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The NF-κB family of transcription factors is crucial for the expression of multiple genes involved in cell survival , proliferation , differentiation , and inflammation . The molecular basis by which NF-κB activates endogenous promoters is largely unknown , but it seems likely that it should include the means to tailor...	Transcriptional activation by the NF-κB family of transcription factors is crucial for the expression of multiple genes involved in cell survival , proliferation , differentiation , and inflammation . The activation domain of the p65 subunit of NF-κB has been extensively studied in vitro and on artificial reporter plas...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology" ]	2009	Two Modes of Transcriptional Activation at Native Promoters by NF-κB p65
Plasmodium vivax is the most prevalent malarial species in South America and exerts a substantial burden on the populations it affects . The control and eventual elimination of P . vivax are global health priorities . Genomic research contributes to this objective by improving our understanding of the biology of P . vi...	Although P . vivax is not as deadly as the more widely studied P . falciparum , it remains a pressing global health problem . Here we report the results of a whole-genome study of P . vivax from Cordóba , Colombia , in South America . This parasite is the most prevalent in this region . We show that the parasite popula...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia
A multitude of proteins and small nucleolar RNAs transiently associate with eukaryotic ribosomal RNAs to direct their modification and processing and the assembly of ribosomal proteins . Utp22 and Rrp7 , two interacting proteins with no recognizable domain , are components of the 90S preribosome or the small subunit pr...	Ribosomes are large RNA–protein complexes that manufacture proteins in all living organisms . Synthesis of large and small ribosomal subunits is a fundamental and enormous task that requires activities of approximately 200 assembly factors in eukaryotic cells . These factors transiently associate with the ribosome , fo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	An RNA-Binding Complex Involved in Ribosome Biogenesis Contains a Protein with Homology to tRNA CCA-Adding Enzyme
Plasmodium falciparum sporozoites that develop and mature inside an Anopheles mosquito initiate a malaria infection in humans . Here we report the first proteomic comparison of different parasite stages from the mosquito—early and late oocysts containing midgut sporozoites , and the mature , infectious salivary gland s...	Human malaria is caused by Plasmodium falciparum , a unicellular protozoan parasite that is transmitted by Anopheles mosquitoes . An infectious mosquito injects saliva containing sporozoite forms of the parasite and these then migrate from the skin to the liver , where they establish an infection . Many intervention st...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/protozoal", "infections", "computational", "biology/systems", "biology", "genetics", "and", "genomics/gene", "expression" ]	2008	Proteomic Profiling of Plasmodium Sporozoite Maturation Identifies New Proteins Essential for Parasite Development and Infectivity
Thymic medullary regions are formed in neonatal mice as islet-like structures , which increase in size over time and eventually fuse a few weeks after birth into a continuous structure . The development of medullary thymic epithelial cells ( TEC ) is dependent on NF-κB associated signaling though other signaling pathwa...	Thymic medulla is known to be an essential site for the deletion of auto-reactive T cells . Whereas it has been well documented that the development of medullary thymic epithelial cells ( mTECs ) depends on NF-κB associated signaling , it remained unclear whether other signaling pathways are also involved . In this con...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	Requirement of Stat3 Signaling in the Postnatal Development of Thymic Medullary Epithelial Cells
Neuroscience models come in a wide range of scales and specificity , from mean-field rate models to large-scale networks of spiking neurons . There are potential trade-offs between simplicity and realism , versatility and computational speed . This paper is about large-scale cortical network models , and the question w...	With the vast numbers of neurons in the cerebral cortex , models in neuroscience are , for practical reasons , often orders of magnitude smaller than the actual network . We examine in this article the scalability of cortical networks . We find that function and dynamics in a network depend on network size . For illust...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "membrane", "potential", "brain", "vertebrates", "electrophysiology", "neuroscience", "animals", "mammals", "primates", "neuronal", "tuning", "computer", "and", "information", "sciences...	2019	A case study in the functional consequences of scaling the sizes of realistic cortical models
MicroRNAs ( miRNAs ) are a class of small non-coding RNAs , which direct post-transcriptional gene silencing ( PTGS ) and function in a vast range of biological events including cancer development . Most miRNAs pair to the target sites through seed region near the 5’ end , leading to mRNA cleavage and/or translation re...	It is generally accepted that miRNAs bind to 3`UTR of target mRNAs and direct post-transcriptional gene silencing ( PTGS ) via its seed sequence . Here we report a new dual regulatory mechanism of miRNA . We described that miR-1254 repressed HO-1 at post-transcriptional level by directly targeting HO-1 3’UTR via its se...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "luciferase", "gene", "regulation", "enzymes", "messenger", "rna", "cell", "processes", "cancers", "and", "neoplasms", "enzymology", "nucleotides", "oncology", "micrornas", "cell", "growth", "proteins", "lung",...	2017	MiR-1254 suppresses HO-1 expression through seed region-dependent silencing and non-seed interaction with TFAP2A transcript to attenuate NSCLC growth
Cell-to-cell spread of HIV , a directed mode of viral transmission , has been observed to be more rapid than cell-free infection . However , a mechanism for earlier onset of viral gene expression in cell-to-cell spread was previously uncharacterized . Here we used time-lapse microscopy combined with automated image ana...	How quickly infection occurs should be an important determinant of viral fitness , but mechanisms which could accelerate the onset of viral gene expression were previously undefined . In this work we use time-lapse microscopy to quantify the timing of the HIV viral cycle and show that onset of viral gene expression can...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "cell", "physiology", "hiv", "infections", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "viral", "structure", "retroviruses", "viruses", "immunodefi...	2016	HIV Cell-to-Cell Spread Results in Earlier Onset of Viral Gene Expression by Multiple Infections per Cell
Quality control ( QC ) is a critical step in large-scale studies of genetic variation . While , on average , high-throughput single nucleotide polymorphism ( SNP ) genotyping assays are now very accurate , the errors that remain tend to cluster into a small percentage of “problem” SNPs , which exhibit unusually high er...	In large-scale studies of population genetic data , particularly genome-wide association studies , considerable effort may be spent on quality control ( QC ) to ensure genotype data are accurate . Typically , QC steps are applied independently to individual marker loci , with data from suspicious loci being excluded fr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics/statistics", "genetics", "and", "genomics/population", "genetics" ]	2008	Linkage Disequilibrium-Based Quality Control for Large-Scale Genetic Studies
Zero-lag synchronization between distant cortical areas has been observed in a diversity of experimental data sets and between many different regions of the brain . Several computational mechanisms have been proposed to account for such isochronous synchronization in the presence of long conduction delays: Of these , t...	Understanding large-scale neuronal dynamics – and how they relate to the cortical anatomy – is one of the key areas of neuroscience research . Despite a wealth of recent research , the key principles of this relationship have yet to be established . Here we employ computational modeling to study neuronal dynamics on sm...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "circuit", "models", "complex", "systems", "physics", "computer", "and", "information", "sciences", "systems", "science", "mathematics", "interdisciplinary", "physics", "computational", "neuroscience", "applied", "mathematics", "biology", "and", "life", "sciences", "physi...	2014	Mechanisms of Zero-Lag Synchronization in Cortical Motifs
During meiosis in most sexually reproducing organisms , recombination forms crossovers between homologous maternal and paternal chromosomes and thereby promotes proper chromosome segregation at the first meiotic division . The number and distribution of crossovers are tightly controlled , but the factors that contribut...	Meiosis is the specialized cell division that gives rise to reproductive cells such as sperm and eggs . During meiosis in most organisms , genetic information is exchanged between homologous maternal and paternal chromosomes through the process of homologous recombination . This recombination forms connections between ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "cell", "biology/nuclear", "structure", "and", "function", "genetics", "and", "genomics/nuclear", "structure", "and", "function", "genetics", "and", "genomics/chromosome", "biology", "biochemistry/replication", "and", "repai...	2008	ATM Promotes the Obligate XY Crossover and both Crossover Control and Chromosome Axis Integrity on Autosomes
Two crucial steps in the virus life cycle are genome encapsidation to form an infective virion and genome exit to infect the next host cell . In most icosahedral double-stranded ( ds ) DNA viruses , the viral genome enters and exits the capsid through a unique vertex . Internal membrane-containing viruses possess addit...	The life cycle of a virus involves serial coordination of viral molecular machines . These machines facilitate functions such as membrane fusion and genome delivery during infection , and capsid formation and genome packaging during replication and shedding . Icosahedral dsDNA viruses use one genome-translocation machi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "microscopy", "proteins", "virology", "protein", "structure", "electron", "microscopy", "biology", "and", "life", "sciences", "microbiology", "computational", "biology", "viral", "structure", "research", "and", "analysis", "methods" ]	2014	A Structural Model of the Genome Packaging Process in a Membrane-Containing Double Stranded DNA Virus
In fission yeast , the formation of centromeric heterochromatin is induced through the RNA interference ( RNAi ) -mediated pathway . Some pre-mRNA splicing mutants ( prp ) exhibit defective formation of centromeric heterochromatin , suggesting that splicing factors play roles in the formation of heterochromatin , or al...	Formation of centromeric heterochromatin is required for correct segregation of sister chromatids during mitosis . In fission yeast , formation of heterochromatin at centromeres is performed through the RNA interference ( RNAi ) system , which involves processing of noncoding RNAs transcribed from the centromeres . We ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "rna", "interference", "chromosome", "structure", "and", "function", "centromeres", "gene", "regulation", "fungi", "model", "organisms", "experimental", "organism", "systems", "epigenetics", "chromatin", "schizosaccharomyces", "heterochromatin", "research", "and", "analysis...	2017	The intron in centromeric noncoding RNA facilitates RNAi-mediated formation of heterochromatin
