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Inflammation is a highly coordinated host response to infection , injury , or cell stress . In most instances , the inflammatory response is pro-survival and is aimed at restoring physiological tissue homeostasis and eliminating invading pathogens , although exuberant inflammation can lead to tissue damage and death . ...	Adenovirus ( Ad ) induces a potent activation of pro-inflammatory cytokines and chemokines upon interaction with tissue macrophages in vivo . However , critical factors affecting cellular inflammatory responses to Ad and their functional significance remain unclear . Here we show that in the model of disseminated infec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "medicine", "and", "health", "sciences" ]	2014	IL-1α and Complement Cooperate in Triggering Local Neutrophilic Inflammation in Response to Adenovirus and Eliminating Virus-Containing Cells
Innate cytokine response provides the first line of defense against influenza virus infection . However , excessive production of cytokines appears to be critical in the pathogenesis of influenza virus . Interferon lambdas ( IFN-λ ) have been shown to be overproduced during influenza virus infection , but the precise p...	Influenza virus infection triggers innate immune responses . However , aberrant host immune responses such as excessive production of cytokines contribute to the pathogenesis of influenza virus . Type III interferons ( IFN-λ ) constitute the major innate immune response to influenza virus infection , but the precise pa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2014	Suppression of Interferon Lambda Signaling by SOCS-1 Results in Their Excessive Production during Influenza Virus Infection
p53 protects us from cancer by transcriptionally regulating tumor suppressive programs designed to either prevent the development or clonal expansion of malignant cells . How p53 selects target genes in the genome in a context- and tissue-specific manner remains largely obscure . There is growing evidence that the abil...	The tumor suppressor gene p53 counteracts tumor growth by activating genes that prevent cell proliferation or induce cell death . How p53 selects genes in the genome to direct cell fate specifically into one or the other direction remains unclear . We show that the ability of p53 molecules to interact and thereby coope...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "medicine", "tumor", "physiology", "gene", "expression", "biology", "basic", "cancer", "research", "molecular", "cell", "biology", "dna", "transcription" ]	2013	Characterization of the p53 Cistrome – DNA Binding Cooperativity Dissects p53's Tumor Suppressor Functions
Fv1 is the prototypic restriction factor that protects against infection by the murine leukemia virus ( MLV ) . It was first identified in cells that were derived from laboratory mice and was found to be homologous to the gag gene of an endogenous retrovirus ( ERV ) . To understand the evolution of the host restriction...	We have followed the evolution of the retroviral restriction gene , Fv1 , by functional analysis . We show that Fv1 can recognize and restrict a wider range of retroviruses than previously thought including examples from the gammaretrovirus , lentivirus and foamy virus genera . Nearly every Fv1 tested showed a differen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "of", "infection", "viral", "clearance", "genetic", "mutation", "virulence", "factors", "and", "mechanisms", "viral", "transmission", "and", "infection", "virology", "genetics", "host-pathogen", "interaction", "biology", "microbiology", "evolutionary",...	2014	Evolution of the Retroviral Restriction Gene Fv1: Inhibition of Non-MLV Retroviruses
Several studies propose an influence of chromatin on pre-mRNA splicing , but it is still unclear how widespread and how direct this phenomenon is . We find here that when assembled in vivo , the U2 snRNP co-purifies with a subset of chromatin-proteins , including histones and remodeling complexes like SWI/SNF . Yet , a...	Splicing is an RNA editing step allowing to produce multiple transcripts from a single gene . The gene itself is organized in chromatin , associating DNA and multiple proteins . Some proteins regulating the compaction of the chromatin also affect RNA splicing . Yet , it was unclear whether these chromatin proteins were...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "regulation", "rna", "extraction", "dna-binding", "proteins", "dna", "transcription", "epigenetics", "extraction", "techniques", "chromatin", "research", "and", "analysis", "methods", "small", "interfering", "rnas", "genome", "complexity", "genomics", "chromosome"...	2016	A Broad Set of Chromatin Factors Influences Splicing
Ras mediates signaling pathways controlling cell proliferation and development by cycling between GTP- and GDP-bound active and inactive conformational states . Understanding the complete reaction path of this conformational change and its intermediary structures is critical to understanding Ras signaling . We characte...	The Ras family of enzymes mediate signaling pathways controlling cell proliferation and development by cycling between active and inactive conformational states . Mutations that affect the ability to switch between states are associated with a variety of cancers . However , details of how the structural changes occur a...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "biophysics/theory", "and", "simulation", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "biochemistry/bioinformatics", "biochemistry/theory", "and", "simulation", "computational", "biology/molecular", "dynamics", "biophysics/cell", "signaling", "and", "tra...	2009	Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics
Condensin-mediated chromosome condensation is essential for genome stability upon cell division . Genetic studies have indicated that the association of condensin with chromatin is intimately linked to gene transcription , but what transcription-associated feature ( s ) direct ( s ) the accumulation of condensin remain...	Failure to condense chromosomes prior to anaphase onset can lead to genome instability . The evolutionary-conserved condensin complex drives chromosome condensation , probably by changing the topology of chromatin around its binding sites . Condensin localizes to regions of high transcription , suggesting that some tra...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chromosome", "structure", "and", "function", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "cell", "processes", "dna", "transcription", "mitosis", "fungi", "chromatin", "schizosaccharomyces", "chromosome", "biology", "gene", "expression", "schizosac...	2014	RNA Processing Factors Swd2.2 and Sen1 Antagonize RNA Pol III-Dependent Transcription and the Localization of Condensin at Pol III Genes
Cleft palate ( CP ) is one of the most commonly occurring craniofacial birth defects in humans . In order to study cleft palate in a naturally occurring model system , we utilized the Nova Scotia Duck Tolling Retriever ( NSDTR ) dog breed . Micro-computed tomography analysis of CP NSDTR craniofacial structures revealed...	Cleft palate is one of the most commonly occurring birth defects in children , and yet its cause is not completely understood . In order to better understand cleft palate we have turned to man's best friend , the domestic dog . Common breeding practices have made the dog a unique animal model to help understand the gen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "developmental", "biology", "animal", "genetics", "organism", "development", "genome", "analysis", "genetics", "biology", "and", "life", "sciences", "molecular", "genetics", "computational", "biology", "genetics", "of", "disease", ...	2014	A LINE-1 Insertion in DLX6 Is Responsible for Cleft Palate and Mandibular Abnormalities in a Canine Model of Pierre Robin Sequence
By aggregating data for complex traits in a biologically meaningful way , gene and gene-set analysis constitute a valuable addition to single-marker analysis . However , although various methods for gene and gene-set analysis currently exist , they generally suffer from a number of issues . Statistical power for most m...	Gene and gene-set analysis are statistical methods for analysing multiple genetic markers simultaneously to determine their joint effect . These methods can be used when the effects of individual markers is too weak to detect , which is a common problem when studying polygenic traits . Moreover , gene-set analysis can ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	MAGMA: Generalized Gene-Set Analysis of GWAS Data
As miRNAs are associated with normal cellular processes , deregulation of miRNAs is thought to play a causative role in many complex diseases . Nevertheless , the precise contribution of miRNAs in fibrotic lung diseases , especially the idiopathic form ( IPF ) , remains poorly understood . Given the poor response rate ...	Fibrosis is the final common pathway in virtually all forms of chronic organ failure , including lung , liver , and kidney , and is a leading cause of morbidity and mortality worldwide . Fibrosis results from the excessive activity of fibroblasts , in particular a differentiated form known as myofibroblast that is resp...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "histology", "functional", "genomics", "interstitial", "lung", "diseases", "gene", "regulation", "genetics", "molecular", "genetics", "biology", "genomics", "genetics", "and", "genomics", "respiratory", "medicine", "pulmonology" ]	2013	miR-199a-5p Is Upregulated during Fibrogenic Response to Tissue Injury and Mediates TGFbeta-Induced Lung Fibroblast Activation by Targeting Caveolin-1
Histoplasmosis is an endemic fungal infection in French Guiana . It is the most common AIDS-defining illness and the leading cause of AIDS-related deaths . Diagnosis is difficult , but in the past 2 decades , it has improved in this French overseas territory which offers an interesting model of Amazonian pathogen ecolo...	Histoplasmosis is an endemic fungal infection in French Guiana . It is the most common AIDS-defining illness and the leading cause of AIDS-related deaths . Diagnosis is difficult , but in the past 2 decades , it has improved . The objectives of the present study were to describe the temporal trends of incidence and mor...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "sexually", "transmitted", "diseases", "aids", "histoplasmosis", "neglected", "tropical", "diseases", "fungal", "diseases", "viral", "diseases", "infectious", "disease", "control", "tropical", "diseases" ]	2014	HIV-Associated Histoplasmosis Early Mortality and Incidence Trends: From Neglect to Priority
Borrelia persica , a bacterium transmitted by the soft tick Ornithodoros tholozani , causes tick-borne relapsing fever in humans in the Middle East , Central Asia and the Indian peninsula . Immunocompetent C3H/HeOuJ mice were infected intradermally with B . persica at varying doses: 1 x 106 , 1 x 104 , 1 x 102 and 4 x ...	The spirochete Borrelia persica is a tick-borne bacterium that is transmitted by the vector Ornithodoros tholozani to its vertebrate host in the Middle East , Central Asia and the Indian peninsula . Current migration of vast numbers of individuals from this area increases the likelihood that B . persica infections will...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "borrelia", "infection", "medicine", "and", "health", "sciences", "body", "fluids", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "immune", "physiology", "pathogens", "immunology", "microbiology", "animal", "models", "bacterial", "diseases...	2016	Borrelia persica Infection in Immunocompetent Mice - A New Tool to Study the Infection Kinetics In Vivo
