VtkSMP: Task-based Parallel Operators for VTK Filters

International audienceNUMA nodes are potentially powerful but taking benefit of their capabilities is challenging due to their architec- ture (multiple computing cores, advanced memory hierarchy). They are nonetheless one of the key components to enable processing the ever growing amount of data produced by scientific simulations. In this paper we study the parallelization of patterns commonly used in VTK algorithms and propose a new multi- threaded plugin for VTK that eases the development of parallel multi-core VTK filters. We specifically focus on task-based approaches and show that with a limited code refactoring effort we can take advantage of NUMA node capabilities. We experiment our patterns on a transform filter, base isosurface extraction filter and a min/max tree accelerated isosurface extraction. We support 3 programming environments, OpenMP, Intel TBB and X-KAAPI, and propose different algorithmic refinements according to the capabilities of the target environment. Results show that we can speed execution up to 30 times on a 48-core machine

VtkSMP: Task-based Parallel Operators for Accelerating VTK Filters

NUMA nodes are potentially powerful but taking benefit of their capabilities is challenging due to their architecture (multiple computing cores, advanced memory hierarchy). They are nonetheless one of the key components to enable processing the ever growing amount of data produced by scientific simulations.In this paper we study the parallelization of patterns commonly used in VTK algorithms and propose a new multi-threaded plugin for VTK that eases the development of parallel multi-core VTK filters. We specifically focus on task-based approaches and show that with a limited code refactoring effort we can take advantage of NUMA node capabilities. We experiment our patterns on a transform filter, base isosurface extraction filter and a min/max tree accelerated isosurface extraction. We support 3 programming environ- ments, OpenMP, Intel TBB and X-KAAPI, and propose different algorithmic refinements according to the capabilities of the target environment. Results show that we can speed execution up to 30 times on a 48-core machine.Les architectures NUMA multicœurs sont potentiellement très puissantes, mais les exploiter pleinement reste difficile étant donné leur complexité (grand nombre de cœurs, hiérarchie mémoire profonde). Un usage efficace des ces ressources est cependant impératif pour pouvoir traiter la masse toujours plus importante de données produites par les simulations numériques.Dans ce papier, nous étudions les différentes environnements de parallélisation qui ont été développés en visualisation scientifique, et tout particulièrement autour de la plateforme VTK. En complément des solutions existantes nous proposons une approche s’appuyant sur la programmation par tâches et le mécanisme d’équilibrage de charge par vol de tâches pour la parallélisation de filtres VTK. Nous expérimentons plusieurs schémas sur les filtres de transformation locale, d’extraction d’iso-surface directe et d’une version optimisée reposant sur une structure accélératrice arborescente de type min/max. Nous évaluons les performances avec 3 environnements, OpenMP, Intel TBB et X-KAAPI. Les résultats mon- trent que l’on peut obtenir des accélérations significatives sur une machine à 48 cœurs

Right-hemispheric brain activation correlates to language performance

Language function in the right-hemispheric homologues of Brocas and Wernickes areas does not only correlate with left-handedness or pathology, but occurs naturally in right-handed healthy subjects as well. In the current study, two non-invasive methods of assessing language lateralization are correlated with behavioral results in order to link hemispheric dominance to language ability in healthy subjects. Functional magnetic resonance imaging (fMRI) together with a sentence-completion paradigm was used to determine region-specific lateralization indices in the left- and right-sided Brocas and Wernickes areas, the frontal temporal lobe, the anterior cingulate cortex and the parietal lobe. In addition, dichotic listening results were used to determine overall language lateralization and to strengthen conclusions by correlating with fMRI indices. Results showed that fMRI lateralization in the superior parietal, the posterior temporal, and the anterior cingulate cortices correlated to dichotic listening. A decreased right ear advantage (REA), which indicates less left- hemispheric dominance in language, correlated with higher performance in most administered language tasks, including reading, language ability, fluency, and non-word discrimination. Furthermore, right hemispheric involvement in the posterior temporal lobe and the homologue of Brocas area suggests better performance in behavioral language tasks. This strongly indicates a supportive role of the right-hemispheric counterparts of Brocas and Wernickes areas in language performance.Original Publication: Helene M van Ettinger-Veenstra, Mattias Ragnehed, Mathias Hällgren, Thomas Karlsson, Anne-Marie Landtblom, Peter Lundberg and Maria Engström, Right-hemispheric brain activation correlates to language performance, 2010, NEUROIMAGE, (49), 4, 3481-3488. http://dx.doi.org/10.1016/j.neuroimage.2009.10.041 Copyright: Elsevier Science B.V., Amsterdam http://www.elsevier.com

Sodium nitroprusside-induced osteoblast apoptosis is mediated by long chain ceramide and is decreased by raloxifene.

Release of high levels of nitric oxide (NO) is associated with osteoblastic cell death. The mechanisms of NO-induced cytotoxicity are not well documented and it is presently not known if estrogenic compounds prevent this effect. We studied the role of ceramides in cell death induced by the NO donor sodium nitroprusside (SNP) and we tested the possibility that 17beta-estradiol, the anti-estrogen ICI 182.780 and two selective estrogen receptor modulators raloxifene and tamoxifen modify osteoblastic cell apoptosis. SNP dose-dependently decreased MC3T3-E1 osteoblast viability, increased NO production in the culture media and enhanced the release of intracellular ceramides C22 and C24. Cell death induced by SNP was partially inhibited when MC3T3-E1 cells were pretreated with raloxifene and tamoxifen but was not modified when the cells were pretreated with 17beta-estradiol or ICI 182.780. Cell death induced by SNP resulted from apoptosis as demonstrated by Annexin-V and propidium iodide labeling and a reduction of SNP-induced MC3T3-E1 apoptosis was confirmed in the presence of raloxifene and tamoxifen. SNP induction of C22 and C24 production was inhibited by a pretreatment with raloxifene but not with 17beta-estradiol. Moreover, the synthetic ceramide C24 (0.75 and 1microM) decreased MC3T3-E1 cell viability and osteoblast cell death induced by C24 was partially decreased by raloxifene and to a lesser extent by 17beta-estradiol. These data demonstrate that SNP-induced cell death is mediated by the long chain ceramides C22 and C24 and that raloxifene protected osteoblast from apoptosis induced by SNP, an effect that might be relevant to its pharmacological properties on bone remodeling

Multiple Synchronous Outbreaks of Puumala Virus, Germany, 2010

To investigate 2,017 cases of hantavirus disease in Germany, we compared 38 new patient-derived Puumala virus RNA sequences identified in 2010 with bank vole–derived small segment RNA sequences. The epidemic process was driven by outbreaks of 6 Puumala virus clades comprising strains of human and vole origin. Each clade corresponded to a different outbreak region