RASopathies are a family of related syndromes caused by mutations in regulators of the RAS/Extracellular Regulated Kinase 1/2 ( ERK1/2 ) signaling cascade that often result in neurological deficits . RASopathy mutations in upstream regulatory components , such as NF1 , PTPN11/SHP2 , and RAS have been well-characterized...	The RASopathies are a large and complex family of syndromes caused by mutations in the RAS/MAPK signaling cascade with no known cure . Individuals with these syndromes often present with heart defects , craniofacial differences , and neurological abnormalities , such as developmental delay , cognitive changes , epileps...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "astrocytes", "vertebrates", "social", "sciences", "mice", "neuroscience", "macroglial", "cells", "animals", "mammals", "learning", "and", "memory", "biological", "locomotion", "animal", "models", "cognitive", "neuroscience", "mo...	2019	The Noonan Syndrome-linked Raf1L613V mutation drives increased glial number in the mouse cortex and enhanced learning
DNA amplification is a molecular process that increases the copy number of a chromosomal tract and often causes elevated expression of the amplified gene ( s ) . Although gene amplification is frequently observed in cancer and other degenerative disorders , the molecular mechanisms involved in the process of DNA copy n...	DNA amplification is a copy-number increase of a DNA segment . Although DNA amplification is frequently observed in cancer and other degenerative disorders , the molecular mechanisms initiating this process are still largely elusive . Here we demonstrate that small DNA fragments with homology to two distant loci on the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology", "model", "organisms", "forms", "of", "dna", "molecular", "genetics", "dna", "dna", "amplification", "biology", "molecular", "biology", "nucleic", "acids", "genetics", "gene", "duplication", "yeast", "and", "fungal", "models", "saccharomyces", "cerevisi...	2012	A Mechanism of Gene Amplification Driven by Small DNA Fragments
The ookinete is a motile stage in the malaria life cycle which forms in the mosquito blood meal from the zygote . Ookinetes use an acto-myosin motor to glide towards and penetrate the midgut wall to establish infection in the vector . The regulation of gliding motility is poorly understood . Through genetic interaction...	Malaria parasites are single celled organisms , which must alternate between vertebrate and mosquito hosts to survive and spread . In both hosts , certain parasite stages can glide through tissues and invade cells . Many components of the molecular motor that powers gliding and invasion are known and we have a good ide...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/morphogenesis", "and", "cell", "biology", "microbiology/parasitology", "cell", "biology/cell", "signaling" ]	2009	A Cyclic GMP Signalling Module That Regulates Gliding Motility in a Malaria Parasite
During embryogenesis the spinal cord shifts position along the anterior-posterior axis relative to adjacent tissues . How motor neurons whose cell bodies are located in the spinal cord while their axons reside in adjacent tissues compensate for such tissue shift is not well understood . Using live cell imaging in zebra...	Embryonic development requires tight coordination between tissues as they frequently grow at different rates . Such differential growth rates can cause shifts between neighboring tissues , and are a particular challenge for individual cells that span multiple tissues , in part because mechanical tension on such cells i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "muscle", "tissue", "nervous", "system", "vertebrates", "neuroscience", "animals", "motor", "neurons", "animal", "models", "osteichthyes", "developmental", "biology", "model", "organisms", "molecular", "motors", "actin", "motors"...	2016	Myosin phosphatase Fine-tunes Zebrafish Motoneuron Position during Axonogenesis
Hantaviruses are endemic throughout the world and hosted by rodents and insectivores . Two human zoonoses , hemorrhagic fever with renal syndrome ( HFRS ) and hantavirus pulmonary syndrome ( HPS ) , are caused by hantaviruses and case fatality rates have reached 12% for HFRS and 50% for HPS in some outbreaks . Symptoma...	Hantaviruses are endemic throughout the world and naturally hosted by rodents . The vast majority of human hantavirus infections are asymptomatic . In Europe , symptomatic hantavirus infections are summarised as hemorrhagic fever with renal syndrome ( HFRS ) mainly due to Puumala , Dobrava-Belgrade and Saaremaa virus ....	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology", "biology", "microbiology" ]	2012	Second External Quality Assurance Study for the Serological Diagnosis of Hantaviruses in Europe
When modeling cell signaling networks , a balance must be struck between mechanistic detail and ease of interpretation . In this paper we apply a fuzzy logic framework to the analysis of a large , systematic dataset describing the dynamics of cell signaling downstream of TNF , EGF , and insulin receptors in human colon...	Cells use networks of interacting proteins to interpret intra-cellular state and extra-cellular cues and to execute cell-fate decisions . Even when individual proteins are well understood at a molecular level , the dynamics and behavior of networks as a whole are harder to understand . However , deciphering the operati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/systems", "biology", "cell", "biology/cell", "signaling" ]	2009	Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling
Genome sequencing of bacterial pathogens has advanced our understanding of their evolution , epidemiology , and response to antibiotic therapy . However , we still have only a limited knowledge of the molecular changes in in vivo evolving bacterial populations in relation to long-term , chronic infections . For example...	Pseudomonas aeruginosa is the dominating pathogen of chronic airway infections in patients with cystic fibrosis ( CF ) . Although bacterial long-term persistence in CF hosts involves mutation and selection of genetic variants with increased fitness in the CF lung environment , our understanding of the within-host evolu...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Genome Analysis of a Transmissible Lineage of Pseudomonas aeruginosa Reveals Pathoadaptive Mutations and Distinct Evolutionary Paths of Hypermutators
Many theoretical and experimental studies suggest that range expansions can have severe consequences for the gene pool of the expanding population . Due to strongly enhanced genetic drift at the advancing frontier , neutral and weakly deleterious mutations can reach large frequencies in the newly colonized regions , as...	When a life form expands its range , the individuals close to the expanding front are more likely to dominate the gene pool of the newly colonized territory . This leads to the sweeping of pioneer genes across the newly colonized , a process which has been named gene surfing . We investigate how this effect interferes ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "population", "genetics", "biology", "evolutionary", "biology", "population", "biology", "evolutionary", "processes", "genetics", "and", "genomics" ]	2012	The Rate of Beneficial Mutations Surfing on the Wave of a Range Expansion
The conserved function of protein phosphorylation , catalysed by members of protein kinase superfamily , is regulated in different ways in different kinase families . Further , differences in activating triggers , cellular localisation , domain architecture and substrate specificity between kinase families are also wel...	Protein kinases are molecular switches that destine crucial decision points in cell signalling pathways . Consequently , they are implicated in the normal functioning of a cell as well as in various cancers if mutated . Kinases constitute a large and diverse superfamily with conserved 3-dimensional structure and cataly...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "taxonomy", "crystal", "structure", "protein", "interactions", "enzymes", "split-decomposition", "method", "condensed", "matter", "physics", "enzymology", "multiple", "alignment", "calculation", "phylogenetics", "data", "management", "physicochemical", "properties", "phylogen...	2018	Recognition of sites of functional specialisation in all known eukaryotic protein kinase families
The hereditary spastic paraplegias ( HSP ) are a clinically and genetically heterogeneous group of disorders characterized by progressive lower limb spasticity . Mutations in subunits of the heterotetrameric ( ε-β4-μ4-σ4 ) adaptor protein 4 ( AP-4 ) complex cause an autosomal recessive form of complicated HSP referred ...	Hereditary spastic paraplegia ( HSP ) is a genetic disorder characterized by progressive stiffness of the legs . To date , mutations in more than 70 genes have been shown to cause HSP . Four of these genes encode the subunits of adaptor protein 4 ( AP-4 ) , a heterotetrameric complex involved in intracellular protein t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "autophagic", "cell", "death", "medicine", "and", "health", "sciences", "cell", "processes", "brain", "vertebrates", "mice", "neuroscience", "animals", "mammals", "fibroblasts", "animal", "models", "model", "organisms", "connective", "tissue", "cells"...	2018	Altered distribution of ATG9A and accumulation of axonal aggregates in neurons from a mouse model of AP-4 deficiency syndrome
Classical non-homologous end joining ( C-NHEJ ) and homologous recombination ( HR ) compete to repair mammalian chromosomal double strand breaks ( DSBs ) . However , C-NHEJ has no impact on HR induced by DNA nicking enzymes . In this case , the replication fork is thought to convert the DNA nick into a one-ended DSB , ...	Genomic instability is a significant contributor to human disease , ranging from hereditary developmental disorders to cancer predisposition . Two major triggers to genomic instability are chromosomal double strand breaks ( DSBs ) and the stalling of replication forks during the DNA synthesis ( S phase ) of the cell cy...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfection", "gene", "regulation", "cloning", "plasmid", "construction", "analysis", "of", "variance", "mathematics", "dna", "replication", "statistics", "(mathematics)", "dna", "construction", "molecular", "biology", "techniques", "dna", "dna", "structure", "research"...	2018	Rad51 recruitment and exclusion of non-homologous end joining during homologous recombination at a Tus/Ter mammalian replication fork barrier
Pungent chemical compounds originating from decaying tissue are strong drivers of animal behavior . Two of the best-characterized death smell components are putrescine ( PUT ) and cadaverine ( CAD ) , foul-smelling molecules produced by decarboxylation of amino acids during decomposition . These volatile polyamines act...	The distinctive dead smell comes largely from molecules like cadaverine and putrescine that are produced during decomposition of organic tissues . These volatile compounds act as powerful chemical signals important for the survival of a wide range of species . Previous studies have identified the trace amine-associated...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "fish", "molecular", "dynamics", "chemical", "compounds", "split-decomposition", "method", "social", "sciences", "vertebrates", "neuroscience", "animals", "organic", "compounds", "animal", "models", "osteichthyes", "multiple", "alignment", "calculation", "model", "organisms...	2018	Identifying human diamine sensors for death related putrescine and cadaverine molecules
The hippocampus is crucial for episodic or declarative memory and the theta rhythm has been implicated in mnemonic processing , but the functional contribution of theta to memory remains the subject of intense speculation . Recent evidence suggests that the hippocampus might function as a network hub for volitional lea...	Neural activity both within and across brain regions can oscillate in different frequency ranges ( such as alpha , gamma , and theta frequencies ) , and these different ranges are associated with distinct functions . In behaving rodents , for example , theta rhythms ( 4–12 Hz ) in the hippocampus are prominent during t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cognitive", "neuroscience", "biology", "neuroscience", "neuroimaging" ]	2012	Movement-Related Theta Rhythm in Humans: Coordinating Self-Directed Hippocampal Learning
Rac GTPases act as master switches to coordinate multiple interweaved signaling pathways . A major function for Rac GTPases is to control neurite development by influencing downstream effector molecules and pathways . In Caenorhabditis elegans , the Rac proteins CED-10 , RAC-2 and MIG-2 act in parallel to control axon ...	Brain development requires that neurite outgrowth and guidance are precisely regulated . Previous studies have shown that molecular switch proteins called Rac GTPases perform redundant functions in controlling neurite development . Using a pair of bilateral neurons in the nematode Caenorhabditis elegans to model neurit...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "cell", "death", "caenorhabditis", "enzymes", "statistics", "cell", "processes", "enzymology", "neuroscience", "animals", "alleles", "animal", "models", "caenorhabditis", "elegans", "statistical", "data", "model", "organisms", "mathematics", "experimental",...	2018	Distinct CED-10/Rac1 domains confer context-specific functions in development
Functional cell-to-cell variability is ubiquitous in multicellular organisms as well as bacterial populations . Even genetically identical cells of the same cell type can respond differently to identical stimuli . Methods have been developed to analyse heterogeneous populations , e . g . , mixture models and stochastic...	In this manuscript , we introduce ODE constrained mixture models for the analysis of population snapshot data of kinetics and dose responses . Population snapshot data can for instance be derived from flow cytometry or single-cell microscopy and provide information about the population structure and the dynamics of sub...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "systems", "biology", "computer", "and", "information", "sciences", "mathematics", "theoretical", "biology", "statistics", "(mathematics)", "population", "modeling", "network", "analysis", "biology", "and", "life", "sciences", "signaling", "networks", "computational", "bi...	2014	ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics
Since its beginning in 1999 , the Schistosomiasis Control Program within the Unified Health System ( PCE-SUS ) has registered a cumulative coverage of just 20% of the population from the Rainforest Zone of Pernambuco ( ZMP ) , northeast Brazil . This jeopardizes the accomplishment of the minimum goal of the Fifty-Fourt...	In 2001 , a World Health Assembly resolution urged member states to ensure treatment against schistosomiasis and soil-transmitted helminthiasis in endemic areas with the goal of attaining a minimum target of at least 75% of all school-aged children by 2010 . In the highly endemic Rainforest Zone of Pernambuco ( ZMP ) ,...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/epidemiology" ]	2009	A Rationale for Schistosomiasis Control in Elementary Schools of the Rainforest Zone of Pernambuco, Brazil
Shade from neighboring plants limits light for photosynthesis; as a consequence , plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light . Collectively the response to foliar shade is called the shade avoidance syndrome ( SAS ) . The SAS includes elongation of a variety of ...	Because plants depend on light for photosynthesis , neighboring plant shade can be detrimental to survival . Many plants sense and respond to neighbor shade to compete for light . Although shade causes responses throughout the plant ( collectively known as the shade avoidance syndrome or SAS ) , most SAS studies have b...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Shade Avoidance Components and Pathways in Adult Plants Revealed by Phenotypic Profiling
Migrating cells and growth cones extend lamellipodial and filopodial protrusions that are required for outgrowth and guidance . The mechanisms of cytoskeletal regulation that underlie cell and growth cone migration are of much interest to developmental biologists . Previous studies have shown that the Arp2/3 complex an...	In the developing nervous system , the growth cone guides axons of neurons to their correct targets in the organism . The growth cone is a highly dynamic specialization at the tip of the axon that senses cues and responds by crawling toward its target , leaving the axon behind . Key to growth cone motility are dynamic ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/neurodevelopment", "developmental", "biology/neurodevelopment", "developmental", "biology/morphogenesis", "and", "cell", "biology" ]	2010	RACK-1 Acts with Rac GTPase Signaling and UNC-115/abLIM in Caenorhabditis elegans Axon Pathfinding and Cell Migration
Recent studies in Mali , Nigeria , and Senegal have indicated that annual ( or biannual ) ivermectin distribution may lead to local elimination of human onchocerciasis in certain African foci . Modelling-based projections have been used to estimate the required duration of ivermectin distribution to reach elimination ....	Studies in Mali , Nigeria , and Senegal suggest that , in some settings , it is possible to eliminate onchocerciasis after 15–17 years of ivermectin distribution . Computer models have been used to estimate the required duration of ivermectin distribution to reach elimination . Some models assume that annual ivermectin...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "medicine", "infectious", "diseases", "computer", "science", "disease", "ecology", "computer", "modeling", "neglected", "tropical", "diseases", "onchocerciasis", "infectious", "disease", "control", "infectious", "disease", "modeling", "parasitic", "dis...	2013	Uncertainty Surrounding Projections of the Long-Term Impact of Ivermectin Treatment on Human Onchocerciasis
As in other eukaryotes , protein kinases play major regulatory roles in filamentous fungi . Although the genomes of many plant pathogenic fungi have been sequenced , systematic characterization of their kinomes has not been reported . The wheat scab fungus Fusarium graminearum has 116 protein kinases ( PK ) genes . Alt...	Fusarium head blight caused by Fusarium graminearum is one of the most important diseases on wheat and barley . Although protein kinases are known to play major regulatory roles in fungi , systematic characterization of fungal kinomes has not been reported in plant pathogens . In this study we generated deletion mutant...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "agriculture", "biology" ]	2011	Functional Analysis of the Kinome of the Wheat Scab Fungus Fusarium graminearum
Alkylpurine glycosylase D ( AlkD ) exhibits a unique base excision strategy . Instead of interacting directly with the lesion , the enzyme engages the non-lesion DNA strand . AlkD induces flipping of the alkylated and opposing base accompanied by DNA stack compression . Since this strategy leaves the alkylated base sol...	DNA repair efficiency is critically dependent on the function of DNA glycosylases . These versatile enzymes perform a remarkably discriminating search for DNA lesions , followed by damage-specific base extrusion into to the enzyme's active site and removal of the damaged bases . Our work elucidates the mechanism of Bac...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Methods" ]	[ "biochemistry", "computational", "chemistry", "molecular", "dynamics", "nucleic", "acids", "biology", "and", "life", "sciences", "dna", "repair", "dna", "physical", "sciences", "chemistry", "biophysics", "biophysical", "simulations" ]	2014	Alkylpurine Glycosylase D Employs DNA Sculpting as a Strategy to Extrude and Excise Damaged Bases
Alternative pre-mRNA splicing expands the coding capacity of eukaryotic genomes , potentially enabling a limited number of genes to govern the development of complex anatomical structures . Alternative splicing is particularly prevalent in the vertebrate nervous system , where it is required for neuronal development an...	Vertebrates possess extraordinarily complex nervous systems that are formed by hundreds of different types of neurons . This neuronal diversity is achieved in part through the expression of specific sets of genes . In addition , neurons use alternative splicing to a much higher degree than other cells to produce neuron...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "sequencing", "techniques", "rna-binding", "proteins", "medicine", "and", "health", "sciences", "ocular", "anatomy", "social", "sciences", "neuroscience", "alternative", "splicing", "sequence", "motif", "analysis",...	2016	The Musashi 1 Controls the Splicing of Photoreceptor-Specific Exons in the Vertebrate Retina
Symbionts that distort their host's sex ratio by favouring the production and survival of females are common in arthropods . Their presence produces intense Fisherian selection to return the sex ratio to parity , typified by the rapid spread of host ‘suppressor’ loci that restore male survival/development . In this stu...	The sex ratio of the offspring produced by an individual can be an evolutionary battleground . In many arthropod species , maternally inherited microbes selectively kill male hosts , and the host may in turn evolve strategies to restore the production or survival of males . When males are rare , the intensity of select...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "signatures", "of", "natural", "selection", "genetic", "polymorphism", "natural", "selection", "symbiosis", "genetics", "biology", "and", "life", "sciences", "population", "genetics", "species", "interactions", "evolutionary", "biology", "evolutionary", "processes", "evol...	2014	The Evolution of Sex Ratio Distorter Suppression Affects a 25 cM Genomic Region in the Butterfly Hypolimnas bolina
HIV causes rapid CD4+ T cell depletion in the gut mucosa , resulting in immune deficiency and defects in the intestinal epithelial barrier . Breakdown in gut barrier integrity is linked to chronic inflammation and disease progression . However , the early effects of HIV on the gut epithelium , prior to the CD4+ T cell ...	The loss of intestinal CD4+ T cells in chronic HIV infection is associated with impaired immune responses to pathogens , aberrant immune activation , and defects in the gut epithelial barrier . While much is known about the pathogenesis of HIV in chronic disease , less is known about the defects that occur prior to gut...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "immunology", "microbiology" ]	2014	Early Mucosal Sensing of SIV Infection by Paneth Cells Induces IL-1β Production and Initiates Gut Epithelial Disruption
The parts of the genome transcribed by a cell or tissue reflect the biological processes and functions it carries out . We characterized the features of mammalian tissue transcriptomes at the gene level through analysis of RNA deep sequencing ( RNA-Seq ) data across human and mouse tissues and cell lines . We observed ...	A variety of genes are active within the nuclei of our cells . Some are needed for the day-to-day maintenance of cell functions , while others have roles that are more specific to certain tissues or particular cell types; for example , only the pancreas produces insulin . As a result , every tissue has its own profile ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/bioinformatics", "genetics", "and", "genomics/gene", "expression" ]	2009	An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data