Ataxia represents a pathological coordination failure that often involves functional disturbances in cerebellar circuits . Purkinje cells ( PCs ) characterize the only output neurons of the cerebellar cortex and critically participate in regulating motor coordination . Although different genetic mutations are known tha...	Cerebellar ataxia describes a combination of motor symptoms and uncoordinated movements that originates from various hereditary and non-hereditary diseases . Although functional disturbances of cerebellar inhibitory output signals are thought to cause ataxia , the underlying molecular mechanisms are barely understood a...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "cell", "biology/membranes", "and", "sorting", "neuroscience", "genetics", "and", "genomics/disease", "models", "neurological", "disorders/movement", "disorders" ]	2009	The Ataxia (axJ) Mutation Causes Abnormal GABAA Receptor Turnover in Mice
Since the late 1980s , wild salmon catch and abundance have declined dramatically in the North Atlantic and in much of the northeastern Pacific south of Alaska . In these areas , there has been a concomitant increase in the production of farmed salmon . Previous studies have shown negative impacts on wild salmonids , b...	The impact of salmon farming on wild salmon and trout is a hotly debated issue in all countries where salmon farms and wild salmon coexist . Studies have clearly shown that escaped farm salmon breed with wild populations to the detriment of the wild stocks , and that diseases and parasites are passed from farm to wild ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "ecology" ]	2008	A Global Assessment of Salmon Aquaculture Impacts on Wild Salmonids
Following productive , lytic infection in epithelia , herpes simplex virus type 1 ( HSV-1 ) establishes a lifelong latent infection in sensory neurons that is interrupted by episodes of reactivation . In order to better understand what triggers this lytic/latent decision in neurons , we set up an organotypic model base...	Upon primary infection of the oronasal mucosa , herpes simplex virus type 1 ( HSV-1 ) rapidly reaches the ganglia of the peripheral nervous system via axonal transport and establishes lifelong latency in surviving neurons . Central to the establishment of latency is the ability of HSV-1 to reliably switch from producti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "of", "infection", "viral", "entry", "host", "cells", "viral", "persistence", "and", "latency", "viral", "transmission", "and", "infection", "virology", "neurovirulence", "biology", "microbiology" ]	2012	Entry of Herpes Simplex Virus Type 1 (HSV-1) into the Distal Axons of Trigeminal Neurons Favors the Onset of Nonproductive, Silent Infection
The learning mechanism in the hippocampus has almost universally been assumed to be Hebbian in nature , where individual neurons in an engram join together with synaptic weight increases to support facilitated recall of memories later . However , it is also widely known that Hebbian learning mechanisms impose significa...	We present a novel hippocampal model based on the oscillatory dynamics of the theta rhythm , which enables the network to learn much more efficiently than the Hebbian form of learning that is widely assumed in most models . Specifically , two pathways , Tri-Synaptic and Mono-Synaptic , alternate in strength during thet...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "circuit", "models", "computer", "science", "psychology", "computer", "modeling", "social", "and", "behavioral", "sciences", "cognitive", "psychology", "neural", "networks", "computational", "neuroscience", "memory", "biology", "computerized", "simulations", "neuroscience",...	2013	Theta Coordinated Error-Driven Learning in the Hippocampus
Strongyloides stercoralis is a widely distributed parasite that infects 30 to 100 million people worldwide . In the United States strongyloidiasis is recognized as an important infection in immigrants and refugees . Public health and commercial reference laboratories need a simple and reliable method for diagnosis of s...	Strongyloidiasis is a neglected tropical disease that affects millions worldwide and needs more attention and better diagnostic methods . Strongyloides stercoralis can undergo an autoinfection cycle and can cause hyperinfection involving the pulmonary and gastrointestinal systems and disseminated infection in other org...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Development of Ss-NIE-1 Recombinant Antigen Based Assays for Immunodiagnosis of Strongyloidiasis
The diagnosis of Chagas disease is complex due to the dynamics of parasitemia in the clinical phases of the disease . The molecular tests have been considered promissory because they detect the parasite in all clinical phases . Trypanosoma cruzi presents significant genetic variability and is classified into six Discre...	Chagas disease is a neglected tropical disease caused by the parasite Trypanosoma cruzi that shows tremendous genetic diversity evinced in at least six Discrete Typing Units and massive genetic diversity within TcI . Two clinical phases exist where acute phase shows high parasitemia and chronic phase shows low and inte...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "parasitemia", "organisms", "protozoans", "neglected", "tropical", "diseases", "molecular", "...	2016	Molecular Diagnosis of Chagas Disease in Colombia: Parasitic Loads and Discrete Typing Units in Patients from Acute and Chronic Phases
Retrograde signaling is essential for neuronal growth , function and survival; however , we know little about how signaling endosomes might be directed from synaptic terminals onto retrograde axonal pathways . We have identified Khc-73 , a plus-end directed microtubule motor protein , as a regulator of sorting of endos...	Retrograde axonal transport is essential for normal synaptic function and neuronal survival . How endosomes are specifically sorted from the synaptic terminal for retrograde axonal transport is currently not known . At the Drosophila neuromuscular junction , receptors for the Bone Morphogenic Protein signaling pathway ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "vesicles", "nervous", "system", "cell", "processes", "electrophysiology", "neuroscience", "motor", "neurons", "developmental", "biology", "molecular", "motors", "nerve", "fibers", "cellular", "structures", "and", "organelles", "...	2018	Kinesin Khc-73/KIF13B modulates retrograde BMP signaling by influencing endosomal dynamics at the Drosophila neuromuscular junction
Reduced insulin/IGF signaling increases lifespan in many animals . To understand how insulin/IGF mediates lifespan in Drosophila , we performed chromatin immunoprecipitation-sequencing analysis with the insulin/IGF regulated transcription factor dFOXO in long-lived insulin/IGF signaling genotypes . Dawdle , an Activin ...	It is widely known that reduced insulin/IGF signaling slows aging in many contexts . This process requires the forkhead transcription factor ( FOXO ) . FOXO modulates the expression of many genes , and the list of those associated with slow aging is impressive . But there are few data indicating the mechanisms or genes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Activin Signaling Targeted by Insulin/dFOXO Regulates Aging and Muscle Proteostasis in Drosophila
For over two decades , a racemic mixture of oxamniquine ( OXA ) was administered to patients infected by Schistosoma mansoni , but whether one or both enantiomers exert antischistosomal activity was unknown . Recently , a ~30 kDa S . mansoni sulfotransferase ( SmSULT ) was identified as the target of OXA action . Here ...	Schistosomes , parasites that cause the disease schistosomiasis in humans , are blood flukes that infect an estimated 200 million people in 76 countries . Control of schistosomiasis is currently based on repeated doses of the drug praziquantel ( PZQ ) . Parasites showing reduced susceptibility to PZQ have been recovere...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Structural and Functional Characterization of the Enantiomers of the Antischistosomal Drug Oxamniquine
Telomerase activity is readily detectable in extracts from human hematopoietic stem and progenitor cells , but appears unable to maintain telomere length with proliferation in vitro and with age in vivo . We performed a detailed study of the telomere length by flow FISH analysis in leukocytes from 835 healthy individua...	Human blood cells all originate from a common precursor , the hematopoietic stem cell . Telomerase , the enzyme responsible for adding telomere repeats to chromosome ends , is active in human hematopoietic stem cells but appears unable to maintain a constant telomere length with age . We first document the telomere len...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "hematopoiesis", "genetics", "genetics", "and", "genomics", "biology", "genetics", "of", "disease", "hematology" ]	2012	Collapse of Telomere Homeostasis in Hematopoietic Cells Caused by Heterozygous Mutations in Telomerase Genes
Steroid hormones are crucial for many biological events in multicellular organisms . In insects , the principal steroid hormones are ecdysteroids , which play essential roles in regulating molting and metamorphosis . During larval and pupal development , ecdysteroids are synthesized in the prothoracic gland ( PG ) from...	Steroid hormones are crucial for development and reproduction in multicellular organisms . The spatially-restricted expression of almost all steroid biosynthesis genes is key to the specialization of steroid producing cells . In the last decade , insects have become the focus for research on the biosynthesis of the pri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Drosophila Zinc Finger Transcription Factor Ouija Board Controls Ecdysteroid Biosynthesis through Specific Regulation of spookier
Dengue is a major public health problem in tropical and subtropical countries . Exploring the relationships between virological features of infection with patient immune status and outcome may help to identify predictors of disease severity and enable rational therapeutic strategies . Clinical features , antibody respo...	Dengue is an acute viral disease that affects tens of millions of people annually in tropical and sub-tropical countries . In some cases , this infection happens to be severe and even life threatening . Severe cases have been associated with higher levels of virus in the blood . Several hypotheses have been proposed to...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "clinical", "research", "design", "virology", "clinical", "trials", "dengue", "fever", "neglected", "tropical", "diseases", "dengue", "biology", "microbiology", "viral", "diseases" ]	2011	Kinetics of Viremia and NS1 Antigenemia Are Shaped by Immune Status and Virus Serotype in Adults with Dengue
In nature , larvae of the fruitfly Drosophila melanogaster are commonly infected by parasitoid wasps , and so have evolved a robust immune response to counter wasp infection . In this response , fly immune cells form a multilayered capsule surrounding the wasp egg , leading to death of the parasite . Many of the molecu...	Organisms such as the fruitfly Drosophila melanogaster have long been used as model systems to understand complex aspects of human biology . Work on Drosophila antimicrobial immunity has led to identification of mechanisms underlying human innate immunity , such as the use of Toll-like receptors for recognizing antigen...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "drosophila", "melanogaster", "model", "organisms", "genetics", "of", "the", "immune", "system", "immunity", "innate", "immunity", "genetics", "parasitology", "immunology", "biology", "zoology", "genetics", "and", "genomics", "immune", "response" ]	2012	Mgat1-dependent N-glycosylation of Membrane Components Primes Drosophila melanogaster Blood Cells for the Cellular Encapsulation Response
The major histocompatibility complex ( MHC ) region is strongly associated with multiple sclerosis ( MS ) susceptibility . HLA-DRB1*15:01 has the strongest effect , and several other alleles have been reported at different levels of validation . Using SNP data from genome-wide studies , we imputed and tested classical ...	Multiple sclerosis ( MS ) is an inflammatory and neurodegenerative disease with a heritable component . Although it has been known for a long time that the strongest MS risk factor maps to the major histocompatibility complex ( MHC ) on chromosome 6 , there are still many unresolved questions as to the identity and the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Fine-Mapping the Genetic Association of the Major Histocompatibility Complex in Multiple Sclerosis: HLA and Non-HLA Effects
Hyaluronan is a polyanionic , megadalton-scale polysaccharide , which initiates cell signaling by interacting with several receptor proteins including CD44 involved in cell-cell interactions and cell adhesion . Previous studies of the CD44 hyaluronan binding domain have identified multiple widespread residues to be res...	Hyaluronan is a natural sugar polymer in our bodies . Besides acting as a space-filling agent for example in multiple connective tissues , it also functions as a cellular cue in cancer and inflammation . Our tissues sense hyaluronan through receptors—proteins that sit at the surface of cells and grab the molecules they...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "crystal", "structure", "chemical", "compounds", "cd", "coreceptors", "condensed", "matter", "physics", "carbohydrates", "organic", "compounds", "materials", "science", "basic", "amino", "acids", "amino", "acids", "crystallography", "coreceptors", "oligomers", "macromolec...	2017	Atomistic fingerprint of hyaluronan–CD44 binding
Cancer-associated fibroblasts ( CAFs ) , the most common constituent of the tumor stoma , are known to promote tumor initiation , progression and metastasis . However , the mechanism of how cancer cells transform normal fibroblasts ( NFs ) into CAFs is largely unknown . In this study , we determined the contribution of...	During tumorigenesis , normal fibroblasts ( NFs ) within the tumor stroma acquire a modified phenotype and become cancer-associated fibroblasts ( CAFs ) . CAFs provide oncogenic signals to facilitate tumor initiation , progression , and metastasis . Here , we set out to determine the factors that mediate the conversion...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "cardiovascular", "physiology", "gene", "regulation", "cancer", "treatment", "immunology", "cancers", "and", "neoplasms", "basic", "cancer", "research", "fibrobla...	2016	Reprogramming of Normal Fibroblasts into Cancer-Associated Fibroblasts by miRNAs-Mediated CCL2/VEGFA Signaling
Patterned spontaneous activity in the developing retina is necessary to drive synaptic refinement in the lateral geniculate nucleus ( LGN ) . Using perforated patch recordings from neurons in LGN slices during the period of eye segregation , we examine how such burst-based activity can instruct this refinement . Retino...	The brain is comprised of an immense number of connections between neurons , and clever strategies are required to achieve the correct wiring during development . One common strategy uses neural activity itself as feedback to instruct individual connections ( synapses ) through synaptic learning rules that delineate wh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "mammals", "physiology", "vertebrates", "neuroscience", "rattus", "(rat)" ]	2007	A Burst-Based “Hebbian” Learning Rule at Retinogeniculate Synapses Links Retinal Waves to Activity-Dependent Refinement
Mycobacterium tuberculosis has evolved many strategies to evade elimination by the host immune system , including the selective repression of macrophage IL-12p40 production . To identify the M . tuberculosis genes responsible for this aspect of immune evasion , we used a macrophage cell line expressing a reporter for I...	Currently , one-third of the world's population has tuberculosis ( TB ) . TB , an ancient foe , has reemerged to become a threat to global public health . A central problem in TB research is to investigate why the host immune system cannot sterilize the infection caused by the bacterium Mycobacterium tuberculosis . Int...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "immunology", "microbiology", "infectious", "diseases" ]	2008	Mycolic Acid Modification by the mmaA4 Gene of M. tuberculosis Modulates IL-12 Production
Although information regarding morphogenesis of the hepatitis C virus ( HCV ) is accumulating , the mechanism ( s ) by which the HCV genome encapsidated remains unknown . In the present study , in cell cultures producing HCV , the molecular ratios of 3’ end- to 5’ end-regions of the viral RNA population in the culture ...	Although cell culture systems provide a powerful tool for deciphering the life cycle of the hepatitis C virus ( HCV ) , the mechanisms of encapsidation of the viral genome into infectious particles remain to be uncovered . The HCV genome is a positive RNA with one single reading frame flanked by 5’- and 3’ untranslated...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "nucleic", "acid", "synthesis", "pathology", "and", "laboratory", "medicine", "3'", "utr", "hepacivirus", "pathogens", "messenger", "rna", "rna", "extraction", "microbiology", "viruses", "rna", "viruses", "untranslated", "regio...	2016	Involvement of the 3’ Untranslated Region in Encapsidation of the Hepatitis C Virus
Drug discovery initiatives , aimed at Chagas treatment , have been hampered by the lack of standardized drug screening protocols and the absence of simple pre-clinical assays to evaluate treatment efficacy in animal models . In this study , we used a simple Enzyme Linked Aptamer ( ELA ) assay to detect T . cruzi biomar...	A marked decrease in incidence of Chagas Disease has been observed in the last decade achieved by vector control strategies; however , there are still geographical areas where the disease reaches endemic proportions . Due to high morbidity and disease burden , other avenues of Chagas control , such as vaccines and ther...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "tropical", "diseases", "biomarkers", "parasitic", "diseases", "parasitic", "protozoans", "drug", "screening", "parasitemia", "protozoans", "pharmaceutics", "neglected", "tropical", "diseases", "pharmacology", "quantitative", "parasi...	2015	Aptamer-Based Detection of Disease Biomarkers in Mouse Models for Chagas Drug Discovery
Phylogenomic research is accelerating the publication of landmark studies that aim to resolve deep divergences of major organismal groups . Meanwhile , systems for identifying and integrating the products of phylogenomic inference–such as newly supported clade concepts–have not kept pace . However , the ability to verb...	Synthetic platforms for phylogenomic knowledge tend to manage conflict between different evolutionary reconstructions in the following way: "If we do not agree , then it is either our view over yours , or we just collapse all conflicting node concepts into polytomies" . We argue that this is not an equitable way to rea...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "taxonomy", "linguistics", "social", "sciences", "neuroscience", "animal", "phylogenetics", "research", "design", "phylogenetics", "data", "management", "cognitive", "psychology", "phylogenetic", "analysis", "zoology", "research", "and", "analysis", "methods", "sequence", ...	2019	Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion
The Drosophila heart tube represents a structure that similarly to vertebrates' primary heart tube exhibits a large lumen; the mechanisms promoting heart tube morphology in both Drosophila and vertebrates are poorly understood . We identified Multiplexin ( Mp ) , the Drosophila orthologue of mammalian Collagen-XV/XVIII...	The formation of the characteristic large heart lumen is common to all heart-containing organisms and is essential for efficient heart function; however , the structural components promoting this process are yet to be elucidated . The Drosophila heart represents a specific compartment within an elongated contractile tu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "organism", "development", "morphogenesis", "organogenesis", "biology", "anatomy", "and", "physiology", "cardiovascular", "system" ]	2013	Multiplexin Promotes Heart but Not Aorta Morphogenesis by Polarized Enhancement of Slit/Robo Activity at the Heart Lumen
The BAR domain protein superfamily is involved in membrane invagination and endocytosis , but its role in organizing membrane proteins has not been explored . In particular , the membrane scaffolding protein BIN1 functions to initiate T-tubule genesis in skeletal muscle cells . Constitutive knockdown of BIN1 in mice is...	Calcium plays a primary role in regulating heart function . During each heartbeat , calcium ions cross the membrane of individual cardiac muscle cells and trigger a rapid increase of calcium within the cell ( called the calcium transient ) . Calcium causes the muscle cells to contract and determines the strength of the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/membranes", "and", "sorting", "cardiovascular", "disorders/myopathies", "cardiovascular", "disorders/heart", "failure", "cell", "biology/cytoskeleton" ]	2010	BIN1 Localizes the L-Type Calcium Channel to Cardiac T-Tubules
Evidence from human genetic studies of several disorders suggests that interactions between alleles at multiple genes play an important role in influencing phenotypic expression . Analytical methods for identifying Mendelian disease genes are not appropriate when applied to common multigenic diseases , because such met...	Susceptibility to many diseases and disorders is caused by breakdown at multiple points in the genetic network . Each of these points of breakdown by itself may have a very modest effect on disease risk but the points may have a much stronger effect through statistical interactions with each other . Genome-wide associa...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/genetics", "of", "the", "immune", "system", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/population", ...	2009	Capturing the Spectrum of Interaction Effects in Genetic Association Studies by Simulated Evaporative Cooling Network Analysis
Vibrio cholerae has evolved to adeptly transition between the human small intestine and aquatic environments , leading to water-borne spread and transmission of the lethal diarrheal disease cholera . Using a host model that mimics the pathology of human cholera , we applied high density transposon mutagenesis combined ...	Cholera is a deadly diarrheal disease that spreads in explosive epidemics and is caused by the water-borne bacterium Vibrio cholerae . Pathogenic strains of V . cholerae can be found in both fresh and salt water estuaries in-between cholera outbreaks . Cholera infections are frequently derived from contaminated fresh w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Gene Fitness Landscapes of Vibrio cholerae at Important Stages of Its Life Cycle
Deficiency of the protein Wolfram syndrome 1 ( WFS1 ) is associated with multiple neurological and psychiatric abnormalities similar to those observed in pathologies showing alterations in mitochondrial dynamics . The aim of this study was to examine the hypothesis that WFS1 deficiency affects neuronal function via mit...	Wolfram syndrome ( WS ) is a genetic disorder characterized by diabetes insipidus , diabetes mellitus , optic atrophy , deafness , and brain atrophy . Brain abnormalities occur at the earliest stage of clinical symptoms , suggesting that Wolfram syndrome has a pronounced impact on early brain development . The majority...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "luciferase", "enzymes", "endoplasmic", "reticulum", "cell", "processes", "enzymology", "neuroscience", "physiological", "processes", "homeostasis", "mitochondria", "molecular", "biology", "techniques", "bioenergetics", "cellular", "...	2016	Role of Mitochondrial Dynamics in Neuronal Development: Mechanism for Wolfram Syndrome
Mutations in certain subunits of the DNA repair/transcription factor complex TFIIH are linked to the human syndromes xeroderma pigmentosum ( XP ) , Cockayne's syndrome ( CS ) , and trichothiodystrophy ( TTD ) . One of these subunits , p8/TTDA , interacts with p52 and XPD and is important in maintaining TFIIH stability ...	TFIIH participates in RNA polymerase II transcription , nucleotide excision repair , and control of the cell cycle . In humans , certain mutations in the XPB and XPD subunits of TFIIH generate the syndromes trichothiodystrophy ( TTD ) , xeroderma pigmentosum ( XP ) , and Cockayne's syndrome ( CS ) . In contrast , mutat...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "developmental", "biology", "molecular", "biology/transcription", "initiation", "and", "activation", "cell", "biology/developmental", "molecular", "mechanisms", "genetics", "and", "genomics/disease", "models", "molecular", "biology/dna", "repair" ]	2008	p8/TTDA Overexpression Enhances UV-Irradiation Resistance and Suppresses TFIIH Mutations in a Drosophila Trichothiodystrophy Model
Identification of the determinants of pathogen reservoir potential is central to understand disease emergence . It has been proposed that host lifespan is one such determinant: short-lived hosts will invest less in costly defenses against pathogens , so that they will be more susceptible to infection , more competent a...	Understanding pathogen emergence is a major goal of pathology , because of the high impact of emerging diseases . Pathogens emerge onto a new host from a reservoir , hence the relevance of identifying the determinants of host's reservoir potential . Host lifespan is considered as one such determinant: short-lived hosts...	[ "Abstract", "Introduction", "Materials", "and", "Experimental", "Methods", "Experimental", "Results", "Model", "Methods", "Model", "Simulation", "Results", "Discussion" ]	[ "evolutionary", "ecology", "plant", "science", "plant", "viral", "pathogens", "ecology", "virology", "plant", "pathogens", "plant", "pathology", "biology", "and", "life", "sciences", "microbiology", "evolutionary", "biology" ]	2014	The Relationship between Host Lifespan and Pathogen Reservoir Potential: An Analysis in the System Arabidopsis thaliana-Cucumber mosaic virus
Hepatitis B virus ( HBV ) is one of the major etiological pathogens for liver cirrhosis and hepatocellular carcinoma . Chronic HBV infection is a key factor in these severe liver diseases . During infection , HBV forms a nuclear viral episome in the form of covalently closed circular DNA ( cccDNA ) . Current therapies ...	Hepatitis B virus ( HBV ) infection remains a worldwide health problem that affects more than 350 million people . HBV is one of the major etiological pathogens for liver cirrhosis and hepatocellular carcinoma . HBV covalently closed circular DNA ( cccDNA ) is a key viral intermediate for persistent infection . However...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "enzymes", "pathogens", "gene", "regulation", "microbiology", "enzymology", "dna-binding", "proteins",...	2018	Flap endonuclease 1 is involved in cccDNA formation in the hepatitis B virus
Experimental studies have demonstrated that nanoparticles can affect the rate of protein self-assembly , possibly interfering with the development of protein misfolding diseases such as Alzheimer's , Parkinson's and prion disease caused by aggregation and fibril formation of amyloid-prone proteins . We employ classical...	Investigation of the effects of nanomaterials on biological systems is crucial due to the increasing exposure to nanostructured materials with the growing developments and applications of nanotechnology in everyday life . Nanoparticles have been shown to have an effect on protein structure and interfere with protein se...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[]	2013	Dimensionality of Carbon Nanomaterials Determines the Binding and Dynamics of Amyloidogenic Peptides: Multiscale Theoretical Simulations
Hereditary spastic paraplegias ( HSPs ) comprise a group of genetically heterogeneous neurodegenerative disorders characterized by spastic weakness of the lower extremities . We have generated a Drosophila model for HSP type 10 ( SPG10 ) , caused by mutations in KIF5A . KIF5A encodes the heavy chain of kinesin-1 , a ne...	Hereditary spastic paraplegias ( HSPs ) comprise a group of inherited neurological diseases . The main feature of HSP is progressive stiffness of the lower limbs due to a dysfunction of nerve cells . We study HSP type 10 , which is caused by mutations in the neuronal motor protein KIF5A . HSP type 10 is inherited in an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "model", "organisms", "neurological", "disorders", "neurology", "biology", "molecular", "cell", "biology", "neuroscience", "genetics", "and", "genomics", "clinical", "genetics" ]	2012	Spastic Paraplegia Mutation N256S in the Neuronal Microtubule Motor KIF5A Disrupts Axonal Transport in a Drosophila HSP Model
The Hippo signaling pathway has a conserved role in growth control and is of fundamental importance during both normal development and oncogenesis . Despite rapid progress in recent years , key steps in the pathway remain poorly understood , in part due to the incomplete identification of components . Through a genetic...	Processes that control cell numbers are essential during normal development , when they are required to generate organs of the correct size , and during cancinogenesis , when they influence tumor growth . The Hippo pathway is an intercellular signaling pathway that relays information about cell-cell contact and cell po...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/organogenesis", "cell", "biology/cell", "growth", "and", "division", "cell", "biology/cell", "signaling" ]	2011	Zyxin Links Fat Signaling to the Hippo Pathway
We present a rigorous statistical model that infers the structure of P . falciparum mixtures—including the number of strains present , their proportion within the samples , and the amount of unexplained mixture—using whole genome sequence ( WGS ) data . Applied to simulation data , artificial laboratory mixtures , and ...	Since the 1960’s researchers have observed that Plasmodium falciparum infections , the cause of most severe malaria , are frequently composed of several different strains of the parasite . In this work , the authors use Bayesian methods on whole genome sequence data to model the structure of these mixtures . Results fr...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "plasmodium", "falciparum", "parasitic", "diseases", "parasitic", "protozoans", "simulation", "and", "modeling", "probability", "distribution", "mathematics", "protozoans", "molecular", "biology", "techniq...	2016	Inferring Strain Mixture within Clinical Plasmodium falciparum Isolates from Genomic Sequence Data
Precise positioning of the cell division site is essential for the correct segregation of the genetic material into the two daughter cells . In the bacterium Myxococcus xanthus , the proteins PomX and PomY form a cluster on the chromosome that performs a biased random walk to midcell and positively regulates cell divis...	In order for the rod-shaped bacterium M . xanthus to reproduce , its genetic content must be duplicated , distributed equally to the two cell halves and then the cell must divide precisely at midcell . Three proteins , called PomX , PomY and PomZ , are important for the localization of the cell division site at midcell...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "dimers", "(chemical", "physics)", "classical", "mechanics", "enzymes", "cell", "cycle", "and", "cell", "division", "cell", "processes", "enzymology", "phosphatases", "simulation", "and", "modeling", "research", "and", "analysis", "methods", "proteins", "chemistry", "...	2018	Regulation of Pom cluster dynamics in Myxococcus xanthus
All State TB control programmes in Nigeria were requested to submit 25–50 smear-positive Ziehl-Neelsen ( ZN ) stained slides for screening during 2013–2014 . DNA was extracted from 929 slides for spoligotyping and drug-resistance analysis using microbead-based flow-cytometry suspension arrays . Spoligotyping results we...	Using a classical genotyping method designated as “spoligotyping” , which targets polymorphic repetitive DNA loci , we present a general snapshot of the genetic diversity of Mycobacterium tuberculosis complex causing tuberculosis in Nigeria . Our results were obtained on a collection of 549 DNAs , extracted from Ziehl-...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "biogeography", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "population", "dynamics", "population", "genetics", "geographical", "locations", "tropical", "diseases", "ethnicities", "bacterial", "diseases", "population", "biology", ...	2018	Mycobacterium tuberculosis complex genotypes circulating in Nigeria based on spoligotyping obtained from Ziehl-Neelsen stained slides extracted DNA
We combined the Hodgkin–Huxley equations and a 36-state model of gap junction channel gating to simulate electrical signal transfer through electrical synapses . Differently from most previous studies , our model can account for dynamic modulation of junctional conductance during the spread of electrical signal between...	In most computational models of neuronal networks , it is assumed that electrical synapses have a constant and ohmic conductance . However , numerous experimental studies demonstrate that connexin-based channels expressed in neuronal gap junctions can change their conductance in response to a transjunctional voltage or...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Discussion" ]	[ "cell", "physiology", "ion", "channel", "gating", "medicine", "and", "health", "sciences", "action", "potentials", "neural", "networks", "nervous", "system", "membrane", "potential", "junctional", "complexes", "electrophysiology", "neuroscience", "gap", "junctions", "io...	2017	Functional asymmetry and plasticity of electrical synapses interconnecting neurons through a 36-state model of gap junction channel gating
The 2014/2015 West African Ebola Virus Disease ( EVD ) outbreak attracted global attention . Numerous opinions claimed that the global response was impaired , in part because , the EVD research was neglected , although quantitative or qualitative studies did not exist . Our objective was to analyse how the EVD research...	Ebola Virus Disease ( EVD ) research publications were used to analyse and visualise collaborations between institutions jointly publishing research results , using freely available social network analysis tools . Constructed co-authorship networks between author affiliated institutions showed EVD research publications...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "united", "states", "bibliometrics", "sociology", "geographical", "locations", "social", "sciences", "north", "america", "network", "analysis", "social", "networks", "information", "technology", "data", "processing", "research", "and", "analysis", "methods", "computer", ...	2017	Analysing published global Ebola Virus Disease research using social network analysis
Insect vitellogenin ( Vg ) has been considered to be synthesized in the fat body . Here , we found that abundant Vg protein is synthesized in Laodelphax striatellus hemocytes as well . We also determined that only the hemocyte-produced Vg binds to Rice stripe virus ( RSV ) in vivo . Examination of the subunit compositi...	Rice stripe virus ( RSV ) , which is completely dependent on Laodelphax striatellus for transmission between host plants , can also be vertically transmitted from the mother insect to its offsprings . Passing through the insect hemolymph is an essential step for both kinds of viral transmission . In this study , we fou...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "invertebrates", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "immunology", "light", "microscopy", "animals", "developmental", "biology", "nymphs", "microscopy", "confocal", "microscopy", "antibodies", "insect", "...	2018	Insect tissue-specific vitellogenin facilitates transmission of plant virus
