Utilisation de grilles de calcul pour la génomique comparative

International audienceLarge scale phylogenomics and comparative genomics require complex computational methods (parsimony, maximum likelihood, bayesian methods, MCMC, etc.) associated with massively distributed calculation. In this respect, grid computing plays a crucial role. Here we present how we processed exhaustive similarity searches on several millions of sequences with BLAST, using two different grids (TIDRA and GRISBI)

Parallelization of monte Carlo simulations and submission to a grid environment

presentation L. Maign

Utilisation de grilles de calcul pour la génomique comparative

International audienceLarge scale phylogenomics and comparative genomics require complex computational methods (parsimony, maximum likelihood, bayesian methods, MCMC, etc.) associated with massively distributed calculation. In this respect, grid computing plays a crucial role. Here we present how we processed exhaustive similarity searches on several millions of sequences with BLAST, using two different grids (TIDRA and GRISBI)

Measurement of eta photoproduction on the proton from threshold to 1500 MeV

Beam asymmetry and differential cross section for the reaction gamma+p->eta+p were measured from production threshold to 1500 MeV photon laboratory energy. The two dominant neutral decay modes of the eta meson, eta->2g and eta->3pi0, were analyzed. The full set of measurements is in good agreement with previously published results. Our data were compared with three models. They all fit satisfactorily the results but their respective resonance contributions are quite different. The possible photoexcitation of a narrow state N(1670) was investigated and no evidence was found.Comment: 18 pages, 14 figures, 4 tables Submitted to EPJ

Circulating adrenomedullin estimates survival and reversibility of organ failure in sepsis: the prospective observational multinational Adrenomedullin and Outcome in Sepsis and Septic Shock-1 (AdrenOSS-1) study

Background: Adrenomedullin (ADM) regulates vascular tone and endothelial permeability during sepsis. Levels of circulating biologically active ADM (bio-ADM) show an inverse relationship with blood pressure and a direct relationship with vasopressor requirement. In the present prospective observational multinational Adrenomedullin and Outcome in Sepsis and Septic Shock 1 (, AdrenOSS-1) study, we assessed relationships between circulating bio-ADM during the initial intensive care unit (ICU) stay and short-term outcome in order to eventually design a biomarker-guided randomized controlled trial. Methods: AdrenOSS-1 was a prospective observational multinational study. The primary outcome was 28-day mortality. Secondary outcomes included organ failure as defined by Sequential Organ Failure Assessment (SOFA) score, organ support with focus on vasopressor/inotropic use, and need for renal replacement therapy. AdrenOSS-1 included 583 patients admitted to the ICU with sepsis or septic shock. Results: Circulating bio-ADM levels were measured upon admission and at day 2. Median bio-ADM concentration upon admission was 80.5 pg/ml [IQR 41.5-148.1 pg/ml]. Initial SOFA score was 7 [IQR 5-10], and 28-day mortality was 22%. We found marked associations between bio-ADM upon admission and 28-day mortality (unadjusted standardized HR 2.3 [CI 1.9-2.9]; adjusted HR 1.6 [CI 1.1-2.5]) and between bio-ADM levels and SOFA score (p < 0.0001). Need of vasopressor/inotrope, renal replacement therapy, and positive fluid balance were more prevalent in patients with a bio-ADM > 70 pg/ml upon admission than in those with bio-ADM ≤ 70 pg/ml. In patients with bio-ADM > 70 pg/ml upon admission, decrease in bio-ADM below 70 pg/ml at day 2 was associated with recovery of organ function at day 7 and better 28-day outcome (9.5% mortality). By contrast, persistently elevated bio-ADM at day 2 was associated with prolonged organ dysfunction and high 28-day mortality (38.1% mortality, HR 4.9, 95% CI 2.5-9.8). Conclusions: AdrenOSS-1 shows that early levels and rapid changes in bio-ADM estimate short-term outcome in sepsis and septic shock. These data are the backbone of the design of the biomarker-guided AdrenOSS-2 trial. Trial registration: ClinicalTrials.gov, NCT02393781. Registered on March 19, 2015

A propos de la saison balnéaire

Calvat . A propos de la saison balnéaire. In: Manuel général de l'instruction primaire : journal hebdomadaire des instituteurs. 69e année, tome 38, 1902. p. 485

Influence d’une distribution bimodale de tailles de grains sur les mécanismes de déformation d’un acier austénitique inoxydable

