 occurs through in situ switches i...	Plasmodium falciparum causes the most severe form of malaria in humans . The high virulence of this unicellular parasite is in part related to the selective expression of members of falciparum-specific gene families . These genes encode proteins that are exported into the cytoplasm and onto the surface of infected red ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/chromatin", "structure", "molecular", "biology/histone", "modification", "cell", "biology/gene", "expression", "cell", "biology/nuclear", "structure", "and", "function", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/nucle...	2009	Plasmodium falciparum Heterochromatin Protein 1 Marks Genomic Loci Linked to Phenotypic Variation of Exported Virulence Factors
Many complex disease syndromes , such as asthma , consist of a large number of highly related , rather than independent , clinical or molecular phenotypes . This raises a new technical challenge in identifying genetic variations associated simultaneously with correlated traits . In this study , we propose a new statist...	An association study examines a phenotype against genotypic variations over a large set of individuals in order to find the genetic variant that gives rise to the variation in the phenotype . Many complex disease syndromes consist of a large number of highly related clinical phenotypes , and the patient cohorts are rou...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "biology/population", "genetics", "genetics", "and", "genomics/bioinformatics", "computational", "biology/genomics", "genetics", "and", "genomics/population", "genetics" ]	2009	Statistical Estimation of Correlated Genome Associations to a Quantitative Trait Network
The control of neglected tropical diseases ( NTDs ) has primarily focused on preventive chemotherapy and case management . Less attention has been placed on the role of ensuring access to adequate water , sanitation , and hygiene and personal preventive measures in reducing exposure to infection . Our aim was to assess...	Consistent use of footwear may help in preventing or slowing down the progression of many neglected tropical diseases ( NTDs ) . We conducted a systematic review and meta-analysis to assess the association between footwear use and infection or disease for those NTDs for which the route of transmission or occurrence may...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "mycetoma", "tropical", "diseases", "parasitic", "diseases", "bacterial", "diseases", "ectoparasitic", "infections", "neglected", "tropical", "diseases", "fungal", "diseases", "veterinary", "science", "infectious", "diseases", "bur...	2014	Association between Footwear Use and Neglected Tropical Diseases: A Systematic Review and Meta-Analysis
Nicotinic acetylcholine receptors ( nAChRs ) of parasitic nematodes are required for body movement and are targets of important “classical” anthelmintics like levamisole and pyrantel , as well as “novel” anthelmintics like tribendimidine and derquantel . Four biophysical subtypes of nAChR have been observed electrophys...	Parasitic nematode infections of humans and animals are world-wide . In humans , they cause disease and perpetuate a cycle of poverty . In animals , the parasites cause welfare problems and production loss . In developing countries , the debilitating effect of nematode parasites in school children limits their educatio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "parasitic", "intestinal", "diseases", "neglected", "tropical", "diseases", "veterinary", "pharmacology", "biology", "molecular", "cell", "biology", "parasitic", "diseases", "veterinary", "science", "helminth", "infection" ]	2014	Investigation of Acetylcholine Receptor Diversity in a Nematode Parasite Leads to Characterization of Tribendimidine- and Derquantel-Sensitive nAChRs
Previously , we reported that little canonical ( H3 . 1–H4 ) 2 tetramers split to form “hybrid” tetramers consisted of old and new H3 . 1–H4 dimers , but approximately 10% of ( H3 . 3–H4 ) 2 tetramers split during each cell cycle . In this report , we mapped the H3 . 3 nucleosome occupancy , the H3 . 3 nucleosome turno...	In our previous study , we unexpectedly discovered that nucleosomes containing the variant H3 . 3 histones experience substantial splitting events , resulting hybrid nucleosomes containing both “old” and “new” H3 . 3–H4 dimers . Here , we mapped the genomic distribution of these splitting events at the genome-wide leve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "chromatin", "epigenetics", "biology" ]	2013	H3.3-H4 Tetramer Splitting Events Feature Cell-Type Specific Enhancers
Canine rabies is a neglected disease causing 55 , 000 human deaths worldwide per year , and 99% of all cases are transmitted by dog bites . In N'Djaména , the capital of Chad , rabies is endemic with an incidence of 1 . 71/1 , 000 dogs ( 95% C . I . 1 . 45–1 . 98 ) . The gold standard of rabies diagnosis is the direct ...	A new diagnostic test for rabies in animals was evaluated in N'Djaména , capital of Chad . The test is based on a direct immuno-histochemical detection of rabies virus in brain tissue ( dRIT ) visible by normal light microscopy . Rabies detection by dRIT light microscopy is 10 times less expensive than fluorescence mic...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/diagnosis", "infectious", "diseases/infectious", "diseases", "of", "the", "nervous", "system", "infectious", "diseases/viral", "infections", "infectious", "diseases/neglected", "tropical", "diseases" ]	2008	Rabies Diagnosis for Developing Countries
