Developing High Performance Computing Resources for Teaching Cluster and Grid Computing courses

High-Performance Computing (HPC) and the ability to process large amounts of data are of paramount importance for UK business and economy as outlined by Rt Hon David Willetts MP at the HPC and Big Data conference in February 2014. However there is a shortage of skills and available training in HPC to prepare and expand the workforce for the HPC and Big Data research and development. Currently, HPC skills are acquired mainly by students and staff taking part in HPC-related research projects, MSc courses, and at the dedicated training centres such as Edinburgh University’s EPCC. There are few UK universities teaching the HPC, Clusters and Grid Computing courses at the undergraduate level. To address the issue of skills shortages in the HPC it is essential to provide teaching and training as part of both postgraduate and undergraduate courses. The design and development of such courses is challenging since the technologies and software in the fields of large scale distributed systems such as Cluster, Cloud and Grid computing are undergoing continuous change. The students completing the HPC courses should be proficient in these evolving technologies and equipped with practical and theoretical skills for future jobs in this fast developing area. In this paper we present our experience in developing the HPC, Cluster and Grid modules including a review of existing HPC courses offered at the UK universities. The topics covered in the modules are described, as well as the coursework projects based on practical laboratory work. We conclude with an evaluation based on our experience over the last ten years in developing and delivering the HPC modules on the undergraduate courses, with suggestions for future work

The 105 month Swift-BAT all-sky hard X-ray survey

We present a catalog of hard X-ray sources detected in the first 105 months of observations with the Burst Alert Telescope (BAT) coded mask imager on board the Swift observatory. The 105 month Swift-BAT survey is a uniform hard X-ray all-sky survey with a sensitivity of $8.40\times 10^{-12}\ {\rm erg\ s^{-1}\ cm^{-2}}$over 90$7.24\times 10^{-12}\ {\rm erg\ s^{-1}\ cm^{-2}}$ over 50% of the sky in the 14-195 keV band. The Swift-BAT 105 month catalog provides 1632 (422 new detections) hard X-ray sources in the 14-195 keV band above the 4.8{\sigma} significance level. Adding to the previously known hard X-ray sources, 34% (144/422) of the new detections are identified as Seyfert AGN in nearby galaxies (z<0.2). The majority of the remaining identified sources are X-ray binaries (7%, 31) and blazars/BL Lac objects (10%, 43). As part of this new edition of the Swift-BAT catalog, we release eight-channel spectra and monthly sampled light curves for each object in the online journal and at the Swift-BAT 105 month Web site.Comment: Accepted for publication in ApJS. The Swift-BAT 105-month Survey public website can be found at this URL: https://swift.gsfc.nasa.gov/results/bs105mon

Cognitive functioning in young children with type 1 diabetes

OBJECTIVE: To assess cognitive functioning in children with type 1 diabetes (T1D) and examine whether glycemic history influences cognitive function. RESEARCH DESIGN AND METHODS: Neuropsychological evaluation of 216 children (healthy controls, n = 72; T1D, n = 144) ages 4-10yrs across five DirecNet sites. Cognitive domains included IQ, Executive Functions, Learning and Memory, and Processing Speed. Behavioral, mood, parental IQ data and T1D glycemic history since diagnosis were collected. RESULTS: The cohorts did not differ in age, gender or parent IQ. Median T1D duration was 2.5yrs and average onset age was 4yrs. After covarying age, gender, and parental IQ, the IQ and the Executive Functions domain scores trended lower (both p = .02, not statistically significant adjusting for multiple comparisons) with T1D relative to controls. Children with T1D were rated by parents as having more depressive and somatic symptoms (p < 0.001). Learning and memory (p = 0.46) and processing speed (p = 0.25) were similar. Trends in the data supported that the degree of hyperglycemia was associated with Executive Functions, and to a lesser extent, Child IQ and Learning and Memory. CONCLUSIONS: Differences in cognition are subtle in young children with T1D within 2 years of onset. Longitudinal evaluations will help determine whether these findings change or become more pronounced with time

Subject Benchmark Statement Forensic Science

This document is a QAA Subject Benchmark Statement for Forensic Science that defines what can be expected of a graduate in the subject, in terms of what they might know, do and understand at the end of their studies. Subject Benchmark Statements also describe the nature and characteristics of awards in a particular subject or area. Subject Benchmark Statements are published in QAA's capacity as a membership organisation on behalf of the higher education sector. A summary of the Statement is also available on the QAA website

Establishing a core outcome set for peritoneal dialysis : report of the SONG-PD (standardized outcomes in nephrology-peritoneal dialysis) consensus workshop

Outcomes reported in randomized controlled trials in peritoneal dialysis (PD) are diverse, are measured inconsistently, and may not be important to patients, families, and clinicians. The Standardized Outcomes in Nephrology-Peritoneal Dialysis (SONG-PD) initiative aims to establish a core outcome set for trials in PD based on the shared priorities of all stakeholders. We convened an international SONG-PD stakeholder consensus workshop in May 2018 in Vancouver, Canada. Nineteen patients/caregivers and 51 health professionals attended. Participants discussed core outcome domains and implementation in trials in PD. Four themes relating to the formation of core outcome domains were identified: life participation as a main goal of PD, impact of fatigue, empowerment for preparation and planning, and separation of contributing factors from core factors. Considerations for implementation were identified: standardizing patient-reported outcomes, requiring a validated and feasible measure, simplicity of binary outcomes, responsiveness to interventions, and using positive terminology. All stakeholders supported inclusion of PD-related infection, cardiovascular disease, mortality, technique survival, and life participation as the core outcome domains for PD

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment