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Chronic soil-transmitted helminth ( STH ) infections are associated with effects on systemic immune responses that could be caused by alterations in immune homeostasis . To investigate this , we measured the impact in children of STH infections on cytokine responses and gene expression in unstimulated blood . Sixty chi...	Soil-transmitted helminth ( STH or intestinal worm ) infections are extremely common infectious diseases of childhood in developing countries . Infections tend be chronic and may last for many years . Chronic STH infections are associated with modulation of the immune response , a consequence of which may be a reduced ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "soil-transmitted", "helminths", "clinical", "immunology", "neglected", "tropical", "diseases", "immunology", "immunomodulation", "immune", "response" ]	2011	Effects of Chronic Ascariasis and Trichuriasis on Cytokine Production and Gene Expression in Human Blood: A Cross-Sectional Study
Multiple PIP2 dependent molecular processes including receptor activated phospholipase C activity occur at the neuronal plasma membranes , yet levels of this lipid at the plasma membrane are remarkably stable . Although the existence of unique pools of PIP2 supporting these events has been proposed , the mechanism by w...	PIP2 has been implicated in multiple functions at the plasma membrane . Some of these require its hydrolysis by receptor-activated phospholipase C , whereas others , such as membrane transport and cytoskeletal function , involve the interaction of the intact lipid with cellular proteins . The mechanistic basis underlyi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A dPIP5K Dependent Pool of Phosphatidylinositol 4,5 Bisphosphate (PIP2) Is Required for G-Protein Coupled Signal Transduction in Drosophila Photoreceptors
The antiviral factor tripartite interaction motif 5α ( Trim5α ) restricts a broad range of retroviruses in a species-specific manner . Although human Trim5α is unable to block HIV-1 infection in human cells , a modest inhibition of HIV-1 replication has been reported . Recently two polymorphisms in the Trim5 gene ( H43...	The clinical course of HIV-1 infection is highly variable between individuals , and host genetic variations may at least account for part of these differences . Recently two single nucleotide polymorphisms in the tripartite interaction motif 5 gene ( Trim5 ) have been reported to affect the antiviral activity of the Tr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "homo", "(human)", "infectious", "diseases", "virology" ]	2008	The Effect of Trim5 Polymorphisms on the Clinical Course of HIV-1 Infection
Free-ranging nonhuman primates are frequent sources of zoonotic pathogens due to their physiologic similarity and in many tropical regions , close contact with humans . Many high-risk disease transmission interfaces have not been monitored for zoonotic pathogens due to difficulties inherent to invasive sampling of free...	Wild nonhuman primates are frequent sources of pathogens that could be transmitted to humans because they are closely genetically related and have intimate contact with humans in many parts of the world . Sampling primates to screen for zoonotic pathogens is logistically challenging because standard invasive sampling t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Optimization of a Novel Non-invasive Oral Sampling Technique for Zoonotic Pathogen Surveillance in Nonhuman Primates
Cervical cancer is a multi-stage disease caused by human papillomaviruses ( HPV ) infection of cervical epithelial cells , but the mechanisms regulating disease progression are not clearly defined . Using 3-dimensional organotypic cultures , we demonstrate that HPV16 E6 and E7 proteins alter the secretome of primary hu...	The human papillomaviruses ( HPV ) are the etiological agents of cervical cancer and the disease progresses through the pre-malignant phases of cervical intraepithelial neoplasia I , II and III ( CINI-III ) , before becoming an invasive carcinoma . Therefore identifying factors , which regulate the transition through t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	HPV16 Down-Regulates the Insulin-Like Growth Factor Binding Protein 2 to Promote Epithelial Invasion in Organotypic Cultures
The Kato-Katz technique is the most widely used diagnostic method in epidemiologic surveys and drug efficacy trials pertaining to intestinal schistosomiasis and soil-transmitted helminthiasis . However , the sensitivity of the technique is low , particularly for the detection of light-intensity helminth infections . Ex...	The World Health Organization ( WHO ) has defined a roadmap for schistosomiasis and soil-transmitted helminthiasis morbidity control and interruption of transmission with targets to be reached by 2025 . Control efforts require reliable estimates of at-risk populations , number of infections , and disease burden estimat...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "helminths", "tropical", "diseases", "hookworms", "parasitic", "diseases", "animals", "neglected", "tropical", "diseases", "infectious", "disease", "control", "public", "and...	2017	Estimating sensitivity of the Kato-Katz technique for the diagnosis of Schistosoma mansoni and hookworm in relation to infection intensity
Taenia solium is known to cause human cysticercosis while T . saginata does not . Comparative in vitro and in vivo studies on the oncosphere and the postoncospheral ( PO ) forms of T . solium and T . saginata may help to elucidate why cysticercosis can occur from one and not the other . The aim of this study was to use...	Taenia solium and Taenia saginata are two parasites that cause the tissue infection cysticercosis in their intermediate hosts , pigs and cows , respectively . One major difference between them is that T . solium can also cause neurocysticercosis in the human brain , while T . saginata cannot . Neurocysticercosis is tho...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "immunology", "tropical", "diseases", "parasitic", "diseases", "parasitology", "solutions", "developmental", "biology"...	2019	In vitro model of postoncosphere development, and in vivo infection abilities of Taenia solium and Taenia saginata
Constraint-based metabolic modeling methods such as Flux Balance Analysis ( FBA ) are routinely used to predict the effects of genetic changes and to design strains with desired metabolic properties . The major bottleneck in modeling genome-scale metabolic systems is the establishment and manual curation of reliable st...	Mathematical models that aim to describe the complete metabolism of a cell help us understand cellular metabolic capabilities and evolution , and aid the biotechnological design of microbial strains with desired properties . Draft models are frequently improved through adjustments that increase the agreement of growth/...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "metabolic", "networks", "gene", "knockout", "carbohydrates", "organic", "compounds", "glucose", "genomic", "databases", "optimization", "monomers", "(chemistry)", "metabolites", "mathematics", "network", "...	2016	Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets
Among all species of Bartonella , human-restricted Bartonella bacilliformis is the most virulent but harbors one of the most reduced genomes . Carrión’s disease , the infection caused by B . bacilliformis , has been afflicting poor rural populations for centuries in the high-altitude valleys of the South American Andes...	How host-restriction , intracellularity and genome reduction interplay to exert or maintain virulence is poorly characterized . The fact that B . bacilliformis is the most pathogenic Bartonella and has a highly reduced genome makes it an attractive model to gain insights into ( patho ) adaptive evolution of intracellul...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "taxonomy", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "genome", "evolution", "pathogens", "population", "genetics", "microbiology", "phylogenetics", "data", "management", "dna", "recombination", "convergent", "evolution", "popu...	2016	Mutation-Driven Divergence and Convergence Indicate Adaptive Evolution of the Intracellular Human-Restricted Pathogen, Bartonella bacilliformis
Phyllotaxis , the arrangement of leaves on a plant stem , is well known because of its beautiful geometric configuration , which is derived from the constant spacing between leaf primordia . This phyllotaxis is established by mutual interaction between a diffusible plant hormone auxin and its efflux carrier PIN1 , whic...	Self-organization of spatially regular patterns is critical for development and differentiation in multicellular organisms . Phyllotaxis , the arrangement of leaves on a plant stem , shows diverse patterns depending on plant species , which attracts many people because of its beautiful geometric configuration . In part...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "plant", "anatomy", "apoplastic", "space", "hormones", "simulation", "and", "modeling", "developmental", "biology", "plant", "science", "plant", "hormones", "cellular", "structures", "and", "organelles", "morphogenesis", "pattern", "formation", "research", "and", "analy...	2018	Spatial regularity control of phyllotaxis pattern generated by the mutual interaction between auxin and PIN1
Filoviruses such as Ebola virus ( EBOV ) cause outbreaks of viral hemorrhagic fevers for which no FDA-approved vaccines or drugs are available . The 2014–2016 EBOV outbreak in West Africa infected approximately 30 , 000 people , killing more than 11 , 000 and affecting thousands more in areas still suffering from the e...	Ebola Virus ( EBOV ) and its related species cause hemorrhagic fevers for which there are no FDA- approved treatments . The 2014–2016 EBOV outbreak in West Africa infected over 30 , 000 people , killing more than 11 , 000 . This was the largest outbreak to date and Liberia was the unfortunate epicenter . In Liberia , E...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "animal", "types", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "domestic", "animals", "geographical", "locations", "microbiology", "vertebrates", "pets", "and", "companion", "animals", "dogs", "animals", "mammals",...	2019	Serological evidence of Ebola virus exposure in dogs from affected communities in Liberia: A preliminary report
The identification of a causal mutation is essential for molecular diagnosis and clinical management of many genetic disorders . However , even if next-generation exome sequencing has greatly improved the detection of nucleotide changes , the biological interpretation of most exonic variants remains challenging . Moreo...	The biological interpretation of most disease-associated variants has become a real challenge , especially with the implementation of next-generation sequencing . Particular attention is typically given to protein-coding changes often neglecting the potential impact of exonic variants on RNA splicing . Here , we used t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	Exonic Splicing Mutations Are More Prevalent than Currently Estimated and Can Be Predicted by Using In Silico Tools
Evolutionary pressures act on protein complex interfaces so that they preserve their complementarity . Nonetheless , the elementary interactions which compose the interface are highly versatile throughout evolution . Understanding and characterizing interface plasticity across evolution is a fundamental issue which cou...	Unraveling how interfaces of protein complexes coevolved is of major importance to improve our ability to predict their structures and design novel binders . Proteins whose interaction was maintained throughout evolution generally have their homologs binding in a similar manner while their sequences can have significan...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "protein", "interactions", "macromolecular", "assemblies", "coevolution", "protein", "structure", "sequence", "analysis", "biology", "proteomics", "biophysics", "macromolecular", "complex", "analysis", "biochemistry", "computational", "biology", "evolutionary", "biology", "ev...	2012	Versatility and Invariance in the Evolution of Homologous Heteromeric Interfaces
