80 research outputs found

    Vers une ontologie des processus de propagation des maladies infectieuses

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    International audiencePlusieurs ontologies sont construites au sein du projet Infectious Disease Ontology (IDO) pour fournir un vocabulaire commun du domaine et une représentation formelle des connaissances permettant de garantir leur partage, l'interopérabilité entre applications et le raisonnement. Dans ce papier, l'ontologie que nous proposons présente la modélisation des connaissances sur la propagation des maladies infectieuses. Le modèle prend en compte la structure multidimensionnelle et la nature complexe de la dynamique de propagation des maladies infectieuses. Nous étudions la propagation à l'échelle de la population tout en montrant ses interdépendances avec les processus sous-jacents aux échelles individuelle et biologique. Le choix de catégorisation des entités du domaine en tant que continuant ou occurrent est étudié. Une extension du modèle à la propagation de la bilharziose au Sénégal est également présentée

    Modélisation ontologique de processus dans le domaine de la veille épidémiologique

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    Session "Posters"National audienceDans ce papier, nous proposons une modélisation ontologique des processus de la veille sur les maladies infectieuses. Nous montrons l'intérêt de formaliser les aspects dynamiques des connaissances du domaine de la veille. Cette modélisation est menée sur trois niveaux : i) conceptuel modélisant des processus de la veille, de la veille sur les maladies infectieuses et de la propagation d'une maladie infectieuse ; ii) semi-formel correspondant à l'élaboration de patrons de processus pour faciliter la réutilisation des modèles conceptuels de?finis, et iii) formel correspondant à la formalisation des patrons élaborés. Ces patrons sont traduits dans le langage PSL pour rendre opérationnelle leur réutilisation et raisonner sur les modèles définis. La pertinence de la réutilisation des patrons est testée dans le domaine de l'épidémiologie de la bilharziose. Notre travail s'inscrit dans une approche de modélisation par spécification de la veille épidémiologique et constitue un apport à la mise en place des systèmes de veille. Une autre contribution est de participer aux travaux dans le domaine des ontologies des processus en prenant en compte les spécificités des phénomènes épidémiologiques

    Potential of Aquatic Plants for Pesticide Removal in Wastewater: A Case Study on Pentachlorophenol

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    Today, soil and water pollution by pesticides is a serious problem worldwide. Compared with conventionally expensive, invasive, and sometimes ineffective techniques for pentachlorophenol (PCP) dealing, such as excavation, dredging and some chemical methods, in situ treatment strategies are more effective at reducing risk and decreasing expenditures on management. Among the in situ treatments, bioremediation (microbial remediation and phytoremediation) is thought to be capable in permanent pollutants elimination at low cost. Therefore, phytoremediation has received more attention in the last decade. Phytoremediation is applicable owing to its esthetic value, environment friendly, manipulation in situ and economic benefit. However, the previous phytoremediation studies mostly focused on the use of terrestrial plants and remediation of heavy metals. Sediments in aquatic environment are regarded as ultimate sink of organic contaminants, but little information is available on the possibility of use of aquatic macrophytes for remediation of organic toxicants in aquatic environment. It is, therefore, necessary to develop phytoremediation method of PCP by using aquatic macrophytes

    Expanded genome-wide comparisons give novel insights into population structure and genetic heterogeneity of Leishmania tropica complex