Capping protein ( CP ) is a heterodimer that regulates actin assembly by binding to the barbed end of F-actin . In cultured nonneuronal cells , each CP subunit plays a critical role in the organization and dynamics of lamellipodia and filopodia . Mutations in either α or β CP subunit result in retinal degeneration in D...	Neuronal growth , migration , and survival depend on the regulated formation of cellular outgrowths called neurites . Extension of normal neurites requires coordinated interactions between cytoskeletal networks made up of microfilaments ( composed of F-actin ) and microtubules ( formed by tubulin ) in structures called...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/neuronal", "and", "glial", "cell", "biology", "cell", "biology/cytoskeleton" ]	2009	Capzb2 Interacts with β-Tubulin to Regulate Growth Cone Morphology and Neurite Outgrowth
In the mosquito , the midgut epithelium is the initial tissue to become infected with an arthropod-borne virus ( arbovirus ) that has been acquired from a vertebrate host along with a viremic bloodmeal . Following its replication in midgut epithelial cells , the virus needs to exit the midgut and infect secondary tissu...	The biological nature of the midgut escape barrier in insects for arthropod-borne viruses has been a mystery for decades . Here we show that the basal lamina ( BL ) surrounding the mosquito midgut acts as a barrier for chikungunya virus , an alphavirus , which has emerged in the New World hemisphere around three years ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "digestion", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "enzymes", "pathogens", "tropical", "diseases", "microbiology", "enzymology", "viral", "structure", "animals", "...	2017	Chikungunya virus dissemination from the midgut of Aedes aegypti is associated with temporal basal lamina degradation during bloodmeal digestion
The blue-light sensitive photoreceptor cryptochrome ( CRY ) may act as a magneto-receptor through formation of radical pairs involving a triad of tryptophans . Previous genetic analyses of behavioral responses of Drosophila to electromagnetic fields using conditioning , circadian and geotaxis assays have lent some supp...	Low frequency electromagnetic fields ( EMFs ) are associated with electrical power lines and have been implicated in the development of childhood leukemias . However , the Earth also has a natural EMF that animals can detect and which they use in order to navigate and orient themselves , particularly during migrations ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetic", "oscillators", "mutation", "behavioral", "neuroscience", "cellular", "neuroscience", "molecular", "neuroscience", "animal", "behavior", "phenotypes", "genetics", "biology", "and", "life", "sciences", "molecular", "genetics", "sensory", "perception", "zoology", ...	2014	Genetic Analysis of Circadian Responses to Low Frequency Electromagnetic Fields in Drosophila melanogaster
In immunocompetent individuals , non-typhoidal Salmonella serovars ( NTS ) are associated with gastroenteritis , however , there is currently an epidemic of NTS bloodstream infections in sub-Saharan Africa . Plasmodium falciparum malaria is an important risk factor for invasive NTS bloodstream in African children . Her...	In children , malaria is a predisposing factor for invasive bacterial infections with non-typhoidal Salmonella ( NTS ) serovars , a frequent cause of morbidity and mortality in sub-Saharan Africa . Since development of vaccines against NTS has been proposed as a strategy to protect African children against disseminated...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Transient Loss of Protection Afforded by a Live Attenuated Non-typhoidal Salmonella Vaccine in Mice Co-infected with Malaria
The facultative intracellular bacterium Listeria monocytogenes ( Lm ) may cause severe infection in humans and livestock . Control of acute listeriosis is primarily dependent on innate immune responses , which are strongly regulated by NF-κB , and tissue protective factors including fibrin . However , molecular pathway...	Listeria monocytogenes causes high mortality in immunocompromised patients and fetuses . Murine studies have revealed that innate immune responses and fibrin , a major product of hepatocytes , are important to control Listeria . In the present study , we analysed whether the deubiquitinating enzyme CYLD impairs protect...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunity", "to", "infections", "immunology", "immunity", "biology" ]	2013	CYLD Enhances Severe Listeriosis by Impairing IL-6/STAT3-Dependent Fibrin Production
Most adenoviruses attach to host cells by means of the protruding fiber protein that binds to host cells via the coxsackievirus and adenovirus receptor ( CAR ) protein . Human adenovirus type 52 ( HAdV-52 ) is one of only three gastroenteritis-causing HAdVs that are equipped with two different fiber proteins , one long...	HAdVs are common pathogens in humans , causing disease mainly in eyes , airways and gastrointestinal tract . Most HAdVs are equipped with twelve protruding fiber proteins that mediate attachment to host cell receptor molecules . Recently , a new human gastroenteritis-associated adenovirus ( HAdV-52 ) was identified and...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Human Adenovirus 52 Uses Sialic Acid-containing Glycoproteins and the Coxsackie and Adenovirus Receptor for Binding to Target Cells
Lymphatic Filariasis and Onchocerciasis ( river blindness ) constitute pressing public health issues in tropical regions . Global elimination programs , involving mass drug administration ( MDA ) , have been launched by the World Health Organisation . Although the drugs used are generally well tolerated , individuals w...	Lymphatic Filariasis ( LF ) is caused by parasitic worms which live in the lymphatic system . Though several body parts may be affected , LF characteristically leads to the enlargement of limbs , causing pain , physical disability and social stigma . Onchocerciasis ( river blindness ) is caused by similar worms which i...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "tropical", "diseases", "parasitic", "diseases", "animals", "mathematics", "filariasis", "statistics", "(mathematics)", "forecasting", "neglected", "tropical", "diseases", "onchocerciasis", "lymphat...	2016	Using Community-Level Prevalence of Loa loa Infection to Predict the Proportion of Highly-Infected Individuals: Statistical Modelling to Support Lymphatic Filariasis and Onchocerciasis Elimination Programs
