559 research outputs found
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
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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
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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
VHEE FLASH sparing effect measured at CLEAR, CERN with DNA damage of pBR322 plasmid as a biological endpoint
Ultra-high dose rate (UHDR) irradiation has been shown to have a sparing effect on healthy tissue, an effect known as ‘FLASH’. This effect has been studied across several radiation modalities, including photons, protons and clinical energy electrons, however, very little data is available for the effect of FLASH with Very High Energy Electrons (VHEE). pBR322 plasmid DNA was used as a biological model to measure DNA damage in response to Very High Energy Electron (VHEE) irradiation at conventional (0.08 Gy/s), intermediate (96 Gy/s) and ultra-high dose rates (UHDR, (2 × 109 Gy/s) at the CERN Linear Electron Accelerator (CLEAR) user facility. UHDRs were used to determine if the biological FLASH effect could be measured in the plasmid model, within a hydroxyl scavenging environment. Two different concentrations of the hydroxyl radical scavenger Tris were used in the plasmid environment to alter the proportions of indirect damage, and to replicate a cellular scavenging capacity. Indirect damage refers to the interaction of ionising radiation with molecules and species to generate reactive species which can then attack DNA. UHDR irradiated plasmid was shown to have significantly reduced amounts of damage in comparison to conventionally irradiated, where single strand breaks (SSBs) was used as the biological endpoint. This was the case for both hydroxyl scavenging capacities. A reduced electron energy within the VHEE range was also determined to increase the DNA damage to pBR322 plasmid. Results indicate that the pBR322 plasmid model can be successfully used to explore and test the effect of UHDR regimes on DNA damage. This is the first study to report FLASH sparing with VHEE, with induced damage to pBR322 plasmid DNA as the biological endpoint. UHDR irradiated plasmid had reduced amounts of DNA single-strand breaks (SSBs) in comparison with conventional dose rates. The magnitude of the FLASH sparing was a 27% reduction in SSB frequency in a 10 mM Tris environment and a 16% reduction in a 100 mM Tris environment
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
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