Sleeping sickness , or human African trypanosomiasis , is caused by two species of Trypanosoma brucei that are transmitted to humans by tsetse flies ( Glossina spp . ) when these insects take a bloodmeal . It is commonly assumed that humans must enter the normal woodland habitat of the flies to become infected , but re...	To identify factors affecting the contact between tsetse and humans in buildings , we caught tsetse that ( i ) accumulated in a large thatched house in Zimbabwe , and ( ii ) alighted on humans in the house during the day . In accord with earlier work , the numbers accumulating increased about 10-fold with rising ambien...	[ "Abstract", "Introduction", "General", "Methods", "Experiments", "and", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases" ]	2013	Factors Affecting the Propensity of Tsetse Flies to Enter Houses and Attack Humans Inside: Increased Risk of Sleeping Sickness in Warmer Climates
Rare variants are of increasing interest to genetic association studies because of their etiological contributions to human complex diseases . Due to the rarity of the mutant events , rare variants are routinely analyzed on an aggregate level . While aggregation analyses improve the detection of global-level signal , t...	While it is known that rare variants play an important role in understanding associations between genotype and complex diseases , pinpointing individual rare variants likely to be responsible for association is still a daunting task . Due to their low frequency in the population and reduced signal , localizing causal r...	[ "Abstract", "Introduction", "Methods", "Discussion" ]	[ "statistics", "variant", "genotypes", "genetic", "mapping", "kernel", "functions", "mathematics", "test", "statistics", "protein", "structure", "protein", "structure", "databases", "research", "and", "analysis", "methods", "operator", "theory", "proteins", "mathematical",...	2019	Identifying individual risk rare variants using protein structure guided local tests (POINT)
Specification of the centromere location in most eukaryotes is not solely dependent on the DNA sequence . However , the non-genetic determinants of centromere identity are not clearly defined . While multiple mechanisms , individually or in concert , may specify centromeres epigenetically , most studies in this area ar...	The epigenetic mark of centromeres , CENP-A , is deposited in S phase in most yeasts by a mechanism that is not completely understood . Here , we identify two CEN7 flanking replication origins , ORI7-L1 and ORI7-RI , proximal to an early replicating centromere ( CEN7 ) in a budding yeast Candida albicans . Replication ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "genetics", "biology", "and", "life", "sciences", "microbiology", "molecular", "cell", "biology" ]	2014	Rad51–Rad52 Mediated Maintenance of Centromeric Chromatin in Candida albicans
Neurological involvement is one of the most important clinical manifestations of syphilis and neurological disease occurs in both early and late syphilis . The impact of HIV co-infection on clinical neurosyphilis remains unclear . The highest prevalence of both syphilis and HIV is in Africa . Therefore it might be expe...	Involvement of the central nervous system is an important manifestation of syphilis which may be more common in patients co-infected with HIV . As most cases of syphilis and HIV are seen in Africa it might be anticipated that neurosyphilis was common there . We reviewed all published material on neurosyphilis in Africa...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "inflammatory", "diseases", "urology", "medicine", "and", "health", "sciences", "body", "fluids", "nervous", "system", "tropical", "diseases", "geographical", "locations", "treponematoses", "bacterial", "diseases", "sexually", "transmitted", "diseases", "neglected", "trop...	2017	Neurosyphilis in Africa: A systematic review
A global increase in invasive infections due to group A Streptococcus ( S . pyogenes or GAS ) has been observed since the 1980s , associated with emergence of a clonal group of strains of the M1T1 serotype . Among other virulence attributes , the M1T1 clone secretes NAD+-glycohydrolase ( NADase ) . When GAS binds to ep...	Invasive infections due to group A Streptococcus ( S . pyogenes or GAS ) have become more frequent since the 1980s due , in part , to the emergence and global spread of closely related strains of the M1T1 serotype . A feature of this clonal group is the production of a secreted enzyme , NAD+-glycohydrolase ( NADase ) ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "lysosomes", "keratinocytes", "toxins", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "pathogens", "group", "a", "streptococcal", "infection", "toxicology", "toxic", "agents", "epithelial", "cells", ...	2016	NAD+-Glycohydrolase Promotes Intracellular Survival of Group A Streptococcus
Infections by enteropathogenic Escherichia coli ( EPEC ) cause diarrhea linked to high infant mortality in developing countries . EPEC adheres to epithelial cells and induces the formation of actin pedestals . Actin polymerization is driven fundamentally through signaling mediated by Tir bacterial effector protein , wh...	Infections by enteropathogenic Escherichia coli are an important cause of diarrhea linked to high infant mortality . Such bacteria attach to cells and form actin-rich structures called pedestals , which contain many proteins that play unknown functions during pedestal formation . Here we studied two nearly identical fo...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "molecular", "complexes", "pathology", "and", "laboratory", "medicine", "microbiology", "basic", "cancer", "research", "oncology", "gastroenterology", "and", "hepatology", "bacterial", "pathogens", "infectious", "diseases", "cell",...	2014	Crk Adaptors Negatively Regulate Actin Polymerization in Pedestals Formed by Enteropathogenic Escherichia coli (EPEC) by Binding to Tir Effector
Neural activity in awake behaving animals exhibits a vast range of timescales that can be several fold larger than the membrane time constant of individual neurons . Two types of mechanisms have been proposed to explain this conundrum . One possibility is that large timescales are generated by a network mechanism based...	Brain activity spans a wide range of timescales , as it is required to interact in complex time-varying environments . However , individual neurons are primarily fast devices: their membrane time constant is of the order of a few tens of milliseconds . Yet , neurons are also subject to additional biophysical processes ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neural", "networks", "engineering", "and", "technology", "signal", "processing", "bifurcation", "theory", "neuroscience", "signal", "filtering", "systems", "science", "mathematics", "algebra", "white", "noise", "computational", "neuroscience", "computer", "and", "informa...	2019	Contrasting the effects of adaptation and synaptic filtering on the timescales of dynamics in recurrent networks
Human immunity to Schistosoma infection requires many years of exposure , and multiple infections and treatments to develop . Unlike humans , rhesus macaques clear an established schistosome infection naturally at the same time acquiring immunity towards re-infection . In macaques , schistosome egg production decreases...	Schistosomes express many glycan antigens to which antibodies are raised by the infected host . These glycans may therefore form potential vaccine targets . Unlike humans where the disease persists chronically if not treated , schistosome-infected rhesus macaques are able to elicit a self-cure process naturally . To fi...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "immune", "physiology", "helminths", "immunology", "vertebrates", "parasitic", "diseases", "animals", "mammals", "primates", "animal", "models", "experimental", "organism", ...	2017	Specific anti-glycan antibodies are sustained during and after parasite clearance in Schistosoma japonicum-infected rhesus macaques
Mediator is a multi-subunit protein complex that regulates gene expression in eukaryotes by integrating physiological and developmental signals and transmitting them to the general RNA polymerase II machinery . We examined , in the fungal pathogen Candida albicans , a set of conditional alleles of genes encoding Mediat...	In this study , we have investigated Mediator function in the human fungal pathogen C . albicans . An initial screening of conditionally regulated Mediator subunits showed that the Med7 of C . albicans was not essential , in contrast to the situation noted for S . cerevisiae . While loss of CaMed7 did not lead to loss ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genomics", "gene", "regulatory", "networks", "fungal", "genetics", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "molecular", "genetics", "molecular", "biology", "techniques", "computational", "biology", "molecular", "biology", "gene", "functi...	2014	A Functional Portrait of Med7 and the Mediator Complex in Candida albicans
Our study aimed to assess the presence of different pathogens in ticks collected in two regions in Côte d’Ivoire . Real-time PCR and standard PCR assays coupled to sequencing were used . Three hundred and seventy eight ( 378 ) ticks ( 170 Amblyomma variegatum , 161 Rhipicepalus microplus , 3 Rhipicephalus senegalensis ...	The management of febrile illnesses represents a veritable challenge in sub Saharan-Africa . Until recently most of them were considered as malaria . However , it was showed that a large part of non-malarial febrile diseases in African rural regions ( for instance , in Senegal ) may be caused by tick-borne infections ....	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2016	Multiple Pathogens Including Potential New Species in Tick Vectors in Côte d’Ivoire
Systemic approaches to the study of a biological cell or tissue rely increasingly on the use of context-specific metabolic network models . The reconstruction of such a model from high-throughput data can routinely involve large numbers of tests under different conditions and extensive parameter tuning , which calls fo...	Metabolism comprises all life-sustaining biochemical processes . It plays an essential role in various aspects of biology , including the development and progression of many diseases . As the metabolism of a living cell involves several thousands of small molecules and their conversion , a full analysis of such a metab...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "algorithms", "systems", "biology", "computer", "science", "metabolic", "networks", "biology", "computational", "biology" ]	2014	Fast Reconstruction of Compact Context-Specific Metabolic Network Models
Postpartum depression is a severe emotional and mental disorder that involves maternal care defects and psychiatric illness . Postpartum depression is closely associated with a combination of physical changes and physiological stress during pregnancy or after parturition in stress-sensitive women . Although postpartum ...	Postpartum depression is a severe emotional and mental disease that can affect women typically after parturition . However , the genetic risk factors associated with the development of postpartum depression are still largely unknown . We discovered a novel function of T cell death-associated gene 51 ( TDAG51 ) in the r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "vertebrates", "electrophysiology", "mice", "neuroscience", "animals", "mammals", "social", "sciences", "ion", "channels", "animal", "behavior", "behavioral", "disorders", "molecular", "biology", "techniques", "zoology", "mood", ...	2019	TDAG51 is a crucial regulator of maternal care and depressive-like behavior after parturition
Recent advances in single-neuron biophysics have enhanced our understanding of information processing on the cellular level , but how the detailed properties of individual neurons give rise to large-scale behavior remains unclear . Here , we present a model of the hippocampal network based on observed biophysical prope...	Understanding how behavior is connected to cellular and network processes is one of the most important challenges in neuroscience , and computational modeling allows one to directly formulate hypotheses regarding the interactions between these scales . We present a model of the hippocampal network , an area of the brai...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computer", "science", "cell", "biology", "computational", "biology", "biophysics", "neuroscience", "rattus", "(rat)" ]	2007	Coincidence Detection of Place and Temporal Context in a Network Model of Spiking Hippocampal Neurons
Continuous taste bud cell renewal is essential to maintain taste function in adults; however , the molecular mechanisms that regulate taste cell turnover are unknown . Using inducible Cre-lox technology , we show that activation of β-catenin signaling in multipotent lingual epithelial progenitors outside of taste buds ...	Taste is a fundamental sense that helps the body determine whether food can be ingested . Taste dysfunction can be a side effect of cancer therapies , can result from an alteration of the renewal capacities of the taste buds , and is often associated with psychological distress and malnutrition . Thus , understanding h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	β-Catenin Signaling Biases Multipotent Lingual Epithelial Progenitors to Differentiate and Acquire Specific Taste Cell Fates
Scientific literature on cystic echinococcosis ( CE ) reporting data on risk factors is limited and to the best of our knowledge , no global evaluation of human CE risk factors has to date been performed . This systematic review ( SR ) summarizes available data on statistically relevant potential risk factors ( PRFs ) ...	Cystic echinococcosis ( CE ) is a chronic zoonotic disease causing serious global socio-economic losses in human and animal hosts . Two main aspects make it extremely difficult to study risk factors associated with human CE , the parasite’s unknown and apparently long incubation period which may last for several years ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "water", "resources", "cross-sectional", "studies", "tropical", "diseases", "vertebrates", "parasitic", "diseases", "dogs", "animals", "mammals", "research", "design", "mathematics", ...	2016	Potential Risk Factors Associated with Human Cystic Echinococcosis: Systematic Review and Meta-analysis
Modification of bacterial surface structures , such as the lipid A portion of lipopolysaccharide ( LPS ) , is used by many pathogenic bacteria to help evade the host innate immune response . Helicobacter pylori , a gram-negative bacterium capable of chronic colonization of the human stomach , modifies its lipid A by re...	Since its discovery in 1982 Helicobacter pylori has been identified as the leading cause of gastritis and peptic ulcer disease , infecting around 50% of the world's population . Infected patients are at increased risk for gastric cancers , allowing for classification of H . pylori as a class I carcinogen by the World H...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "immunology", "microbiology", "host-pathogen", "interaction", "bacterial", "biochemistry", "bacterial", "pathogens", "microbial", "physiology", "medical", "microbiology", "microbial", "pathogens", "biology", "biochemistry", "gram", "negative", "immunity", "inn...	2011	Helicobacter pylori versus the Host: Remodeling of the Bacterial Outer Membrane Is Required for Survival in the Gastric Mucosa
Multiplicity of infection ( MOI ) refers to the average number of distinct parasite genotypes concurrently infecting a patient . Although several studies have reported on MOI and the frequency of multiclonal infections in Plasmodium falciparum , there is limited data on Plasmodium vivax . Here , MOI and the frequency o...	Previous studies on rodent malarias and mathematical models have postulated a link between multiclonal infections and disease severity . This association has been tested in Plasmodium falciparum mostly in Africa with limited information on P . vivax . Furthermore , there is a paucity of information from areas with low ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2016	Multiplicity of Infection and Disease Severity in Plasmodium vivax
Integration of synaptic currents across an extensive dendritic tree is a prerequisite for computation in the brain . Dendritic tapering away from the soma has been suggested to both equalise contributions from synapses at different locations and maximise the current transfer to the soma . To find out how this is achiev...	Neurons take a great variety of shapes that allow them to perform their different computational roles across the brain . The most distinctive visible feature of many neurons is the extensively branched network of cable-like projections that make up their dendritic tree . A neuron receives current-inducing synaptic cont...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "dendritic", "structure", "nervous", "system", "radii", "electrophysiology", "geometry", "neuroscience", "optimization", "mathematics", "ganglion", "cells", "neuronal", "dendrites", "animal", "cells", "cellular", "neuroscience", "c...	2016	Optimal Current Transfer in Dendrites
Computational predictions of the functional impact of genetic variation play a critical role in human genetics research . For nonsynonymous coding variants , most prediction algorithms make use of patterns of amino acid substitutions observed among homologous proteins at a given site . In particular , substitutions obs...	The rapid pace of technological advances in DNA sequencing methods is leading to the discovery of genetic variants at a remarkable rate . Indeed , it is conceivable that entire individual genomes will be sequenced routinely in the near future . While these platforms greatly increase our ability to catalog variation , t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "evolutionary", "biology/human", "evolution", "genetics", "and", "genomics/functional", "genomics", "evolutionary", "biology/genomics", "computational"...	2010	The Use of Orthologous Sequences to Predict the Impact of Amino Acid Substitutions on Protein Function
Genome wide maps of nucleosome occupancy in yeast have recently been produced through deep sequencing of nuclease-protected DNA . These maps have been obtained from both crosslinked and uncrosslinked chromatin in vivo , and from chromatin assembled from genomic DNA and nucleosomes in vitro . Here , we analyze these map...	Genomic DNA is largely covered by proteins that compete with one another for binding to regulatory sequences . Most of these proteins are in the form of nucleosomes . How nucleosomes come to occupy particular sites and thereby compete with sequence specific transcription factors is a central problem in developing a sys...	[ "Abstract", "Introduction", "Results", "Methods", "Discussion" ]	[ "biochemistry/transcription", "and", "translation", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/chromosome", "biology", "computational", "biology/transcriptional", "regulation" ]	2010	Blurring of High-Resolution Data Shows that the Effect of Intrinsic Nucleosome Occupancy on Transcription Factor Binding is Mostly Regional, Not Local
The vitellarium is a highly proliferative organ , producing cells which are incorporated along with a fertilized ovum into the schistosome egg . Vitellarial growth fails to occur in virgin female schistosomes in single sex ( female-only ) infections , and involution of this tissue , which is accompanied by physical shr...	Schistosomes are parasitic trematode worms that infect more that 200 million people in 76 countries of the tropics and subtropics . These parasites are unusual amongst trematodes in having separate sexes . Mating of male and female schistosome involves the female residing within a specialized canal on the ventral surfa...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology" ]	2012	Cell Death and Reproductive Regression in Female Schistosoma mansoni
The trehalose metabolic enzymes have been considered as potential targets for drug or vaccine in several organisms such as Mycobacterium , plant nematodes , insects and fungi due to crucial role of sugar trehalose in embryogenesis , glucose uptake and protection from stress . Trehalose-6-phosphate phosphatase ( TPP ) i...	Lymphatic filariasis , one of the neglected tropical diseases , is the second leading cause of permanent and long term disability . Control of the disease relies on the mass administration of drugs which mainly act on the microfilariae without substantial effect on adult worms . Drugs need to be continued for several y...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biotechnology", "biology", "zoology", "parasitology" ]	2012	In Vitro Silencing of Brugia malayi Trehalose-6-Phosphate Phosphatase Impairs Embryogenesis and In Vivo Development of Infective Larvae in Jirds
Protein quality control requires constant surveillance to prevent misfolding , aggregation , and loss of cellular function . There is increasing evidence in metazoans that communication between cells has an important role to ensure organismal health and to prevent stressed cells and tissues from compromising lifespan ....	The protein quality control machinery is responsible for preventing the accumulation of misfolded and damaged proteins and loss of cellular function . The capacity of cellular surveillance is limited however , leading to increased appearance of protein aggregates and risk for age-associated diseases . Here , we show th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Neuronal Reprograming of Protein Homeostasis by Calcium-Dependent Regulation of the Heat Shock Response
Phylodynamics seeks to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest . One way to accomplish this task formulates an observed sequence data likelihood exploiting a coalescent model for the sampled individuals’ genealogy and then integrating...	Phylodynamics seeks to estimate changes in population size from genetic data sampled from individuals across a particular population . One approach to accomplish this task uses a model called the coalescent , which relates the shape of the individuals’ shared ancestral tree to genetic diversity , which is in turn relat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "influenza", "population", "dynamics", "population", "genetics", "simulation", "and", "modeling", "mathematics", "statistics", "(mathematics)", "effective", "population", "size", "molecular", "biology", ...	2016	Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference
It has been empirically established that the cerebral cortical areas defined by Brodmann one hundred years ago solely on the basis of cellular organization are closely correlated to their function , such as sensation , association , and motion . Cytoarchitectonically distinct cortical areas have different densities and...	Neurons , or nerve cells in the brain , communicate with each other using stereotyped electric pulses , called spikes . It is believed that neurons convey information mainly through the frequency of the transmitted spikes , called the firing rate . In addition , neurons may communicate some information through the fine...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "neuroscience/neuronal", "signaling", "mechanisms", "neuroscience/theoretical", "neuroscience", "computational", "biology/computational", "neuroscience" ]	2009	Relating Neuronal Firing Patterns to Functional Differentiation of Cerebral Cortex
