270 research outputs found
The HARNESS Workbench: Unified and Adaptive Access to Diverse HPC Platforms
The primary goal of the Harness WorkBench (HWB) project is to investigate innovative software environments that will help enhance the overall productivity of applications science on diverse HPC platforms. Two complementary frameworks were designed: one, a virtualized command toolkit for application building, deployment, and execution, that provides a common view across diverse HPC systems, in particular the DOE leadership computing platforms (Cray, IBM, SGI, and clusters); and two, a unified runtime environment that consolidates access to runtime services via an adaptive framework for execution-time and post processing activities. A prototype of the first was developed based on the concept of a 'system-call virtual machine' (SCVM), to enhance portability of the HPC application deployment process across heterogeneous high-end machines. The SCVM approach to portable builds is based on the insertion of toolkit-interpretable directives into original application build scripts. Modifications resulting from these directives preserve the semantics of the original build instruction flow. The execution of the build script is controlled by our toolkit that intercepts build script commands in a manner transparent to the end-user. We have applied this approach to a scientific production code (Gamess-US) on the Cray-XT5 machine. The second facet, termed Unibus, aims to facilitate provisioning and aggregation of multifaceted resources from resource providers and end-users perspectives. To achieve that, Unibus proposes a Capability Model and mediators (resource drivers) to virtualize access to diverse resources, and soft and successive conditioning to enable automatic and user-transparent resource provisioning. A proof of concept implementation has demonstrated the viability of this approach on high end machines, grid systems and computing clouds
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Cooperative fault-tolerant distributed computing U.S. Department of Energy Grant DE-FG02-02ER25537 Final Report
The Harness project has developed novel software frameworks for the execution of high-end simulations in a fault-tolerant manner on distributed resources. The H2O subsystem comprises the kernel of the Harness framework, and controls the key functions of resource management across multiple administrative domains, especially issues of access and allocation. It is based on a “pluggable” architecture that enables the aggregated use of distributed heterogeneous resources for high performance computing. The major contributions of the Harness II project result in significantly enhancing the overall computational productivity of high-end scientific applications by enabling robust, failure-resilient computations on cooperatively pooled resource collections
2014 Epilepsy Benchmarks Area III: Improve Treatment Options for Controlling Seizures and Epilepsy-Related Conditions Without Side Effects
The Epilepsy Benchmark goals in Area III focus on making progress in understanding and controlling seizures and related conditions as well as on developing biomarkers and new therapies that will reduce seizures and improve outcomes for individuals with epilepsy. Area III emphasizes a need to better understand the ways in which seizures start, propagate, and terminate and whether those network processes are common or unique in different forms of epilepsy. The application of that knowledge to improved seizure prediction and detection will also play a role in improving patient outcomes. Animal models of treatment-resistant epilepsy that are aligned with etiologies and clinical features of human epilepsies are especially encouraged as necessary tools to understand mechanisms and test potential therapies. Antiseizure therapies that target (either alone or in combination) novel or multiple seizure mechanisms are prioritized in this section of the Benchmarks. Area III goals also highlight validation of biomarkers of treatment response and safety risk, effective self-management, and patient-centered outcome measures as important areas of emphasis for the next five to ten years
Rebuilding the Post-Pandemic Economy
After suffering the worst economic shock since the Great Depression, the American economy is recovering in fits and starts. While many businesses are reopening their doors and thriving, continued uncertainty about the course of the virus, the inflation outlook, labor shortages, and many other factors are hampering a full return to normal activity. The COVID-19 pandemic reinforced and exacerbated many of the biggest structural economic challenges in our society. It precipitated the largest economic relief and stimulus spending in US history and transformed the way that millions of Americans live and work, with automation, e-commerce, and telework all playing a bigger role.The policy volume Rebuilding the Post Pandemic Economy examines important questions about how the post-pandemic economy will take shape. What are some initial lessons we can take away from the novel government programs that were deployed to provide economic relief and stimulus? How can we implement new infrastructure investments to maximize efficiency and equity, and best respond to the climate crisis? After a year of widespread school closures, what have we learned about the role of K-12 education in perpetuating or reducing social and economic inequities? And how should American trade policies evolve to promote economic recovery and strengthen America's role in the global economy
Case Series of Fertility Treatment in HIV-Discordant Couples (Male Positive, Female Negative): The Ontario Experience
The success of combination antiretroviral therapies for the treatment of human immunodeficiency virus (HIV) has resulted in prolonged life expectancy (over 40 years from diagnosis) and an improved quality of life for people living with HIV. The risk of vertical HIV transmission during pregnancy has been reduced to less than 1%. As a result of these breakthroughs and as many of these individuals are of reproductive age, fertility issues are becoming increasingly important for this population. One population in which conception planning and reduction of horizontal HIV transmission warrants further research is HIV-discordant couples where the male partner is HIV-positive and the female partner is HIV-negative. Sperm washing is a technique carried out in a fertility clinic that separates HIV from the seminal fluid. Although sperm washing followed by intrauterine insemination significantly reduces the risk of horizontal HIV transmission, there has been limited access to the procedure in North America. Furthermore, little is known about the conception decision-making experiences of HIV-discordant couples who might benefit from sperm washing. Chart reviews and semi-structured interviews were completed with 12 HIV-discordant couples in Ontario, Canada. Couples were recruited through HIV clinics and one fertility clinic that offered sperm washing. Participants identified a number of factors that affected their decision-making around pregnancy planning. Access to sperm washing and other fertility services was an issue (cost, travel and few clinics). Participants identified a lack of information on the procedure (availability, safety). Sources of support (social networks, healthcare providers) were unevenly distributed, especially among those who did not disclose their HIV status to friends and family. Finally, the stigmatisation of HIV continues to have a negative affect on HIV-discordant couples and their intentions to conceive. Access to sperm washing and fertility service is significantly limited for this population and is accompanied with a number of challenges
Sperm midpiece apoptotic markers: impact on fertilizing potential in in vitro fertilization and intracytoplasmic sperm injection
Sociodemographic differences in linkage error: An examination of four large-scale datasets
© 2018 The Author(s). Background: Record linkage is an important tool for epidemiologists and health planners. Record linkage studies will generally contain some level of residual record linkage error, where individual records are either incorrectly marked as belonging to the same individual, or incorrectly marked as belonging to separate individuals. A key question is whether errors in linkage quality are distributed evenly throughout the population, or whether certain subgroups will exhibit higher rates of error. Previous investigations of this issue have typically compared linked and un-linked records, which can conflate bias caused by record linkage error, with bias caused by missing records (data capture errors). Methods: Four large administrative datasets were individually de-duplicated, with results compared to an available 'gold-standard' benchmark, allowing us to avoid methodological issues with comparing linked and un-linked records. Results were compared by gender, age, geographic remoteness (major cities, regional or remote) and socioeconomic status. Results: Results varied between datasets, and by sociodemographic characteristic. The most consistent findings were worse linkage quality for younger individuals (seen in all four datasets) and worse linkage quality for those living in remote areas (seen in three of four datasets). The linkage quality within sociodemographic categories varied between datasets, with the associations with linkage error reversed across different datasets due to quirks of the specific data collection mechanisms and data sharing practices. Conclusions: These results suggest caution should be taken both when linking younger individuals and those in remote areas, and when analysing linked data from these subgroups. Further research is required to determine the ramifications of worse linkage quality in these subpopulations on research outcomes
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