Componentising a scientific application for the grid

CoreGRID is a Network of Excellence funded by the European Commission under the Sixth Framework Programm

Visualizing mineralization in deformed opercular bones of larval gilthead sea bream (Sparus aurata)

During the rearing process of gilthead sea bream (Sparus aurata), abnormal development of the opercular bone is particularly common (Aquaculture 156, 1997, 165). In order to alleviate its occurrence in rearing facilities, it's crucial to identify the very first physical signs of deviation in normal skeletal development. Nano-CT-scanning was tested for its applicability to quantify deviations in bone mineralization levels. Seven opercles were dissected from larvi of 65 days post hatching, randomly sampled at the commercial sea bream hatchery Maricoltura di Rosignano Solvay (Livorno, Italy). The samples were nano-CT-scanned and computationally reconstructed. Mineralization intensity was colorcoded using Amira software, resulting in a detailed visualization of opercular morphology and mineralization patterns. In conclusion, nano-CT-scanning promises to be a good tool to both describe morphology and detect mineralization levels in the early onset of deformities

Dynamically-Fulfilled Application Constraints through Technical Services - Towards Flexible Component Deployments

We propose in this paper, a mechanism for Grid computing frameworks, for specifying environmental requirements that may set and be optimized by deployers. Specified by designers by parameterizing deployment abstractions, the constraints can be dynamically mapped onto the infrastructure. This work is integrated in the ProActive middleware with the concept of technical services. We illustrate this mechanism with a concrete use case: deploying a component-based application with fault-tolerance on an heterogeneous grid provided by the ProActive Peer-to-Peer infrastructure

Dynamically-Fulfilled Application Constraints through Technical Services - Towards Flexible Component Deployments

We propose in this paper, a mechanism for Grid computing frameworks, for specifying environmental requirements that may set and be optimized by deployers. Specified by designers by parameterizing deployment abstractions, the constraints can be dynamically mapped onto the infrastructure. This work is integrated in the ProActive middleware with the concept of technical services. We illustrate this mechanism with a concrete use case: deploying a component-based application with fault-tolerance on an heterogeneous grid provided by the ProActive Peer-to-Peer infrastructure

Cine and tagged cardiovascular magnetic resonance imaging in normal rat at 1.5 T: a rest and stress study

BACKGROUND: The purpose of this study was to measure regional contractile function in the normal rat using cardiac cine and tagged cardiovascular magnetic resonance (CMR) during incremental low doses of dobutamine and at rest. METHODS: Five rats were investigated for invasive left ventricle pressure measurements and five additional rats were imaged on a clinical 1.5 T MR system using a cine sequence (11-20 phases per cycle, 0.28/0.28/2 mm) and a C-SPAMM tag sequence (18-25 phases per cycle, 0.63/1.79/3 mm, tag spacing 1.25 mm). For each slice, wall thickening (WT) and circumferential strains (CS) were calculated at rest and at stress (2.5, 5 and 10 microg/min/kg of dobutamine). RESULTS: Good cine and tagged images were obtained in all the rats even at higher heart rate (300-440 bpm). Ejection fraction and left ventricular (LV) end-systolic volume showed significant changes after each dobutamine perfusion dose (p < 0.001). Tagged CMR had the capacity to resolve the CS transmural gradient and showed a significant increase of both WT and CS at stress compared to rest. Intra and interobserver study showed less variability for the tagged technique. In rats in which a LV catheter was placed, dobutamine produced a significant increase of heart rate, LV dP/dtmax and LV pressure significantly already at the lowest infusion dose. CONCLUSION: Robust cardiac cine and tagging CMR measurements can be obtained in the rat under incremental dobutamine stress using a clinical 1.5 T MR scanner

Programming, Composing, Deploying for the Grid

Grids raise new challenges in the following way: heterogeneity of underlying machines/networks and runtime environments (types and performance characteristics), not a single administrative domain, versatility. So the need to have appropriate programming and runtime solutions in order to write, deploy then execute applications on such heterogeneous distributed hardware in an effective and efficient manner. We propose in this article a solution to those challenges which takes the form of a programming and deployment framework featuring parallel, mobile, secure and distributed objects and components

