A Three Step Blind Approach for Improving HPC Systems' Energy Performance

International audienceNowadays, there is no doubt that energy consumption has become a limiting factor in the design and operation of high performance computing (HPC) systems. This is evidenced by the rise of efforts both from the academia and the industry to reduce the energy consumption of those systems. Unlike hardware solutions, software initiatives targeting HPC systems' energy consumption reduction despite their effectiveness are often limited for reasons including: (i) the program specific nature of the solution proposed; (ii) the need of deep understanding of applications at hand; (iii) proposed solutions are often difficult to use by novices and/or are designed for single task environments. This paper propose a three step blind system-wide, application independent, fine-grain, and easy to use (user friendly) methodology for improving energy performance of HPC systems. The methodology typically breaks into phase detection, phase characterization, and phase identification and system reconfiguration. And it is blind in the sense that it does not require any knowledge from users. It relies upon reconfigurable capabilities offered by the majority of HPC subsystems -- including the processor, storage, memory, and communication subsystems -- to reduce the overall energy consumption of the system (excluding network equipments) at runtime. We also present an implementation of our methodology through which we demonstrate its effectiveness via static analyses and experiments using benchmarks representative of HPC workloads

Testing for the occurrence of pilchard herpesvirus (PHV) in South African sardine Sardinops sagax

Catches of South African sardine Sardinops sagax have declined in recent years from about 200 000 t harvested annually during the period 2002–2006 to less than 100 000 t. Consequently, some companies are now importing sardine from sources elsewhere in the world to meet local demand for canned sardine and bait. This importation has the potential for the introduction of sardine pathogens, in particular the pilchard herpesvirus (PHV), which could have a negative impact on the currently small South African sardine population. The aims of the current study were to determine whether PHV is present in the local sardine population and to assess the extent to which sardine is being imported into the country and whether imported fish are from countries where the virus is known to be endemic. Fish sampled from South Africa’s western (n = 150), southern (n = 182) and eastern (n = 96) putative stocks of S. sagax were analysed for the presence of PHV using real-time quantitative polymerase chain reaction (qPCR). The origin and amount of potentially infected material imported into South Africa during the period 2010–2014 was also assessed. None of the South African sardine collected during this study tested positive for PHV, suggesting that active PHV was not prevalent in the local population of S. sagax at the time of this study. Between 56 000 and 71 000 t of frozen sardine was imported annually into South Africa from countries where S. sagax occurs, including some from areas (Australia and New Zealand) where sardine infection by PHV is known to be endemic. Hence, it is plausible that the PHV pathogen, capable of perpetuating infections in local sardine populations, could be imported into South Africa along with the importation of frozen sardine. Should local sardine be naïve to the virus, as suggested by this study, then the population is at risk of infection and precautions against such must be taken.DHE

Genes Suggest Ancestral Colour Polymorphisms Are Shared across Morphologically Cryptic Species in Arctic Bumblebees

email Suzanne orcd idCopyright: © 2015 Williams et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Prevalence and gender distribution of the metabolic syndrome

<p>Abstract</p> <p>Background</p> <p>The Metabolic syndrome (MetS) is a cardiovascular risk factor of public health significance and of recent has become a topical issue. The prevalence of diabetes mellitus (DM) is on the increase and with this scenario, a possible increase in burden of DM which may be largely attributed to cardiovascular complications is expected. The objective of this report is to determine the prevalence of the MetS and compare gender characteristics in subjects with type 2 DM.</p> <p>Methods</p> <p>Subjects with type 2 DM were recruited from an urban hospital for the study. Clinical data was obtained by interviewing the patients and referring to their Case folders. The anthropometric indices and blood pressure measurements were documented. Laboratory parameters analysed for included total cholesterol, high density and low density cholesterol, triglyceride and glycosylated haemoglobin. Statistical analysis included usage of Student's t test and chi square.</p> <p>Results</p> <p>963 patients with type 2 DM aged between 35-85 years were recruited for the study. The main outcome measures included the prevalence of the metabolic syndrome and the gender differences of its components. The prevalence of the metabolic syndrome was 86%. The frequency of occurrence of the MetS was similar for men (83%) and women (86%) and increased with age in both sexes. The prevalence of MetS increased from 11% among participants aged 20 through 29 years to 89% in participants aged 70 through 79. In our patients with DM, the commonest occurring and least detected MetS defining parameters are central obesity and elevated triglyceride levels respectively. The components of the MetS that differed significantly in both sexes was HDL-C. The combination of the components of the MetS were comparable in both genders and 5.8% of the subjects with the MetS had all components of the MetS.</p> <p>Conclusion</p> <p>The prevalence of the MetS in type 2DM is high in both genders and increases with age thus posing a potential high cardiovascular risk in this group of patients. The modifiable risk factors for the MetS should be a focus point in the management of subjects with type 2 DM,</p

Control of intestinal stem cell function and proliferation by mitochondrial pyruvate metabolism.