While hippocampal and cortical mechanisms of memory consolidation have long been studied , their interaction is poorly understood . We sought to investigate potential interactions with respect to trace dominance , strengthening , and interference associated with postencoding novelty or sleep . A learning procedure was ...	Memories are initially stored in a hippocampal–cortical network; however , which brain area is important for long-term storage depends on what happens after learning . For example , replay of recent memories during sleep is thought to lead to consolidation in the cortex . In contrast , postlearning novelty is thought t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "medicine", "and", "health", "sciences", "sleep", "deprivation", "sleep", "immediate", "early", "genes", "brain", "social", "sciences", "neuroscience", "learning", "and", "memory", "physiological", "processes", "cognitive", "psychology", "cognition", "memory...	2017	The Yin and Yang of Memory Consolidation: Hippocampal and Neocortical
Investigating the pleiotropic effects of genetic variants can increase statistical power , provide important information to achieve deep understanding of the complex genetic structures of disease , and offer powerful tools for designing effective treatments with fewer side effects . However , the current multiple pheno...	Association analysis of multiple phenotypes will unravel the genetic pleiotropic structures of multiple phenotypes , provide a powerful tool for developing drug with fewer side effects . To increase the power of the tests for high dimensional association analysis of multiple phenotypes with next-generation sequencing d...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "multivariate", "analysis", "mathematics", "statistics", "(mathematics)", "test", "statistics", "genome", "analysis", "information", "technology", "research", "and", "analysis", "methods", "computer", "and", "information", "sciences", "data", "reduction", "mathematical", ...	2017	A quadratically regularized functional canonical correlation analysis for identifying the global structure of pleiotropy with NGS data
Acute regional ischemia in the heart can lead to cardiac arrhythmias such as ventricular fibrillation ( VF ) , which in turn compromise cardiac output and result in secondary global cardiac ischemia . The secondary ischemia may influence the underlying arrhythmia mechanism . A recent clinical study documents the effect...	Cardiac arrhythmias are an important cause of death in the industrialized world . The most dangerous type of cardiac arrhythmias is ventricular fibrillation . If left untreated , it leads to death within just few minutes . In most of the cases ventricular fibrillation occurs as a result of cardiac ischemia , which is a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cardiology", "medicine", "and", "health", "sciences", "arrhythmia", "physiology", "biology", "and", "life", "sciences", "cardiovascular", "diseases", "electrophysiology", "biophysics", "biophysical", "simulations" ]	2014	Effect of Global Cardiac Ischemia on Human Ventricular Fibrillation: Insights from a Multi-scale Mechanistic Model of the Human Heart
Natural selection favors efficient expression of encoded proteins , but the causes , mechanisms , and fitness consequences of evolved coding changes remain an area of aggressive inquiry . We report a large-scale reversal in the relative translational accuracy of codons across 12 fly species in the Drosophila/Sophophora...	Ribosomes translate mRNA into protein using tRNAs , and these tRNAs often translate multiple synonymous codons . Although synonymous codons specify the same amino acid , tRNAs read codons with differing speed and accuracy , and so some codons may be more accurately translated than their synonyms . Such variation in the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "molecular", "evolution", "biology", "and", "life", "sciences" ]	2014	A Nutrient-Driven tRNA Modification Alters Translational Fidelity and Genome-wide Protein Coding across an Animal Genus
Structural colors are generated by scattering of light by variations in tissue nanostructure . They are widespread among animals and have been studied most extensively in butterflies and moths ( Lepidoptera ) , which exhibit the widest diversity of photonic nanostructures , resultant colors , and visual effects of any ...	Biological structural colors are generated when light is scattered by nanostructures in tissues . Such colors have diverse functions for communication both among and between species . Structural colors are most complex in extant butterflies and moths ( lepidopterans ) , but the evolution of such colors and their functi...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "paleoecology", "evolutionary", "ecology", "invertebrate", "paleontology", "paleobiology", "entomology", "paleontology", "earth", "sciences", "biology", "evolutionary", "biology", "zoology", "taphonomy" ]	2011	Fossilized Biophotonic Nanostructures Reveal the Original Colors of 47-Million-Year-Old Moths
Dot1 is an evolutionarily conserved histone methyltransferase specific for lysine 79 of histone H3 ( H3K79 ) . In Saccharomyces cerevisiae , Dot1-mediated H3K79 methylation is associated with telomere silencing , meiotic checkpoint control , and DNA damage response . The biological function of H3K79 methylation in mamm...	Histone methylation plays a critical role in the regulation of gene expression and chromatin structure . Among the sites of histone methylation , lysine 79 of histone H3 ( H3K79 ) is unique in that it is not located within the H3 N-terminal tail but in the globular domain . Our knowledge about H3K79 methylation comes p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "developmental", "biology/embryology", "developmental", "biology/stem", "cells" ]	2008	The Histone H3K79 Methyltransferase Dot1L Is Essential for Mammalian Development and Heterochromatin Structure
Copy number polymorphism ( CNP ) is ubiquitous in eukaryotic genomes , but the degree to which this reflects the action of positive selection is poorly understood . The first gene in the Plasmodium folate biosynthesis pathway , GTP-cyclohydrolase I ( gch1 ) , shows extensive CNP . We provide compelling evidence that gc...	Recent comparative genomic hybridization studies have revealed extensive copy number variation in eukaryotic genomes . The first gene in the Plasmodium folate biosynthesis pathway , GTP-cyclohydrolase I ( gch1 ) , shows extensive copy number polymorphism ( CNP ) . We provide compelling evidence that gch1 CNP is adaptiv...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "infectious", "diseases/antimicrobials", "and", "drug", "resistance", "genetics", "and", "genomics/population", "genetics" ]	2008	Adaptive Copy Number Evolution in Malaria Parasites
The loss of dopaminergic neurons is a hallmark of Parkinson’s disease , the aetiology of which is associated with increased levels of oxidative stress . We used C . elegans to screen for genes that protect dopaminergic neurons against oxidative stress and isolated glit-1 ( gliotactin ( Drosophila neuroligin-like ) homo...	Neurons use dopamine as a chemical messenger to mediate diverse behaviours . The gradual loss of dopaminergic neurons in specific brain areas is a hallmark of Parkinson’s disease . The increased occurrence of highly reactive oxygen radicals , also called oxidative stress , is assumed to contribute to the demise of dopa...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "death", "invertebrates", "neurochemistry", "chemical", "compounds", "oxidative", "stress", "caenorhabditis", "dopaminergics", "cell", "processes", "neuroscience", "organic", "compounds", "animals", "hormones", "animal", "models", "developmental", "biology", "caenor...	2018	Mutations in Caenorhabditis elegans neuroligin-like glit-1, the apoptosis pathway and the calcium chaperone crt-1 increase dopaminergic neurodegeneration after 6-OHDA treatment
Stress responses are crucial processes that require activation of genetic programs that protect from the stressor . Stress responses are also energy consuming and can thus be deleterious to the organism . The mechanisms coordinating energy consumption during stress response in multicellular organisms are not well under...	Stress responses require proper activation of genetic programs to protect the organism from the stressor . However , the mechanisms controlling energy consumption during stress responses are not well understood . Here , we investigate the role of epigenetic modifier G9a in regulating metabolism and gene transcription d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "invertebrates", "cellular", "stress", "responses", "rna", "interference", "oxidative", "stress", "gene", "regulation", "cell", "processes", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "experimental", "org...	2019	The histone methyltransferase G9a regulates tolerance to oxidative stress–induced energy consumption
ClinicalTrials . gov NCT02397772 Periodic large-scale administration of anthelmintic medication to populations at risk can effectively reduce the disease burden of soil-transmitted helminth ( STH ) infections [1] , which together are responsible for an estimated 4 . 98 million years lived with disability each year [2] ...	Soil-transmitted helminth ( STH ) infections , including Trichuris trichiura , Ascaris lumbricoides and the hookworms Ancylostoma duodenale and Necator americanus , remain endemic in many regions of sub-Saharan Africa ( SSA ) , including parts of Kenya . The current WHO-recommended treatment strategy focuses on morbidi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "education", "helminths", "sociology", "tropical", "diseases", "hookworms", "geographical", "locations", "social", "sciences", "parasitic", "diseases", "animals", "health", "care", "ascaris", "ascaris", "lumbricoid...	2019	Community-level epidemiology of soil-transmitted helminths in the context of school-based deworming: Baseline results of a cluster randomised trial on the coast of Kenya
Strongyloides seroprevalence is hyper-endemic in many Australian Aboriginal and Torres Strait Islander communities , ranging from 35–60% . We report the impact on Strongyloides seroprevalence after two oral ivermectin mass drug administrations ( MDAs ) delivered 12 months apart in a remote Australian Aboriginal communi...	We were invited by one community in East Arnhem Land to develop and deliver an ivermectin MDA to reduce the prevalence of Strongyloides and scabies . We demonstrated a sustained reduction in Strongyloides seroprevalence following the ivermectin MDA . Strongyloides is endemic in many Australian Aboriginal and Torres Str...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "census", "parasitic", "diseases", "animals", "ethnicities", "research", "design", "indigenous", "australians", "ectoparasitic", "infections", "...	2017	Strongyloides seroprevalence before and after an ivermectin mass drug administration in a remote Australian Aboriginal community
Yeast mating type is determined by the genotype at the mating type locus ( MAT ) . In homothallic ( self-fertile ) Saccharomycotina such as Saccharomyces cerevisiae and Kluveromyces lactis , high-efficiency switching between a and α mating types enables mating . Two silent mating type cassettes , in addition to an acti...	The mating system of Saccharomycotina has evolved from the ancestral heterothallic system as seen in Yarrowia lipolytica to homothallism as seen in Saccharomyces cerevisiae . The acquisition of silent cassettes was an important step towards homothallism . However , some Saccharomycotina species that diverged from the c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "fungal", "genomics", "fungal", "genomes", "fungal", "genetics", "genetics", "biology", "and", "life", "sciences", "molecular", "genetics", "evolutionary", "biology", "evolutionary", "genetics" ]	2014	Inversion of the Chromosomal Region between Two Mating Type Loci Switches the Mating Type in Hansenula polymorpha
