Portage de StarPU sur la bibliothèque de communication NewMadeleine

National audienceDe nombreux calculs sont complexe a paralléliser. De plus les structures des machines sont de plus en plus hétérogènes, avec la présence d'accélérateurs (GPU, ...). Un ordonnanceur de tache comme StarPU permet de répartir efficacement les calculs a l’intérieur d'un nœud. Son module StarPU-MPI permet d’étendre cette répartition sur plusieurs nœuds, en échangeant les données nécessaires avec la librairie de communication MPI.Cependant de nombreuses implémentions de MPI manquent d'efficacité pour un grand nombre de requêtes en attente.Notre port de StarPU-MPI sous NewMadeleine permet de résoudre ce problème, et d'améliorer le recouvrement (effectuer du calcul durant les communication) des communications

Analyse de l’influence de l’oscillation Arctique sur la variabilité interannuelle des précipitations dans le bassin versant de la rivière Saint-François (Québec, Canada) au moyen de la méthode des corrélations canoniques

Le bassin versant de la rivière Saint-François, situé sur la rive sud (rive droite) du fleuve Saint-Laurent (Québec, Canada), couvre une superficie d’environ 10 000 km2. Dans le but de déceler les facteurs climatiques qui influencent les précipitations dans ce bassin versant, nous avons analysé la succession des périodes pluviométriques sèches et humides par la technique des moyennes glissantes sur cinq ans, d’une part, et la relation entre quatre indices climatiques (oscillation arctique, oscillation australe, oscillation nord-atlantique et la température des eaux océaniques de surface) et ces périodes pluviométriques au moyen de l’analyse des corrélations canoniques, d’autre part. Nous avons analysé les données pluviométriques mesurées à trois stations représentatives des régimes pluviométriques du bassin versant : Sherbrooke, Disraeli et Drummondville. Ces données couvrent une période de 76 ans (1914-1990).En ce qui concerne la variabilité interannuelle des précipitations, nous avons détecté deux types de changement. Le premier type de changement, survenu autour de 1950, concerne la répartition des précipitations à l’échelle du bassin versant (changement spatial). Avant 1950, la succession des périodes sèches et humides des précipitations n’était pas synchrone (opposition des périodes) mais elle l’est devenue après 1950. Le second type de changement a été observé autour des années 1935 et 1970. Il correspond à un changement des totaux pluviométriques au niveau des stations (changement quantitatif). Avant et après 1935 et 1970, on passe ainsi des périodes sèches aux périodes humides ou vice versa selon les stations. En tenant compte de ces trois dates, nous avons observé la succession des périodes sèches et humides suivantes : 1) Avant 1950, entre 1914 et 1935, nous avons observé une période sèche aux stations de Disraeli et de Sherbrooke mais une période humide à la station de Drummondville. Entre 1936-1950, ces périodes se sont inversées : humide à Disraeli et Sherbrooke mais sèche à Drummondville; 2) Après 1950, entre 1951 et 1970, les précipitations étaient déficitaires aux trois stations. En revanche, elles sont devenues excédentaires après 1970.L’analyse des corrélations canoniques entre les précipitations et les indices climatiques a révélé les faits significatifs suivants : 1) Avant et après 1950, les précipitations sont positivement corrélées à l’oscillation arctique (OA), mais cette corrélation est plus faible après qu’avant 1950. Ainsi, l’augmentation des valeurs de OA entraînerait une hausse de fréquence des masses d’air en provenant du sud dans le bassin versant; 2) Lorsqu’on considère les périodes sèches et humides, OA est toujours positivement corrélée aux périodes sèches à la station de Sherbrooke.The Saint-François River watershed, located on the south shore of the St. Lawrence River (Québec, Canada), covers an area of about 10,000 km2. To detect the climatic factors that influence precipitation in this watershed, we analyzed the succession of dry and wet pluviometric periods by a method of simple moving averages computed over five years. In addition, the relationship between four climatic indices (Arctic Oscillation, Southern Oscillation, North Atlantic Oscillation and Sea Surface Temperature) and these pluviometric periods was analyzed by means of canonical correlation analysis. We analyzed the pluviometric data measured over a 76-year period (1914-1990) at three stations representative of the watershed’s pluviometric regimes: Sherbrooke, Disraeli and Drummondville.Two types of change in the inter-annual variability of precipitation were detected. The first type of change, occuring circa 1950, concernend the distribution of precipitation throughout the watershed, i.e. spatial change. Before 1950, the succession of dry and wet precipitation periods was asynchronous (opposition of periods), but became synchronous after 1950. The second type of change, corresponding to a change in the pluviometric totals at the stations, i.e. quantitative change, was observed circa 1935 and 1970. There was, therefore, a shift from dry to wet periods or vice versa, prior to and following 1935 and 1970, depending on the station. By accounting for these three dates, we observed the succession of the following dry periods and wet periods. First, before 1950 and between 1914 and 1935, we observed a dry period at the Disraeli and Sherbrooke stations and a wet period at the Drummondville station. Between 1936 and 1950, these periods were reversed: wet periods at Disraeli and Sherbrooke but a dry period at Drummondville. Second, after 1950 and between 1951 and 1970, there was a precipitation deficit at all three stations, which, however, moved into a surplus phase after 1970.The canonical correlation analysis of precipitation levels and the climate indices revealed the following significant facts: 1) prior to and following 1950, precipitation was positively correlated to the Arctic Oscillation (AO) indices, but this correlation was weaker after 1950 than before; and 2) with respect to the wet and dry periods, the AO index is still positively correlated with the dry periods at the Sherbrooke station

