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

Deep learning classification of chest x-ray images

We propose a deep learning based method for classification of commonly occurring pathologies in chest X-ray images. The vast number of publicly available chest X-ray images provides the data necessary for successfully employing deep learning methodologies to reduce the misdiagnosis of thoracic diseases. We applied our method to the classification of two example pathologies, pulmonary nodules and cardiomegaly, and we compared the performance of our method to three existing methods. The results show an improvement in AUC for detection of nodules and cardiomegaly compared to the existing methods.Comment: 4 pages, 4 figures, 2 tables, conference , SSIAI 202

Comparison of SST diurnal variation models over the Tropical Warm Pool region

Four sea surface temperature (SST) diurnal variation (DV) models have been compared against Multi-functional Transport Satellite - 1R (MTSAT-1R) SST measurements over the Tropical Warm Pool region (TWP, 90°E-170°E, 25°S-15°N) for four months from January to April 2010. The four models include one empirical model formulated by Chelle Gentemann (hereafter CG03), one physical model proposed by Zeng and Beljaars in 2005 (ZB05) and its updated version (ZB+T), and one air-sea coupled model (the Met Office Unified Model Global Coupled configuration 2, GC2) with ZB05 warm layer scheme added on top of the standard configuration. The sensitivity of the v3 MTSAT-1R data to the “true” changes in SST is first investigated using drifting buoys and is estimated to be 0.60 ± 0.05. This being significantly different from 1, the models are validated against MTSAT-1R data and the same data scaled by the inverse of the sensitivity (representing an estimate of the true variability). Results indicate that all models are able to capture the general DV patterns but with differing accuracies and features. Specifically, CG03 and ZB+T underestimate strong (> 2 K) DV events’ amplitudes especially if we assume that sensitivity-scaled MTSAT-1R variability is most realistic. ZB05 can effectively capture the DV cycles under most DV and wind conditions, as well as the DV spatial distribution. GC2 tends to overestimate small-moderate (< 2 K) DV events but can reasonably predict large DV events. 1-3 hr lags in warming start and peak times are found in GC2

Physiological concentrations of bile acids down-regulate agonist induced secretion in colonic epithelial cells

In patients with bile acid malabsorption, high concentrations of bile acids enter the colon and stimulate Cl− and fluid secretion, thereby causing diarrhoea. However, deoxycholic acid (DCA), the predominant colonic bile acid, is normally present at lower concentrations where its role in regulating transport is unclear. Thus, the current study set out to investigate the effects of physiologically relevant DCA concentrations on colonic epithelial secretory function. Cl− secretion was measured as changes in short-circuit current across voltage-clamped T84 cell monolayers. At high concentrations (0.5–1 mM), DCA acutely stimulated Cl− secretion but this effect was associated with cell injury, as evidenced by decreased transepithelial resistance (TER) and increased lactate dehydrogenase (LDH) release. In contrast, chronic (24 hrs) exposure to lower DCA concentrations (10–200 μM) inhibited responses to Ca2+ and cAMP-dependent secretagogues without altering TER, LDH release, or secretagogue-induced increases in intracellular second messengers. Other bile acids – taurodeoxycholic acid, chenodeoxycholic acid and cholic acid – had similar antisecretory effects. DCA (50 μM) rapidly stimulated phosphorylation of the epidermal growth factor receptor (EGFr) and both ERK and p38 MAPKs (mitogen-activated protein kinases). The EGFr inhibitor, AG1478, and the protein synthesis inhibitor, cycloheximide, reversed the antisecretory effects of DCA, while the MAPK inhibitors, PD98059 and SB203580, did not. In summary, our studies suggest that, in contrast to its acute prosecretory effects at pathophysiological concentrations, lower, physiologically relevant, levels of DCA chronically down-regulate colonic epithelial secretory function. On the basis of these data, we propose a novel role for bile acids as physiological regulators of colonic secretory capacity

How to Select a Termite Control Service

6 pp., 6 photosThis publication explains how to choose a termite control service and what control options are available for homeowners

Plasma kininogen and kininogen fragments are biomarkers of progressive renal decline in type-1 diabetes

The ability of microalbuminuria to predict early progressive renal function decline in type-1 diabetic patients has been questioned. To resolve this, we determined the plasma proteome differences between microalbuminuric patients with type-1 diabetes and stable renal function (controls) and patients at risk for early progressive renal function decline (cases) and asked whether these differences have value as surrogate biomarkers. Mass spectrometry was used to analyze small (less than 3 kDa) plasma peptides isolated from well-matched case and control plasma obtained at the beginning of an 8-12 year follow-up period. Spearman analysis of plasma peptide abundance and the rate of renal function decline during follow-up identified seven masses with a significant negative correlation with early progressive renal function decline. Tandem mass spectrometry identified three fragments of high molecular weight kininogen. Increased plasma high molecular weight kininogen in the cases was confirmed by immunoblot. One peptide, des-Arg9-BK(1-8), induced Erk1/2 phosphorylation when added apically to two proximal tubular cell lines grown on permeable inserts. Thus, we have identified plasma protein fragments, some of which have biological activity with moderate to strong correlation, with early progressive renal function decline in microalbuminuric patients with type-1 diabetes. Other peptides are candidates for validation as candidate biomarkers of diabetes-associated renal dysfunction