Enzymes stabilize transition states of reactions while limiting binding to ground states , as is generally required for any catalyst . Alkaline Phosphatase ( AP ) and other nonspecific phosphatases are some of Nature's most impressive catalysts , achieving preferential transition state over ground state stabilization o...	Enzymes use a variety of tools and strategies to enhance ( catalyze ) biological reactions; these include the use of general acids and bases , cofactors , and the employment of remote binding interactions to position substrates near reactive chemical groups . Phosphatases are some of Nature's best enzymes , affording e...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "biochemistry", "enzyme", "structure", "hydrolysis", "biocatalysis", "thermodynamics", "enzymes", "catalysis", "chemistry", "chemical", "reactions", "biology", "enzyme", "kinetics", "biophysics", "physical", "chemistry" ]	2013	Ground State Destabilization by Anionic Nucleophiles Contributes to the Activity of Phosphoryl Transfer Enzymes
CENP-A ( CID in flies ) is the histone H3 variant essential for centromere specification , kinetochore formation , and chromosome segregation during cell division . Recent studies have elucidated major cell cycle mechanisms and factors critical for CENP-A incorporation in mitosis , predominantly in cultured cells . How...	Centromeres are regions of eukaryotic chromosomes that recruit the kinetochores and are essential for faithful segregation of DNA during all cell divisions . The centromere-specific histone H3 variant CENP-A accumulates at the centromere , defining this region , and is maintained throughout cellular generations by epig...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "mitosis", "meiosis", "drosophila", "melanogaster", "model", "organisms", "molecular", "cell", "biology", "cell", "division", "cell", "biology", "chromosome", "biology", "centromeres", "biology" ]	2012	The Cell Cycle Timing of Centromeric Chromatin Assembly in Drosophila Meiosis Is Distinct from Mitosis Yet Requires CAL1 and CENP-C
The tumor necrosis factor-receptor-associated factor 2 ( TRAF2 ) - and Nck-interacting kinase ( TNIK ) is a ubiquitously expressed member of the germinal center kinase family . The TNIK functions in hematopoietic cells and the role of TNIK-TRAF interaction remain largely unknown . By functional proteomics we identified...	The germinal center kinase family member TNIK was discovered in a yeast-two-hybrid screen for interaction partners of the adapter proteins TRAF2 and Nck , and here we show it is one of the missing molecular players in two key signaling pathways in B-lymphocytes . We found that TNIK is crucial for the activities of the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immune", "cells", "protein", "interactions", "viruses", "and", "cancer", "immunology", "microbiology", "c-jun", "n-terminal", "kinase", "signaling", "cascade", "cell", "growth", "biology", "proteomics", "pathogenesis", "biochemistry", "signal", "transduction", "b", "ce...	2012	The Germinal Center Kinase TNIK Is Required for Canonical NF-κB and JNK Signaling in B-Cells by the EBV Oncoprotein LMP1 and the CD40 Receptor
A promising strategy for drug abuse treatment is to accelerate the drug metabolism by administration of a drug-metabolizing enzyme . The question is how effectively an enzyme can actually prevent the drug from entering brain and producing physiological effects . In the present study , we have developed a pharmacokineti...	In this computational study , we have examined , for the first time , the potential effects of a drug-metabolizing enzyme on drug pharmacokinetics in human , showing that a high-activity drug-metabolizing enzyme can completely/effectively prevent the drug of abuse from entering brain to produce physiological effects . ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "neuroscience", "biology", "computational", "biology" ]	2012	Modeling of Pharmacokinetics of Cocaine in Human Reveals the Feasibility for Development of Enzyme Therapies for Drugs of Abuse
Manipulating the dynamics of neural systems through targeted stimulation is a frontier of research and clinical neuroscience; however , the control schemes considered for neural systems are mismatched for the unique needs of manipulating neural dynamics . An appropriate control method should respect the variability in ...	Stimulating a neural system and observing its effect through simultaneous observation offers the promise to better understand how neural systems perform computations , as well as for the treatment of neurological disorders . A powerful perspective for understanding a neural system’s behavior undergoing stimulation is t...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "decision", "making", "engineering", "and", "technology", "electronics", "neurodegenerative", "diseases", "signal", "processing", "integrators", "social", "sciences", "neuroscience", "noise", "reduction", "systems", "science", "mat...	2019	Myopic control of neural dynamics
Skin pigment patterns of vertebrates are a classic system for understanding fundamental mechanisms of morphogenesis , differentiation , and pattern formation , and recent studies of zebrafish have started to elucidate the cellular interactions and molecular mechanisms underlying these processes . In this species , hori...	Pigment patterns are some of the most distinctive , diverse and aesthetically pleasing traits of vertebrates . In turn , these patterns offer an outstanding opportunity to understand the mechanisms underlying the development of adult form and how such mechanisms change evolutionarily . Among the especially wide-ranging...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "biology", "morphogenesis", "pattern", "formation", "cell", "differentiation" ]	2013	Interactions with Iridophores and the Tissue Environment Required for Patterning Melanophores and Xanthophores during Zebrafish Adult Pigment Stripe Formation
The murine leukaemia virus ( MLV ) gag gene encodes a small protein called p12 that is essential for the early steps of viral replication . The N- and C-terminal regions of p12 are sequentially acting domains , both required for p12 function . Defects in the C-terminal domain can be overcome by introducing a chromatin ...	All retroviral genomes contain a gag gene that codes for the Gag polyprotein . Gag is cleaved upon viral maturation to release individual proteins , including matrix , capsid and nucleocapsid , providing the structural components of the virion . In murine leukaemia virus ( MLV ) , Gag cleavage releases an additional pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "components", "viral", "core", "viruslike", "particles", "encapsidation", "virology", "biology", "and", "life", "sciences", "capsids", "microbiology", "viral", "replication", "complex", "viral", "structure", "viral", "replication" ]	2014	The N-Terminus of Murine Leukaemia Virus p12 Protein Is Required for Mature Core Stability
Rabbit hemorrhagic disease , first described in China in 1984 , causes hemorrhagic necrosis of the liver . Its etiological agent , rabbit hemorrhagic disease virus ( RHDV ) , belongs to the Lagovirus genus in the family Caliciviridae . The detailed molecular structure of any lagovirus capsid has yet to be determined . ...	Rabbit hemorrhagic disease ( RHD ) , first described in China in 1984 , causes hemorrhagic necrosis of the liver within three days after infection and with a mortality rate that exceeds 90% . RHD has spread to large parts of the world and threatens the rabbit industry and related ecology . Its etiological agent , rabbi...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "viral", "core", "virology", "biology", "microbiology", "viral", "structure" ]	2013	Atomic Model of Rabbit Hemorrhagic Disease Virus by Cryo-Electron Microscopy and Crystallography
Understanding the genetic basis of phenotypic adaptation to changing environments is an essential goal of population and quantitative genetics . While technological advances now allow interrogation of genome-wide genotyping data in large panels , our understanding of the process of polygenic adaptation is still limited...	Many traits are controlled by a large number of genes , and environmental changes can lead to shifts in trait optima . How populations adapt to these shifts depends on a number of parameters including the genetic basis of the trait as well as population demography . We simulate a number of trait architectures and popul...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "animal", "types", "quantitative", "trait", "loci", "population", "genetics", "domestic", "animals", "animals", "model", "organisms", "experimental", "organism", "systems", "evolutionary", "adaptation", "population", "biology", "plants", "zoology", "research", "and", "a...	2018	Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima
This study investigates the contributions of network topology features to the dynamic behavior of hierarchically organized excitable networks . Representatives of different types of hierarchical networks as well as two biological neural networks are explored with a three-state model of node activation for systematicall...	Many complex biological networks are characterized by the coexistence of topological features such as modules and central hub nodes . What are the relative contributions of these structural features to the networks' dynamic behavior ? We used a computational model to simulate the general activation and inactivation beh...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/metabolic", "networks", "computational", "biology/systems", "biology", "computational", "biology/computational", "neuroscience" ]	2008	Organization of Excitable Dynamics in Hierarchical Biological Networks
Standard theories of decision-making involving delayed outcomes predict that people should defer a punishment , whilst advancing a reward . In some cases , such as pain , people seem to prefer to expedite punishment , implying that its anticipation carries a cost , often conceptualized as ‘dread’ . Despite empirical su...	People often prefer to ‘get pain out of the way’ , treating pain in the future as more significant than pain now . One explanation , termed ‘dread’ , is that anticipating pain is unpleasant or disadvantageous , rather like pain itself . Human brain imaging studies support the existence of dread , though it is unknown w...	[ "Abstract", "Introduction", "Discussion", "Methods" ]	[]	2013	Dread and the Disvalue of Future Pain
Human BCL7 gene family consists of BCL7A , BCL7B , and BCL7C . A number of clinical studies have reported that BCL7 family is involved in cancer incidence , progression , and development . Among them , BCL7B , located on chromosome 7q11 . 23 , is one of the deleted genes in patients with Williams-Beuren syndrome . Alth...	BCL7B , a member of the human BCL7 gene family , is deleted in patients with Williams-Beuren syndrome . Although several clinical studies have suggested that malignant diseases occurring in patients with Williams-Beuren syndrome are associated with aberrations in BCL7B , little is known regarding the physiological func...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "cancer", "genetics", "genetics", "biology", "and", "life", "sciences", "cell", "differentiation" ]	2015	The Tumor Suppressor BCL7B Functions in the Wnt Signaling Pathway
Astrocytes , a glial cell type of the central nervous system , have emerged as detectors and regulators of neuronal information processing . Astrocyte excitability resides in transient variations of free cytosolic calcium concentration over a range of temporal and spatial scales , from sub-microdomains to waves propaga...	Astrocytes process information in the brain via calcium signals that can modulate neuronal communication . Astrocytic calcium signals are associated with brain functioning , including memory and learning , and are altered in the diseased brain . Astrocytic calcium signals display a huge spatio-temporal diversity , whic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "astrocytes", "endoplasmic", "reticulum", "cell", "processes", "electrophysiology", "neuroscience", "macroglial", "cells", "simulation", "and", "modeling", "ion", "channels", "calcium", "signaling", "cellular", "structures", "and",...	2019	Simulation of calcium signaling in fine astrocytic processes: Effect of spatial properties on spontaneous activity