The glucocorticoid receptor ( GR ) associates with glucocorticoid response elements ( GREs ) and regulates selective gene transcription in a cell-specific manner . Native GREs are typically thought to be composite elements that recruit GR as well as other regulatory factors into functional complexes . We assessed wheth...	The glucocorticoid receptor ( GR ) regulates a myriad of physiological functions , such as cell differentiation and metabolism , achieved through modulating transcription in a cell- and gene-specific manner . However , the determinants that specify cell- and gene-specific GR transcriptional regulation are not well esta...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "none", "cell", "biology", "molecular", "biology", "dog", "computational", "biology", "evolutionary", "biology", "homo", "(human)", "rattus", "(rat)", "mus", "(mouse)" ]	2007	Determinants of Cell- and Gene-Specific Transcriptional Regulation by the Glucocorticoid Receptor
Zwitterionic capsular polysaccharides ( ZPS ) of commensal bacteria are characterized by having both positive and negative charged substituents on each repeating unit of a highly repetitive structure that has an α-helix configuration . In this paper we look at the immune response of CD8+ T cells to ZPSs . Intraperitone...	One of the most difficult challenges for the mammalian immune system is to protect its host from pathogens and cancer while at the same time avoiding a self-destructive or overwhelming immune response . In addition to so-called central tolerance induced in the thymus , the immune system relies on peripheral control mec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/immunomodulation", "infectious", "diseases/bacterial", "infections", "immunology/immunity", "to", "infections", "infectious", "diseases/gastrointestinal", "infections", "immunology/leukocyte", "activation" ]	2009	Streptococcus pneumoniae Serotype 1 Capsular Polysaccharide Induces CD8+CD28− Regulatory T Lymphocytes by TCR Crosslinking
Colon cancer accounts for more than 10% of all cancer deaths annually . Our genetic evidence from Drosophila and previous in vitro studies of mammalian Atonal homolog 1 ( Atoh1 , also called Math1 or Hath1 ) suggest an anti-oncogenic function for the Atonal group of proneural basic helix-loop-helix transcription factor...	Like most cancers , colon cancer displays a loss of differentiation , and the stronger this property , the more aggressive the cancer . This suggests that the loss of the capacity to differentiate may be a critical and possibly early event during the formation of these tumors . The key gene instructing secretory cell f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "molecular", "biology", "genetics", "and", "genomics" ]	2009	Atonal homolog 1 Is a Tumor Suppressor Gene
Piwi proteins associate with piRNAs and functions in epigenetic programming , post-transcriptional regulation , transposon silencing , and germline development . However , it is not known whether the diverse functions of these proteins are molecularly separable . Here we report that Piwi interacts with Tudor-SN ( Tudor...	Piwi proteins bind to a large class of small noncoding RNAs called Piwi-interacting RNAs ( piRNAs ) . These proteins have emerged as major players in germline development , stem cell self-renewal , transposon silencing , and gene regulation . However , it is not known whether these functions of Piwi proteins represent ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	Tudor-SN Interacts with Piwi Antagonistically in Regulating Spermatogenesis but Synergistically in Silencing Transposons in Drosophila
Cartilage and bone are formed into a remarkable range of shapes and sizes that underlie many anatomical adaptations to different lifestyles in vertebrates . Although the morphological blueprints for individual cartilage and bony structures must somehow be encoded in the genome , we currently know little about the detai...	Every bone in the skeleton has a specific shape and size . These characteristic features must be under separate genetic control , because individual bones can undergo striking morphological changes in different species . Researchers have long postulated that the morphology of individual bones arises from the local acti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/comparative", "genomics", "developmental", "biology/morphogenesis", "and", "cell", "biology", "genetics", "and", "genomics/functional", "genomics" ]	2008	Shaping Skeletal Growth by Modular Regulatory Elements in the Bmp5 Gene
L . tropica can cause both cutaneous and visceral leishmaniasis in humans . Although the L . tropica-induced cutaneous disease has been long known , its potential to visceralize in humans was recognized only recently . As nothing is known about the genetics of host responses to this infection and their clinical impact ...	Leishmaniasis , a disease caused by Leishmania ssp . is among the most neglected infectious diseases . In humans , L . tropica causes cutaneous form of leishmaniasis , but can damage internal organs too . The reasons for this variability are not known , and its genetic basis was never investigated . Therefore , analysi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "host-pathogen", "interaction", "microbiology", "parasitic", "diseases", "parastic", "protozoans", "genome", "analysis", "tools", "leishmania", "trait", "locus", "analysis", "neglected", "tropical", "diseases", "veterinary", "science", "infectious", "diseases", ...	2013	Mapping the Genes for Susceptibility and Response to Leishmania tropica in Mouse
Previously we have described the V2-directed CAP256-VRC26 lineage that includes broadly neutralizing antibodies ( bNAbs ) that neutralize globally diverse strains of HIV . We also identified highly mutated “off-track” lineage members that share high sequence identity to broad members but lack breadth . Here , we define...	Broadly neutralizing antibodies ( bNAbs ) develop in some HIV infected individuals , partly due to their complex evolutionary pathways that are characterized by extensive somatic hypermutation ( SHM ) . Furthermore , bNAbs within a lineage may form a minor subset , amidst many strain-specific “siblings” , indicating th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chemical", "neutralization", "organismal", "evolution", "medicine", "and", "health", "sciences", "microbial", "mutation", "immune", "physiology", "crystal", "structure", "immunology", "condensed", "matter", "physics", "microbiology", "microbial", "evolution", "crystallogra...	2019	Somatic hypermutation to counter a globally rare viral immunotype drove off-track antibodies in the CAP256-VRC26 HIV-1 V2-directed bNAb lineage
Leptospirosis is an extremely widespread zoonotic infection with outcomes ranging from subclinical infection to fatal Weil's syndrome . Despite the global impact of the disease , key aspects of its pathogenesis remain unclear . To examine in detail the earliest steps in the host response to leptospires , we used fluore...	Leptospirosis is a common bacterial infection in many tropical regions of the world that causes serious and often fatal disease in humans . The infection is transmitted by carrier animals , especially rats and other rodents , that release the leptospire bacteria from their kidneys into their urine . Humans are infected...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "immunology/leukocyte", "activation", "infectious", "diseases/bacterial", "infections", "immunology/innate", "immunity" ]	2009	Leptospira interrogans Stably Infects Zebrafish Embryos, Altering Phagocyte Behavior and Homing to Specific Tissues
A common yet poorly understood evolutionary transition among flowering plants is a switch from outbreeding to an inbreeding mode of mating . The model plant Arabidopsis thaliana evolved to an inbreeding state through the loss of self-incompatibility , a pollen-rejection system in which pollen recognition by the stigma ...	The mating system adopted by a species has a profound influence on extent of polymorphism , population structure , and evolutionary potential . In flowering plants , the switch from outbreeding to inbreeding has occurred repeatedly , yet little is known about the underlying genetic events . This is true even for the mo...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "plant", "biology/plant", "genomes", "and", "evolution", "evolutionary", "biology/plant", "genomes", "and", "evolution", "evolutionary", "biology/sexual", "behavior", "genetics", "and", "genomics/plant", "genomes", "and", "evolution", "evolutionary", "biology/plant", "genet...	2009	Independent S-Locus Mutations Caused Self-Fertility in Arabidopsis thaliana
The Caenorhabditis elegans inner nuclear envelope protein matefin/SUN-1 plays a conserved , pivotal role in the process of genome haploidization . CHK-2–dependent phosphorylation of SUN-1 regulates homologous chromosome pairing and interhomolog recombination in Caenorhabditis elegans . Using time-lapse microscopy , we ...	During meiosis , homologous chromosomes from each parent must pair , synapse , and recombine before being assorted to the gametes . In Caenorhabditis elegans , to find the correct pairing partner , telomere-led chromosome movement occurs in a restricted subvolume of the nucleus . This feature is comparable to the widel...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/chromosome", "biology", "cell", "biology/nuclear", "structure", "and", "function" ]	2010	Leptotene/Zygotene Chromosome Movement Via the SUN/KASH Protein Bridge in Caenorhabditis elegans
NF449 , a sulfated compound derived from the antiparasitic drug suramin , was previously reported to inhibit infection by enterovirus A71 ( EV-A71 ) . In the current work , we found that NF449 inhibits virus attachment to target cells , and specifically blocks virus interaction with two identified receptors—the P-selec...	Enterovirus A71 is epidemic in the Asia-Pacific region , and has been responsible for thousands of cases of fatal neurological disease in young children . There are no specific therapies available . We previously identified NF449 as a compound with anti-EV-A71 activity , although its mechanism of action was uncertain ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Suramin Derivative NF449 Interacts with the 5-fold Vertex of the Enterovirus A71 Capsid to Prevent Virus Attachment to PSGL-1 and Heparan Sulfate
Vpr is a conserved primate lentiviral protein that promotes infection of T lymphocytes in vivo by an unknown mechanism . Here we demonstrate that Vpr and its cellular co-factor , DCAF1 , are necessary for efficient cell-to-cell spread of HIV-1 from macrophages to CD4+ T lymphocytes when there is inadequate cell-free vi...	Human immunodeficiency virus ( HIV-1 ) , the leading infectious killer worldwide , dysregulates the immune system primarily through infection and depletion of CD4+ T cells . The conserved HIV-1 Vpr protein has been previously shown to promote T cell infection and disease progression in an animal model; however , infect...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Vpr Promotes Macrophage-Dependent HIV-1 Infection of CD4+ T Lymphocytes
The F-type ATP synthase complex is a rotary nano-motor driven by proton motive force to synthesize ATP . Its F1 sector catalyzes ATP synthesis , whereas the Fo sector conducts the protons and provides a stator for the rotary action of the complex . Components of both F1 and Fo sectors are highly conserved across prokar...	Synthesis of ATP , the currency of the cellular energy economy , is carried out by a rotary nano-motor , the ATP synthase complex , which uses proton flow to drive the rotation of protein subunits so as to produce ATP . There are two main components in mitochondrial F-type ATP synthase complexes , each made up of a num...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/molecular", "evolution", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "biophysics/macromolecular", "assemblies", "and", "machines", "biochemistry/biocatalysis", "genetics", "and", "genomics/gene", "discovery", "biophysics/protein", "chemistry",...	2010	Highly Divergent Mitochondrial ATP Synthase Complexes in Tetrahymena thermophila