In nearly all metazoans , the earliest stages of development are controlled by maternally deposited mRNAs and proteins . The zygotic genome becomes transcriptionally active hours after fertilization . Transcriptional activation during this maternal-to-zygotic transition ( MZT ) is tightly coordinated with the degradati...	Following fertilization , the one-celled zygote must be rapidly reprogrammed to enable the development of a new , unique organism . During these initial stages of development there is little or no transcription of the zygotic genome , and maternally deposited products control this process . Among the essential maternal...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "messenger", "rna", "invertebrate", "genomics", "animals", "dna", "transcription", "animal", "models", "developmental", "biology", "mutation", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "embryos", "drosophila"...	2017	A conserved maternal-specific repressive domain in Zelda revealed by Cas9-mediated mutagenesis in Drosophila melanogaster
About 8% of the human genome is made up of endogenous retroviruses ( ERVs ) . Though most human endogenous retroviruses ( HERVs ) are thought to be irrelevant to our biology notable exceptions include members of the HERV-H family that are necessary for the correct functioning of stem cells . ERVs are commonly found in ...	Animal genomes contain ancient pathogens known as endogenous retroviruses ( ERVs ) . Though the widespread abundance of ERVs is due to their ability to self replicate , some ERVs are known to have become important to host processes including placentation , and in the case of HERV-H , the functioning of human stem cells...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "taxonomy", "split-decomposition", "method", "vertebrates", "marmosets", "animals", "mammals", "animal", "phylogenetics", "primates", "animal", "models", "multiple", "alignment", "calculation", "phylogenetics", "data", "management", "model", "org...	2016	Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved
Leucine-rich repeat kinase 2 ( LRRK2 ) is a key molecule in the pathogenesis of familial and idiopathic Parkinson’s disease ( PD ) . We have identified two novel LRRK2-associated proteins , a HECT-type ubiquitin ligase , HERC2 , and an adaptor-like protein with six repeated Neuralized domains , NEURL4 . LRRK2 binds to ...	LRRK2 is linked to autosomal dominant late-onset Parkinson’s disease , suggesting that LRRK2 gain-of-function mutations lead to age-dependent degeneration of the midbrain dopaminergic neurons . In this study , we describe two novel LRRK2-associated proteins HERC2 and NEURL4 , which are a ubiquitin ligase and an adaptor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Parkinson’s Disease-Associated Protein Kinase LRRK2 Modulates Notch Signaling through the Endosomal Pathway
Leishmaniasis is a neglected tropical disease affecting millions of individuals worldwide . P2X7 receptor has been linked to the elimination of Leishmania amazonensis . Biological responses evoked by P2X7 receptor activation have been well-documented , including apoptosis , phagocytosis , cytokine release , such as IL-...	Leishmania spp . is a protozoan parasite that infects human and causes several diseases . Leishmania amazonensis causes cutaneous leishmaniasis ( CL ) and mucocutaneous leishmaniasis ( MCL ) . Leishmania parasites preferentially infect macrophages . In macrophages , several mechanisms have been described as controlling...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "vacuoles", "immunology", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "protozoan", "life", "cycles", "immune", "receptor", "signaling", "developmental", "biology", "pro...	2019	Non-canonical NLRP3 inflammasome activation and IL-1β signaling are necessary to L. amazonensis control mediated by P2X7 receptor and leukotriene B4
Chagas disease , also known as American Trypanosomiasis , is a chronic parasitic disease caused by the flagellated protozoan Trypanosoma cruzi that affects about 8 million people around the world where more than 25 million are at risk of contracting the infection . Despite of being endemic on 21 Latin-American countrie...	Chagas disease is a neglected tropical disease caused by the parasite Trypanosoma cruzi that affects more than 8 million people around the world . Unfortunately , the diagnosis is generally performed too late , when anti-parasitic drugs are no longer effective . About 30–40% of infected individuals progress toward a sy...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "immune", "cells", "immunology", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "vaccines", "protozoans", "neglected", "tropica...	2018	Trypanosoma cruzi 80 kDa prolyl oligopeptidase (Tc80) as a novel immunogen for Chagas disease vaccine
Sigma factors are essential global regulators of transcription initiation in bacteria which confer promoter recognition specificity to the RNA polymerase core enzyme . They provide effective mechanisms for simultaneously regulating expression of large numbers of genes in response to challenging conditions , and their p...	Pseudomonas aeruginosa is well known for its high adaptability to a large range of environmental conditions , including those encountered within the human host . Transcription initiation represents a major regulatory target which drives versatility , and enables bacterial adaptation to challenging conditions and expres...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Elucidation of Sigma Factor-Associated Networks in Pseudomonas aeruginosa Reveals a Modular Architecture with Limited and Function-Specific Crosstalk
The ability to produce timely and accurate flu forecasts in the United States can significantly impact public health . Augmenting forecasts with internet data has shown promise for improving forecast accuracy and timeliness in controlled settings , but results in practice are less convincing , as models augmented with ...	It has been demonstrated in retrospective settings that flu forecasting can be improved by augmenting forecasting models with internet-based nowcasts ( i . e . , one-week-ahead forecasts generated with internet data ) . The improvement of internet-assisted forecasting models , however , has not translated to overall im...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "united", "states", "medicine", "and", "health", "sciences", "statistics", "influenza", "sociology", "geographical", "locations", "social", "sciences", "north", "america", "online", "encyclopedias", "mathematics", "forecasting", "internet", "regional", "geography", "resea...	2019	Even a good influenza forecasting model can benefit from internet-based nowcasts, but those benefits are limited
Expansions of trinucleotide CAG/CTG repeats in somatic tissues are thought to contribute to ongoing disease progression through an affected individual's life with Huntington's disease or myotonic dystrophy . Broad ranges of repeat instability arise between individuals with expanded repeats , suggesting the existence of...	The genetic instability of repetitive DNA sequences in particular genes can lead to numerous neurodegenerative , neurological , and neuromuscular diseases . These diseases show progressively increasing severity of symptoms through the life of the affected individual , a phenomenon that is linked with increasing instabi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2013	MSH3 Polymorphisms and Protein Levels Affect CAG Repeat Instability in Huntington's Disease Mice
The spatial organization of metabolism is common to all domains of life . Enteric and other bacteria use subcellular organelles known as bacterial microcompartments to spatially organize the metabolism of pathogenicity-relevant carbon sources , such as 1 , 2-propanediol . The organelles are thought to sequester a priva...	Many bacterial species , such as Salmonella enterica ( responsible for over 1 million illnesses per year in the United States ) and Yersinia pestis ( the causative agent of bubonic plague ) , have a suite of unique metabolic capabilities allowing them to proliferate in the hostile environment of the host gut . Bacteria...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "enzymes", "cell", "processes", "permeability", "enzymology", "organic", "compounds", "toxicology", "toxicity", "active", "transport", "materials", "science", ...	2017	A systems-level model reveals that 1,2-Propanediol utilization microcompartments enhance pathway flux through intermediate sequestration
In the present study , an integrated hierarchical approach was applied to: ( 1 ) identify pathways associated with susceptibility to schizophrenia; ( 2 ) detect genes that may be potentially affected in these pathways since they contain an associated polymorphism; and ( 3 ) annotate the functional consequences of such ...	Large-scale genetic studies of complex diseases such as schizophrenia have identified a variety of susceptibility loci . Since many of the respective variants have only a weak influence on disease risk , pathophysiological interpretation of the results is problematic . Investigation of the joint effects of multiple fun...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "psychology", "medicine", "and", "health", "sciences", "social", "sciences", "genetics", "biology", "and", "life", "sciences", "computational", "biology", "mental", "health", "and", "psychiatry", "neuroscience" ]	2014	Integrated Pathway-Based Approach Identifies Association between Genomic Regions at CTCF and CACNB2 and Schizophrenia
Rapid diversification often involves complex histories of gene flow that leave variable and conflicting signatures of evolutionary relatedness across the genome . Identifying the extent and source of variation in these evolutionary relationships can provide insight into the evolutionary mechanisms involved in rapid rad...	Groups of closely related species can rapidly evolve to occupy diverse ecological roles , but the ecological and genetic conditions that trigger this diversification are still highly debated . We examined patterns of molecular evolution across the genomes of a recent radiation of pupfishes that includes two trophic spe...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "genome", "evolution", "population", "genetics", "computational", "biology", "geographical", "locations", "north", "america", "aquatic", "environments", "bodies", "of", "water", "pop...	2017	Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic adaptive radiation of trophic specialist pupfishes
Epstein-Barr virus ( EBV ) infection converts resting human B cells into permanently proliferating lymphoblastoid cell lines ( LCLs ) . The Epstein-Barr virus nuclear antigen 2 ( EBNA2 ) plays a key role in this process . It preferentially binds to B cell enhancers and establishes a specific viral and cellular gene exp...	Epstein-Barr virus ( EBV ) infection is closely linked to cancer development . At particular risk are immunocompromised individuals like post-transplant patients which can develop B cell lymphomas . In healthy individuals EBV preferentially infects B cells and establishes a latent infection without causing apparent cli...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "binding", "cell", "physiology", "medicine", "and", "health", "sciences", "immune", "cells", "gene", "regulation", "regulatory", "proteins", "immunology", "dna-binding", "proteins", "hormones", "transcription", "factors", "epigenetics", "estrog...	2017	EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells
Environmental perturbations have large effects on both organismal and cellular traits , including gene expression , but the extent to which the environment affects RNA processing remains largely uncharacterized . Recent studies have identified a large number of genetic variants associated with variation in RNA processi...	Changes in a cell’s environment and genetic variation have been shown to impact gene expression . Here , we demonstrate that environmental perturbations also lead to extensive changes in alternative RNA processing across a large number of cellular environments that we investigated . These changes often occur in a non-r...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "materials" ]	[ "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "dna", "transcription", "transcription", "factors", "sequence", "motif", "analysis", "research", "and", "analysis", "methods", "sequence", "analysis", "selenium", "genome", "complexity", "genomics"...	2017	Environmental perturbations lead to extensive directional shifts in RNA processing
International sustainable development goals for the elimination of viral hepatitis as a public health problem by 2030 highlight the pressing need to optimize strategies for prevention , diagnosis and treatment . Selected or transmitted resistance associated mutations ( RAMs ) and vaccine escape mutations ( VEMs ) in he...	The Global Hepatitis Health Sector Strategy is aiming for the elimination of viral hepatitis as a public health threat by 2030 . However , mutations associated with drug resistance and vaccine escape may reduce the success of existing treatment and prevention strategies . In the current literature , the prevalence , di...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "geographical", "locations", "microbiology", "hepatitis", "b", "virus", "retroviruses", "viruses", "immunodeficiency", "viruses", "vaccines", "mutation", "rna", "viruses", ...	2018	A systematic review of hepatitis B virus (HBV) drug and vaccine escape mutations in Africa: A call for urgent action
Conventional drug design embraces the “one gene , one drug , one disease” philosophy . Polypharmacology , which focuses on multi-target drugs , has emerged as a new paradigm in drug discovery . The rational design of drugs that act via polypharmacological mechanisms can produce compounds that exhibit increased therapeu...	Proteins play a critical role in human disease; bacteria , viruses , and parasites have unique proteins that can interfere with human health , and dysfunctional human proteins can likewise lead to illness . In order to find cures , scientists often try to identify small molecules ( drugs ) that can inhibit disease-caus...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "pharmacology/drug", "resistance", "pharmacology/drug", "development", "pharmacology", "computational", "biology", "pharmacology/adverse", "reactions", "biochemistry/drug", "discovery" ]	2010	A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology
Use-dependent downregulation of neuronal activity ( negative feedback ) can act as a homeostatic mechanism to maintain neuronal activity at a particular specified value . Disruption of this negative feedback might lead to neurological pathologies , such as epilepsy , but the precise mechanisms by which this feedback ca...	Use-dependent downregulation of neuronal excitability ( negative feedback ) can act to maintain neuronal activity within specified levels . Disruption of this homeostasis can lead to neurological disorders , such as epilepsy . Here , we report a novel mechanism for negative feedback control of excitability in the Droso...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/neuronal", "and", "glial", "cell", "biology", "neuroscience/motor", "systems", "cell", "biology/cell", "growth", "and", "division", "neuroscience/neural", "homeostasis", "neuroscience/neurodevelopment", "neuroscience/neuronal", "signaling", "mechanisms", "neuro...	2008	A PI3-Kinase–Mediated Negative Feedback Regulates Neuronal Excitability
Visual attention is thought to be driven by the interplay between low-level visual features and task dependent information content of local image regions , as well as by spatial viewing biases . Though dependent on experimental paradigms and model assumptions , this idea has given rise to varying claims that either bot...	In our lifetime we make about 5 billion eye movements . Yet our knowledge about what determines where we look at is surprisingly sketchy . Some traditional approaches assume that gaze is guided by simple image properties like local contrast ( low-level features ) . Recent arguments emphasize the influence of tasks ( hi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/cognitive", "neuroscience" ]	2010	Influence of Low-Level Stimulus Features, Task Dependent Factors, and Spatial Biases on Overt Visual Attention
Disrupting erythrocyte invasion by Plasmodium falciparum is an attractive approach to combat malaria . P . falciparum EBA-175 ( PfEBA-175 ) engages the host receptor Glycophorin A ( GpA ) during invasion and is a leading vaccine candidate . Antibodies that recognize PfEBA-175 can prevent parasite growth , although not ...	Malaria is a devastating parasitic disease that kills one million people annually . The parasites invade and multiply within red blood cells , leading to the clinical symptoms of malaria . Therefore , preventing red blood cell , entry through vaccines is an attractive approach to controlling the disease . Although wide...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "infectious", "diseases", "immunology", "biology", "microbiology", "biophysics" ]	2013	Structural and Functional Basis for Inhibition of Erythrocyte Invasion by Antibodies that Target Plasmodium falciparum EBA-175