Valgus and varus deformity after wide-local excision, brachytherapy and external beam irradiation in two children with lower extremity synovial cell sarcoma: case report

BACKGROUND: Limb-salvage is a primary objective in the management of extremity soft-tissue sarcoma in adults and children. Wide-local excision combined with radiation therapy is effective in achieving local tumor control with acceptable morbidity and good functional outcomes for most patients. CASE PRESENTATION: Two cases of deformity after wide-local excision, brachytherapy and external beam irradiation for lower-extremity synovial cell sarcoma are presented and discussed to highlight contributing factors, time course of radiation effects and orthopedic management. In an effort to spare normal tissues from the long-term effects of radiation therapy, more focal irradiation techniques have been applied to patients with musculoskeletal tumors including brachytherapy and conformal radiation therapy. As illustrated in this report, the use of these techniques results in the asymmetric irradiation of growth plates and contributes to the development of valgus or varus deformity and leg-length discrepancies. CONCLUSIONS: Despite good functional outcomes, progressive deformity in both patients required epiphysiodesis more than 3 years after initial management. There is a dearth of information related to the effects of radiation therapy on the musculoskeletal system in children. Because limb-sparing approaches are to be highlighted in the next generation of cooperative group protocols for children with musculoskeletal tumors, documentation of the effects of surgery and radiation therapy will lead to improved decision making in the selection of the best treatment approach and in the follow-up of these patients

Packed Red Blood Cell Transfusion Associates with Acute Kidney Injury After Transcatheter Aortic Valve Replacement

Background: Acute kidney injury after cardiac surgery significantly associates with morbidity and mortality. Despite not requiring cardiopulmonary bypass, transcatheter aortic valve replacement patients have an incidence of post-procedural acute kidney injury similar to patients who undergo open surgical aortic valve replacement. Packed red blood cell transfusion has been associated with morbidity and mortality after cardiac surgery. We hypothesized that packed red blood cell transfusion independently associates with acute kidney injury after transcatheter aortic valve replacement, after accounting for other risk factors. Methods: This is a single-center retrospective cohort study of 116 patients undergoing transcatheter aortic valve replacement. Post-transcatheter aortic valve replacement acute kidney injury was defined by Kidney Disease: Improving Global Outcomes serum creatinine-based criteria. Univariate comparisons between patients with and without post-transcatheter aortic valve replacement acute kidney injury were made for clinical characteristics. Multivariable logistic regression was used to assess independent association of packed red blood cell transfusion with post-transcatheter aortic valve replacement acute kidney injury (adjusting for pre-procedural renal function and other important clinical parameters). Results: Acute kidney injury occurred in 20 (17.2%) subjects. Total number of packed red blood cells transfused independently associated with post-procedure acute kidney injury (OR = 1.67 per unit, 95% CI 1.13–2.47, P = 0.01) after adjusting for pre-procedure estimated glomerular filtration rate (OR = 0.97 per ml/min/1.73m2, 95% CI 0.94–1.00, P = 0.05), nadir hemoglobin (OR = 0.88 per g/dL increase, CI 0.61–1.27, P = 0.50), and post-procedure maximum number of concurrent inotropes and vasopressors (OR = 2.09 per inotrope or vasopressor, 95% CI 1.19–3.67, P = 0.01). Conclusion: Packed red blood cell transfusion, along with post-procedure use of inotropes and vasopressors, independently associate with acute kidney injury after transcatheter aortic valve replacement. Further studies are needed to elucidate the pathobiology underlying these associations

OPTIma:a tracking solution for proton computed tomography in high proton flux environments

Currently there is a large discrepancy between the currents that are used for treatments in proton beam therapy facilities and the ultra low beam currents required for many proton CT imaging systems. Here we provide details of the OPTIma silicon strip based tracking system, which has been designed for performing proton CT imaging in conditions closer to the high proton flux environments of modern spot scanning treatment facilities. Details on the physical design, sensor testing, modelling, and track reconstruction are provided along with Monte-Carlo simulation studies of the expected performance for proton beam currents of up to 50 pA at the nozzle when using a σ = ∼10 mm spot scanning cyclotron system. Using a detailed simulation of the proposed OPTIma system, a discrepancy of less than 1% on the Relative Stopping Power is found for various tissues when embedded within a 150 mm diameter Perspex sphere. It is found that by accepting up to 7 protons per bunch it is possible to operate at cyclotron beam currents up to 5 times higher than would be possible with a single proton based readout, significantly reducing the total beam time required to produce an image, while also reducing the discrepancy between the beam currents required for treatment and those used for proton CT

Young children and tablets: the views of parents and teachers

Touch screen tablets are now widely available and due to the increasing use of these technologies in homes and early years centres, it is important to consider parent and teacher views about their use. This paper reports on an interview study which explored the perspectives of four parents of children aged 20–36 months and their two teachers in one early learning centre in the north of England. Key findings were that parents and teachers had a positive perspective on young children’s use of tablets and viewed them as educationally valuable. They expressed that they did not wish children to be left behind in learning about new technologies and emphasized having a ‘balanced’ approach to tablets. However, there were also concerns voiced over the potential overuse and misuse of tablets at home suggesting more guidance for parents is needed to support young children’s experiences with tablets