Many species of bacteria harbor multiple prophages in their genomes . Prophages often carry genes that confer a selective advantage to the bacterium , typically during host colonization . Prophages can convert to infectious viruses through a process known as induction , which is relevant to the spread of bacterial viru...	Many viruses that infect bacteria ( bacteriophages ) can direct the integration of their DNA into the bacterial chromosome . This condition , known as lysogeny , is relevant to bacterial evolution , as it is one of the main pathways leading to the incorporation of foreign DNA in nature . Indeed , bacteriophages often c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "microbial", "mutation", "genetic", "mutation", "microbiology", "host-pathogen", "interaction", "gene", "function", "microbial", "evolution", "molecular", "genetics", "bacterial", "pathogens", "gene", "expression", "biology", "genetic", "screens", "genetics"...	2011	Bacteriophage Crosstalk: Coordination of Prophage Induction by Trans-Acting Antirepressors
Monospermic fertilization is mediated by the extracellular zona pellucida composed of ZP1 , ZP2 and ZP3 . Sperm bind to the N-terminus of ZP2 which is cleaved after fertilization by ovastacin ( encoded by Astl ) exocytosed from egg cortical granules to prevent sperm binding . AstlNull mice lack the post-fertilization b...	Monospermic fertilization is essential for the onset of development . Egg cortical granules exocytose their contents after fertilization to prevent polyspermy by modifying the extracellular zona pellucida ( ZP1 , ZP2 , ZP3 ) . Little is known about the biology of these subcellular organelles which are unique to oocytes...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Conclusions", "Materials", "and", "Methods" ]	[ "cell", "processes", "light", "microscopy", "germ", "cells", "animal", "models", "developmental", "biology", "oocytes", "model", "organisms", "microscopy", "experimental", "organism", "systems", "confocal", "microscopy", "embryos", "sperm", "research", "and", "analysis"...	2017	A Unique Egg Cortical Granule Localization Motif Is Required for Ovastacin Sequestration to Prevent Premature ZP2 Cleavage and Ensure Female Fertility in Mice
The majority of life on Earth depends directly or indirectly on the sun as a source of energy . The initial step of photosynthesis is facilitated by light-harvesting complexes , which capture and transfer light energy into the reaction centers ( RCs ) . Here , we analyzed the organization of photosynthetic ( PS ) compl...	The majority of life on Earth depends directly or indirectly on the sun as a source of energy . Phototrophic organisms use energy from light to power various cellular and metabolic processes . The initial step of photosynthesis is facilitated by light-harvesting complexes , which capture and transfer light energy into ...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "absorption", "spectra", "plant", "growth", "and", "development", "energy", "transfer", "absorption", "spectroscopy", "phototropism", "light", "plant", "physiology", "pigments", "electromagnetic", "radiation", "developmental", "biology", "plant", "science", "organism", "d...	2017	Unique double concentric ring organization of light harvesting complexes in Gemmatimonas phototrophica
Helminth parasites cause untold morbidity and mortality to billions of people and livestock . Anthelmintic drugs are available but resistance is a problem in livestock parasites , and is a looming threat for human helminths . Testing the efficacy of available anthelmintic drugs and development of new drugs is hindered ...	Parasitic worms cause untold morbidity and mortality on billions of people and livestock . Drugs are available but resistance is problematic in livestock parasites and is a looming threat for human helminths . Currently , new drug discovery and resistance monitoring is hindered as drug efficacy is assessed by observing...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biotechnology/applied", "microbiology", "microbiology/parasitology" ]	2010	A Novel High Throughput Assay for Anthelmintic Drug Screening and Resistance Diagnosis by Real-Time Monitoring of Parasite Motility
The World Health Organization ( WHO ) currently recommends height or age-based dosing as alternatives to weight-based dosing for mass drug administration lymphatic filariasis ( LF ) elimination programs . The goals of our study were to compare these alternative dosing strategies to weight-based dosing and to develop an...	Lymphatic filariasis is a debilitating parasitic disease that affects over 65 million people globally . To eliminate this disease the World Health Organization ( WHO ) recommends treating entire communities with drug combinations that include ivermectin and diethylcarbamazine . Ideally , the amount of drug administered...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "dose", "prediction", "methods", "tropical", "diseases", "geographical", "locations", "india", "parasitic", "diseases", "indonesia", "clinical", "medicine", "filariasis", "pharmaceutics", "drug", "administration", "neglected", "tro...	2019	Dosing pole recommendations for lymphatic filariasis elimination: A height-weight quantile regression modeling approach
A model-based gating strategy is developed for sorting cells and analyzing populations of single cells . The strategy , named CCAST , for Clustering , Classification and Sorting Tree , identifies a gating strategy for isolating homogeneous subpopulations from a heterogeneous population of single cells using a data-deri...	Sorting out homogenous subpopulations in a heterogeneous population of single cells enables downstream characterization of specific cell types , such as cell-type specific genomic profiling . This study proposes a data-driven gating strategy , CCAST , for sorting out homogeneous subpopulations from a heterogeneous popu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "computational", "biology" ]	2014	CCAST: A Model-Based Gating Strategy to Isolate Homogeneous Subpopulations in a Heterogeneous Population of Single Cells
Several plant species require microbial associations for survival under different biotic and abiotic stresses . In this study , we show that Enterobacter sp . SA187 , a desert plant endophytic bacterium , enhances yield of the crop plant alfalfa under field conditions as well as growth of the model plant Arabidopsis th...	Plants as sessile organisms are facing multiple stresses during their lifetime . Among them , abiotic stresses , such as salt stress , can cause severe crop yield reduction , leading to food security issues in many regions of the world . In order to respond to growing food demands , especially in the context of the glo...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "plant", "anatomy", "ecology", "and", "environmental", "sciences", "chemical", "compounds", "ethylene", "brassica", "plant", "physiology", "organic", "compounds", "hormones", "root", "hairs", "plant", "science", "model", "organisms", "fractional", "precipitation", "plan...	2018	Ethylene induced plant stress tolerance by Enterobacter sp. SA187 is mediated by 2‐keto‐4‐methylthiobutyric acid production
The parasite Trypanosoma brucei rhodesiense and its insect vector Glossina morsitans morsitans were used to evaluate the effect of parasite clearance ( resistance ) as well as the cost of midgut infections on tsetse host fitness . Tsetse flies are viviparous and have a low reproductive capacity , giving birth to only 6...	In many cases , parasites adapt to their hosts' biology over time and the extent of their harmful effects gradually diminishes . Insect-transmitted parasites such as African trypanosomes , however , are unusually pathogenic for their mammalian hosts because they rely on their invertebrate hosts for transmission to the ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "microbiology/immunity", "to", "infections", "immunology/immune", "response", "microbiology/innate", "immunity", "immunology/innate", "immunity", "microbiology/parasitology", "ecology/population", "ecology", "immunology/immunity", "to", "infections" ]	2008	Infections with Immunogenic Trypanosomes Reduce Tsetse Reproductive Fitness: Potential Impact of Different Parasite Strains on Vector Population Structure
Aggregation of alpha-synuclein ( ASYN ) in Lewy bodies and Lewy neurites is the typical pathological hallmark of Parkinson's disease ( PD ) and other synucleinopathies . Furthermore , mutations in the gene encoding for ASYN are associated with familial and sporadic forms of PD , suggesting this protein plays a central ...	The accumulation of aggregated proteins in the brain is common across several neurodegenerative disorders . In Parkinson's disease ( PD ) , the protein alpha-synuclein ( ASYN ) is the major component of aggregates known as Lewy bodies . It is currently unclear whether protein aggregates are protective or detrimental fo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "neuroscience", "neuroscience", "biology", "and", "life", "sciences" ]	2014	Systematic Comparison of the Effects of Alpha-synuclein Mutations on Its Oligomerization and Aggregation
Parasites of the phylum Apicomplexa cause diseases that impact global health and economy . These unicellular eukaryotes possess a relict plastid , the apicoplast , which is an essential organelle and a validated drug target . However , much of its biology remains poorly understood , in particular its elaborate compartm...	Apicomplexa are a group of parasites that cause important diseases , including malaria and several AIDS associated opportunistic infections . The parasites depend on an algal endosymbiont , the apicoplast , and this provides an Achilles' heel for drug development . We use Toxoplasma gondii as a model to characterize th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "structures", "subcellular", "organelles", "toxoplasma", "gondii", "parasite", "evolution", "microbiology", "parasitology", "gene", "function", "parastic", "protozoans", "emerging", "infectious", "diseases", "molecular", "genetics", "biology", "cell", "biology",...	2011	A Systematic Screen to Discover and Analyze Apicoplast Proteins Identifies a Conserved and Essential Protein Import Factor
Breast cancer is the most common solid organ malignancy and the most frequent cause of cancer death among women worldwide . Previous research has yielded insights into its genetic etiology , but there remains a gap in the understanding of genetic factors that contribute to risk , and particularly in the biological mech...	There is a clear genetic basis of breast cancer , and previous work has identified numerous genetic variants that increase risk of this common disease . However , much of the underlying genetic variation in breast cancer remains unexplained . To address this void , as part of the National Cancer Institute’s “Up for a C...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "breast", "tumors", "reproductive", "system", "body", "fluids", "cancers", "and", "neoplasms", "oncology", "mathematics", "statistics", "(mathematics)", "genome", "analysis", "research", "...	2017	Cis-eQTL-based trans-ethnic meta-analysis reveals novel genes associated with breast cancer risk