Repair of DNA double-strand breaks ( DSBs ) by homologous recombination ( HR ) in haploid cells is generally restricted to S/G2 cell cycle phases , when DNA has been replicated and a sister chromatid is available as a repair template . This cell cycle specificity depends on cyclin-dependent protein kinases ( Cdk1 in Sa...	Homologous recombination ( HR ) provides an important mechanism to eliminate deleterious lesions , such as DNA double-strand breaks ( DSBs ) . DSB repair by HR uses homologous DNA sequences as a template to form recombinants that are either crossover or noncrossover with regard to flanking parental sequences . Furtherm...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology", "model", "organisms", "dna", "chromosome", "biology", "biology", "molecular", "biology", "cell", "biology", "nucleic", "acids", "yeast", "and", "fungal", "models", "dna", "repair", "saccharomyces", "cerevisiae", "dna", "recombination", "molecular", "ce...	2011	Distinct Cdk1 Requirements during Single-Strand Annealing, Noncrossover, and Crossover Recombination
The complex connectivity of the cerebral cortex is a topic of much study , yet the link between structure and function is still unclear . The processing capacity and throughput of information at individual brain regions remains an open question and one that could potentially bridge these two aspects of neural organizat...	The brain may be thought of as a network of regions that communicate with each other to produce emergent phenomena such as perception and cognition . Many potentially interesting aspects of brain networks , such as how information is emitted at different nodes , also tend to be of interest in various types of telecommu...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "connectomics", "neuroanatomy", "computational", "neuroscience", "biology", "neuroscience", "neuroimaging" ]	2011	Extracting Message Inter-Departure Time Distributions from the Human Electroencephalogram
Forecasting the impacts of climate change on Aedes-borne viruses—especially dengue , chikungunya , and Zika—is a key component of public health preparedness . We apply an empirically parameterized model of viral transmission by the vectors Aedes aegypti and Ae . albopictus , as a function of temperature , to predict cu...	The established scientific consensus indicates that climate change will severely exacerbate the risk and burden of Aedes-transmitted viruses , including dengue , chikungunya , Zika , and other significant threats to global health security . Here , we show more subtle impacts of climate change on transmission , caused p...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "viral", "transmission", "and", "infection", "chikungunya", "infection", "atmospheric", "science", "pathogens", "geographical", "locat...	2019	Global expansion and redistribution of Aedes-borne virus transmission risk with climate change
This year , Brazil will host about 600 , 000 foreign visitors during the 2014 FIFA World Cup . The concern of possible dengue transmission during this event has been raised given the high transmission rates reported in the past by this country . We used dengue incidence rates reported by each host city during previous ...	This year the 2014 FIFA World Cup will be hosted by Brazil , a country that has reported a higher number of dengue cases annually than any other country worldwide over the last decade . About 600 , 000 foreign tourists are expected and may be at risk for this disease . Games will be played in 12 different cities across...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "spatial", "epidemiology", "vector-borne", "diseases", "tropical", "diseases", "geographical", "locations", "forecasting", "neglected", "tropical", "diseases", "infectious", "disease", "contro...	2014	Risk of Dengue for Tourists and Teams during the World Cup 2014 in Brazil
Fusarium graminearum is a fungal pathogen that causes Fusarium head blight ( FHB ) in wheat and barley . Autophagy is a highly conserved vacuolar degradation pathway essential for cellular homeostasis in which Atg9 serves as a multispanning membrane protein important for generating membranes for the formation of phagop...	Autophagy is an intracellular degradation pathway conserved in eukaryotes , but the mechanism of autophagy or autophagosome formation in the wheat head blight fungus Fusarium graminearum remains unclear . One fundamental question in the autophagy field lies on how the formation of autophagosome and recycling of cellula...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "cell", "death", "autophagic", "cell", "death", "medicine", "and", "health", "sciences", "fusarium", "pathology", "and", "laboratory", "medicine", "pathogens", "cell", "processes", "microbiology", "fusarium", "graminearum", "fungal", "structure", ...	2018	Small GTPase Rab7-mediated FgAtg9 trafficking is essential for autophagy-dependent development and pathogenicity in Fusarium graminearum
Cryptosporidium is a leading cause of childhood diarrhea in low-resource settings , and has been repeatedly associated with impaired physical and cognitive development . In May 2013 , an outbreak of diarrhea caused by Cryptosporidium hominis was identified in the Arctic region of Nunavik , Quebec . Human cryptosporidio...	In mid-2013 , an outbreak of moderate-to-severe diarrhea caused by Cryptosporidium was identified in the Arctic region of Nunavik , Quebec , and it predominantly affected young children . Cryptosporidium is a leading cause of childhood diarrhea in low-resource settings , but was previously unknown in this region . This...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "canada", "pathology", "and", "laboratory", "medicine", "pathogens", "geographical", "locations", "microbiology", "cryptosporidium", "parasitic", "diseases", "parasitic", "protozoans", "north", "america", ...	2016	Cryptosporidium hominis Is a Newly Recognized Pathogen in the Arctic Region of Nunavik, Canada: Molecular Characterization of an Outbreak
Progress in decoding neural signals has enabled the development of interfaces that translate cortical brain activities into commands for operating robotic arms and other devices . The electrical stimulation of sensory areas provides a means to create artificial sensory information about the state of a device . Taken to...	Brain-machine interfaces establish new communication channels between the brain and the external world with the goal of restoring sensory and motor functions for people with severe paralysis or sensory impairments . Current methodologies are based on decoding the motor intent from the recorded neural activity and trans...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "neuroscience", "biomedical", "engineering", "motor", "systems", "control", "engineering", "biological", "systems", "engineering", "computational", "neuroscience", "coding", "mechanisms", "bioengineering", "biology", "computer", "science", "bionics", "control...	2012	Shaping the Dynamics of a Bidirectional Neural Interface
Disease caused by the dengue virus ( DENV ) is a significant cause of morbidity throughout the world . Although prior research has focused on the association of specific DENV serotypes ( DENV-1 , DENV-2 , DENV-3 , and DENV-4 ) with the development of severe outcomes such as dengue hemorrhagic fever and dengue shock syn...	Dengue virus ( DENV ) causes disease in millions of people annually and disproportionately affects those in the developing world . DENVs may be divided into four serotypes ( DENV-1 , DENV-2 , DENV-3 , and DENV-4 ) and a geographical region may be affected by one or more DENV serotypes simultaneously . Infection with DE...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "dengue", "viral", "diseases" ]	2012	Correlation of Serotype-Specific Dengue Virus Infection with Clinical Manifestations
Canine rabies transmission was interrupted in N’Djaména , Chad , following two mass vaccination campaigns . However , after nine months cases resurged with re-establishment of endemic rabies transmission to pre-intervention levels . Previous analyses investigated district level spatial heterogeneity of vaccination cove...	Rabies transmission between dogs and from dogs to humans can be interrupted by mass vaccination of dogs . Novel geo-referenced contact sensors tracked the contacts and locations of several hundred dogs in N’Djaména , the capital of Chad . With the data generated by the sensors we developed a contact network model for r...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "animal", "types", "medicine", "and", "health", "sciences", "immunology", "tropical", "diseases", "vertebrates", "pets", "and", "companion", "animals", "dogs", "animals", "mammals", "preventive", "medicine", "rabies", "raccoons", "network", "analysis", "neglected", "t...	2018	The importance of dog population contact network structures in rabies transmission
50% of leprosy patients suffer from episodes of Type 1/ reversal reactions ( RR ) and Type 2/ Erythema Nodosum Leprosum ( ENL ) reactions which lead to morbidity and nerve damage . CD4+ subsets of Th17 cells and CD25+FOXP3+ regulatory T cells ( Tregs ) have been shown to play a major role in disease associated immunopa...	Reversal reactions ( RR; Type 1 ) and Erythema Nodosum Leprosum ( ENL; Type 2 ) are two types of leprosy reactions which appear episodically in a proportion of leprosy patients and lead to high morbidity and peripheral nerve damage that require immediate medical attention , ENL seen in anergic lepromatous patients , sh...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "flow", "cytometry", "cell", "motility", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "immune", "cells", "immunology", "tropical", "diseases", "cloning", "bacterial", "diseases", "develop...	2016	Leprosy Reactions Show Increased Th17 Cell Activity and Reduced FOXP3+ Tregs with Concomitant Decrease in TGF-β and Increase in IL-6
Herpesviruses form different gH/gL virion envelope glycoprotein complexes that serve as entry complexes for mediating viral cell-type tropism in vitro; their roles in vivo , however , remained speculative and can be addressed experimentally only in animal models . For murine cytomegalovirus two alternative gH/gL comple...	The role of viral glycoprotein entry complexes in viral tropism in vivo is a question central to understanding virus pathogenesis and transmission for any virus . Studies were limited by the difficulty in distinguishing between viral entry into first-hit target cells and subsequent cell-to-cell spread within tissues . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Non-redundant and Redundant Roles of Cytomegalovirus gH/gL Complexes in Host Organ Entry and Intra-tissue Spread
In mammals , imprinted gene expression results from the sex-specific methylation of imprinted control regions ( ICRs ) in the parental germlines . Imprinting is linked to therian reproduction , that is , the placenta and imprinting emerged at roughly the same time and potentially co-evolved . We assessed the transcript...	In mammals , a subset of genes is expressed from only one chromosomal copy , depending on its parental origin . This process , known as genomic imprinting , results from DNA methylation marks deposited in gametes at regulatory sequences called imprinting control regions ( ICRs ) . Most of the DNA methylation controllin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/germ", "cells", "developmental", "biology/embryology", "genetics", "and", "genomics/comparative", "genomics", "genetics", "and", "genomics/functional", "genomics", "developmental", "biology/developmental", "evolution", "developmental", "biology/molecular",...	2010	The Parental Non-Equivalence of Imprinting Control Regions during Mammalian Development and Evolution
