51 research outputs found
Portage de StarPU sur la bibliothĂšque de communication NewMadeleine
National audienceDe nombreux calculs sont complexe a parallĂ©liser. De plus les structures des machines sont de plus en plus hĂ©tĂ©rogĂšnes, avec la prĂ©sence d'accĂ©lĂ©rateurs (GPU, ...). Un ordonnanceur de tache comme StarPU permet de rĂ©partir efficacement les calculs a lâintĂ©rieur d'un nĆud. Son module StarPU-MPI permet dâĂ©tendre cette rĂ©partition sur plusieurs nĆuds, en Ă©changeant les donnĂ©es nĂ©cessaires avec la librairie de communication MPI.Cependant de nombreuses implĂ©mentions de MPI manquent d'efficacitĂ© pour un grand nombre de requĂȘtes en attente.Notre port de StarPU-MPI sous NewMadeleine permet de rĂ©soudre ce problĂšme, et d'amĂ©liorer le recouvrement (effectuer du calcul durant les communication) des communications
Analyse de lâinfluence de lâoscillation Arctique sur la variabilitĂ© interannuelle des prĂ©cipitations dans le bassin versant de la riviĂšre Saint-François (QuĂ©bec, Canada) au moyen de la mĂ©thode des corrĂ©lations canoniques
Le bassin versant de la riviĂšre Saint-François, situĂ© sur la rive sud (rive droite) du fleuve Saint-Laurent (QuĂ©bec, Canada), couvre une superficie dâenviron 10 000 km2. Dans le but de dĂ©celer les facteurs climatiques qui influencent les prĂ©cipitations dans ce bassin versant, nous avons analysĂ© la succession des pĂ©riodes pluviomĂ©triques sĂšches et humides par la technique des moyennes glissantes sur cinq ans, dâune part, et la relation entre quatre indices climatiques (oscillation arctique, oscillation australe, oscillation nord-atlantique et la tempĂ©rature des eaux ocĂ©aniques de surface) et ces pĂ©riodes pluviomĂ©triques au moyen de lâanalyse des corrĂ©lations canoniques, dâautre part. Nous avons analysĂ© les donnĂ©es pluviomĂ©triques mesurĂ©es Ă trois stations reprĂ©sentatives des rĂ©gimes pluviomĂ©triques du bassin versant : Sherbrooke, Disraeli et Drummondville. Ces donnĂ©es couvrent une pĂ©riode de 76 ans (1914-1990).En ce qui concerne la variabilitĂ© interannuelle des prĂ©cipitations, nous avons dĂ©tectĂ© deux types de changement. Le premier type de changement, survenu autour de 1950, concerne la rĂ©partition des prĂ©cipitations Ă lâĂ©chelle du bassin versant (changement spatial). Avant 1950, la succession des pĂ©riodes sĂšches et humides des prĂ©cipitations nâĂ©tait pas synchrone (opposition des pĂ©riodes) mais elle lâest devenue aprĂšs 1950. Le second type de changement a Ă©tĂ© observĂ© autour des annĂ©es 1935 et 1970. Il correspond Ă un changement des totaux pluviomĂ©triques au niveau des stations (changement quantitatif). Avant et aprĂšs 1935 et 1970, on passe ainsi des pĂ©riodes sĂšches aux pĂ©riodes humides ou vice versa selon les stations. En tenant compte de ces trois dates, nous avons observĂ© la succession des pĂ©riodes sĂšches et humides suivantes : 1) Avant 1950, entre 1914 et 1935, nous avons observĂ© une pĂ©riode sĂšche aux stations de Disraeli et de Sherbrooke mais une pĂ©riode humide Ă la station de Drummondville. Entre 1936-1950, ces pĂ©riodes se sont inversĂ©es : humide Ă Disraeli et Sherbrooke mais sĂšche Ă Drummondville; 2) AprĂšs 1950, entre 1951 et 1970, les prĂ©cipitations Ă©taient dĂ©ficitaires aux trois stations. En revanche, elles sont devenues excĂ©dentaires aprĂšs 1970.Lâanalyse des corrĂ©lations canoniques entre les prĂ©cipitations et les indices climatiques a rĂ©vĂ©lĂ© les faits significatifs suivants : 1) Avant et aprĂšs 1950, les prĂ©cipitations sont positivement corrĂ©lĂ©es Ă lâoscillation arctique (OA), mais cette corrĂ©lation est plus faible aprĂšs quâavant 1950. Ainsi, lâaugmentation des valeurs de OA entraĂźnerait une hausse de frĂ©quence des masses dâair en provenant du sud dans le bassin versant; 2) Lorsquâon considĂšre les pĂ©riodes sĂšches et humides, OA est toujours positivement corrĂ©lĂ©e aux pĂ©riodes sĂšches Ă la station de Sherbrooke.The Saint-François River watershed, located on the south shore of the St. Lawrence River (QuĂ©bec, 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 watershedâs 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
Datation par la méthode U/Th d'un travertin quaternaire du Sud-Est marocain : implications paléoclimatiques pendant le PléistocÚne moyen et supérieur
RĂ©ponse au commentaire de Brahim Akdim et RamĂłn Julia sur la note <i>Datation par la mĂ©thode U/Th d'un travertin quaternaire du Sud-Est marocain : implications palĂ©oclimatiques pendant le PlĂ©istocĂšne moyen et supĂ©rieur</i> [C. R. Geoscience 335 (2003) 469â478]
Port-en-Bessin-Huppain â Le Mont-Castel
Le Mont-Castel est un plateau cĂŽtier dâune vingtaine dâhectares qui domine la commune de Port-en-Bessin Ă une dizaine de kilomĂštres Ă lâouest de la capitale de citĂ© gallo-romaine des BaĂŻocasses Bayeux/Augustodurum. Il sâintĂšgre au fond dâune plaine dâenviron 400 ha entourĂ©e dâune couronne de reliefs bien marquĂ©s sur lesquels au moins deux autres sites fortifiĂ©s ont dĂ©jĂ Ă©tĂ© repĂ©rĂ©s : le Mont-Cauvin, sur la commune dâĂtreham (Bronze final IIIb, prospections aĂ©riennes G. Hulin et S. Normant 200..
Port-en-Bessin-Huppain â Le Mont Castel
Depuis trois ans, le site du Mont Castel fait lâobjet de fouilles archĂ©ologiques programmĂ©es Ă la fin de lâĂ©tĂ©. Cette annĂ©e, câest principalement lâoccupation de la fin de lâindĂ©pendance gauloise qui a fait lâobjet dâun travail de fond. Il est dĂ©sormais possible de dresser dans ces grandes lignes les modalitĂ©s dâoccupation du site. Nous rappellerons toutefois, avant de prĂ©senter lâoccupation de La TĂšne D2b, que le site est fortifiĂ© et occupĂ© dĂšs le Bronze final IIIa et fait lâobjet 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 âtwo-donor floxingâ 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
Response to correspondence on Reproducibility of CRISPR-Cas9 Methods for Generation of Conditional Mouse Alleles: A Multi-Center Evaluation
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)
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