A subset of human papillomavirus ( HPV ) infections is causally related to the development of human epithelial tumors and cancers . Like a number of pathogens , HPV entry into target cells is initiated by first binding to heparan sulfonated proteoglycan ( HSPG ) cell surface attachment factors . The virus must then mov...	A subset of the >120 different types of human papillomaviruses ( HPVs ) are the most common cause of sexually transmitted infections . Certain HPVs are also associated with approximately 5% of all cancers worldwide . Like many pathogens , HPVs bind first to heparan sulfate proteoglycans ( HSPGs ) on cells before moving...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "dermatology", "infectious", "diseases", "otorhinolaryngology", "women's", "health", "obstetrics", "and", "gynecology", "biology", "microbiology", "molecular", "cell", "biology", "otolaryngology" ]	2012	Essential Roles for Soluble Virion-Associated Heparan Sulfonated Proteoglycans and Growth Factors in Human Papillomavirus Infections
As nascent proteins are synthesized by the ribosome , they depart via an exit tunnel running through the center of the large subunit . The exit tunnel likely plays an important part in various aspects of translation . Although water plays a key role in many bio-molecular processes , the nature of water confined to the ...	The physical properties of water are of critical importance to biomolecular processes such as protein folding and protein-ligand binding . The predominant view of water from a structural biological perspective , however , is that of a two-state model: water is either a tightly bound molecule ( as seen in x-ray crystall...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/molecular", "dynamics", "biophysics/macromolecular", "assemblies", "and", "machines", "biophysics/protein", "folding" ]	2010	Non-Bulk-Like Solvent Behavior in the Ribosome Exit Tunnel
Foot-and-mouth disease remains a major plague of livestock and outbreaks are often economically catastrophic . Current inactivated virus vaccines require expensive high containment facilities for their production and maintenance of a cold-chain for their activity . We have addressed both of these major drawbacks . Firs...	Picornaviruses are small RNA viruses , responsible for important human and animal diseases for example polio , some forms of the common cold and foot-and-mouth disease . Safe and effective picornavirus vaccines could in principle be produced from recombinant virus-like particles , which lack the viral genome and so can...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "viral", "vaccines", "veterinary", "diseases", "virology", "veterinary", "virology", "biology", "microbiology", "viral", "structure", "biophysics", "viral", "diseases", "veterinary", "science" ]	2013	Rational Engineering of Recombinant Picornavirus Capsids to Produce Safe, Protective Vaccine Antigen
MicroRNAs ( miRNAs ) are stable , small non-coding RNAs that modulate many downstream target genes . Recently , circulating miRNAs have been detected in various body fluids and within exosomes , prompting their evaluation as candidate biomarkers of diseases , especially cancer . Kaposi's sarcoma ( KS ) is the most comm...	Circulating microRNAs ( miRNAs ) , such as those found in exosomes , have emerged as diagnostic tools and hold promise as minimally invasive , stable biomarkers . Transfer of tumor-derived exosomal miRNAs to surrounding cells may be an important form of cellular communication . Kaposi's sarcoma-associated herpesvirus (...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "of", "infection", "medicine", "infectious", "diseases", "viral", "persistence", "and", "latency", "virology", "viruses", "and", "cancer", "host-pathogen", "interaction", "biology", "microbiology", "viral", "disease", "diagnosis" ]	2013	Systemically Circulating Viral and Tumor-Derived MicroRNAs in KSHV-Associated Malignancies
We investigated eight families with a novel subtype of congenital generalized lipodystrophy ( CGL4 ) of whom five members had died from sudden cardiac death during their teenage years . ECG studies revealed features of long-QT syndrome , bradycardia , as well as supraventricular and ventricular tachycardias . Further s...	Patients with generalized lipodystrophy have a marked lack of body fat . Several gene defects have been described that impede fat synthesis and maturation of fat cells . Here we report on mutations in a novel gene , called PTRF-CAVIN , causing congenital generalized lipodystrophy type 4 ( CGL4 ) that is additionally as...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "biology/cell", "signaling", "cardiovascular", "disorders/arrhythmias,", "electrophysiology,", "and", "pacing", "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/gene", "function", "cell", "biology/gene", "expression", "genetics", ...	2010	Fatal Cardiac Arrhythmia and Long-QT Syndrome in a New Form of Congenital Generalized Lipodystrophy with Muscle Rippling (CGL4) Due to PTRF-CAVIN Mutations
The mitochondrial electron transport chain transforms energy satisfying cellular demand and generates reactive oxygen species ( ROS ) that act as metabolic signals or destructive factors . Therefore , knowledge of the possible modes and bifurcations of electron transport that affect ROS signaling provides insight into ...	The mitochondrial respiratory chain shows a variety of modes of behavior . In living cells , flashes of ROS production and oscillations accompanied by a decrease of transmembrane potential can be registered . The mechanisms of such complex behavior are difficult to rationalize without a mathematical formalization of mi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "macromolecular", "assemblies", "mathematics", "bioenergetics", "biophysics", "simulations", "biology", "energy-producing", "processes", "differential", "equations", "biophysics", "systems", "biology", "biochemistry", "biophysic", "al", "simulations", "calculus", "computational...	2012	Multistationary and Oscillatory Modes of Free Radicals Generation by the Mitochondrial Respiratory Chain Revealed by a Bifurcation Analysis
Salmonella enterica subspecies enterica is traditionally subdivided into serovars by serological and nutritional characteristics . We used Multilocus Sequence Typing ( MLST ) to assign 4 , 257 isolates from 554 serovars to 1092 sequence types ( STs ) . The majority of the isolates and many STs were grouped into 138 gen...	Microbiologists have used serological and nutritional characteristics to subdivide pathogenic bacteria for nearly 100 years . These subdivisions in Salmonella enterica are called serovars , some of which are thought to be associated with particular diseases and epidemiology . We used MultiLocus Sequence-based Typing ( ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "medicine", "public", "health", "and", "epidemiology", "microbial", "mutation", "infectious", "disease", "epidemiology", "population", "genetics", "microbiology", "salmonellosis", "bacterial", "diseases", "mutation", "gastroenterology", "and", "hepatology", ...	2012	Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica
Understanding how mutator strains emerge in bacterial populations is relevant both to evolutionary theory and to reduce the threat they pose in clinical settings . The rise of mutator alleles is understood as a result of their hitchhiking with linked beneficial mutations , although the factors that govern this process ...	Natural and laboratory populations of bacteria can readily give rise to strains with high mutation rates . The evolution of these mutator bacteria—of particular concern in clinical situations—has been understood exclusively in terms of their increased capacity to generate beneficial mutations , such as those that confe...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "microbiology", "evolutionary", "biology", "genetics", "and", "genomics" ]	2013	Mutational Spectrum Drives the Rise of Mutator Bacteria
Set point viral load in HIV patients ranges over several orders of magnitude and is a key determinant of disease progression in HIV . A number of recent studies have reported high heritability of set point viral load implying that viral genetic factors contribute substantially to the overall variation in viral load . T...	Following an initial peak in viremia , the viral load in HIV infected patients settles down to a set point which remains more or less stable during chronic HIV infection . This set point viral load is one of the key factors determining the rate of disease progression . The extent to which it is determined by the virus ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	High Heritability Is Compatible with the Broad Distribution of Set Point Viral Load in HIV Carriers
This study was conducted with the aim to understand some of the cultural belief systems in the management of wounds and patients practices that could contaminate wounds at the Obom sub-district of the Ga South Municipality of Ghana . This was an ethnographic study using in-depth interviews , Focus Group Discussions and...	The study revealed a number of cultural practices and beliefs which influenced patients' wound care and health seeking behaviour . These included the beliefs that prohibit certain category of people such as pregnant women , lactating mothers and women who menstruate from dressing wounds . Respondents believed that some...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "maternal", "health", "obstetrics", "and", "gynecology", "sociology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "herbs", "health", "care", "bacterial", "diseases", "physiological", "processes", "h...	2016	Cultural Understanding of Wounds, Buruli Ulcers and Their Management at the Obom Sub-district of the Ga South Municipality of the Greater Accra Region of Ghana
A disabling and disfiguring disease that “begins where the road ends” , yaws is targeted by WHO for eradication by the year 2020 . The global campaign is not yet financed . To evaluate yaws eradication within the context of the post-2015 development agenda , we perform a somewhat allegorical cost-effectiveness analysis...	A disabling and disfiguring disease that “begins where the road ends” ( among poor and isolated communities ) , yaws is targeted by WHO for eradication by the year 2020 . The global campaign is not yet financed . We provide benchmarks for the cost and health effects of global yaws eradication , based on evidence from f...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "treponematoses", "bacterial", "diseases", "infectious", "diseases", "medicine", "and", "health", "sciences", "health", "economics", "neglected", "tropical", "diseases", "tropical", "diseases", "social", "sciences", "yaws", "economics", "health", "care" ]	2014	Where the Road Ends, Yaws Begins? The Cost-effectiveness of Eradication versus More Roads
A wide range of organisms use sex pheromones to communicate with each other and to identify appropriate mating partners . While the evolution of chemical communication has been suggested to cause sexual isolation and speciation , the mechanisms that govern evolutionary transitions in sex pheromone production are poorly...	Mate selection is a complex process involving communication between potential partners on many levels , such as visual , aural , and olfactory cues . Many animals use chemical signals in the form of pheromones to communicate and correctly recognize individuals of the appropriate species and sex during reproduction . Ev...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "genetics", "and", "genomics/gene", "expression", "evolutionary", "biology/sexual", "behavior", "molecular", "biology/molecular", "evolution", "developmental", "biology/developmental", "evolution", "evolutionary", "biology", "developmental", "biology/m...	2009	Rapid Evolution of Sex Pheromone-Producing Enzyme Expression in Drosophila
