Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets

Contains additional information and discussion on gPCA (Reese et al., 2013). Table S1. Demonstrates the inverse proportionality between gPCA p-value and the associated ‘delta’ score, reflecting unadjusted relative magnitude of batch effects (Reese et al., 2013). The table shows the scores for all three datasets. Figure S1. Contains an Illustration to further help interpret gPCA p-value vs preserved data variance plots. (DOCX 60 kb

In-situ visualization using Damaris: the Code Saturne use case

PRACE White PaperInternational audienceAs the exascale era approaches, maintaining scalable performance in data management tasks (storage, visualization, analysis, etc.) remains a key challenge in sustaining high performance for the application execution. To address this challenge, the Damaris middleware leverages dedicated computational resources in multicore nodes to offload data management tasks, including I/O, data compression, scheduling of data movements, in-situ analysis, and visualization. In this study we evaluate the benefits of Damaris to improve the efficiency of in-situ visualization for Code_Saturne, a fluid dynamics modeling environment. The experiments show Damaris to adequately hide the I/O processing of various Paraview processing pipelines in Code_Saturne. In all cases the Damaris enabled version of Code_Saturne was found to be more efficient than the identical non-Damaris capable version when running the same Paraview pipeline

Effects of Fish Oil Supplementation on Post-Resistance Exercise Muscle Soreness in Untrained Females

The anti-inflammatory properties of omega-3 fatty acids contained in fish oil may help alleviate symptoms of delayed onset of muscle soreness (DOMS) and improve recovery from exercise. PURPOSE: To examine the effects of fish oil supplementation on the time-course of post-resistance exercise muscle soreness in young untrained females. METHODS: Seventeen non-resistance trained females (age 23.6 ± 3.0 y, % fat 27.4 ± 3.2, weight 60.2 ± 9.6 kg) were randomized into one of two groups: fish oil (6 g/d; 5:1 EPA:DHA) or placebo (6 g/d corn/soy oil). After consuming the supplements for one week, participants underwent a single bout of resistance exercise designed to induce muscle damage. Subjects performed 10 sets to failure of biceps curl machine and leg extensions using 50% of the previously measured 1-repetition maximum. Over the next week, subjective muscle soreness of the upper and lower body was measured via a grounded 10-cm visual analog scale. At 48 hours and 1 week post-exercise, subjects performed a test to determine soreness during functional movements. The comparison-wise error rate was set at p \u3c 0.10. RESULTS: Muscle soreness increased significantly in both groups and peaked at 48 hours post-exercise. The fish oil group perceived less muscle soreness in the lower body than the placebo group (p= 0.06), but there was no difference in the upper body (p= 0.27). The fish oil group reported less perceived soreness during functional movements (p= 0.07 for upper and lower body soreness). Effect sizes, indicating the reduction in muscle soreness that may be attributed to fish oil (Δ effect size between groups), was 0.75 (95% CI: -0.70 – 2.20) for the arms and 0.77 (-0.76 – 2.33) for the legs. The effect size for the functional tests was 0.63 (-0.71 – 1.97) for the arms and 0.57 (-0.85 – 1.99) for the legs. CONCLUSION: Supplementing the diet with 6 grams per day of fish oil may alleviate the muscle soreness experienced after resistance training in young untrained females, but additional studies with larger sample sizes should be conducted to confirm these findings

The CUAVA-2 CubeSat: A Second Attempt to Fly the Remote Sensing, Space Weather Study and Earth Observation Instruments

This paper presents the 6U CubeSat mission conducted by the ARC Training Centre for CubeSats, UAVs, and their Applications (CUAVA) at the University of Sydney. CUAVA-2, the second CubeSat project following the CUAVA-1 mission, builds upon lessons learned from its predecessor. CUAVA-1, the first satellite launched by CUAVA, carried first-generation payloads for earth observation goals and technology demonstrations but experienced communication difficulties. A fault root analysis was performed on CUAVA-1 to inform the design of CUAVA-2. The CUAVA-2 satellite incorporates a hyperspectral imager for applications in agriculture, forestry, coastal and marine environments, urban areas, water hazard assessment, and mineral exploration. It also includes a GPS reflectometry payload for remote sea state determination, as well as secondary payloads for technology demonstration and space weather study. This paper discusses the fault analysis findings, lessons learned, and design inputs from CUAVA-1, showcasing their integration into the CUAVA-2 satellite, which is scheduled for launch in February 2024

A genome-wide association study for diabetic nephropathy genes in African Americans