The brain constantly generates predictions about the environment to guide action . Unexpected events lead to surprise and can necessitate the modification of ongoing behavior . Surprise can occur for any sensory domain , but it is not clear how these separate surprise signals are integrated to affect motor output . By ...	Surprise is an elementary cognitive computation that the brain performs to guide behavior . We investigated how the brain tracks surprise across different senses: Do unexpected sounds make subsequent unexpected visual stimuli less surprising ? Or does the brain maintain separate expectations of environmental regulariti...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "reaction", "time", "brain", "electrophysiology", "social", "sciences", "electrophysiology", "brain", "neuroscience", "cognitive", "neuroscience", "clinical", "medicine", "cognition", "brain", "mapping", "bioassays", "and", "physio...	2019	Frontal cortex tracks surprise separately for different sensory modalities but engages a common inhibitory control mechanism
Legionella pneumophila is an environmental bacterium and the causative agent of Legionnaires’ disease . Previous genomic studies have shown that recombination accounts for a high proportion ( >96% ) of diversity within several major disease-associated sequence types ( STs ) of L . pneumophila . This suggests that recom...	Legionella pneumophila is an environmental bacterium that causes Legionnaires’ disease , a serious and potentially fatal pneumonia . Previous studies have shown that members of this species undergo a process called recombination , whereby DNA is imported from another bacterial cell into the recipient genome . The impor...	[ "Abstract", "Introduction", "Results", "&", "discussion", "Materials", "&", "methods" ]	[ "taxonomy", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "membrane", "proteins", "genomic", "databases", "phylogenetics", "data", "management", "outer", "membrane", "proteins", "phylogenetic", "analysi...	2017	Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila
Epstein-Barr virus ( EBV ) , an oncogenic human herpesvirus , induces cell proliferation after infection of resting B lymphocytes , its reservoir in vivo . The viral latent proteins are necessary for permanent B cell growth , but it is unknown whether they are sufficient . EBV was recently found to encode microRNAs ( m...	To persist in their hosts , herpes viruses must avoid recognition by the host's immune system . Down-regulation of viral antigen production through expression of viral miRNAs is a particularly elegant mechanism as these genetic elements do not encode proteins and remain therefore invisible to the immune system . Upon p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/persistence", "and", "latency", "virology/viruses", "and", "cancer", "virology" ]	2011	A Viral microRNA Cluster Strongly Potentiates the Transforming Properties of a Human Herpesvirus
Tiller angle is one of the most important components of the ideal plant architecture that can greatly enhance rice grain yield . Understanding the genetic basis of tiller angle and mining favorable alleles will be helpful for breeding new plant-type varieties . Here , we performed genome-wide association studies ( GWAS...	Tiller angle is the key component of plant architecture that greatly affect grain yield . However , few tiller angle-related genes that can be used for improving rice plant architecture have been isolated based on natural variation . Here , we identified 7 common tiller angle-related QTLs by a genome-wide association s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "plant", "anatomy", "quantitative", "trait", "loci", "population", "genetics", "cereal", "crops", "plant", "science", "rice", "model", "organisms", "genome", "analysis", "crops", "population", "biology", "plants", "research", "...	2016	A Novel Tiller Angle Gene, TAC3, together with TAC1 and D2 Largely Determine the Natural Variation of Tiller Angle in Rice Cultivars
Arthropod-borne flaviviruses such as yellow fever ( YFV ) , Zika and dengue viruses continue to cause significant human disease globally . These viruses are transmitted by mosquitoes when a female imbibes an infected blood-meal from a viremic vertebrate host and expectorates the virus into a subsequent host . Bamaga vi...	Mosquito-borne flaviviruses include medically significant members such as the dengue viruses , yellow fever virus and Zika virus . These viruses regularly cause outbreaks globally , notably in tropical regions . The ability of mosquitoes to transmit these viruses to vertebrate hosts plays a major role in determining th...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "dengue", "virus", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "vertebrates", "saliva", "animals", "viruses", "rna", "viruses", "insect", "vectors", "infectious", ...	2018	The recently identified flavivirus Bamaga virus is transmitted horizontally by Culex mosquitoes and interferes with West Nile virus replication in vitro and transmission in vivo
The human genitourinary tract is a common anatomical niche for polymicrobial infection and a leading site for the development of bacteremia and sepsis . Most uncomplicated , community-acquired urinary tract infections ( UTI ) are caused by Escherichia coli , while another bacterium , Proteus mirabilis , is more often a...	The human urinary tract is a leading source for polymicrobial infections and for the development of bacteremia and sepsis . Treating these potentially dangerous infections have recently become more challenging due to the appearance of uropathogenic strains that are resistant to the many of the most commonly prescribed ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbial", "metabolism", "medicine", "and", "health", "sciences", "microbial", "physiology", "pathology", "and", "laboratory", "medicine", "host-pathogen", "interactions", "medical", "microbiology", "microbial", "pathogens", "biology", "and", "life", "sciences", "microb...	2015	Preferential Use of Central Metabolism In Vivo Reveals a Nutritional Basis for Polymicrobial Infection
Schistosomiasis , caused by infection with the blood fluke Schistosoma , is responsible for greater than 200 , 000 human deaths per annum . Objective high-throughput screens for detecting novel anti-schistosomal targets will drive ‘genome to drug’ lead translational science at an unprecedented rate . Current methods fo...	With only one effective drug , praziquantel , currently used to treat most worldwide cases of schistosomiasis , there exists a pressing need to identify alternative anthelmintics before the development of praziquantel-resistant schistosomes removes our ability to combat this neglected tropical disease . At present , th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/helminth", "infections", "infectious", "diseases/neglected", "tropical", "diseases" ]	2010	Development and Validation of a Quantitative, High-Throughput, Fluorescent-Based Bioassay to Detect Schistosoma Viability
An important function of all organisms is to ensure that their genetic material remains intact and unaltered through generations . This is an extremely challenging task since the cell's DNA is constantly under assault by endogenous and environmental agents . To protect against this , cells have evolved effective mechan...	UV is responsible for DNA damage and genetic alterations of key players of the Nucleotide Excision Repair ( NER ) machinery promote the development of UV-induced skin cancers . The NER is the major DNA–repair process involved in the recognition and removal of UV-mediated DNA damage . Different factors participating in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "dermatology", "biology", "molecular", "cell", "biology" ]	2012	USF-1 Is Critical for Maintaining Genome Integrity in Response to UV-Induced DNA Photolesions
Genome-wide association studies ( GWAS ) have identified many genetic susceptibility loci for colorectal cancer ( CRC ) . However , variants in these loci explain only a small proportion of familial aggregation , and there are likely additional variants that are associated with CRC susceptibility . Genome-wide studies ...	Alcohol consumption and smoking are associated with CRC risk . We performed a genome-wide analysis for interaction between genetic variants and alcohol consumption and cigarette smoking to identify potential new genetic regions associated with CRC . About 8 , 000 CRC cases and 8 , 800 controls were included in alcohol-...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "cancers", "and", "neoplasms", "diet", "habits", "oncology", "nutrition", "genome", "analysis", "smoking", "habits", "digestive", "system", "genetic", "epidemiology", "genomics", "behavior...	2016	Genome-Wide Interaction Analyses between Genetic Variants and Alcohol Consumption and Smoking for Risk of Colorectal Cancer
Decades ago , the “immortal strand hypothesis” was proposed as a means by which stem cells might limit acquiring mutations that could give rise to cancer , while continuing to proliferate for the life of an organism . Originally based on observations in embryonic cells , and later studied in terms of stem cell self-ren...	For each chromosome , the complementary DNA strands consist of a “younger” strand synthesized during the most recent round of DNA replication and an “older” strand synthesized during a previous cell division . When the strands separate to serve as templates for DNA synthesis during a subsequent round of replication , t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "in", "vitro", "cell", "biology" ]	2007	High Incidence of Non-Random Template Strand Segregation and Asymmetric Fate Determination In Dividing Stem Cells and their Progeny
Assembly of the ribosome from its protein and RNA constituents has been studied extensively over the past 50 years , and experimental evidence suggests that prokaryotic ribosomal proteins undergo conformational changes during assembly . However , to date , no studies have attempted to elucidate these conformational cha...	Ribosomes are complex cellular machines that synthesize new proteins in the cell . The accurate and efficient assembly of ribosomal proteins ( r-proteins ) and ribosomal RNA ( rRNA ) to form a functional ribosome is important for cell growth , metabolic reactions , and other cellular processes . Additionally , some ant...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "macromolecular", "complex", "analysis", "rna", "structure", "biophysic", "al", "simulations", "protein", "structure", "biology", "computational", "biology", "macromolecular", "structure", "analysis" ]	2012	A Computational Investigation on the Connection between Dynamics Properties of Ribosomal Proteins and Ribosome Assembly
Onchocerciasis , or river blindness , has historically been an important cause of blindness , skin disease and economic disruption in Africa and the Americas . It is caused by the filarial parasite Onchocerca volvulus , which is transmitted by black flies in the genus Simulium . Over the past decade , several internati...	Onchocerciasis or river blindness is historically one of the most important causes of blindness and skin disease in the developing world . It is caused by infection with the filarial parasite Onchocerca volvulus . The finding that ivermectin was an effective and safe treatment for onchocerciasis and the decision by its...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "onchocerca", "volvulus", "education", "helminths", "sociology", "tropical", "diseases", "geographical", "locations", "uganda", "black", "flies", "social", "sciences", "parasitic", "diseases", "animals", "onchocerc...	2019	Optimization and evaluation of the Esperanza Window Trap to reduce biting rates of Simulium damnosum sensu lato in Northern Uganda
