Virtualizing the Stampede2 Supercomputer with Applications to HPC in the Cloud

Methods developed at the Texas Advanced Computing Center (TACC) are described and demonstrated for automating the construction of an elastic, virtual cluster emulating the Stampede2 high performance computing (HPC) system. The cluster can be built and/or scaled in a matter of minutes on the Jetstream self-service cloud system and shares many properties of the original Stampede2, including: i) common identity management, ii) access to the same file systems, iii) equivalent software application stack and module system, iv) similar job scheduling interface via Slurm. We measure time-to-solution for a number of common scientific applications on our virtual cluster against equivalent runs on Stampede2 and develop an application profile where performance is similar or otherwise acceptable. For such applications, the virtual cluster provides an effective form of "cloud bursting" with the potential to significantly improve overall turnaround time, particularly when Stampede2 is experiencing long queue wait times. In addition, the virtual cluster can be used for test and debug without directly impacting Stampede2. We conclude with a discussion of how science gateways can leverage the TACC Jobs API web service to incorporate this cloud bursting technique transparently to the end user.Comment: 6 pages, 0 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, US

Stimulated Muscle Contractions Regulate Membrane-Bound and Soluble TLR4 to Prevent LPS-Induced Signaling and Myotube Atrophy in Skeletal Muscle Cells

Toll-like receptor 4 (TLR4) activation by lipopolysaccharides (LPS) contributes to chronic inflammation and causes upregulation of muscle atrophy signaling pathways. Exercise can suppress LPS/TLR4 axis activation by reducing the expression of TLR4 on immune cells. It is unknown how this regulation occurs, and it is not clear how exercise affects TLR4 on skeletal muscle. PURPOSE: To uncover the nature and mechanisms by which exercise affects TLR4 expression and intracellular signaling using cell culture models and human experiments. METHODS: C2C12 myotubes were subjected to electrical pulse stimulation (EPS) with and without subsequent treatment with 500 ng/mL lipopolysaccharide (LPS) along with corresponding control conditions. To investigate the effect of muscle contraction on the regulation of TLR4 in-vivo, we analyzed PBMC and serum samples from eight recreationally active men that completed 60-minutes of cycling at a moderate intensity (65% of VO2max). RESULTS: In-vitro, LPS decreased membrane-bound TLR4, increased TLR4 signaling (decreased inhibitor of κBα), and induced myotube atrophy. However, stimulated muscle contractions decreased membrane-bound TLR4, increased soluble TLR4 (sTLR4), and prevented LPS-induced signaling and myotube atrophy. In human participants, a single bout of moderate-intensity exercise decreased membrane-bound TLR4 on PBMCs and increased serum-borne sTLR4. CONCLUSION: These experiments support exercise may exert a novel anti-catabolic/ anti-inflammatory effect by increasing sTLR4 and decreasing TLR4 expressed on the muscle membrane. These results could help improve interventions for conditions associated with TLR4-mediated inflammation and muscle atrophy, such as diabetes, sarcopenia, and cancer cachexia

Seagrass mapping synthesis: a resource for coastal management in the Great Barrier Reef World Heritage Area

This project provides an up to date synthesis of the available information on seagrass in the Great Barrier Reef World Heritage Area (GBRWHA). It brings together more than 30 years of spatial information and data collection into easy to use spatial GIS layers that provide key information on species, meadow type and age and reliability of the data. The project provides: Seagrass site and meadow-specific data in Geographic Information System (GIS) layers to provide seagrass data to inform research analysis and management advice. A site layer that includes >66,000 individual survey sites with information including latitude/longitude, Natural Resource Management region, site depth, seagrass presence/absence, dominant seagrass species, presence/absence of individual species, survey date, survey method, and data custodian. A meadow layer that includes 1169 individual and/or composite seagrass meadows with information including individual meadow persistence, meadow location (intertidal/subtidal), meadow density based on mean biomass and/or mean percent cover, meadow area, dominant seagrass species, seagrass species present, range of survey dates, survey method, and data custodian. Metadata to enable interpretation of the information and to identify the original data custodians for assistance with interpretation. Outcomes: This study consolidates all available seagrass spatial data for the GBRWHA collected from 1984 to December 2014 by the TropWATER Seagrass Group and CSIRO in a GIS database. It assembles and documents the state of spatial knowledge of seagrass in the GBRWHA. The spatial data is based on methods developed by TropWATER and CSIRO for seagrass habitat surveys of subtidal meadows, and TropWATER methods for intertidal surveys. Methods include sampling by boat (free divers, underwater video camera, grabs, sled with net sampling), helicopter and walking. 447,530 hectares of seagrasses were mapped (modelled deep water seagrass areas are not included in area figures in this report) within the GBRWHA; much of which provides habitat for commercial and traditional fishery species, and an important food resource for dugong and green turtle populations. Data is included for twelve seagrass species from three families. Seagrass was present at 39% of all sites visited. The study identifies areas where much of the data available for management is more than 20 years old or where there are specific habitats unsurveyed. Large areas of central and northern Queensland require updating. Several key habitat types such as reef platform seagrass meadows are poorly represented in the data