The cross-species transmission of viruses from one host species to another is responsible for the majority of emerging infections . However , it is unclear whether some virus families have a greater propensity to jump host species than others . If related viruses have an evolutionary history of co-divergence with their...	Emerging infectious diseases are often characterized by host switching events , in which a pathogen jumps from its original host to infect a novel species . However , given the ecological and genetic barriers a virus must overcome to jump species and adapt to new hosts , it might be reasonable to assume that successful...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taxonomy", "organismal", "evolution", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "microbiology", "animal", "phylogenetics", "viruses", "phylogenetics", "data", "management", "rna", ...	2017	Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families
The potential use of clinically approved beta-lactams for Buruli ulcer ( BU ) treatment was investigated with representative classes analyzed in vitro for activity against Mycobacterium ulcerans . Beta-lactams tested were effective alone and displayed a strong synergistic profile in combination with antibiotics current...	Buruli ulcer ( BU ) is a chronic debilitating disease of the skin and soft tissue , mainly affecting children and young adults in tropical regions . Before 2004 , the only treatment option was surgery; a major breakthrough was the discovery that BU could be cured in most cases with a standard treatment that involved 8 ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "drugs", "tropical", "diseases", "microbiology", "animal", "models", "bacterial", "diseases", "streptomycin", "model", "organisms", "pharmaceutics", "antibiotics", "experimental", "organism", "systems", "neglected",...	2019	Triple oral beta-lactam containing therapy for Buruli ulcer treatment shortening
Embryonic stem cells ( ESC ) have the potential to self-renew indefinitely and to differentiate into any of the three germ layers . The molecular mechanisms for self-renewal , maintenance of pluripotency and lineage specification are poorly understood , but recent results point to a key role for epigenetic mechanisms ....	Stem cell differentiation and the maintenance of self-renewal are intrinsically complex processes that require coordinated regulation on many different cellular levels . Here we focus on the relationship between two important layers and follow it over the first five days of differentiation . The first layer – measured ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/systems", "biology", "computational", "biology/genomics" ]	2010	Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells
Positive-strand and double-strand RNA viruses typically compartmentalize their replication machinery in infected cells . This is thought to shield viral RNA from detection by innate immune sensors and favor RNA synthesis . The picture for the non-segmented negative-strand ( NNS ) RNA viruses , however , is less clear ....	Positive-strand and double-strand RNA viruses compartmentalize their replication machinery in infected cells . This compartmentalization is thought to favor the catalysis of RNA synthesis , and sequester viral RNA molecules from detection by innate immune sensors . For the negative-strand RNA viruses that replicate in ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/viral", "replication", "and", "gene", "regulation", "virology" ]	2010	Protein Expression Redirects Vesicular Stomatitis Virus RNA Synthesis to Cytoplasmic Inclusions
Chagas disease is a significant health problem in Latin America and the available treatments have significant issues in terms of toxicity and efficacy . There is thus an urgent need to develop new treatments either via a repurposing strategy or through the development of new chemical entities . A key first step is the ...	Chagas disease is an important health problem in Latin America . The disease is caused by the parasite Trypanosoma cruzi , which is transmitted to people via insects of the Triatomine family . There are currently only two treatments available , Nifurtimox and Benznidazole . These have serious problems including poor ef...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "vero", "cells", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "biological", "cultures", "tropical", "diseases", "microbiology", "parasitic", "diseases", "protozoan", "life", "cycles",...	2016	Identification of Trypanocidal Activity for Known Clinical Compounds Using a New Trypanosoma cruzi Hit-Discovery Screening Cascade
Transcription factors have two functional constraints on their evolution: ( 1 ) their binding sites must have enough information to be distinguishable from all other sequences in the genome , and ( 2 ) they must bind these sites with an affinity that appropriately modulates the rate of transcription . Since both are de...	The main role of transcription factors is to modulate the expression levels of functionally related genes in response to environmental and cellular cues . For this process to be precise , the transcription factor needs to locate and bind specific DNA sequences in the genome and needs to bind these sites with a strength...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "molecular", "cell", "biology", "evolutionary", "biology", "proteins", "gene", "expression", "genetics", "molecular", "genetics", "biology", "biophysics", "molecular", "biology", "genetics", "and", "genomics" ]	2012	Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA–Binding Domain
