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

Performance and Scalability of a Component-Based Grid Application

Component-based development has emerged as an effective approach to building flexible systems, but there is little experience in applying this approach to Grid programming. This paper presents our experience with reengineering a high performance numerical solver to become a component-based Grid application. The adopted component model is an extension of the generic Fractal model that specifically targets grid environments. The paper provides qualitative and quantitative evidence that componentisation has improved the modifiability and reusability of the application while not significantly affecting performance. 1

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

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

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

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