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    Leishmania tropica is one of the main causative agents of cutaneous leishmaniasis (CL). Population structures of L. tropica appear to be genetically highly diverse. However, the relationship between L. tropica strains genomic diversity, protein coding gene evolution and biogeography are still poorly understood. In this study, we sequenced the genomes of three new clinical L. tropica isolates, two derived from a recent outbreak of CL in camps hosting Syrian refugees in Lebanon and one historical isolate from Azerbaijan to further refine comparative genome analyses. In silico multilocus microsatellite typing (MLMT) was performed to integrate the current diversity of genome sequence data in the wider available MLMT genetic population framework. Single nucleotide polymorphism (SNPs), gene copy number variations (CNVs) and chromosome ploidy were investigated across the available 18 L. tropica genomes with a main focus on protein coding genes. MLMT divided the strains in three populations that broadly correlated with their geographical distribution but not populations defined by SNPs. Unique SNPs profiles divided the 18 strains into five populations based on principal component analysis. Gene ontology enrichment analysis of the protein coding genes with population specific SNPs profiles revealed various biological processes, including iron acquisition, sterols synthesis and drug resistance. This study further highlights the complex links between L. tropica important genomic heterogeneity and the parasite broad geographic distribution. Unique sequence features in protein coding genes identified in distinct populations reveal potential novel markers that could be exploited for the development of more accurate typing schemes to further improve our knowledge of the evolution and epidemiology of the parasite as well as highlighting protein variants of potential functional importance underlying L. tropica specific biology

    GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5Ęą and 3Ęą ends of its target genes

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    The modification of histones by acetyl groups has a key role in the regulation of chromatin structure and transcription. The Arabidopsis thaliana histone acetyltransferase GCN5 regulates histone modifications as part of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) transcriptional coactivator complex. GCN5 was previously shown to acetylate lysine 14 of histone 3 (H3K14ac) in the promoter regions of its target genes even though GCN5 binding did not systematically correlate with gene activation. Here, we explored the mechanism through which GCN5 controls transcription. First, we fine-mapped its GCN5 binding sites genome-wide and then used several global methodologies (ATAC-seq, ChIP-seq and RNA-seq) to assess the effect of GCN5 loss-of-function on the expression and epigenetic regulation of its target genes. These analyses provided evidence that GCN5 has a dual role in the regulation of H3K14ac levels in their 5′ and 3′ ends of its target genes. While the gcn5 mutation led to a genome-wide decrease of H3K14ac in the 5′ end of the GCN5 down-regulated targets, it also led to an increase of H3K14ac in the 3′ ends of GCN5 up-regulated targets. Furthermore, genome-wide changes in H3K14ac levels in the gcn5 mutant correlated with changes in H3K9ac at both 5′ and 3′ ends, providing evidence for a molecular link between the depositions of these two histone modifications. To understand the biological relevance of these regulations, we showed that GCN5 participates in the responses to biotic stress by repressing salicylic acid (SA) accumulation and SA-mediated immunity, highlighting the role of this protein in the regulation of the crosstalk between diverse developmental and stress-responsive physiological programs. Hence, our results demonstrate that GCN5, through the modulation of H3K14ac levels on its targets, controls the balance between biotic and abiotic stress responses and is a master regulator of plant-environmental interactions

    HSFA1a modulates plant heat stress responses and alters the 3D chromatin organization of enhancer-promoter interactions

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    The complex and dynamic three-dimensional organization of chromatin within the nucleus makes understanding the control of gene expression challenging, but also opens up possible ways to epigenetically modulate gene expression. Because plants are sessile, they evolved sophisticated ways to rapidly modulate gene expression in response to environmental stress, that are thought to be coordinated by changes in chromatin conformation to mediate specific cellular and physiological responses. However, to what extent and how stress induces dynamic changes in chromatin reorganization remains poorly understood. Here, we comprehensively investigated genome-wide chromatin changes associated with transcriptional reprogramming response to heat stress in tomato. Our data show that heat stress induces rapid changes in chromatin architecture, leading to the transient formation of promoter-enhancer contacts, likely driving the expression of heat-stress responsive genes. Furthermore, we demonstrate that chromatin spatial reorganization requires HSFA1a, a transcription factor (TF) essential for heat stress tolerance in tomato. In light of our findings, we propose that TFs play a key role in controlling dynamic transcriptional responses through 3D reconfiguration of promoter-enhancer contacts

    Étude de la contribution des échanges thermiques radiatifs aux processus de propagation des flammes de poussières : application aux explosions de poussières d’aluminium