In order to investigate how the movement of dogs affects the geographically inter-provincial spread of rabies in Mainland China , we propose a multi-patch model to describe the transmission dynamics of rabies between dogs and humans , in which each province is regarded as a patch . In each patch the submodel consists o...	In 1999 , human rabies cases were reported in about 120 counties in Mainland China , mainly in the southern provinces . Now outbreaks of human rabies have been reported in about 1000 counties and the disease has spread geographically from the south to the north . Phylogeographic analyses of rabies virus strains indicat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Modeling the Geographic Spread of Rabies in China
Cryptococcus neoformans is the most common cause of fungal meningitis , with high mortality and morbidity . The reason for the frequent occurrence of Cryptococcus infection in the central nervous system ( CNS ) is poorly understood . The facts that human and animal brains contain abundant inositol and that Cryptococcus...	Cryptococcus neoformans is an AIDS-associated human fungal pathogen that annually causes over 1 million cases of meningitis world-wide , and more than 600 , 000 attributable deaths . Cryptococcus often causes lung and brain infection and is the leading cause of fungal meningitis in immunosuppressed patients . Why Crypt...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "cryptococcosis", "medicine", "infectious", "diseases", "fungal", "diseases" ]	2013	Brain Inositol Is a Novel Stimulator for Promoting Cryptococcus Penetration of the Blood-Brain Barrier
Human T-cell leukemia virus type 1 ( HTLV-1 ) infects CD4+ T cells and induces proliferation of infected cells in vivo , which leads to the onset of adult T-cell leukemia ( ATL ) in some infected individuals . The HTLV-1 bZIP factor ( HBZ ) gene , which is encoded in the minus strand of HTLV-1 , plays critical roles in...	HTLV-1 is a T-cell-tropic , latently infectious virus that causes a T-cell malignancy , ATL , and inflammatory diseases . The mechanisms by which HTLV-1 evades the immune response and establishes chronic infection are not yet understood . Recent studies have demonstrated that TIGIT , a co-inhibitory molecule , is expre...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	HTLV-1 bZIP Factor Impairs Anti-viral Immunity by Inducing Co-inhibitory Molecule, T Cell Immunoglobulin and ITIM Domain (TIGIT)
While nucleosome positioning on eukaryotic genome play important roles for genetic regulation , molecular mechanisms of nucleosome positioning and sliding along DNA are not well understood . Here we investigated thermally-activated spontaneous nucleosome sliding mechanisms developing and applying a coarse-grained molec...	Nucleosomes are fundamental units of chromatin folding consisting of double-stranded DNA wrapped ~1 . 7 times around a histone octamer . By densely populating the eukaryotic genome , nucleosomes enable efficient genome compaction inside the cellular nucleus . However , the portion of DNA occupied by a nucleosome can ha...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "chemical", "bonding", "crystal", "structure", "chemical", "compounds", "phosphates", "condensed", "matter", "physics", "dna-binding", "proteins", "sequence", "motif", "analysis", "epigenetics", "crystallography", "thermodynamics", "chromatin", "hydrogen", "bonding", "resea...	2017	Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations
Ae . albopictus , an invasive mosquito vector now endemic to much of the northeastern US , is a significant public health threat both as a nuisance biter and vector of disease ( e . g . chikungunya virus ) . Here , we aim to quantify the relationships between local environmental and meteorological conditions and the ab...	This paper examines the ecological underpinnings of the invasive mosquito Ae . albopictus and the associated risk of arboviral transmission in New York City . We aim to quantify the relationships between local environmental and meteorological conditions and Ae . albopctus abundance . Further , we explicitly determine r...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "atmospheric", "science", "pathogens", "tropical", "diseases", "microbiology", "animals", "alphaviruses", "viruses", "chikungun...	2017	Local environmental and meteorological conditions influencing the invasive mosquito Ae. albopictus and arbovirus transmission risk in New York City
The RNA binding protein T-STAR was created following a gene triplication 520–610 million years ago , which also produced its two parologs Sam68 and SLM-1 . Here we have created a T-STAR null mouse to identify the endogenous functions of this RNA binding protein . Mice null for T-STAR developed normally and were fertile...	Alternative splicing plays a key role in animal development and is largely controlled by the expression of RNA binding proteins . Most RNA binding proteins exist as families of sister proteins called paralogs , which result from gene amplification , including T-STAR , which is closely related to Sam68 and SLM-1 . T-STA...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "animal", "genetics", "reproductive", "system", "functional", "genomics", "gene", "regulation", "anatomy", "and", "physiology", "neuroscience", "gene", "function", "developmental", "biology", "molecular", "development", "molecular", "ge...	2013	The Tissue-Specific RNA Binding Protein T-STAR Controls Regional Splicing Patterns of Neurexin Pre-mRNAs in the Brain
Dengue virus ( DENV ) is a re-emerging arthropod borne flavivirus that infects more than 300 million people worldwide , leading to 50 , 000 deaths annually . Because dendritic cells ( DC ) in the skin and blood are the first target cells for DENV , we sought to investigate the early molecular events involved in the hos...	Dengue virus ( DENV ) , the leading arthropod-borne viral infection in the world , represents a major human health concern with a global at risk population of over 3 billion people . Currently , there are no antivirals or vaccines available to treat patients with dengue fever , nor is it possible to predict which patie...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "medicine", "and", "health", "sciences" ]	2014	Cellular Oxidative Stress Response Controls the Antiviral and Apoptotic Programs in Dengue Virus-Infected Dendritic Cells
The ability for a host to recognize infection is critical for virus clearance and often begins with induction of inflammation . The PB1-F2 of pathogenic influenza A viruses ( IAV ) contributes to the pathophysiology of infection , although the mechanism for this is unclear . The NLRP3-inflammasome has been implicated i...	Influenza virus is a highly contagious respiratory pathogen that can cause pandemics , resulting in the deaths of millions worldwide . Previously we demonstrated that PB1-F2 protein produced by pathogenic influenza induces overwhelming inflammatory responses to infection , which enhances disease . The way in which PB1-...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunopathology", "animal", "models", "of", "infection", "virulence", "factors", "and", "mechanisms", "immunity", "virology", "innate", "immunity", "immunology", "host-pathogen", "interaction", "biology", "microbiology", "immune", "response" ]	2013	Activation of the NLRP3 Inflammasome by IAV Virulence Protein PB1-F2 Contributes to Severe Pathophysiology and Disease
Transmitted by blood-sucking insects , the unicellular parasite Trypanosoma cruzi is the causative agent of Chagas' disease , a malady manifested in a variety of symptoms from heart disease to digestive and urinary tract dysfunctions . The reasons for such organ preference have been a matter of great interest in the fi...	Chagas' disease , caused by the protozoon Trypanosoma cruzi , is an ailment affecting approximately 12–14 million people in Iberoamerica and is becoming increasingly important in North America and Europe as a result of migratory currents . The parasite invades mainly cells of the heart or the walls of the digestive tra...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry", "infectious", "diseases", "infectious", "diseases/neglected", "tropical", "diseases", "cell", "biology/extra-cellular", "matrix", "infectious", "diseases/protozoal", "infections" ]	2010	Role of the gp85/Trans-Sialidases in Trypanosoma cruzi Tissue Tropism: Preferential Binding of a Conserved Peptide Motif to the Vasculature In Vivo
Listeria monocytogenes ( Lm ) is a saprophyte and intracellular pathogen . Transition to the pathogenic state relies on sensing of host-derived metabolites , yet it remains unclear how these are recognized and how they mediate virulence gene regulation . We previously found that low availability of isoleucine signals L...	Bacterial pathogens must adapt to their host environment to carry out a successful infection . Sensing host-derived signals precedes adaptation , and triggers switching to the virulent state . Within mammalian cells L . monocytogenes responds to branched-chain amino acids ( BCAA ) deficiency by inducing virulence gene ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "aliphatic", "amino", "acids", "gene", "regulation", "pathogens", "messenger", "rna", "rna", "extraction", "organic", "compounds", "dna", "transcription", "...	2018	Controlled branched-chain amino acids auxotrophy in Listeria monocytogenes allows isoleucine to serve as a host signal and virulence effector
The intrinsic flexibility of proteins allows them to undergo large conformational fluctuations in solution or upon interaction with other molecules . Proteins also commonly assemble into complexes with diverse quaternary structure arrangements . Here we investigate how the flexibility of individual protein chains influ...	Proteins often interact with other proteins and assemble into complexes . Here we show that the flexibility of individual proteins is important for their recruitment to complexes , as it facilitates the formation of asymmetric interfaces between different subunits . The role of flexibility becomes increasingly importan...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Conclusions", "Methods" ]	[ "macromolecular", "complex", "analysis", "biochemistry", "protein", "interactions", "molecular", "complexes", "proteins", "evolutionary", "modeling", "protein", "structure", "biology", "and", "life", "sciences", "comparative", "genomics", "computational", "biology", "evolut...	2014	Protein Flexibility Facilitates Quaternary Structure Assembly and Evolution
The essential herpesvirus adaptor protein HVS ORF57 , which has homologs in all other herpesviruses , promotes viral mRNA export by utilizing the cellular mRNA export machinery . ORF57 protein specifically recognizes viral mRNA transcripts , and binds to proteins of the cellular transcription-export ( TREX ) complex , ...	Herpes viruses invade cells , hijacking cellular components to sustain their lifecycle and replicate . A critical step of infection is the export of viral mRNA from the nucleus to the cytoplasm , where the molecular machinery to produce proteins is located . To provide a link between their mRNA and cellular components ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "medicine", "biochemistry", "rna", "infectious", "diseases", "rna", "transport", "protein", "interactions", "nucleic", "acids", "proteins", "herpes", "simplex", "protein", "structure", "macromolecular", "assemblies", "biology", "vi...	2014	Competitive and Cooperative Interactions Mediate RNA Transfer from Herpesvirus Saimiri ORF57 to the Mammalian Export Adaptor ALYREF

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