Tropheryma whipplei is known as the cause of Whipple's disease , but it is also an emerging pathogen , detected in stool , that causes various chronic localized infections without histological digestive involvement and is associated with acute infections , including gastroenteritis and bacteremia . We conducted a study...	Tropheryma whipplei is known as the cause of Whipple's disease . It is also an emerging pathogen , detected in stool that causes various chronic localized infections without histological digestive involvement and is associated with acute infections , including gastroenteritis and bacteremia . We have studied the presen...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "neglected", "tropical", "diseases" ]	2011	Tropheryma whipplei: A Common Bacterium in Rural Senegal
Babesia microti is tick-borne disease that is an emerging threat to public health due to increasing prevalence and expanding geographic range . Detection and constant surveillance of babesiosis is imperative for predicting pathogen expansion . Leveraging our whole genome sequence ( WGS ) analyses of B . microti , we de...	Babesia microti is an emerging tick-borne disease and is becoming a public health problem . Over the past two decades , the I . scapularis tick population , which is primarily responsible for human infection , has exploded , doubling the number of babesiosis and other I . scapularis-borne disease cases to approximately...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "united", "states", "medicine", "and", "health", "sciences", "parasite", "groups", "geographical", "locations", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "babesiosis", "organisms", "north", "america", "apicomplexa", "protozoans", "genome", "analy...	2019	Development of a SNP barcode to genotype Babesia microti infections
An unprecedented Zika virus epidemic occurred in the Americas during 2015-2016 . The size of the epidemic in conjunction with newly recognized health risks associated with the virus attracted significant attention across the research community . Our study complements several recent studies which have mapped epidemiolog...	Since May 2015 , when Zika was first reported in Brazil , the virus has spread to over 60 countries and territories , and imported cases of Zika have been increasingly reported worldwide . However , there is still much uncertainty behind the mechanisms which dictated the rapid emergence of the epidemic . This work intr...	[ "Abstract", "Introduction", "Method", "Results", "and", "discussion" ]	[ "medicine", "and", "health", "sciences", "air", "travel", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "economic", "analysis", "pathogens", "spatial", "epidemiology", "microbiology", "social", "sciences", "geographical", "lo...	2018	Inferring the risk factors behind the geographical spread and transmission of Zika in the Americas
This work describes the use of entomological studies combined with in silico models ( computer simulations derived from numerical models ) to assess the efficacy of a novel device for controlled release of spatial repellents . Controlled Release Devices ( CRDs ) were tested with different concentrations of metofluthrin...	Spatial Repellents ( SRs ) represent another tool to fight vector-borne diseases , such as malaria and dengue . Newly developed active ingredients were designed to repel or kill vectors in space , creating a shield effect , unlike topical repellents , such as DEET , that rely on vectors to be near or in physical contac...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "invertebrates", "medicine", "and", "health", "sciences", "classical", "mechanics", "fluid", "mechanics", "condensed", "matter", "physics", "vector-borne", "diseases", "animals", "simulation", "and", "modeling", "vaporization", "population", "biology", ...	2019	A combined experimental-computational approach for spatial protection efficacy assessment of controlled release devices against mosquitoes (Anopheles)
Unlike the pandemic form of HIV-1 ( group M ) , group O viruses are endemic in west central Africa , especially in Cameroon . However , little is known about group O’s genetic evolution , and why this highly divergent lineage has not become pandemic . Using a unique and large set of group O sequences from samples colle...	HIV-1 group O is one of the causal agents of AIDS , together with HIV-1 groups M ( responsible for the pandemic ) , N and P ( 15 and 2 cases detected respectively , from Cameroon ) and HIV-2 groups A to I ( mostly found in West Africa ) , each group resulting from a distinct cross species transmission event from non-hu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Two-Phase Emergence of Non Pandemic HIV-1 Group O in Cameroon
Human cytomegalovirus ( HCMV ) infection is associated epidemiologically with poor outcome of renal allografts due to mechanisms which remain largely undefined . Transforming growth factor-β1 ( TGF-β1 ) , a potent fibrogenic cytokine , is more abundant in rejecting renal allografts that are infected with either HCMV or...	Human cytomegalovirus ( HCMV ) is a common virus that establishes lifelong persistence in the host . Although asymptomatic in healthy people , HCMV can reactivate and cause disease in immunosuppressed patients , such as those undergoing kidney transplantation . HCMV infection is associated with inferior renal allograft...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology", "infectious", "diseases/viral", "infections", "nephrology/dialysis", "and", "renal", "transplantation" ]	2010	Human Cytomegalovirus Induces TGF-β1 Activation in Renal Tubular Epithelial Cells after Epithelial-to-Mesenchymal Transition
Interferon stimulated genes ( ISGs ) target viruses at various stages of their infectious life cycles , including at the earliest stage of viral entry . Here we identify ArfGAP with dual pleckstrin homology ( PH ) domains 2 ( ADAP2 ) as a gene upregulated by type I IFN treatment in a STAT1-dependent manner . ADAP2 func...	The induction of antiviral innate immune signaling is a primary defense strategy employed by host cells to restrict virus infections . This system is triggered by the presence of ‘non-self’ components such as viral nucleic acids and culminates in the induction of type I interferons ( IFNs ) . Type I IFNs themselves pos...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	ADAP2 Is an Interferon Stimulated Gene That Restricts RNA Virus Entry
Cohesin is a chromatin-associated protein complex that mediates sister chromatid cohesion by connecting replicated DNA molecules . Cohesin also has important roles in gene regulation , but the mechanistic basis of this function is poorly understood . In mammalian genomes , cohesin co-localizes with CCCTC binding factor...	Recent work has shown that cohesin , a protein best known for its role in holding sister chromatids together , and CTCF , a protein implicated in the formation of chromatin loops , localize to the same regions of DNA in mammalian genomes . This observation raised the intriguing possibility that cohesin might facilitate...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "genetics", "and", "genomics/chromosome", "biology", "molecular", "biology/dna", "methylation", "genetics", "and", "genomics/epigenetics", "genetics", "and", "genomics/cancer", "genetics", "molecular", "biology/chromatin", "st...	2009	Cohesin Is Required for Higher-Order Chromatin Conformation at the Imprinted IGF2-H19 Locus
Parvoviruses exploit transferrin receptor type-1 ( TfR ) for cellular entry in carnivores , and specific interactions are key to control of host range . We show that several key mutations acquired by TfR during the evolution of Caniforms ( dogs and related species ) modified the interactions with parvovirus capsids by ...	Parvoviruses in cats and dogs have been studied as a model system to understand how viruses gain the ability to infect new host species . By studying the evolution of the transferrin receptor , which the virus uses to enter a cell , we discovered that the ancestors of dogs were likely infected by a parvovirus millions ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "Materials" ]	[ "viral", "attachment", "viral", "evolution", "host", "cells", "viral", "transmission", "and", "infection", "virology", "emerging", "viral", "diseases", "biology", "microbiology" ]	2012	Evolutionary Reconstructions of the Transferrin Receptor of Caniforms Supports Canine Parvovirus Being a Re-emerged and Not a Novel Pathogen in Dogs
We have compared 12 genome-scale models of the Saccharomyces cerevisiae metabolic network published since 2003 to evaluate progress in reconstruction of the yeast metabolic network . We compared the genomic coverage , overlap of annotated metabolites , predictive ability for single gene essentiality with a selection of...	Scientists have been mapping the chemical reactions cells use to grow and manage waste since before enzymes were first identified more than 150 years ago . The model yeast Saccharomyces cerevisiae has one of the most extensively studied metabolic networks , including at least 25 metabolic network models published since...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction
The mechanism ( s ) by which bacterial communities impact susceptibility to infectious diseases , such as HIV , and maintain female genital tract ( FGT ) health are poorly understood . Evaluation of FGT bacteria has predominantly been limited to studies of species abundance , but not bacterial function . We therefore s...	The female genital tract ( FGT ) is a key mucosal surface in the context of HIV transmission . Lactobacillus species are beneficial to the FGT , while Garderella vaginalis and other anaerobic bacteria are detrimental . Bacterial vaginosis ( BV ) is an inflammatory condition characterized by an outgrowth of G . vaginali...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "urology", "medicine", "and", "health", "sciences", "gut", "bacteria", "bacterial", "vaginosis", "physiological", "processes", "gene", "sequencing", "sexually", "transmitted", "diseases", "molecular", "biology", "techniques", "cellular", "struc...	2016	Microbiome Composition and Function Drives Wound-Healing Impairment in the Female Genital Tract
One-third of the 4 , 225 protein-coding genes of Escherichia coli K-12 remain functionally unannotated ( orphans ) . Many map to distant clades such as Archaea , suggesting involvement in basic prokaryotic traits , whereas others appear restricted to E . coli , including pathogenic strains . To elucidate the orphans' b...	One goal of modern biology is to chart groups of proteins that act together to perform biological processes via direct and indirect interactions . Such groupings are sometimes called functional modules . The types of protein interactions within modules include physical interactions that generate protein complexes and b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "biochemistry", "computational", "biology", "evolutionary", "biology", "genetics", "and", "genomics" ]	2009	Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins
The progressive decline of CD4+ T cells is a hallmark of disease progression in human immunodeficiency virus ( HIV ) and simian immunodeficiency virus ( SIV ) infection . Whereas the acute phase of the infection is dominated by virus-mediated depletion of memory CD4+ T cells , chronic infection is often associated with...	Despite intensive study , the mechanisms of CD4+ T cell depletion in human immunodeficiency virus ( HIV ) infection remain elusive . The identification of the CD4 receptor as the primary receptor for HIV seemed initially to explain the loss of CD4+ T cell lymphocytes in AIDS . However , the number of infected cells at ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "virology/immunodeficiency", "viruses", "virology/virulence", "factors", "and", "mechanisms", "virology/animal", "models", "of", "infection", "virology/host", "antiviral", "responses" ]	2009	Association of Progressive CD4+ T Cell Decline in SIV Infection with the Induction of Autoreactive Antibodies