This work focuses on the mechanical behavior of austenitic stainless steels with a bimodal grain size distribution. A first part, self-sufficient, is dedicated to the improvement of the elaboration process and a second part, more consequent, proposed an in-depth numerical analysis of the deformation mechanisms governing the constitutive behaviour of these alloys. In this study, the samples are elaborated by powder metallurgy and SPS. One section describes the different strategies adopted to limit the oxidation of the material during elaboration. Among these ways of improvement, we can mention : the ball milling step, the choice of powders, the passivation and the glove box. The addition of an additional powder agglomeration step is also considered to improve the contrast of grain sizes between ultrafine grains and grains of conventional size. The addition of an agglomeration step is also considered to improve the grain size contrast between ultrafine grains and grains of conventional size. The numerical section aims at understanding the mechanisms by analysing the local behaviors, their intensity as well as their spatial distribution in a quantitative way. For this, the constitutive modelling of bimodal microstructures is based on a full field modelling and the use of a modified Méric-Cailletaud crystal plasticity model to take into account a grain size effect. Different microstructures have been studied to understand the influence of various microstructural parameters associated with bimodal microstructures. Subsequently, these microstructures were loaded in shear and in biaxial tension to describe the influence of the loading on the local behavior.Cette étude porte sur le comportement mécanique d’un acier austénitique inoxydable 316L à distribution bimodale de tailles de grains. Une première partie, autosuffisante, traite de l’amélioration du procédé d’élaboration et une seconde, plus conséquente, s’intéresse à la compréhension des mécanismes de déformation de ces alliages par une approche numérique. Pour cette étude, les échantillons d’analyse sont élaborés par métallurgie des poudres. Un chapitre est dédié à la description des différentes stratégies suivies pour limiter l’oxydation du matériau au cours de son élaboration. Parmi ces voies d’amélioration on peut citer : l’étape de broyage, le choix des poudres, la passivation et la boîte à gants. L’ajout d’une étape supplémentaire d’agglomération des poudres est également considéré pour améliorer le contraste de tailles de grains entre grains ultrafins et grains de tailles conventionnelles. La partie numérique porte sur la compréhension des mécanismes par l’analyse des comportements locaux, leur intensité comme leur répartition spatiale et ce de manière quantitative. Pour cela, la modélisation du comportement des microstructures bimodales repose sur une modélisation à champs complets et l’utilisation du modèle de plasticité cristalline de Méric-Cailletaud modifié pour prendre en compte un effet de taille de grains. Différentes microstructures ont été étudiées pour comprendre l’influence des divers paramètres microstructuraux associés aux microstructures bimodales. Par la suite, ces microstructures ont été sollicitées en cisaillement et en traction biaxiale pour décrire l’influence du chargement sur les comportements locaux

Un document pris sur le vif

Calvat I. Un document pris sur le vif . In: Manuel général de l'instruction primaire : journal hebdomadaire des instituteurs. 68e année, tome 37, 1901. pp. 664-666

Impact of the grain-size bimodality on the strain mechanisms of an austenitic stainless steel

Cette étude porte sur le comportement mécanique d’un acier austénitique inoxydable 316L à distribution bimodale de tailles de grains. Une première partie, autosuffisante, traite de l’amélioration du procédé d’élaboration et une seconde, plus conséquente, s’intéresse à la compréhension des mécanismes de déformation de ces alliages par une approche numérique. Pour cette étude, les échantillons d’analyse sont élaborés par métallurgie des poudres. Un chapitre est dédié à la description des différentes stratégies suivies pour limiter l’oxydation du matériau au cours de son élaboration. Parmi ces voies d’amélioration on peut citer : l’étape de broyage, le choix des poudres, la passivation et la boîte à gants. L’ajout d’une étape supplémentaire d’agglomération des poudres est également considéré pour améliorer le contraste de tailles de grains entre grains ultrafins et grains de tailles conventionnelles. La partie numérique porte sur la compréhension des mécanismes par l’analyse des comportements locaux, leur intensité comme leur répartition spatiale et ce de manière quantitative. Pour cela, la modélisation du comportement des microstructures bimodales repose sur une modélisation à champs complets et l’utilisation du modèle de plasticité cristalline de Méric-Cailletaud modifié pour prendre en compte un effet de taille de grains. Différentes microstructures ont été étudiées pour comprendre l’influence des divers paramètres microstructuraux associés aux microstructures bimodales. Par la suite, ces microstructures ont été sollicitées en cisaillement et en traction biaxiale pour décrire l’influence du chargement sur les comportements locaux.This work focuses on the mechanical behavior of austenitic stainless steels with a bimodal grain size distribution. A first part, self-sufficient, is dedicated to the improvement of the elaboration process and a second part, more consequent, proposed an in-depth numerical analysis of the deformation mechanisms governing the constitutive behaviour of these alloys. In this study, the samples are elaborated by powder metallurgy and SPS. One section describes the different strategies adopted to limit the oxidation of the material during elaboration. Among these ways of improvement, we can mention : the ball milling step, the choice of powders, the passivation and the glove box. The addition of an additional powder agglomeration step is also considered to improve the contrast of grain sizes between ultrafine grains and grains of conventional size. The addition of an agglomeration step is also considered to improve the grain size contrast between ultrafine grains and grains of conventional size. The numerical section aims at understanding the mechanisms by analysing the local behaviors, their intensity as well as their spatial distribution in a quantitative way. For this, the constitutive modelling of bimodal microstructures is based on a full field modelling and the use of a modified Méric-Cailletaud crystal plasticity model to take into account a grain size effect. Different microstructures have been studied to understand the influence of various microstructural parameters associated with bimodal microstructures. Subsequently, these microstructures were loaded in shear and in biaxial tension to describe the influence of the loading on the local behavior