A genome-wide association study was performed using the Affymetrix 6.0 chip to identify genes associated with diabetic nephropathy in African Americans. Association analysis was performed adjusting for admixture in 965 type 2 diabetic African American patients with end-stage renal disease (ESRD) and in 1029 African Americans without type 2 diabetes or kidney disease as controls. The top 724 single nucleotide polymorphisms (SNPs) with evidence of association to diabetic nephropathy were then genotyped in a replication sample of an additional 709 type 2 diabetes-ESRD patients and 690 controls. SNPs with evidence of association in both the original and replication studies were tested in additional African American cohorts consisting of 1246 patients with type 2 diabetes without kidney disease and 1216 with non-diabetic ESRD to differentiate candidate loci for type 2 diabetes-ESRD, type 2 diabetes, and/or all-cause ESRD. Twenty-five SNPs were significantly associated with type 2 diabetes-ESRD in the genome-wide association and initial replication. Although genome-wide significance with type 2 diabetes was not found for any of these 25 SNPs, several genes, including RPS12, LIMK2, and SFI1 are strong candidates for diabetic nephropathy. A combined analysis of all 2890 patients with ESRD showed significant association SNPs in LIMK2 and SFI1 suggesting that they also contribute to all-cause ESRD. Thus, our results suggest that multiple loci underlie susceptibility to kidney disease in African Americans with type 2 diabetes and some may also contribute to all-cause ESRD

A cross-institutional analysis of the effects of broadening trainee professional development on research productivity

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Brandt, P. D., Sturzenegger Varvayanis, S., Baas, T., Bolgioni, A. F., Alder, J., Petrie, K. A., Dominguez, I., Brown, A. M., Stayart, C. A., Singh, H., Van Wart, A., Chow, C. S., Mathur, A., Schreiber, B. M., Fruman, D. A., Bowden, B., Wiesen, C. A., Golightly, Y. M., Holmquist, C. E., Arneman, D., Hall, J. D., Hyman, L. E., Gould, K. L., Chalkley, R., Brennwald, P. J., Layton, R. L. A cross-institutional analysis of the effects of broadening trainee professional development on research productivity. Plos Biology, 19(7), (2021): e3000956, https://doi.org/10.1371/journal.pbio.3000956.PhD-trained scientists are essential contributors to the workforce in diverse employment sectors that include academia, industry, government, and nonprofit organizations. Hence, best practices for training the future biomedical workforce are of national concern. Complementing coursework and laboratory research training, many institutions now offer professional training that enables career exploration and develops a broad set of skills critical to various career paths. The National Institutes of Health (NIH) funded academic institutions to design innovative programming to enable this professional development through a mechanism known as Broadening Experiences in Scientific Training (BEST). Programming at the NIH BEST awardee institutions included career panels, skill-building workshops, job search workshops, site visits, and internships. Because doctoral training is lengthy and requires focused attention on dissertation research, an initial concern was that students participating in additional complementary training activities might exhibit an increased time to degree or diminished research productivity. Metrics were analyzed from 10 NIH BEST awardee institutions to address this concern, using time to degree and publication records as measures of efficiency and productivity. Comparing doctoral students who participated to those who did not, results revealed that across these diverse academic institutions, there were no differences in time to degree or manuscript output. Our findings support the policy that doctoral students should participate in career and professional development opportunities that are intended to prepare them for a variety of diverse and important careers in the workforce.Funding sources included the Common Fund NIH Director’s Biomedical Research Workforce Innovation Broadening Experiences in Scientific Training (BEST) Award. The following institutional NIH BEST awards (alphabetical by institution) included: DP7OD020322 (Boston University; AFB, ID, BMS, LEH); DP7OD020316 (University of Chicago; CAS); DP7OD018425 (Cornell University; SSV); DP7OD018428 (Virginia Polytechnic Institute; AVW, BB); DP7OD020314 (Rutgers University; JA); DP7OD020315 (University of Rochester; TB); DP7OD018423 (Vanderbilt University; KAP, AMB, KLG, RC); DP7OD020321 (University of California, Irvine; HS, DAF); DP7OD020317 (University of North Carolina, Chapel Hill; PDB, PJB, RLL); DP7 OD018427 (Wayne State University; CSC, AM). National Institutes of Health (NIH) General Medical Sciences - Science of Science Policy Approach to Analyzing and Innovating the Biomedical Research Enterprise (SCISIPBIO) Award (GM-19-011) - 1R01GM140282-01 (University of North Carolina at Chapel Hill; RLL, PDB, PJB)