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    Ces travaux de thèse sont consacrés à l’examen du rôle du rayonnement thermique dans le processus de propagation des flammes issues de la combustion des particules d’aluminium dans l’air. Le sujet étant complexe et d’un intérêt industriel, il nécessite de prendre en compte le couplage de nombreux phénomènes physico-chimiques afin de prédire finement les conséquences des explosions de poussières. Une analyse bibliographique approfondie est proposée, concernant les mécanismes d’inflammation et de combustion des particules d’aluminium et aussi concernant les connaissances relatives à la propagation des flammes de poussières. La question spécifique de la nature des échanges thermiques et de l’influence du rayonnement thermique est étudiée. La revue bibliographique souligne les approximations et les hypothèses simplificatrices utilisées dans la littérature permettant donc de définir les pistes d’améliorations. Compte tenu des limitations importantes concernant la physique de ces flammes, un outil de simulation de physique numérique nommé « RADIAN », proche de la simulation numérique directe, a été développé proposant un couplage fin entre les différents modes d’échanges thermiques et la combustion pour modéliser la propagation de la flamme dans un nuage de poussières. La méthode des éléments discrets (MED) est utilisée pour modéliser numériquement les échanges radiatifs entre les particules et les échanges conductifs entre gaz et particules. La méthode des différences finies est utilisée pour modéliser numériquement la conduction thermique dans la phase gazeuse et la combustion. Un modèle radiatif est proposé se basant sur la théorie de Mie sur les interactions rayonnement-particules. Les résultats des simulations sont comparés avec des solutions analytiques et des données expérimentales de la littérature. Mais en plus, une étude expérimentale est aussi conduite afin de mesurer la distribution du flux radiatif devant la flamme et la vitesse de combustion laminaire pour des flammes Méthane-Sic, Méthane-Alumine et Al-air. Un bon accord entre les simulations et les expériences est démontré. La loi de Beer-Lambert relative au transfert radiatif devant le front de flamme s’avère inapplicable et une nouvelle solution analytique est proposée. La présence de particules absorbantes du rayonnement promeut la propagation de la flamme. En particulier, il a été montré expérimentalement et confirmé numériquement que les mélanges riches d’AL-air sont susceptibles d’accélérer rapidement.In this thesis, the role of thermal radiation in aluminum-air flames propagation is studied. The subject being complex and of industrial interest, it requires the coupling of many physiochemical phenomena to accurately predict the consequences of dust explosions. A thorough literature review is proposed about the ignition and the combustion of aluminum particles and about the available theoretical models of dust flames propagation. The specific question of the nature of thermal exchanges and the influence of thermal radiation is studied. The bibliographic review underlines the simplifying assumptions and hypotheses used in the literature making possible the definition of improvement areas. Because of the limited amount of knowledge available to address these questions, a numerical tool “RADIAN” is developed enabling an accurate coupling between the different modes of heat exchange and combustion. The Discrete Element Method (DEM) is used to numerically model the radiative exchanges between particles and the gas-particle thermal conduction. The Finite Difference method is used to numerically model the thermal conduction through the gas phase and combustion. A radiative model based on Mie theory for radiation-particles interactions is incorporated. The results of the simulations are compared with available analytical solutions and experimental data. An original experimental study is also conducted to measure the distribution of irradiance ahead of the flame front and the laminar burning velocity for methane-air-Sic, methane-air-alumina and Al-air flames. A good agreement between numerical simulations and experiments is demonstrated. The Beer-Lambert’s law for radiative transfer in front of the flame front is found to be inapplicable and a new analytical solution is proposed. The presence of absorbing particles may promote the flame propagation. In particular, it is shown experimentally and confirmed theoretically/numerically that Al-air rich mixtures are likely to rapidly accelerate

    Towards Lambda-Based Near Real-Time OLAP over Big Data

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    Towards Lambda-Based Near Real-Time OLAP over Big Dat

    Multidimensional Database Modeling: Literature Survey and Research Agenda for the Big Data Era

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    The purpose of this paper is twofold: First, to survey the literature on Multidimensional Database Modeling fundamentals, and Second, to sketch a research agenda which challenges Big Data four V\u2019s, namely Volume, Velocity, Veracity, and Variety
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