Port-en-Bessin-Huppain – Le Mont-Castel

Le Mont-Castel est un plateau côtier d’une vingtaine d’hectares qui domine la commune de Port-en-Bessin à une dizaine de kilomètres à l’ouest de la capitale de cité gallo-romaine des Baïocasses Bayeux/Augustodurum. Il s’intègre au fond d’une plaine d’environ 400 ha entourée d’une couronne de reliefs bien marqués sur lesquels au moins deux autres sites fortifiés ont déjà été repérés : le Mont-Cauvin, sur la commune d’Étreham (Bronze final IIIb, prospections aériennes G. Hulin et S. Normant 200..

Port-en-Bessin-Huppain – Le Mont Castel

Depuis trois ans, le site du Mont Castel fait l’objet de fouilles archéologiques programmées à la fin de l’été. Cette année, c’est principalement l’occupation de la fin de l’indépendance gauloise qui a fait l’objet d’un travail de fond. Il est désormais possible de dresser dans ces grandes lignes les modalités d’occupation du site. Nous rappellerons toutefois, avant de présenter l’occupation de La Tène D2b, que le site est fortifié et occupé dès le Bronze final IIIa et fait l’objet durant le ..

Reproducibility of CRISPR-Cas9 methods for generation of conditional mouse alleles: A multi-center evaluation

Background CRISPR-Cas9 gene-editing technology has facilitated the generation of knockout mice, providing an alternative to cumbersome and time-consuming traditional embryonic stem cell-based methods. An earlier study reported up to 16% efficiency in generating conditional knockout (cKO or floxed) alleles by microinjection of 2 single guide RNAs (sgRNA) and 2 single-stranded oligonucleotides as donors (referred herein as “two-donor floxing” method). Results We re-evaluate the two-donor method from a consortium of 20 laboratories across the world. The dataset constitutes 56 genetic loci, 17,887 zygotes, and 1718 live-born mice, of which only 15 (0.87%) mice contain cKO alleles. We subject the dataset to statistical analyses and a machine learning algorithm, which reveals that none of the factors analyzed was predictive for the success of this method. We test some of the newer methods that use one-donor DNA on 18 loci for which the two-donor approach failed to produce cKO alleles. We find that the one-donor methods are 10- to 20-fold more efficient than the two-donor approach. Conclusion We propose that the two-donor method lacks efficiency because it relies on two simultaneous recombination events in cis, an outcome that is dwarfed by pervasive accompanying undesired editing events. The methods that use one-donor DNA are fairly efficient as they rely on only one recombination event, and the probability of correct insertion of the donor cassette without unanticipated mutational events is much higher. Therefore, one-donor methods offer higher efficiencies for the routine generation of cKO animal models.This work was supported by the National Collaborative Research Infrastructure (NCRIS) via the Australian Phenomics Network (APN) (to Gaetan Burgio and Paul Thomas), by an Institutional Development Award (PI: Shelley Smith) P20GM103471 (to CBG, RMQ, DWH, JDE, and RR), by NIGMS 1P30GM110768-01 and P30CA036727 (as part of support to University of Nebraska Mouse Genome Engineering and DNA Sequencing Cores), the British Heart Foundation FS12-57, FS12/57/29717, and CH/13/2/30154 and the program grant RG/15/12/31616 (to Kathryn Hentges and Bernard Keavney), the Wellcome Trust grants 107849/Z/ 15/Z, 097820/Z11/B, and 105610/Z/14/Z, the Medical Research Council MR/ N029992/1 (to DB and CBL), the National BioResource Project of Ministry of Education, Culture, Sports, Science and Technology/Japan Agency for Medical Research and Development (MEXT/AMED), Japan, the Canadian Institutes of Health Research MOP#142452 (MCB and LJM). LJM is a member of the Research Centre of the McGill University Health Centre which is supported in part by FQRS. Dr. William Thompson was supported by the Indiana Clinical and Translational Sciences Institute, funded in part by grant #UL1 TR001108 from the National Institute of Health (NIH), National Center for Advancing Translational Sciences, Clinical and Translational Sciences Award. KC Kent Lloyd is supported by the NIH (UM1OD023221), and work contributed by staff from the UC Davis Mouse Biology Program (MBP) is supported by a grant from the American College of Laboratory Animal Medicine. The work contributed from Xiande Liu, Chad Smith, Eric Jonasch, Xuesong Zhang, and Jan ParkerThornburg is supported by the NIH under the award number P30CA16672 (XL, CS, EJ, XZ, JPT) and R50CA211121 (JPT). Joseph Miano is supported by the NIH under the award number HL138987. R Sedlacek was supported by LM2015040 (Czech Centre for Phenogenomics), CZ.1.05/1.1.00/02.0109 (BIOCEV), and CZ.1.05/2.1.00/19.0395 by the Ministry of Education, Youth and Sports (MEYS) and by Academy of Sciences of the Czech Republic (RVO 68378050). David Ray was supported by a Wellcome Trust Investigator (107849/Z/15/Z) and the Medical Research Council (MR/P011853/1 and MR/P023576/) grants. Andrew Loudon was supported by a Wellcome Trust Investigator (107849/Z/15/Z), Biotechnology and Biological Sciences Research Council (BB/N015584/1), Medical Research Council (MR/P023576/1). The work contributed from Gloria Lopez-Castejon is supported by the Wellcome Trust (104192/Z/14/Z) and the Royal Society. Pilar Alcaide was supported by the NIH (HL 123658). The work contributed from Surinder K. Batra is supported by the NIH under the award number P01 CA217798