Synthesizing 35 years of seagrass spatial data from the Great Barrier Reef World Heritage Area, Queensland, Australia

The Great Barrier Reef World Heritage Area in Queensland, Australia contains globally significant seagrasses supporting key ecosystem services, including habitat and food for threatened populations of dugong and turtle. We compiled 35 years of data in a spatial database, including 81,387 data points with georeferenced seagrass and species presence/absence, depth, dominant sediment type, and collection date. We include data collected under commercial contract that have not been publicly available. Twelve seagrass species were recorded. The deepest seagrass was found at 76 m. Seagrass meadows are at risk from anthropogenic, climate and weather processes. Our database is a valuable resource that provides coastal managers and the global marine community with a long-term spatial resource describing seagrass populations from the mid-1980s against which to benchmark change. We address the data issues involved in hindcasting over 30 years to ensure confidence in the accuracy and reliability of data included

Following the banking cycle of umbilical cord blood in India: the disparity between prebanking persuasion and post-banking utilization

To address critique of the rare uptake of umbilical cord blood (UCB) in private banks, hybrid-banking models would combine the advantages of ‘public UCB banking’ and private UCB banking by responding to both market forces and public needs. We question both by following the cycle of UCB banking in India: the circulation and stagnation of UCB as waste, gift, biological insurance, enclaved good, source of saving lives, and commodity through various practices of public, private and hybrid UCB banking. Making the journey from ‘recruitment’, ‘collection’ and ‘banking’ to ‘research’ and ‘therapy’ allowed us to identify concerns about the transparency of this cycle. Drawing on archival research and fieldwork interviews with different stakeholders in UCB banks in India, this article shows how private/hybrid cord blood banks are competing for their market share and its implication for the circulation of UCB: speculation, stagnation and opacity

Detection of chemical warfare agent simulants and hydrolysis products in biological samples by paper spray mass spectrometry

Paper spray ionization coupled to a high resolution tandem mass spectrometer (a quadrupole orbitrap) was used to identify and quantitate chemical warfare agent (CWA) simulants and their hydrolysis products in blood and urine. Three CWA simulants, dimethyl methylphosphonate (DMMP), trimethyl phosphate (TMP), and diisopropyl methylphosphonate (DIMP), and their isotopically labeled standards were analyzed in human whole blood and urine. Calibration curves were generated and tested with continuing calibration verification standards. Limits of detection for these three compounds were in the low ng mL−1 range for the direct analysis of both blood and urine samples. Five CWA hydrolysis products, ethyl methylphosphonic acid (EMPA), isopropyl methylphosphonic acid (IMPA), isobutyl methylphosphonic acid (iBuMPA), cyclohexyl methylphosphonic acid (CHMPA), and pinacolyl methylphosphonic acid (PinMPA), were also analyzed. Calibration curves were generated in both positive and negative ion modes. Limits of detection in the negative ion mode ranged from 0.36 ng mL−1 to 1.25 ng mL−1 in both blood and urine for the hydrolysis products. These levels were well below those found in victims of the Tokyo subway attack of 2 to 135 ng mL−1. Improved stability and robustness of the paper spray technique in the negative ion mode was achieved by the addition of chlorinated solvents. These applications demonstrate that paper spray mass spectrometry (PS-MS) can be used for rapid, sample preparation-free detection of chemical warfare agents and their hydrolysis products at physiologically relevant concentrations in biological samples

Feed-Forward Inhibition of Androgen Receptor Activity by Glucocorticoid Action in Human Adipocytes

SummaryWe compared transcriptomes of terminally differentiated mouse 3T3-L1 and human adipocytes to identify cell-specific differences. Gene expression and high content analysis (HCA) data identified the androgen receptor (AR) as both expressed and functional, exclusively during early human adipocyte differentiation. The AR agonist dihydrotestosterone (DHT) inhibited human adipocyte maturation by downregulation of adipocyte marker genes, but not in 3T3-L1. It is interesting that AR induction corresponded with dexamethasone activation of the glucocorticoid receptor (GR); however, when exposed to the differentiation cocktail required for adipocyte maturation, AR adopted an antagonist conformation and was transcriptionally repressed. To further explore effectors within the cocktail, we applied an image-based support vector machine (SVM) classification scheme to show that adipocyte differentiation components inhibit AR action. The results demonstrate human adipocyte differentiation, via GR activation, upregulates AR but also inhibits AR transcriptional activity