Using Pilot Systems to Execute Many Task Workloads on Supercomputers

High performance computing systems have historically been designed to support applications comprised of mostly monolithic, single-job workloads. Pilot systems decouple workload specification, resource selection, and task execution via job placeholders and late-binding. Pilot systems help to satisfy the resource requirements of workloads comprised of multiple tasks. RADICAL-Pilot (RP) is a modular and extensible Python-based pilot system. In this paper we describe RP's design, architecture and implementation, and characterize its performance. RP is capable of spawning more than 100 tasks/second and supports the steady-state execution of up to 16K concurrent tasks. RP can be used stand-alone, as well as integrated with other application-level tools as a runtime system

Effects of extracurricular activities on postsecondary completion for students withdisabilities

This study focuses on participation in extracurricular activities as a way of improving the educational outcomes of children with disabilities. In regard to students in the general population, adolescent involvement in extracurricular activities have been shown to have a positive association with school involvement and adolescent self-esteem, academic achievement, and adolescent development. Using the Educational Longitudinal Study (ELS) dataset, this study conducts logistic regression analyses to examine the relationship between participation in high school-sponsored extracurricular activities and postsecondary degree completion for students with disabilities. Findings show a statistically significant association between postsecondary degree completion for students with disabilities and extracurricular activity participation, including extent and type of extracurricular activity. Students with disabilities who participate in high school extracurricular activities may have increased likelihood of completing a postsecondary degree. Implications for policy, practice, and future research are discussed. [This is a post-print of an article published by Taylor & Francis in The Journal of Educational Research on August 19, 2016, available online: https://doi.org/10.1080/00220671.2015.1058221

Navigator utilization among African-American Breast cancer patients at a Comprehensive Cancer Center

Background: Patient navigation has been demonstrated to improve access to standard-of-care oncologic therapy. However, many patients — particularly those of African-American race — often do not have access to navigation upon receiving a diagnosis of cancer. As the most common cancer among African-American women is breast cancer, we sought to assess the rate of patient navigation among African-American breast cancer patients at our institution, which resides in a regional ZIP code comprised of 46% African-American residents. Materials and methods: African-American breast cancer patients who had been discussed at our weekly breast cancer multidisciplinary tumor board over a recent three-month period were assessed by a patient navigator representing the Navigator-Assisted Hypofractionation (NAVAH) program to determine their access to navigation in their cancer care. Responses were assessed from a breast cancer support group and culled to determine a baseline proportion of navigation utilization. Results: A total of 18 women of African-American race having been diagnosed with breast cancer were identified and assessed. Of these a total of 4 noted that they had received navigation, yielding a navigation utilization percentage of 22.2% among African-American breast cancer patients at our institution. Conclusion: The rate of navigation utilization among African-American breast cancer patients is poor. Despite our center residing in a region comprised of increased African-Americans, such predominance has not translated into optimizing navigation access for African-American breast cancer patients. This 22% rate of navigation utilization serves as a starting benchmark for initiatives such as the NAVAH program to provide tangible improvement in this patient population

Online Content : Physical and Structural Techniques Applied to Nucleic Acids

This chapter looks at the physical and structural techniques that can be applied to nucleic acids. The first few sections focus on spectroscopic techniques, nuclear magnetic resonance, mass spectrometry and diffraction techniques. The following sections explore cryogenic electron microscopy, optical microscopy, atomic force microscopy and electrophoresis. Chromatographic methods, centrifugation and light scattering techniques are also discussed. Finally, the chapter concludes with sections on thermodynamic analysis, molecular mechanics and dynamics, and QM/MM methods for modelling nucleic acids reactions

Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology

The rates of intramolecular proton transfer are calculated on a full-dimensional reactive electronic potential energy surface that incorporates high-level ab initio calculations along the reaction path and by using classical transition state theory, path-integral quantum transition state theory, and the quantum instanton approach. The specific example problem studied is malonaldehyde. Estimates of the kinetic isotope effect using the latter two methods are found to be in reasonable agreement with each other. Improvements and extensions of this practical, yet chemically accurate framework for the calculations of quantized, reactive dynamics are also discussed

Navigator-assisted hypofractionation (NAVAH) to address radiation therapy access disparities facing African-Americans with breast cancer

Background: African-Americans have the highest overall cancer death rate and shortest survival time of any racial or ethnic group in the United States. The most common cancer studied in African-American radiation therapy (RT) access disparities research is breast cancer. The goal of this study is to evaluate the impact of patient navigation on RT access for African-American breast cancer patients. Material and methods: This study is a prospective survey-based evaluation of the impact of patient navigation on access to hypofractionated RT and financial toxicity in African-American breast cancer patients. The impact of patient navigation on RT access will be collated and analyzed from survey results pre-RT versus post-RT as well as for patients with versus without receipt of patient navigation. The validated COST-Functional Assessment of Chronic Illness Therapy score will be used to compare hypofractionation versus standard fractionated RT financial toxicity for patients with early-stage breast cancer who have received lumpectomy. Discussion: This is the first study to investigate the impact of patient navigation on reducing RT access disparities facing African-American breast cancer patients. The natural progression of this work will be to expand this model to include additional breast cancer populations most vulnerable to suffering RT access disparities (Native American, Hispanic American, Appalachian) within the United States

Sequence-dependent DNA deformability studied using molecular dynamics simulations

Proteins recognize specific DNA sequences not only through direct contact between amino acids and bases, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetrameric sequences sandwiched between CGCG sequences. The deformability of dimeric steps obtained by the simulations is consistent with that by the crystal structures. The simulation results further showed that the conformation and deformability of the tetramers can highly depend on the flanking base pairs. The conformations of xATx tetramers show the most rigidity and are not affected by the flanking base pairs and the xYRx show by contrast the greatest flexibility and change their conformations depending on the base pairs at both ends, suggesting tetramers with the same central dimer can show different deformabilities. These results suggest that analysis of dimeric steps alone may overlook some conformational features of DNA and provide insight into the mechanism of indirect readout during protein–DNA recognition. Moreover, the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of protein–DNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids

How Thioredoxin Dissociates Its Mixed Disulfide

The dissociation mechanism of the thioredoxin (Trx) mixed disulfide complexes is unknown and has been debated for more than twenty years. Specifically, opposing arguments for the activation of the nucleophilic cysteine as a thiolate during the dissociation of the complex have been put forward. As a key model, the complex between Trx and its endogenous substrate, arsenate reductase (ArsC), was used. In this structure, a Cys29Trx-Cys89ArsC intermediate disulfide is formed by the nucleophilic attack of Cys29Trx on the exposed Cys82ArsC-Cys89ArsC in oxidized ArsC. With theoretical reactivity analysis, molecular dynamics simulations, and biochemical complex formation experiments with Cys-mutants, Trx mixed disulfide dissociation was studied. We observed that the conformational changes around the intermediate disulfide bring Cys32Trx in contact with Cys29Trx. Cys32Trx is activated for its nucleophilic attack by hydrogen bonds, and Cys32Trx is found to be more reactive than Cys82ArsC. Additionally, Cys32Trx directs its nucleophilic attack on the more susceptible Cys29Trx and not on Cys89ArsC. This multidisciplinary approach provides fresh insights into a universal thiol/disulfide exchange reaction mechanism that results in reduced substrate and oxidized Trx