Steroid hormones act , through their respective nuclear receptors , to regulate target gene expression . Despite their critical role in development , physiology , and disease , however , it is still unclear how these systemic cues are refined into tissue-specific responses . We identified a mutation in the evolutionari...	Pulses of steroid hormones regulate a variety of biological processes , but how these simple global cues are converted into specific local responses remains unclear . While steroid responses have traditionally been thought to be regulated at the transcriptional level , here we demonstrate that translational control pla...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "regulation", "anatomy", "and", "physiology", "hormones", "endocrine", "physiology", "gene", "function", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "organism", "development", "molecular", "development", "mol...	2012	Translational Control by the DEAD Box RNA Helicase belle Regulates Ecdysone-Triggered Transcriptional Cascades
In the nervous system , glial cells provide crucial insulation and trophic support to neurons and are important for neuronal survival . In reaction to a wide variety of insults , glial cells respond with changes in cell morphology and metabolism to allow repair . Additionally , these cells can acquire migratory and pro...	For a functional nervous system , neurons transmit information from cell to cell while glial cells provide crucial insulation and trophic support to neurons , which is important for neuronal survival . Glial cells are one of the most plastic cell types being able to adapt and respond to changing environmental stimuli ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "nuclear", "staining", "social", "sciences", "neuroscience", "animals", "animal", "models", "c-jun", "n-terminal", "kinase", "signaling", "cascade", "developmental", "biology", "drosophila", ...	2017	dMyc is required in retinal progenitors to prevent JNK-mediated retinal glial activation
Recent work has shown that the accuracy of ab initio structure prediction can be significantly improved by integrating evolutionary information in form of intra-protein residue-residue contacts . Following this seminal result , much effort is put into the improvement of contact predictions . However , there is also a s...	Recently , a breakthrough has been achieved in modeling the atomic 3D structures of proteins from their sequence alone without requiring any experimental work on the protein itself . To achieve this goal , a database of evolutionary related sequences is analyzed to find co-evolving residues , giving insight into which ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[]	2015	Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction
Fine-scale temporal organization of cortical activity in the gamma range ( ∼25–80Hz ) may play a significant role in information processing , for example by neural grouping ( ‘binding’ ) and phase coding . Recent experimental studies have shown that the precise frequency of gamma oscillations varies with input drive ( ...	Almost 350 years ago the physicist and polymath Christiaan Huygens first observed the synchronization between two pendulum clocks attached to a common support . Since then synchronization has been recognized as a universal phenomenon from astronomy to biology . The phase-locking ( synchrony ) and the phase-relation bet...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Input-Dependent Frequency Modulation of Cortical Gamma Oscillations Shapes Spatial Synchronization and Enables Phase Coding
Hepatitis C virus ( HCV ) is a major cause of liver disease worldwide . A better understanding of its life cycle , including the process of host cell entry , is important for the development of HCV therapies and model systems . Based on the requirement for numerous host factors , including the two tight junction protei...	HCV is a serious public health problem . Although new treatments have recently become available , it is clear that effective therapies will require combinations of inhibitors targeting diverse stages of the viral life cycle . While the HCV cell entry process is considered a suitable antiviral target , a lack of underst...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "attachment", "coreceptors", "viral", "entry", "host", "cells", "viral", "transmission", "and", "infection", "virology", "biology", "microbiology" ]	2013	Temporal Analysis of Hepatitis C Virus Cell Entry with Occludin Directed Blocking Antibodies
STAT1 is a critical transcription factor for regulating host antiviral defenses . STAT1 activation is largely dependent on phosphorylation at tyrosine 701 site of STAT1 ( pY701-STAT1 ) . Understanding how pY701-STAT1 is regulated by intracellular signaling remains a major challenge . Here we find that pY701-STAT1 is th...	Phosphorylated STAT1 at tyrosine 701 site ( pY701-STAT1 ) is critical for regulating many cellular functions including antiviral immunity . Maintaining sufficient pY701-STAT1 levels in the nucleus is essential to sustain efficient interferons ( IFNs ) signaling and antiviral functions . Therefore , it is important to c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "vesicular", "stomatitis", "virus", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "293t", "cells", "pathogens", "biological", "cultures", "immunology", "immunoblotting", "microbiology", "viruses"...	2016	Deubiquitinase USP2a Sustains Interferons Antiviral Activity by Restricting Ubiquitination of Activated STAT1 in the Nucleus