The interplay of different virus species in a host cell after infection can affect the adaptation of each virus . Endogenous viral elements , such as endogenous pararetroviruses ( PRVs ) , have arisen from vertical inheritance of viral sequences integrated into host germline genomes . As viral genomic fossils , these s...	This paper addresses the adaptive strategies of ancient defective viruses recorded in grass genomes . We mined numerous virus segments from various grass genomes and assembled several defective pararetrovirus ( non-autonomous PRV ) species . We attempted to understand how these non-autonomous PRVs can complete parasiti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taxonomy", "oryza", "computational", "biology", "microbiology", "phylogenetics", "data", "management", "phylogenetic", "analysis", "genome", "analysis", "paleontology", "sequence", "motif", "analysis", "paleogenetics", "plants", "microbial", "genomics", "research", "and", ...	2017	Genomic fossils reveal adaptation of non-autonomous pararetroviruses driven by concerted evolution of noncoding regulatory sequences
The physiopathology of dengue hemorrhagic fever ( DHF ) , a severe form of Dengue Fever , is poorly understood . We are unable to identify patients likely to progress to DHF for closer monitoring and early intervention during epidemics , so most cases are sent home . This study explored whether patients with selected c...	Dengue is an arboviral disease that affects large areas of countries in tropical and subtropical regions of the world . Around 500 , 000 cases and 22 , 000 deaths of dengue hemorrhagic fever ( DHF ) /Dengue Shock Syndrome ( DSS ) , the most severe presentations of this disease , occur annually . It is unclear why some ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/viral", "infections", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2010	Allergies and Diabetes as Risk Factors for Dengue Hemorrhagic Fever: Results of a Case Control Study
Embryonic development requires a correct balancing of maternal and paternal genetic information . This balance is mediated by genomic imprinting , an epigenetic mechanism that leads to parent-of-origin-dependent gene expression . The parental conflict ( or kinship ) theory proposes that imprinting can evolve due to a c...	In plants and mammals , embryo development occurs under the protection and nourishment of maternal tissues . In polygamous species , this can lead to competition between siblings for privileged access to maternal nutrients . According to the parental conflict theory—a variation of the kinship theory—the asymmetric gene...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "plant", "anatomy", "quantitative", "trait", "loci", "population", "genetics", "gene", "pool", "pollen", "developmental", "biology", "plant", "science", "plant", "genomics", "epigenetics", "population", "biology", "embryos", "embryology", "genomic", "im...	2016	Quantitative Genetics Identifies Cryptic Genetic Variation Involved in the Paternal Regulation of Seed Development
Polycomb proteins play an essential role in maintaining the repression of developmental genes in self-renewing embryonic stem cells . The exact mechanism allowing the derepression of polycomb target genes during cell differentiation remains unclear . Our project aimed to identify Cbx8 binding sites in differentiating m...	Cell fate transitions have long been known to be accompanied by alterations in chromatin structure . But only during the last few years has it become clear that chromatin modifications form the molecular basis of an epigenetic memory that defines cell identity . The Polycomb Group Proteins ( PcGs ) form two major prote...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "chromosome", "biology", "genetics", "biology", "and", "life", "sciences", "epigenetics", "molecular", "cell", "biology", "chromatin", "histone", "modification" ]	2014	A Cbx8-Containing Polycomb Complex Facilitates the Transition to Gene Activation during ES Cell Differentiation
Sprouting angiogenesis , where new blood vessels grow from pre-existing ones , is a complex process where biochemical and mechanical signals regulate endothelial cell proliferation and movement . Therefore , a mathematical description of sprouting angiogenesis has to take into consideration biological signals as well a...	Sprouting angiogenesis—a process by which new blood vessels grow from existing ones—is an ubiquitous phenomenon in health and disease of higher organisms , playing a crucial role in organogenesis , wound healing , inflammation , as well as on the onset and progression of over 50 different diseases such as cancer , rheu...	[ "Abstract", "Introduction", "Models", "Results", "and", "Discussion" ]	[]	2015	The Force at the Tip - Modelling Tension and Proliferation in Sprouting Angiogenesis
Multicellular tubes consist of polarized cells wrapped around a central lumen and are essential structures underlying many developmental and physiological functions . In Drosophila compound eyes , each ommatidium forms a luminal matrix , the inter-rhabdomeral space , to shape and separate the key phototransduction orga...	Biological tubes are integral units of tissues and organs such as lung , kidney , and the cardiovascular system . The fundamental design of tubes involves a central lumen wrapped by a sheet of cells . To function properly , the tubes require a precise genetic control over their creation , the diametric growth and maint...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "cell", "biology", "biology", "and", "life", "sciences", "developmental", "biology" ]	2014	The Actomyosin Machinery Is Required for Drosophila Retinal Lumen Formation
Apicomplexans employ a peripheral membrane system called the inner membrane complex ( IMC ) for critical processes such as host cell invasion and daughter cell formation . We have identified a family of proteins that define novel sub-compartments of the Toxoplasma gondii IMC . These IMC Sub-compartment Proteins , ISP1 ...	Apicomplexans are the cause of important diseases in humans and animals including malaria ( Plasmodium falciparum ) , which claims over a million human lives each year , and toxoplasmosis ( Toxoplasma gondii ) , which causes birth defects and neurological disorders . These parasites possess a unique cortical system of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/membranes", "and", "sorting", "cell", "biology/microbial", "growth", "and", "development", "infectious", "diseases/protozoal", "infections", "microbiology/cellular", "microbiology", "and", "pathogenesis", "cell", "biology/cytoskeleton" ]	2010	A Novel Family of Toxoplasma IMC Proteins Displays a Hierarchical Organization and Functions in Coordinating Parasite Division
Integration of genome-wide association studies ( GWAS ) and expression quantitative trait loci ( eQTL ) studies is needed to improve our understanding of the biological mechanisms underlying GWAS hits , and our ability to identify therapeutic targets . Gene-level association methods such as PrediXcan can prioritize can...	We develop a new method , MultiXcan , to test the mediating role of gene expression variation on complex traits , integrating information available across multiple tissue studies . We show this approach has higher power than traditional single-tissue methods . We extend this method to use only summary-statistics from p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "statistics", "sociology", "computational", "biology", "social", "sciences", "random", "variables", "covariance", "singular", "value", "decomposition", "mathematics", "forecasting", "algebra", "genome", "analysis", "research", "and",...	2019	Integrating predicted transcriptome from multiple tissues improves association detection
Dengue is associated with explosive urban epidemics and has become a major public health problem in many tropical developing countries , including Brazil . The laboratory diagnosis of dengue can be carried out using several approaches , however sensitive and specific assays useful to diagnose in the early stage of feve...	Dengue is the one of the most prevalent arthropod-borne viral diseases in tropical regions of the world . Manifestations may vary from asymptomatic to potentially fatal complications . Laboratorial diagnosis is essential to diagnose dengue and differentiate it from other diseases . Dengue virus non-structural protein 1...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/diagnosis" ]	2010	Comparison of Three Commercially Available Dengue NS1 Antigen Capture Assays for Acute Diagnosis of Dengue in Brazil
In budding yeast , meiotic commitment is the irreversible continuation of the developmental path of meiosis . After reaching meiotic commitment , cells finish meiosis and gametogenesis , even in the absence of the meiosis-inducing signal . In contrast , if the meiosis-inducing signal is removed and the mitosis-inducing...	There are two main types of cell division cycles , mitosis and meiosis . During mitosis , DNA is replicated and then chromosomes segregate , producing two daughter cells with the same ploidy as the progenitor cell . During meiosis , DNA is replicated and then chromosomes undergo two rounds of segregation , producing fo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences" ]	2014	Positive Feedback of NDT80 Expression Ensures Irreversible Meiotic Commitment in Budding Yeast
During interphase chromosomes decondense , but fluorescent in situ hybridization experiments reveal the existence of distinct territories occupied by individual chromosomes inside the nuclei of most eukaryotic cells . We use computer simulations to show that the existence and stability of territories is a kinetic effec...	Eukaryotic genomes are organized in sets of chromosomes . Each chromosome consists of a single continuous DNA double-helix and associated proteins that organize locally in the form of a chromatin fiber . During cell division ( mitosis ) chromosomes adopt a compact form that is suitable for transport . During periods of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/molecular", "dynamics", "computational", "biology/macromolecular", "structure", "analysis", "biophysics/theory", "and", "simulation", "physics/condensed", "matter" ]	2008	Structure and Dynamics of Interphase Chromosomes
Aspergillus fumigatus forms ubiquitous airborne conidia that humans inhale on a daily basis . Although respiratory fungal infection activates the adaptor proteins CARD9 and MyD88 via C-type lectin , Toll-like , and interleukin-1 family receptor signals , defining the temporal and spatial pattern of MyD88- and CARD9-cou...	Our understanding of how epithelial and hematopoietic cells in the lung coordinate immunity against inhaled fungal conidia ( spores ) remains limited . The mold Aspergillus fumigatus is a major cause of infectious mortality in immune compromised patients . Host defense against A . fumigatus involves the activation of t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Compartment-Specific and Sequential Role of MyD88 and CARD9 in Chemokine Induction and Innate Defense during Respiratory Fungal Infection
Tuberculous latency and reactivation play a significant role in the pathogenesis of tuberculosis , yet the mechanisms that regulate these processes remain unclear . The Mycobacterium tuberculosis universal stress protein ( USP ) homolog , rv2623 , is among the most highly induced genes when the tubercle bacillus is sub...	Mycobacterium tuberculosis poses serious threats to public health worldwide . The ability of this pathogen to establish in the host a clinically silent , persistent latent infection that can subsequently reactivate to cause diseases constitutes a major challenge in controlling tuberculosis . Our study showed that an M ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/protein", "folding", "biochemistry/protein", "chemistry", "pathology/histopathology", "infectious", "diseases/bacterial", "infections", "microbiology/microbial", "growth", "and", "development", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2009	Mycobacterium tuberculosis Universal Stress Protein Rv2623 Regulates Bacillary Growth by ATP-Binding: Requirement for Establishing Chronic Persistent Infection