Avian lungs are remarkably different from mammalian lungs in that air flows unidirectionally through rigid tubes in which gas exchange occurs . Experimental observations have been able to determine the pattern of gas flow in the respiratory system , but understanding how the flow pattern is generated and determining th...	Birds and mammals have similar metabolic demands and cardiovascular systems , but they have evolved drastically different respiratory systems . A key difference in birds is that gas exchange occurs in rigid tubes , through which air flows unidirectionally during both inspiration and expiration . How this unidirectional...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "livestock", "medicine", "and", "health", "sciences", "dynamics", "classical", "mechanics", "fluid", "mechanics", "vertebrates", "animals", "physiological", "processes", "respiratory", "system", "breathing", "respiration", "waterfowl", "air", "flow", "birds", "ducks", "...	2016	Robust Unidirectional Airflow through Avian Lungs: New Insights from a Piecewise Linear Mathematical Model
Canine rabies was reintroduced to the city of Arequipa , Peru in March 2015 . The Ministry of Health has conducted a series of mass dog vaccination campaigns to contain the outbreak , but canine rabies virus transmission continues in Arequipa’s complex urban environment , putting the city’s 1 million inhabitants at ris...	Canine rabies was reintroduced in Arequipa , Peru in March 2015 , a rare event in an area previously declared free of transmission . In Arequipa , annual mass dog vaccination is practiced as a preventive strategy , with additional campaigns being implemented since the recent detection of the virus . However , these add...	[ "Abstract", "Introduction", "Methods", "Discussion", "Conclusions" ]	[ "animal", "types", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "vertebrates", "pets", "and", "companion", "animal...	2017	Barriers to dog rabies vaccination during an urban rabies outbreak: Qualitative findings from Arequipa, Peru
Cyanide-resistant non-phosphorylating respiration is known in mitochondria from plants , fungi , and microorganisms but is absent in mammals . It results from the activity of an alternative oxidase ( AOX ) that conveys electrons directly from the respiratory chain ( RC ) ubiquinol pool to oxygen . AOX thus provides a b...	In mammalian mitochondria , the energy-producing machinery is powered by the electron transfer to molecular oxygen , a mechanism whose terminal step is mediated by the cyanide-sensitive cytochrome c oxidase ( COX ) . In plants , fungi , microorganisms , and some lower animals ( but not in mammals ) , in addition to the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "biochemistry", "animal", "genetics", "model", "organisms", "genetics", "biology", "mouse", "genetics", "and", "genomics" ]	2013	Alternative Oxidase Expression in the Mouse Enables Bypassing Cytochrome c Oxidase Blockade and Limits Mitochondrial ROS Overproduction
Two important ideas about associative learning have emerged in recent decades: ( 1 ) Animals are Bayesian learners , tracking their uncertainty about associations; and ( 2 ) animals acquire long-term reward predictions through reinforcement learning . Both of these ideas are normative , in the sense that they are deriv...	How do we learn about associations between events ? The seminal Rescorla-Wagner model provided a simple yet powerful foundation for understanding associative learning . However , much subsequent research has uncovered fundamental limitations of the Rescorla-Wagner model . One response to these limitations has been to r...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[]	2015	A Unifying Probabilistic View of Associative Learning
The splice isoforms of vascular endothelial growth A ( VEGF ) each have different affinities for the extracellular matrix ( ECM ) and the coreceptor NRP1 , which leads to distinct vascular phenotypes in model systems expressing only a single VEGF isoform . ECM-immobilized VEGF can bind to and activate VEGF receptor 2 (...	Angiogenesis , the growth of new blood vessels from the existing vasculature , is critical for maintenance of health and response to injury . In ischemic disease , this process is impaired , but therapies targeting a key family of proteins , the vascular endothelial growth factors ( VEGF ) , have failed to translate cl...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "binding", "phosphorylation", "cell", "physiology", "medicine", "and", "health", "sciences", "placental", "growth", "factor", "body", "fluids", "vegf", "signaling", "endothelial", "cells", "epithelial", "cells", "endocrine", "physiology", "growth", "factors", ...	2017	A computational analysis of in vivo VEGFR activation by multiple co-expressed ligands
Although Plasmodium vivax is responsible for the majority of malaria infections outside Africa , little is known about its evolution and pathway to humans . Its closest genetic relative , P . vivax-like , was discovered in African great apes and is hypothesized to have given rise to P . vivax in humans . To unravel the...	Among the 5 species responsible for malaria in humans , Plasmodium vivax is the most prevalent outside Africa . It causes severe and incapacitating clinical symptoms with significant effects on human health . Yet little is known about its evolution , adaptation , and emergence in humans . The recent discovery in Africa...	[ "Abstract", "Genome", "assemblies", "Gene", "synteny", "and", "gene", "composition", "Phylogenetic", "relationships", "to", "other", "Relationships", "to", "worldwide", "human", "A", "still", "uncertain", "origin", "of", "Conclusion", "Materials", "and", "methods" ]	[ "taxonomy", "parasite", "groups", "medicine", "and", "health", "sciences", "methods", "and", "resources", "plasmodium", "parasite", "evolution", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "apicomplexa", "phylogenetics", "data", "management", "prot...	2018	Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution
The agents of paracoccidioidomycosis , historically identified as Paracoccidioides brasiliensis , are in fact different phylogenetic species . This study aims to evaluate associations between Paracoccidioides phylogenetic species and corresponding clinical data . Paracoccidioides strains from INI/Fiocruz patients ( 199...	Paracoccidioidomycosis ( PCM ) is a severe systemic mycosis caused by different phylogenetic species . According to previous studies , these species could have an impact in PCM clinical features . This study aims to investigate possible associations between Paracoccidioides species and corresponding clinical data . The...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[]	2019	Clinical features and genetic background of the sympatric species Paracoccidioides brasiliensis and Paracoccidioides americana
As the Drosophila embryo transitions from the use of maternal RNAs to zygotic transcription , domains of open chromatin , with relatively low nucleosome density and specific histone marks , are established at promoters and enhancers involved in patterned embryonic transcription . However it remains unclear how regions ...	DNA in the nuclei of animals and other eukaryotes is not floating around freely . Rather it is wrapped around proteins called histones that are in turn compacted into higher order structures called chromatin . Highly compact chromatin can restrict which genes and regulatory regions are accessible to the machinery that ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "materials" ]	[ "invertebrates", "in", "situ", "hybridization", "molecular", "probe", "techniques", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "animals", "invertebrate", "genomics", "animal", "models", "developmental", "biology", "drosophila", "melanogaster"...	2018	Patterns of chromatin accessibility along the anterior-posterior axis in the early Drosophila embryo
Increasing energy expenditure through brown adipocyte recruitment is a promising approach to combat obesity . We report here the comprehensive profiling of the epigenome and transcriptome throughout the lineage commitment and differentiation of C3H10T1/2 mesenchymal stem cell line into brown adipocytes . Through direct...	Obesity and its related metabolic diseases are growing problems worldwide . Brown adipose tissue ( BAT ) with its capability of burning off fat to generate heat is now at the center of research interest as target of therapeutic intervention for obesity treatment . In order to get a better understanding of the molecular...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "characterization", "gene", "regulation", "long", "non-coding", "rnas", "cell", "differentiation", "developmental", "biology", "regulator", "genes", "adipocytes", "connective", "tissue", "cells", "gene", "types", "res...	2016	Comparative Transcriptomic and Epigenomic Analyses Reveal New Regulators of Murine Brown Adipogenesis
The accumulation of mutant mitochondrial DNA ( mtDNA ) molecules in aged cells has been associated with mitochondrial dysfunction , age-related diseases and the ageing process itself . This accumulation has been shown to often occur clonally , where mutant mtDNA grow in number and overpopulate the wild-type mtDNA . How...	Mitochondria are responsible for most energy generation in human and animal cells . Loss or pathological alteration of mitochondrial function is a hallmark of many age-related diseases . Mitochondrial dysfunction may be a central and conserved feature of the ageing process . As part of quality control ( QC ) , mitochon...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Context-Dependent Role of Mitochondrial Fusion-Fission in Clonal Expansion of mtDNA Mutations
There is epidemiological evidence that patients with certain Central Nervous System ( CNS ) disorders have a lower than expected probability of developing some types of Cancer . We tested here the hypothesis that this inverse comorbidity is driven by molecular processes common to CNS disorders and Cancers , and that ar...	A lower-than-expected probability of developing certain types of Cancer has been observed in patients with CNS disorders , including Alzheimer's disease , Parkinson's disease or Schizophrenia . Understanding such a protective effect could be the key to finding novel treatments for both types of conditions , for instanc...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Methods" ]	[ "cancer", "genetics", "gene", "expression", "genetics", "biology", "computational", "biology", "gene", "networks" ]	2014	Molecular Evidence for the Inverse Comorbidity between Central Nervous System Disorders and Cancers Detected by Transcriptomic Meta-analyses
Deregulation of the Wnt signal transduction pathway underlies numerous congenital disorders and cancers . Axin , a concentration-limiting scaffold protein , facilitates assembly of a “destruction complex” that prevents signaling in the unstimulated state and a plasma membrane-associated “signalosome” that activates sig...	Axin is a scaffold protein with essential roles in Wnt signal transduction . In the classical model , the transition from the unstimulated to stimulated state is thought to be achieved by recruitment of Axin from cytosol to plasma membrane . We find that a pool of endogenous Drosophila Axin is localized in puncta juxta...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "molecular", "probe", "techniques", "membrane", "staining", "immunoblotting", "cloning", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "molecular", "biology", "techniques", "embryos", "cellula...	2016	Dual Roles for Membrane Association of Drosophila Axin in Wnt Signaling
