RSV: OSG Fabric Monitoring and Interoperation with WLCG Monitoring Systems

Presented at CHEP 2009 (Computing in High Energy and Nuclear Physics)

Survey of TeraGrid Job Distribution: Toward Specialized Serial Machines as TeraGrid Resources

Presented at TeraGrid 2007.As we proceed towards the age of petascale computing, it is important to be aware that even today more than half of national cyberinfrastructure users are serial users who run single processor code; more over, coarse-grained parallel application do not necessarily benefit from a high-speed low-latency interconnect. While a majority of compute resources on the TeraGrid today are massive parallel machines with high-speed low-latency interconnects like Myrinet or Infiniband, optimized to run large fine-grained parallel applications that use hundreds of processors/cores in parallel, usage patterns indicate that there is still considerable demand that could be just as effectively met by large computational resources with no special high-speed or low-latency interconnects. Research allocations involving large serial applications or coarse-grained parallel applications could be allocated to these machines, thus possibly leading to decreased wait times for massive parallel and large serial jobs. This change in focus would also lower the financial barrier for potential new resource providers to the national cyberinfrastructure, by allowing them to reallocate funds from the interconnect to additional computational capacity

Indiana University's Advanced Cyberinfrastructure

This is an archived document. The most current version may be found at http://pti.iu.edu/ciThe purpose of this document is to introduce researchers to Indiana University’s cyberinfrastructure – to clarify what these facilities make possible, to discuss how to use them and the professional staff available to work with you. The resources described here are complex and varied, among the most advanced in the world. The intended audience is anyone unfamiliar with IU’s cyberinfrastructure

A.: Cluster utility: A new metric to guide sequence clustering

Automatic sequence clustering has become increasingly important in analyzing the ever increasing number of biological sequences. Although there has been significant progress recently in developing high performance sequence clustering algorithms, correctly clustering a large number of sequences still remains a huge challenge. More often than not, the clusters generated end up being incorrect or fragmented. We have developed a new metric called the cluster utility to guide cluster splitting. We have illustrated the effectiveness of this technique by implementing it in the BAG clustering algorithm. Experiments with the entire COG database show that the proposed technique can effectively guide correct sequence clustering even while keeping the number of fragmented clusters significantly low

StarDock: shipping customized computing environments to the data

Surging data volumes make it increasingly unfeasible to transfer astronomical datasets to the local systems of individual scientists. Centralized pipelines offer some relief, but lack flexibility to fulfill the needs of all users. We have developed a system that leverages the Docker container application virtualization software. Along with a suite of commonly used astronomy applications, users can configure a container with their own custom software and analysis tools. Our StarDock system will move the users container to the data, and expose the requested dataset, allowing our users to safely and securely process their data without needlessly transferring hundreds of gigabytes

Sparsentan in patients with IgA nephropathy: a prespecified interim analysis from a randomised, double-blind, active-controlled clinical trial

Background: Sparsentan is a novel, non-immunosuppressive, single-molecule, dual endothelin and angiotensin receptor antagonist being examined in an ongoing phase 3 trial in adults with IgA nephropathy. We report the prespecified interim analysis of the primary proteinuria efficacy endpoint, and safety. Methods: PROTECT is an international, randomised, double-blind, active-controlled study, being conducted in 134 clinical practice sites in 18 countries. The study examines sparsentan versus irbesartan in adults (aged ≥18 years) with biopsy-proven IgA nephropathy and proteinuria of 1·0 g/day or higher despite maximised renin-angiotensin system inhibitor treatment for at least 12 weeks. Participants were randomly assigned in a 1:1 ratio to receive sparsentan 400 mg once daily or irbesartan 300 mg once daily, stratified by estimated glomerular filtration rate at screening (30 to 1·75 g/day). The primary efficacy endpoint was change from baseline to week 36 in urine protein-creatinine ratio based on a 24-h urine sample, assessed using mixed model repeated measures. Treatment-emergent adverse events (TEAEs) were safety endpoints. All endpoints were examined in all participants who received at least one dose of randomised treatment. The study is ongoing and is registered with ClinicalTrials.gov, NCT03762850. Findings: Between Dec 20, 2018, and May 26, 2021, 404 participants were randomly assigned to sparsentan (n=202) or irbesartan (n=202) and received treatment. At week 36, the geometric least squares mean percent change from baseline in urine protein-creatinine ratio was statistically significantly greater in the sparsentan group (-49·8%) than the irbesartan group (-15·1%), resulting in a between-group relative reduction of 41% (least squares mean ratio=0·59; 95% CI 0·51-0·69; p<0·0001). TEAEs with sparsentan were similar to irbesartan. There were no cases of severe oedema, heart failure, hepatotoxicity, or oedema-related discontinuations. Bodyweight changes from baseline were not different between the sparsentan and irbesartan groups. Interpretation: Once-daily treatment with sparsentan produced meaningful reduction in proteinuria compared with irbesartan in adults with IgA nephropathy. Safety of sparsentan was similar to irbesartan. Future analyses after completion of the 2-year double-blind period will show whether these beneficial effects translate into a long-term nephroprotective potential of sparsentan. Funding: Travere Therapeutics