Cardiac troponin and skeletal muscle oxygenation in severe post-partum haemorrhage

International audienceIntroductionCardiac troponin has been shown to be elevated in one-half of the parturients admitted for post-partum haemorrhage. The purpose of the study was to assess whether increased cardiac troponin was associated with a simultaneous alteration in haemoglobin tissue oxygen saturation in peripheral muscles in post-partum haemorrhage.MethodsTissue haemoglobin oxygen saturation of thenar eminence muscle (StO2) was measured via near-infrared spectroscopy technology. Two sets of StO2 parameters (both isolated baseline and during forearm ischaemia-reperfusion tests) were collected at two time points: upon intensive care unit admission and prior to intensive care unit discharge. Comparisons were performed using Wilcoxon paired tests, and univariate associations were assessed using logistic regression model and Wald tests.ResultsThe 42 studied parturients, admitted for post-partum haemorrhage, had clinical and biological signs of severe blood loss. Initial cardiac troponin I was increased in 24/42 parturients (0.43 ± 0.60 μrg/l). All measured parameters of muscular haemoglobin oxygen saturation, including Srecovery, were also altered at admission and improved together with improved haemodynamics, when bleeding was controlled. Multivariate analysis showed that muscular Srecovery ConclusionsOur study confirmed the high incidence of increased cardiac troponin, and demonstrated the simultaneous impairment in the reserve of oxygen delivery to peripheral muscles in parturients admitted for severe post-partum haemorrhage

The phenome analysis of mutant alleles in Leucine-Rich Repeat Receptor-Like Kinase genes in rice reveals new potential targets for stress tolerant cereals

AbstractPlants are constantly exposed to a variety of biotic and abiotic stresses that reduce their fitness and performance. At the molecular level, the perception of extracellular stimuli and the subsequent activation of defense responses require a complex interplay of signaling cascades, in which protein phosphorylation plays a central role. Several studies have shown that some members of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) family are involved in stress and developmental pathways. We report here a systematic analysis of the role of the members of this gene family by mutant phenotyping in the monocotyledon model plant rice, Oryza sativa. We have then targeted 176 of the ∼320 LRR-RLK genes (55.7%) and genotyped 288 mutant lines. Position of the insertion was confirmed in 128 lines corresponding to 100 LRR-RLK genes (31.6% of the entire family). All mutant lines harboring homozygous insertions have been screened for phenotypes under normal conditions and under various abiotic stresses. Mutant plants have been observed at several stages of growth, from seedlings in Petri dishes to flowering and grain filling under greenhouse conditions. Our results show that 37 of the LRR-RLK rice genes are potential targets for improvement especially in the generation of abiotic stress tolerant cereals

Oryza Tag Line, a phenotypic mutant database for the Génoplante rice insertion line library

To organize data resulting from the phenotypic characterization of a library of 30 000 T-DNA enhancer trap (ET) insertion lines of rice (Oryza sativa L cv. Nipponbare), we developed the Oryza Tag Line (OTL) database (http://urgi.versailles.inra.fr/OryzaTagLine/). OTL structure facilitates forward genetic search for specific phenotypes, putatively resulting from gene disruption, and/or for GUSA or GFP reporter gene expression patterns, reflecting ET-mediated endogenous gene detection. In the latest version, OTL gathers the detailed morpho-physiological alterations observed during field evaluation and specific screens in a first set of 13 928 lines. Detection of GUS or GFP activity in specific organ/tissues in a subset of the library is also provided. Search in OTL can be achieved through trait ontology category, organ and/or developmental stage, keywords, expression of reporter gene in specific organ/tissue as well as line identification number. OTL now contains the description of 9721 mutant phenotypic traits observed in 2636 lines and 1234 GUS or GFP expression patterns. Each insertion line is documented through a generic passport data including production records, seed stocks and FST information. 8004 and 6101 of the 13 928 lines are characterized by at least one T-DNA and one Tos17 FST, respectively that OTL links to the rice genome browser OryGenesDB