Ribose 5-phosphate isomerase is an enzyme involved in the non-oxidative branch of the pentose phosphate pathway , and catalyzes the inter-conversion of D-ribose 5-phosphate and D-ribulose 5-phosphate . Trypanosomatids , including the agent of African sleeping sickness namely Trypanosoma brucei , have a type B ribose-5-...	Within the non-oxidative branch of the pentose phosphate pathway , ribose 5-phosphate isomerase catalyzes the inter-conversion of ribose 5-phosphate and ribulose 5-phosphate . There are two types of ribose 5-phosphate isomerase , namely A and B . The presence of type B in Trypanosoma brucei , and its absence in humans ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "molecular", "biology", "biology", "and", "life", "sciences", "parasitology" ]	2015	Ribose 5-Phosphate Isomerase B Knockdown Compromises Trypanosoma brucei Bloodstream Form Infectivity
In central neurons , the threshold for spike initiation can depend on the stimulus and varies between cells and between recording sites in a given cell , but it is unclear what mechanisms underlie this variability . Properties of ionic channels are likely to play a role in threshold modulation . We examined in models t...	Neurons communicate primarily with stereotypical electrical impulses , action potentials , which are fired when a threshold level of excitation is reached . This threshold varies between cells and over time as a function of previous stimulations , which has major functional implications on the integrative properties of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/theoretical", "neuroscience", "computational", "biology/computational", "neuroscience" ]	2010	A Threshold Equation for Action Potential Initiation
Knowledge of the Free Energy Landscape topology is the essential key to understanding many biochemical processes . The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions . In this work , we present a novel framework to unveil t...	A complete description of complex polymers , such as proteins , includes information about their structure and their dynamics . In particular it is of utmost importance to answer the following questions: What are the structural conformations possible ? Is there any relevant hierarchy among these conformers ? What are t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "biology/molecular", "dynamics", "computational", "biology/macromolecular", "structure", "analysis", "biophysics/theory", "and", "simulation", "biophysics/protein", "folding" ]	2009	Exploring the Free Energy Landscape: From Dynamics to Networks and Back
Leprosy Type 1 reactions are difficult to treat and only 70% of patients respond to steroid treatment . Azathioprine has been used as an immune-suppressant and we tested its efficacy in treating leprosy T1R . Randomised controlled trial adding azathioprine to steroid treatment for leprosy reactions . This trial was con...	Type 1 reactions affect leprosy patients and are due to increased inflammation in skin and nerves that can cause disfiguring skin lesions and loss of sensation and loss of power in the hands and the feet . These disabilities can lead to deformity and severe disability . It is important to improve the treatment for T1 r...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "clinical", "research", "design", "pathology", "and", "laboratory", "medicine", "immunology", "tropical", "diseases", "neuroscience", "organic", "compounds", "anemia", "bacterial", "diseases", "research", ...	2017	AZALEP a randomized controlled trial of azathioprine to treat leprosy nerve damage and Type 1 reactions in India: Main findings
Scabies afflicts millions of people worldwide , but it is very difficult to diagnose by the usual skin scrape test , and a presumptive diagnosis is often made based on clinical signs such as rash and intense itch . A sensitive and specific blood test to detect scabies would allow a physician to quickly make a correct d...	Scabies , caused by the mite S . scabiei that burrows in the skin of humans , is a contagious skin disease that affects millions of people worldwide . It is a significant public health burden in economically disadvantaged populations , and outbreaks are common in nursing homes , daycare facilities , schools and workpla...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	The Potential for a Blood Test for Scabies
The transition from single-cell to multicellular behavior is important in early development but rarely studied . The starvation-induced aggregation of the social amoeba Dictyostelium discoideum into a multicellular slug is known to result from single-cell chemotaxis towards emitted pulses of cyclic adenosine monophosph...	Cells are often coupled to each other in cell collectives , such as aggregates during early development , tissues in the developed organism , and tumors in disease . How do cells communicate over macroscopic distances much larger than the typical cell—cell distance to decide how they should behave ? Here , we developed...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "cell", "motility", "medicine", "and", "health", "sciences", "dictyostelium", "fruiting", "body", "dictyosteliomycota", "microbiology", "simulation", "and", "modeling", "fluorophotometry", "physiological", "processes", "developmental", "biology", "dict...	2017	A critical-like collective state leads to long-range cell communication in Dictyostelium discoideum aggregation
Mitochondrial processing peptidases are heterodimeric enzymes ( α/βMPP ) that play an essential role in mitochondrial biogenesis by recognizing and cleaving the targeting presequences of nuclear-encoded mitochondrial proteins . The two subunits are paralogues that probably evolved by duplication of a gene for a monomer...	In classic model organisms , cleavage of signals that are required to deliver nuclear-encoded proteins to mitochondria is mediated by an enzyme comprising two different subunits , called α or β , neither of which is functional by itself . Here , we have characterized a novel enzyme that functions in the mitosome , a hi...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "biochemistry/molecular", "evolution", "cell", "biology", "microbiology/parasitology" ]	2008	Reductive Evolution of the Mitochondrial Processing Peptidases of the Unicellular Parasites Trichomonas vaginalis and Giardia intestinalis
A diverse suite of effector immune responses provide protection against various pathogens . However , the array of effector responses must be immunologically regulated to limit pathogen- and immune-associated damage . CD4+Foxp3+ regulatory T cells ( Treg ) calibrate immune responses; however , how Treg cells adapt to c...	The diversity of pathogens that the immune system encounters are controlled by a diverse suite of immunological effector responses . Preserving a well-controlled protective immune response is essential . Too vigorous an effector response can be as damaging as too little . Regulatory T cells ( Treg ) calibrate immune re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "parastic", "protozoans", "immunopathology", "adaptive", "immunity", "immune", "cells", "leishmania", "immunity", "t", "cells", "immunology", "protozoology", "biology", "microbiology", "immunoregulation", "host-pathogen", "interaction", "immune", "response" ]	2013	miR-182 and miR-10a Are Key Regulators of Treg Specialisation and Stability during Schistosome and Leishmania-associated Inflammation
Intestinal epithelial cells ( IECs ) compose the first barrier against microorganisms in the gastrointestinal tract . Although the NF-κB pathway in IECs was recently shown to be essential for epithelial integrity and intestinal immune homeostasis , the roles of other inflammatory signaling pathways in immune responses ...	The cellular responses of intestinal epithelial cells ( IECs ) to microorganisms in the gastrointestinal tract are mediated by activation of a number of intracellular signaling pathways . It was shown that the NF-κB pathway in IECs is essential for epithelial integrity and intestinal immune homeostasis , and here we sh...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "gastroenterology", "and", "hepatology/gastrointestinal", "infections", "immunology/immune", "response", "infectious", "diseases/bacterial", "infections", "immunology/immunity", "to", "infections", "infectious", "diseases/gastrointestinal", "infections" ]	2010	Epithelial p38α Controls Immune Cell Recruitment in the Colonic Mucosa
Sensory processing is associated with gamma frequency oscillations ( 30–80 Hz ) in sensory cortices . This raises the question whether gamma oscillations can be directly involved in the representation of time-varying stimuli , including stimuli whose time scale is longer than a gamma cycle . We are interested in the ab...	Sensory processing of time-varying stimuli , such as speech , is associated with high-frequency oscillatory cortical activity , the functional significance of which is still unknown . One possibility is that the oscillations are part of a stimulus-encoding mechanism . Here , we investigate a computational model of such...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "neuroscience/theoretical", "neuroscience", "neuroscience/sensory", "systems", "computational", "biology/computational", "neuroscience", "computational", "biology", "neuroscience", "computational", "biology/systems", "biology" ]	2009	Representation of Time-Varying Stimuli by a Network Exhibiting Oscillations on a Faster Time Scale
In the early 20th century , there were few therapeutic options for mental illness and asylum numbers were rising . This pessimistic outlook favoured the rise of the eugenics movement . Heredity was assumed to be the principal cause of mental illness . Politicians , scientists and clinicians in North America and Europe ...	Psychiatric genetics was established as a scientific discipline in the early 20th century . The intention was to provide evidence for the inheritance of mental illnesses . This was to open up new paths in prevention , since therapeutic options at the time were meagre . Applying modern study designs and statistical meth...	[ "Abstract", "Introduction" ]	[]	2015	Ernst Rüdin’s Unpublished 1922-1925 Study “Inheritance of Manic-Depressive Insanity”: Genetic Research Findings Subordinated to Eugenic Ideology
Single-cell mRNA sequencing can uncover novel cell-to-cell heterogeneity in gene expression levels in seemingly homogeneous populations of cells . However , these experiments are prone to high levels of unexplained technical noise , creating new challenges for identifying genes that show genuine heterogeneous expressio...	Gene expression signatures have historically been used to generate molecular fingerprints that characterise distinct tissues . Moreover , by interrogating these molecular signatures it has been possible to understand how a tissue’s function is regulated at the molecular level . However , even between cells from a seemi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	BASiCS: Bayesian Analysis of Single-Cell Sequencing Data
Most yeast ribosomal protein genes are duplicated and their characterization has led to hypotheses regarding the existence of specialized ribosomes with different subunit composition or specifically-tailored functions . In yeast , ribosomal protein genes are generally duplicated and evidence has emerged that paralogs m...	Translation is the process by which proteins are made within a cell . Ribosomes are the main macromolecular complexes involved in this process . Ribosomes are composed of ribosomal RNA and ribosomal proteins . Ribosomal proteins are generally thought to be structural components of the ribosome but recent findings have ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "biochemistry", "protein", "synthesis", "model", "organisms", "proteins", "gene", "expression", "genetics", "regulatory", "proteins", "biology", "mouse", "rna", "stability" ]	2013	The Ribosomal Protein Rpl22 Controls Ribosome Composition by Directly Repressing Expression of Its Own Paralog, Rpl22l1

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