Using rare genetic mutations to revisit structural brain asymmetry

Asymmetry between the left and right hemisphere is a key feature of brain organization. Hemispheric functional specialization underlies some of the most advanced human-defining cognitive operations, such as articulated language, perspective taking, or rapid detection of facial cues. Yet, genetic investigations into brain asymmetry have mostly relied on common variants, which typically exert small effects on brain-related phenotypes. Here, we leverage rare genomic deletions and duplications to study how genetic alterations reverberate in human brain and behavior. We designed a pattern-learning approach to dissect the impact of eight high-effect-size copy number variations (CNVs) on brain asymmetry in a multi-site cohort of 552 CNV carriers and 290 non-carriers. Isolated multivariate brain asymmetry patterns spotlighted regions typically thought to subserve lateralized functions, including language, hearing, as well as visual, face and word recognition. Planum temporale asymmetry emerged as especially susceptible to deletions and duplications of specific gene sets. Targeted analysis of common variants through genome-wide association study (GWAS) consolidated partly diverging genetic influences on the right versus left planum temporale structure. In conclusion, our gene-brain-behavior data fusion highlights the consequences of genetically controlled brain lateralization on uniquely human cognitive capacities

Cartography and long term trends (1998-2011) of particulate-bound polycyclic aromatic hydrocarbons (PAHs) in the ambient air of France

In Europe, PAHs are regulated and their ambient air monitoring has been mandatory since 2004 (European Directive 2004/107/CE). As to date, no national cartography has ever been reported for any country and the study of long temporal trends of PAHs is poorly documented in literature. The long term evolution of the contribution of B[a]P to the ambient air PAH mixture has not yet been properly documented in literature even if this compound has been chosen as the marker for the suite of PAH compounds. Based on the data from the statutory monitoring performed by the local air quality network, the objective of this work was to complete a French cartography of atmospheric PAHs and to study their spatial and temporal variations in concentrations and profiles (B[a]P/?7PAHs and B[a]P/PM10). Temporal trends were investigated on selected monitoring sites (monitoring periods > 5 years) factoring in the emission time trends, location and seasonal effect. Results obtained showed that, at a national scale, B[a]P annual mean concentration levels are lower than the European Directive target value of 1 ng m-3. Only industrial sites and some urban sites located in specific regions, characterized by their considerable industrial activity, their relief and/or their geographical location, showed higher annual mean concentrations. The highest contributions of B[a]P/PM10 ratios were observed on industrial sites, and its large seasonal variations observed on urban, suburban and rural locations highlighted the major contribution of residential heating to the toxicity of the PM in winter period. A statistical time-series model was applied to decompose and analyze long term trends. Results obtained showed a significant decrease in PAH concentration levels (- 1 ng m-3 in 10 years) for all the selected sites. Only half of them showed a significant decrease of the contribution of B[a]P on PM. Finally, results showed that the choice of B[a]P as representative of PAH chronicle contamination is questionable. Differences in temporal evolution of the contribution of B[a]P to the mixture of PAH was clearly observed between monitoring sites from different regions. This work was supported by the French Ministry of Ecology, Sustainable Development and Energy (MEDDE) and by the French central laboratory of air quality monitoring (LCSQA)