Despite internal complexity , tumor growth kinetics follow relatively simple laws that can be expressed as mathematical models . To explore this further , quantitative analysis of the most classical of these were performed . The models were assessed against data from two in vivo experimental systems: an ectopic syngene...	Tumor growth curves display relatively simple time curves that can be quantified using mathematical models . Herein we exploited two experimental animal systems to assess the descriptive and predictive power of nine classical tumor growth models . Several goodness-of-fit metrics and a dedicated error model were employe...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "oncology", "medicine", "and", "health", "sciences", "mathematics", "theoretical", "biology", "tumor", "physiology", "calculus", "biology", "and", "life", "sciences", "physical", "sciences", "basic", "cancer", "research", "differential", "equations" ]	2014	Classical Mathematical Models for Description and Prediction of Experimental Tumor Growth
Salmonella Typhimurium sequence type ( ST ) 313 causes invasive nontyphoidal Salmonella ( iNTS ) disease in sub-Saharan Africa , targeting susceptible HIV+ , malarial , or malnourished individuals . An in-depth genomic comparison between the ST313 isolate D23580 and the well-characterized ST19 isolate 4/74 that causes ...	Invasive nontyphoidal Salmonella ( iNTS ) is associated with a major and largely unreported tropical disease that is responsible for hundreds of thousands of deaths per year in Africa . The main causative agent is a pathovariant of Salmonella Typhimurium called ST313 , which is closely related to the well-characterized...	[ "Abstract", "Introduction", "Results", "Perspective", "Materials", "and", "methods" ]	[ "blood", "cells", "sequencing", "techniques", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "plasmid", "construction", "bacterial", "diseases", "enterobacteriaceae", "ge...	2019	Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580
In mammals , both testis and ovary arise from a sexually undifferentiated precursor , the genital ridge , which first appears during mid-gestation as a thickening of the coelomic epithelium on the ventromedial surface of the mesonephros . At least four genes ( Lhx9 , Sf1 , Wt1 , and Emx2 ) have been demonstrated to be ...	During mammalian fetal development , the precursor of the testis or ovary first appears as a simple thickening , in a specific region , of the epithelial cell layer that lines the body cavity . The resulting structure is called the genital ridge , which then differentiates into either testis or ovary , depending on whe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "function", "developmental", "biology", "embryology", "histology", "animal", "genetics", "sexual", "differentiation", "genetics", "molecular", "genetics", "biology", "morphogenesis", "sex", "determination" ]	2013	Gata4 Is Required for Formation of the Genital Ridge in Mice
Nutrient stresses trigger a variety of developmental switches in the budding yeast Saccharomyces cerevisiae . One of the least understood of such responses is the development of complex colony morphology , characterized by intricate , organized , and strain-specific patterns of colony growth and architecture . The gene...	Baker's yeast forms smooth round colonies when grown in favorable conditions . When starved for one or more nutrients , yeast can alter its growth pattern to produce complex structures consisting of numerous interacting cells . One mode of growth , the colony morphology response , produces visually striking , lacy colo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "signaling", "cell", "biology/morphogenesis", "and", "cell", "biology", "genetics", "and", "genomics/complex", "traits", "cell", "biology/developmental", "molecular", "mechanisms", "evolutionary", "biology/pattern", "formation", "microbiology/microbial",...	2010	Environmental and Genetic Determinants of Colony Morphology in Yeast
Yeast successfully adapts to an environmental stress by altering physiology and fine-tuning metabolism . This fine-tuning is achieved through regulation of both gene expression and protein activity , and it is shaped by various physiological requirements . Such requirements impose a sustained evolutionary pressure that...	Although different environmental stresses trigger specific sets of protective changes in the gene expression of yeast , the adaptive responses to these stresses also share some common features . We hypothesize that minimization of metabolic costs may contribute to shaping such adaptive responses . If this is so , then ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry/transcription", "and", "translation", "microbiology/microbial", "evolution", "and", "genomics", "computational", "biology/systems", "biology", "evolutionary", "biology/bioinformatics" ]	2010	Minimization of Biosynthetic Costs in Adaptive Gene Expression Responses of Yeast to Environmental Changes
Chemotherapy resistance is a major challenge to the effective treatment of cancer . Thus , a systematic pipeline for the efficient identification of effective combination treatments could bring huge biomedical benefit . In order to facilitate rational design of combination therapies , we developed a comprehensive compu...	Combination chemotherapy is frequently used in the fight against cancer as treatment with multiple chemotherapy drugs of different molecular mechanisms reduces the chance of resistance . The complex mechanisms involved makes it essential to develop a comprehensive computational model that comprehends experimental data ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "cancer", "treatment", "cell", "processes", "clinical", "oncology", "simulation", "and", "modeling", "oncology", "clinical", "medicine", "pharmaceutics", "artificial", "intelligence", "pharmacology", "research", ...	2019	Designing combination therapies with modeling chaperoned machine learning
Mutations in the splicing factor SF3B1 are found in several cancer types and have been associated with various splicing defects . Using transcriptome sequencing data from chronic lymphocytic leukemia , breast cancer and uveal melanoma tumor samples , we show that hundreds of cryptic 3’ splice sites ( 3’SSs ) are used i...	A key goal of cancer genomics studies is to identify genes that are recurrently mutated at a rate above background and likely contribute to cancer development . Many such recurrently mutated genes have been identified over the last few years , but we often do not know the underlying mechanisms by which they contribute ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers
In mouse female preimplantation embryos , the paternal X chromosome ( Xp ) is silenced by imprinted X chromosome inactivation ( iXCI ) . This requires production of the noncoding Xist RNA in cis , from the Xp . The Xist locus on the maternally inherited X chromosome ( Xm ) is refractory to activation due to the presenc...	In sexual reproduction , maternal and paternal haploid sets of DNA are combined in one new diploid individual . However , not only DNA , but also epigenetic information , defined by DNA and histone modifications , is transferred to the zygote . Specific inactivation of the paternally inherited X chromosome ( Xp ) in th...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "germ", "cells", "zygotes", "developmental", "biology", "oocytes", "epigenetics", "embryos", "sperm", "spermatids", "embryology", "sex", "chromosomes", "animal", "cells", "chromosome", "biology", "fertilization", "x", "chromosomes", "cell", "biology", "ova", "genetics",...	2016	Round Spermatid Injection Rescues Female Lethality of a Paternally Inherited Xist Deletion in Mouse
Dengue fever induces a robust immune response , including massive T cell activation . The level of T cell activation may , however , be associated with more severe disease . In this study , we explored the level of CD8+ T lymphocyte activation in the first six days after onset of symptoms during a DENV2 outbreak in ear...	Dengue is a disease affecting approximately 400 million people annually , especially in tropical and subtropical areas of the globe . The immune response against the dengue virus is still under investigation and it is important to understand why the disease can be fatal in a small proportion of cases . In this work , w...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	CD8+ T Lymphocyte Expansion, Proliferation and Activation in Dengue Fever
Large , naturally evolved biomolecular networks typically fulfil multiple functions . When modelling or redesigning such systems , functional subsystems are often analysed independently first , before subsequent integration into larger-scale computational models . In the design and analysis process , it is therefore im...	To better understand the dynamic behaviour of cells and their interaction with the environment , mathematical models describing the interplay between proteins , metabolites or signalling molecules are used extensively in Systems Biology . Typically , such models focus on single functional subsystems and neglect the res...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Quantification of Interactions between Dynamic Cellular Network Functionalities by Cascaded Layering
Cellular adaptation relies on the development of proper regulatory schemes for accurate control of gene expression levels in response to environmental cues . Over- or under-expression can lead to diminished cell fitness due to increased costs or insufficient benefits . Positive autoregulation is a common regulatory sch...	Different proteins are expressed at different levels that may have evolved for optimal fitness under specific environmental conditions . Additionally , cells regulate protein expression levels in response to environmental changes . For signaling proteins whose benefits are not immediately proportional to their expressi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Evolutionary Tuning of Protein Expression Levels of a Positively Autoregulated Two-Component System
Mitochondrial dynamics is an essential physiological process controlling mitochondrial content mixing and mobility to ensure proper function and localization of mitochondria at intracellular sites of high-energy demand . Intriguingly , for yet unknown reasons , severe impairment of mitochondrial fusion drastically affe...	Mammalian mitochondria contain multiple copies of the mitochondrial genome ( mtDNA ) , which encodes genes that are essential for the oxidative phosphorylation system . An important feature of mtDNA is that it is evenly distributed throughout the mitochondrial network . Dynamin-related GTPase proteins help control the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "mitochondrial", "dna", "molecular", "probe", "techniques", "cardiovascular", "anatomy", "light", "microscopy", "mutation", "membrane", "fusion", "dna", "replication", "microscopy", "forms", "of", "dna", "mitochondria", "dna", ...	2019	Mitochondrial fusion is required for regulation of mitochondrial DNA replication
There is an urgent need to field test dengue vaccines to determine their role in the control of the disease . Our aims were to study dengue epidemiology and prepare the site for a dengue vaccine efficacy trial . We performed a prospective cohort study of children in primary schools in central Thailand from 2006 through...	There is an urgent need to field test dengue vaccine . Efficacy trials need to be conducted in study sites with sufficiently high dengue incidence to make a robust estimate of vaccine efficacy and where all dengue virustypes circulate frequently . In this paper , we report on dengue disease surveillance on approximatel...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "pediatrics", "and", "child", "health", "public", "health", "pediatrics" ]	2012	Dengue Infection in Children in Ratchaburi, Thailand: A Cohort Study. I. Epidemiology of Symptomatic Acute Dengue Infection in Children, 2006–2009
Current WHO recommendations for lymphatic filariasis ( LF ) surveillance advise programs to implement activities to monitor for new foci of transmission after stopping mass drug administration ( MDA ) . A current need in the global effort to eliminate LF is to standardize diagnostic tools and surveillance activities be...	Lymphatic filariasis ( LF ) , endemic in 72 countries , is a debilitating mosquito-transmitted parasitic disease caused by filarial worms . The Global Program to Eliminate Lymphatic Filariasis ( GPELF ) aims to interrupt transmission through mass drug administration ( MDA ) and to reduce suffering caused by the disease...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "american", "samoa", "invertebrates", "children", "medicine", "and", "health", "sciences", "immune", "physiology", "body", "fluids", "education", "immunology", "sociology", "geographical", "locations", "social", "sciences", "animals", "age", "groups", "immunoprecipitation...	2018	Comparison of antigen and antibody responses in repeat lymphatic filariasis transmission assessment surveys in American Samoa
Central nervous system ( CNS ) melioidosis is rare . However , delayed diagnosis and treatment could lead to fatality . To identify knowledge of CNS melioidosis , we systematically review case reports and case series . We searched through PubMed , Web of Science and Thai-Journal Citation Index databases as well as Goog...	Melioidosis is an infectious disease caused by the bacterium , Burkholderia pseudomallei . It is the disease of the tropical region especially Southeast Asia and northern Australia where the microbes are present in soil and water . Melioidosis can cause a variety of symptoms depending on the site of infection . Brain a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "nervous", "system", "melioidosis", "brain", "cranial", "nerves", "encephalomyelitis", "bacterial", "diseases", "signs", "and", "symptoms", "abscesses", "infectious"...	2019	Central nervous system melioidosis: A systematic review of individual participant data of case reports and case series
The cellular immune response against parasitoid wasps in Drosophila involves the activation , mobilization , proliferation and differentiation of different blood cell types . Here , we have assessed the role of Edin ( elevated during infection ) in the immune response against the parasitoid wasp Leptopilina boulardi in...	The events leading to a successful encapsulation of parasitoid wasp eggs in the larvae of the fruit fly Drosophila melanogaster are insufficiently understood . The formation of a capsule seals off the wasp egg , and this process is often functionally compared to the formation of granulomas in vertebrates . Like granulo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Edin Expression in the Fat Body Is Required in the Defense Against Parasitic Wasps in Drosophila melanogaster
Epstein-Barr Nuclear Antigen 1 ( EBNA1 ) is essential for Epstein-Barr virus to immortalize naïve B-cells . Upon binding a cluster of 20 cognate binding-sites termed the family of repeats , EBNA1 transactivates promoters for EBV genes that are required for immortalization . A small domain , termed UR1 , that is 25 amin...	Epstein-Barr virus ( EBV ) infects human B-cells and immortalizes them . Immortalization results in diseases that range from infectious mononucleosis to malignancies such as lymphomas . During immortalization , EBV expresses a small number of viral genes that modulate cellular proliferation and differentiation . One of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/persistence", "and", "latency", "virology/viral", "replication", "and", "gene", "regulation", "molecular", "biology/transcription", "initiation", "and", "activation", "virology/viruses", "and", "cancer", "biochemistry/transcription", "and", "translation" ]	2009	Zinc Coordination Is Required for and Regulates Transcription Activation by Epstein-Barr Nuclear Antigen 1
The major transition to eusociality required the evolution of a switch to canalize development into either a reproductive or a helper , the nature of which is currently unknown . Following predictions from the ‘theory of facilitated variation’ , we identify sex differentiation pathways as promising candidates because o...	Division of labor into reproductive queens and helper workers in the societies of ants , bees and wasps is achieved by phenotypic plasticity , which allows individuals to embark on discrete developmental trajectories in response to variable signals . These signals can be genetic , epigenetic or environmental , thereby ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "invertebrates", "insect", "metamorphosis", "gene", "regulation", "animals", "alternative", "splicing", "developmental", "biology", "pupae", "zoology", "morphogenesis", "hymenoptera", "ants", "gene", "expression", "evolutionary", "genetics", "insects", "arthropoda", "bioche...	2016	Evolution of Social Insect Polyphenism Facilitated by the Sex Differentiation Cascade
Current limitations in quantitatively predicting biological behavior hinder our efforts to engineer biological systems to produce biofuels and other desired chemicals . Here , we present a new method for calculating metabolic fluxes , key targets in metabolic engineering , that incorporates data from 13C labeling exper...	While metabolic fluxes constitute the most direct window into a cell’s metabolism , their accurate measurement is non trivial . The gold standard for flux measurement involves providing a labeled feed where some of the carbon atoms have been substituted by isotopes with higher atomic mass ( 13C instead of 12C ) . The e...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Method to Constrain Genome-Scale Models with 13C Labeling Data
While RNA interference ( RNAi ) has been deployed to facilitate gene function studies in diverse helminths , parasitic nematodes appear variably susceptible . To test if this is due to inter-species differences in RNAi effector complements , we performed a primary sequence similarity survey for orthologs of 77 Caenorha...	Many organisms regulate gene expression through an RNA interference ( RNAi ) pathway , first characterized in the nematode Caenorhabditis elegans . This pathway can be triggered experimentally using double-stranded ( ds ) RNA to selected gene targets , thereby allowing researchers to ‘silence’ individual genes and so i...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "biology", "genomics", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2011	RNAi Effector Diversity in Nematodes
Strongyloides stercoralis is the only soil-transmitted helminth with the ability to replicate within its host , leading to long-lasting and potentially fatal infections . It is ubiquitous and its worldwide prevalence has recently been estimated to be at least half that of hookworm . Information on the epidemiology of S...	Strongyloides stercoralis is an intestinal parasite that can replicate within its host , leading to long-lasting and potentially life-threatening infections . Occurring worldwide , it thrives where the climate is warm and sanitation is poor . S . stercoralis is not well detected by standard field techniques and its glo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "geographical", "locations", "parasitic", "diseases", "animals", "health", "care", "physiological", "processes", "developmental", "biology", "sanitation", "infectious", "disease", "control", "strongyloides", "stercor...	2016	Ivermectin Treatment and Sanitation Effectively Reduce Strongyloides stercoralis Infection Risk in Rural Communities in Cambodia
Zika virus ( ZIKV ) is an emerging mosquito-borne flavivirus linked to devastating neurologic diseases . Immune responses to flaviviruses may be pathogenic or protective . Our understanding of human immune responses to ZIKV in vivo remains limited . Therefore , we performed a longitudinal molecular and phenotypic chara...	Zika virus ( ZIKV ) is an emerging flaviviral infection that causes significant clinical disease . It is estimated that approximately one half of the world’s population is at risk for ZIKV infection . There are only a limited number of studies describing the human immune response to ZIKV infection . Carlin et al . comb...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "dengue", "virus", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "cytokines", "pathogens", "immunology", "microbiology", "viruses", "dev...	2018	A longitudinal systems immunologic investigation of acute Zika virus infection in an individual infected while traveling to Caracas, Venezuela
Knotted proteins , because of their ability to fold reversibly in the same topologically entangled conformation , are the object of an increasing number of experimental and theoretical studies . The aim of the present investigation is to assess , on the basis of presently available structural data , the extent to which...	Out of the tens of thousands of known protein structures , only a few hundred are knotted . The latter epitomize , better than unknotted proteins , the degree of coordinated motion of the backbone required to fold reversibly in a specific native conformation , which indeed must contain a precise knot in a specific prot...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biophysics", "computational", "biology" ]	2010	Knotted vs. Unknotted Proteins: Evidence of Knot-Promoting Loops
It is well established that Epstein-Barr virus nuclear antigen 3C ( EBNA3C ) can act as a potent repressor of gene expression , but little is known about the sequence of events occurring during the repression process . To explore further the role of EBNA3C in gene repression–particularly in relation to histone modifica...	The Epstein-Barr nuclear protein EBNA3C is a well-characterised repressor of host gene expression in B cells growth-transformed by EBV . It is also well established that EBNA3C can interact with the cellular factor RBPJ , a DNA-binding factor in the Notch signalling pathway conserved from worms to humans . However , pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[]	2016	EBNA3C Directs Recruitment of RBPJ (CBF1) to Chromatin during the Process of Gene Repression in EBV Infected B Cells
Visual short-term memory tasks depend upon both the inferior temporal cortex ( ITC ) and the prefrontal cortex ( PFC ) . Activity in some neurons persists after the first ( sample ) stimulus is shown . This delay-period activity has been proposed as an important mechanism for working memory . In ITC neurons , interveni...	To know whether one is looking at an object seen a few seconds ago or not depends on visual short-term memory . To study short-term memory , we recorded single neuronal activity from two brain areas of monkeys , the TE and the perirhinal cortex of the temporal lobe , known to be important in visual pattern recognition ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience", "neuroscience/cognitive", "neuroscience", "neuroscience/sensory", "systems", "neuroscience/theoretical", "neuroscience" ]	2008	Short-Term Memory Trace in Rapidly Adapting Synapses of Inferior Temporal Cortex
Recent studies have demonstrated how the competition for the finite pool of available gene expression factors has important effect on fundamental gene expression aspects . In this study , based on a whole-cell model simulation of translation in S . cerevisiae , we evaluate for the first time the expected effect of mRNA...	Each cell contains a limited number of macromolecules and factors that participate in the gene expression process . These expression resources are shared between the different molecules that encode the genetic code , resulting in non-trivial couplings and competitions between the different gene expression stages . Such...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "synthetic", "genetic", "systems", "engineering", "and", "technology", "synthetic", "biology", "messenger", "rna", "population", "genetics", "gene", "pool", "fungi", "model", "organisms", "experimental", "organism", "systems", "population", "biology", "synthetic", "gene...	2018	Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources

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