Hedgehog ( Hh ) proteins control animal development and tissue homeostasis . They activate gene expression by regulating processing , stability , and activation of Gli/Cubitus interruptus ( Ci ) transcription factors . Hh proteins are secreted and spread through tissue , despite becoming covalently linked to sterol dur...	Hedgehog ( Hh ) proteins are conserved secreted signaling molecules that regulate embryonic development and adult tissue homeostasis . Ectopic Hh signaling promotes tumorigenesis , and secretion of mammalian Sonic Hedgehog ( Shh ) by many tumors supports their growth and survival . As Hh proteins are covalently modifie...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "morphogens", "biochemistry", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "proteins", "signaling", "molecular", "development", "lipoproteins", "biology" ]	2013	Secretion and Signaling Activities of Lipoprotein-Associated Hedgehog and Non-Sterol-Modified Hedgehog in Flies and Mammals
Despite many aspects of the regulation of segmentation being conserved among arthropods , the evolution of novel gene functions has played an important role in the evolution of developmental regulation and the emergence of new segmental structures . Moreover the study of such novel gene functions can be informative wit...	The development and segmentation of the head of the fly Drosophila is one of the best-studied examples of how tissues become genetically specified during embryonic development . However , the mechanisms for head segmentation vary considerably among the arthropods . This is on the one hand surprising because the head co...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "organismal", "evolution", "segmentation", "gene", "function", "developmental", "biology", "organism", "development", "body", "plan", "organization", "zoology", "morphogenesis", "pattern", "formation", "biology", "entomology", "animal", "evolution", "genetics", "evolutionar...	2011	Novel Function of Distal-less as a Gap Gene during Spider Segmentation
Cytoplasmic dynein is a giant ATP-driven molecular motor that proceeds to the minus end of the microtubule ( MT ) . Dynein hydrolyzes ATP in a ring-like structure , containing 6 AAA+ ( ATPases associated with diverse cellular activities ) modules , which is ~15 nm away from the MT binding domain ( MTBD ) . This archite...	The linear molecular motor dynein is an intriguing allosteric model protein . ATP hydrolysis , catalyzed by modules in the AAA+ ring , regulates the binding to the rail molecule , microtubule , which is ~15 nm away from the AAA+ ring . The molecular mechanisms underpinning this long-distance communication are unclear ....	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "kinesins", "crystal", "structure", "split-decomposition", "method", "condensed", "matter", "physics", "simulation", "and", "modeling", "multiple", "alignment", "calculation", "dyneins", "molecular", "motors", "crystallography", "motor", "proteins", "research", "and", "an...	2017	Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations
Antiretroviral therapy ( ART ) effectively controls HIV infection , suppressing HIV viral loads . Suspension of therapy is followed by rebound of viral loads to high , pre-therapy levels . However , there is significant heterogeneity in speed of rebound , with some rebounds occurring within days , weeks , or sometimes ...	Antiretroviral therapy ( ART ) effectively controls HIV infection , holding HIV viral loads to levels undetectable by commercial assays . Therapy interruption is followed by rebound of viral loads to high , pre-therapy levels , but there is significant heterogeneity in the timing of the rebound to those high levels . S...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "cell", "activation", "antiviral", "therapy", "pathogens", "immunology", "microbiology", "biomarkers", "retroviruses",...	2019	Predictions of time to HIV viral rebound following ART suspension that incorporate personal biomarkers
People with HIV infection are at increased risk for community-acquired methicillin-resistant Staphylococcus aureus ( CA-MRSA ) skin and soft tissue infections ( SSTIs ) . Lower CD4 T-cell counts , higher peak HIV RNA levels and epidemiological factors may be associated with increased risk but no specific immune defect ...	Methicillin-resistant Staphylococcus aureus ( MRSA ) causes infections of the skin and associated tissue . HIV-infected people are at increased risks of these infections for unclear reasons . We recruited participants with or without HIV infection who had a MRSA skin or soft tissue infection , MRSA colonization , or ne...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "t", "helper", "cells", "hiv", "infections", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "biopsy", "pathogens", "immunology", "microbiology", "staphylococcus", "aureus", "surgical", "and",...	2016	MRSA Infections in HIV-Infected People Are Associated with Decreased MRSA-Specific Th1 Immunity
When environmental conditions deteriorate and become inhospitable , generic survival strategies for populations of bacteria may be to enter a dormant state that slows down metabolism , to develop a general tolerance to hostile parameters that characterize the habitat , and to impose a regime to eliminate damaged member...	A little poison may be generically beneficial to bacterial populations . By eliminating damaged members and by promoting survival of the fittest , selective poisoning may significantly contribute to multi-cellular bacterial behavior . Here , we report that the pseudomonas quinolone signal ( PQS ) exhibits both benefici...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "microbiology" ]	2008	The Pseudomonas Quinolone Signal (PQS) Balances Life and Death in Pseudomonas aeruginosa Populations

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