Efficacy and safety of sparsentan versus irbesartan in patients with IgA nephropathy (PROTECT): 2-year results from a randomised, active-controlled, phase 3 trial

Background Sparsentan, a novel, non-immunosuppressive, single-molecule, dual endothelin angiotensin receptor antagonist, significantly reduced proteinuria versus irbesartan, an angiotensin II receptor blocker, at 36 weeks (primary endpoint) in patients with immunoglobulin A nephropathy in the phase 3 PROTECT trial's previously reported interim analysis. Here, we report kidney function and outcomes over 110 weeks from the double-blind final analysis. Methods PROTECT, a double-blind, randomised, active-controlled, phase 3 study, was done across 134 clinical practice sites in 18 countries throughout the Americas, Asia, and Europe. Patients aged 18 years or older with biopsy-proven primary IgA nephropathy and proteinuria of at least 1·0 g per day despite maximised renin–angiotensin system inhibition for at least 12 weeks were randomly assigned (1:1) to receive sparsentan (target dose 400 mg oral sparsentan once daily) or irbesartan (target dose 300 mg oral irbesartan once daily) based on a permuted-block randomisation method. The primary endpoint was proteinuria change between treatment groups at 36 weeks. Secondary endpoints included rate of change (slope) of the estimated glomerular filtration rate (eGFR), changes in proteinuria, a composite of kidney failure (confirmed 40% eGFR reduction, end-stage kidney disease, or all-cause mortality), and safety and tolerability up to 110 weeks from randomisation. Secondary efficacy outcomes were assessed in the full analysis set and safety was assessed in the safety set, both of which were defined as all patients who were randomly assigned and received at least one dose of randomly assigned study drug. This trial is registered with ClinicalTrials.gov, NCT03762850. Findings Between Dec 20, 2018, and May 26, 2021, 203 patients were randomly assigned to the sparsentan group and 203 to the irbesartan group. One patient from each group did not receive the study drug and was excluded from the efficacy and safety analyses (282 [70%] of 404 included patients were male and 272 [67%] were White) . Patients in the sparsentan group had a slower rate of eGFR decline than those in the irbesartan group. eGFR chronic 2-year slope (weeks 6–110) was −2·7 mL/min per 1·73 m2 per year versus −3·8 mL/min per 1·73 m2 per year (difference 1·1 mL/min per 1·73 m2 per year, 95% CI 0·1 to 2·1; p=0·037); total 2-year slope (day 1–week 110) was −2·9 mL/min per 1·73 m2 per year versus −3·9 mL/min per 1·73 m2 per year (difference 1·0 mL/min per 1·73 m2 per year, 95% CI −0·03 to 1·94; p=0·058). The significant reduction in proteinuria at 36 weeks with sparsentan was maintained throughout the study period; at 110 weeks, proteinuria, as determined by the change from baseline in urine protein-to-creatinine ratio, was 40% lower in the sparsentan group than in the irbesartan group (−42·8%, 95% CI −49·8 to −35·0, with sparsentan versus −4·4%, −15·8 to 8·7, with irbesartan; geometric least-squares mean ratio 0·60, 95% CI 0·50 to 0·72). The composite kidney failure endpoint was reached by 18 (9%) of 202 patients in the sparsentan group versus 26 (13%) of 202 patients in the irbesartan group (relative risk 0·7, 95% CI 0·4 to 1·2). Treatment-emergent adverse events were well balanced between sparsentan and irbesartan, with no new safety signals. Interpretation Over 110 weeks, treatment with sparsentan versus maximally titrated irbesartan in patients with IgA nephropathy resulted in significant reductions in proteinuria and preservation of kidney function.</p