Most differentiated cells convert glucose to pyruvate in the cytosol through glycolysis, followed by pyruvate oxidation in the mitochondria. These processes are linked by the mitochondrial pyruvate carrier (MPC), which is required for efficient mitochondrial pyruvate uptake. In contrast, proliferative cells, including many cancer and stem cells, perform glycolysis robustly but limit fractional mitochondrial pyruvate oxidation. We sought to understand the role this transition from glycolysis to pyruvate oxidation plays in stem cell maintenance and differentiation. Loss of the MPC in Lgr5-EGFP-positive stem cells, or treatment of intestinal organoids with an MPC inhibitor, increases proliferation and expands the stem cell compartment. Similarly, genetic deletion of the MPC in Drosophila intestinal stem cells also increases proliferation, whereas MPC overexpression suppresses stem cell proliferation. These data demonstrate that limiting mitochondrial pyruvate metabolism is necessary and sufficient to maintain the proliferation of intestinal stem cells

Quantifying and filtering knowledge generated by literature based discovery

Background Literature based discovery (LBD) automatically infers missed connections between concepts in literature. It is often assumed that LBD generates more information than can be reasonably examined. Methods We present a detailed analysis of the quantity of hidden knowledge produced by an LBD system and the effect of various filtering approaches upon this. The investigation of filtering combined with single or multi-step linking term chains is carried out on all articles in PubMed. Results The evaluation is carried out using both replication of existing discoveries, which provides justification for multi-step linking chain knowledge in specific cases, and using timeslicing, which gives a large scale measure of performance. Conclusions While the quantity of hidden knowledge generated by LBD can be vast, we demonstrate that (a) intelligent filtering can greatly reduce the number of hidden knowledge pairs generated, (b) for a specific term, the number of single step connections can be manageable, and (c) in the absence of single step hidden links, considering multiple steps can provide valid links

Xanthine oxidase inhibition and white matter hyperintensity progression following ischaemic stroke and transient ischaemic attack (XILO-FIST): a multicentre, double-blinded, randomised, placebo-controlled trial

BACKGROUND: People who experience an ischaemic stroke are at risk of recurrent vascular events, progression of cerebrovascular disease, and cognitive decline. We assessed whether allopurinol, a xanthine oxidase inhibitor, reduced white matter hyperintensity (WMH) progression and blood pressure (BP) following ischaemic stroke or transient ischaemic attack (TIA). METHODS: In this multicentre, prospective, randomised, double-blinded, placebo-controlled trial conducted in 22 stroke units in the United Kingdom, we randomly assigned participants within 30-days of ischaemic stroke or TIA to receive oral allopurinol 300 mg twice daily or placebo for 104 weeks. All participants had brain MRI performed at baseline and week 104 and ambulatory blood pressure monitoring at baseline, week 4 and week 104. The primary outcome was the WMH Rotterdam Progression Score (RPS) at week 104. Analyses were by intention to treat. Participants who received at least one dose of allopurinol or placebo were included in the safety analysis. This trial is registered with ClinicalTrials.gov, NCT02122718. FINDINGS: Between 25th May 2015 and the 29th November 2018, 464 participants were enrolled (232 per group). A total of 372 (189 with placebo and 183 with allopurinol) attended for week 104 MRI and were included in analysis of the primary outcome. The RPS at week 104 was 1.3 (SD 1.8) with allopurinol and 1.5 (SD 1.9) with placebo (between group difference −0.17, 95% CI −0.52 to 0.17, p = 0.33). Serious adverse events were reported in 73 (32%) participants with allopurinol and in 64 (28%) with placebo. There was one potentially treatment related death in the allopurinol group. INTERPRETATION: Allopurinol use did not reduce WMH progression in people with recent ischaemic stroke or TIA and is unlikely to reduce the risk of stroke in unselected people. FUNDING: The British Heart Foundation and the UK Stroke Association

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

Jet energy measurement with the ATLAS detector in proton-proton collisions at root s=7 TeV

The jet energy scale and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of √s = 7TeV corresponding to an integrated luminosity of 38 pb-1. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0. 4 or R=0. 6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pT≥20 GeV and pseudorapidities {pipe}η{pipe}<4. 5. The jet energy systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams, exploiting the transverse momentum balance between central and forward jets in events with dijet topologies and studying systematic variations in Monte Carlo simulations. The jet energy uncertainty is less than 2. 5 % in the central calorimeter region ({pipe}η{pipe}<0. 8) for jets with 60≤pT<800 GeV, and is maximally 14 % for pT<30 GeV in the most forward region 3. 2≤{pipe}η{pipe}<4. 5. The jet energy is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pT, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pT jets recoiling against a high-pT jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, aiming for an improved jet energy resolution and a reduced flavour dependence of the jet response. The systematic uncertainty of the jet energy determined from a combination of in situ techniques is consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pT jets. Special cases such as event topologies with close-by jets, or selections of samples with an enhanced content of jets originating from light quarks, heavy quarks or gluons are also discussed and the corresponding uncertainties are determined. © 2013 CERN for the benefit of the ATLAS collaboration