Acquisition of a High-Speed, High Capacity Storage System to Support Scientific Computing: The Data Capacitor Final Report

Final report to the National Science Foundation on ACI-0521433.National Science Foundatio

Use of IU parallel computing resources and high performance file systems - July 2013 to Dec 2014

This report details use of IU's parallel computing resources and high performance file systems from July 2013 through December 2014

What is Cyberinfrastructure?

Cyberinfrastructure is a word commonly used but lacking a single, precise definition. One recognizes intuitively the analogy with infrastructure, and the use of cyber to refer to thinking or computing – but what exactly is cyberinfrastructure as opposed to information technology infrastructure? Indiana University has developed one of the more widely cited definitions of cyberinfrastructure: "Cyberinfrastructure consists of computing systems, data storage systems, advanced instruments and data repositories, visualization environments, and people, all linked together by software and high performance networks to improve research productivity and enable breakthroughs not otherwise possible." A second definition, more inclusive of scholarship generally and educational activities, has also been published and is useful in describing cyberinfrastructure: "Cyberinfrastructure consists of systems, data and information management, advanced instruments, visualization environments, and people, all linked together by software and advanced networks to improve scholarly productivity and enable knowledge breakthroughs and discoveries not otherwise possible." In this paper, we describe the origin of the term cyberinfrastructure based on the history of the root word infrastructure, discuss several terms related to cyberinfrastructure, and provide several examples of cyberinfrastructure

Indiana University Pervasive Technology Institute – Research Technologies: XSEDE Service Provider and XSEDE subcontract report (PY1: 1 July 2011 to 30 June 2012)

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NSF or XSEDE leadership.This document is a summary of the activities of the Research Technologies division of UITS, a Service & Cyberinfrastructure Center affiliated with the Indiana University Pervasive Technology Institute, as part of the eXtreme Science and Engineering Discovery Environment (XSEDE) during XSEDE Program Year 1 (1 July 2011 – 30 June 2012). This document consists of three parts: - Section 2 of this document describes IU’s activities as an XSEDE Service Provider, using the format prescribed by XSEDE for reporting such activities. - Section 3 of this document describes IU’s activities as part of XSEDE management, operations, and support activities funded under a subcontract from the National Center for Supercomputer Applications (NCSA), the lead organization for XSEDE. This section is organized by the XSEDE Work Breakdown Structure (WBS) plan. - Appendix 1 is a summary table of IU’s education, outreach, and training events funded and supported in whole or in part by IU’s subcontract from NCSA as part of XSEDE.This document was developed with support from National Science Foundation (NSF) grant OCI-1053575

The unexpected resurgence of Weyl geometry in late 20-th century physics

Weyl's original scale geometry of 1918 ("purely infinitesimal geometry") was withdrawn by its author from physical theorizing in the early 1920s. It had a comeback in the last third of the 20th century in different contexts: scalar tensor theories of gravity, foundations of gravity, foundations of quantum mechanics, elementary particle physics, and cosmology. It seems that Weyl geometry continues to offer an open research potential for the foundations of physics even after the turn to the new millennium.Comment: Completely rewritten conference paper 'Beyond Einstein', Mainz Sep 2008. Preprint ELHC (Epistemology of the LHC) 2017-02, 92 pages, 1 figur

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.

Multiple sclerosis is a common disease of the central nervous system in which the interplay between inflammatory and neurodegenerative processes typically results in intermittent neurological disturbance followed by progressive accumulation of disability. Epidemiological studies have shown that genetic factors are primarily responsible for the substantially increased frequency of the disease seen in the relatives of affected individuals, and systematic attempts to identify linkage in multiplex families have confirmed that variation within the major histocompatibility complex (MHC) exerts the greatest individual effect on risk. Modestly powered genome-wide association studies (GWAS) have enabled more than 20 additional risk loci to be identified and have shown that multiple variants exerting modest individual effects have a key role in disease susceptibility. Most of the genetic architecture underlying susceptibility to the disease remains to be defined and is anticipated to require the analysis of sample sizes that are beyond the numbers currently available to individual research groups. In a collaborative GWAS involving 9,772 cases of European descent collected by 23 research groups working in 15 different countries, we have replicated almost all of the previously suggested associations and identified at least a further 29 novel susceptibility loci. Within the MHC we have refined the identity of the HLA-DRB1 risk alleles and confirmed that variation in the HLA-A gene underlies the independent protective effect attributable to the class I region. Immunologically relevant genes are significantly overrepresented among those mapping close to the identified loci and particularly implicate T-helper-cell differentiation in the pathogenesis of multiple sclerosis

The higher-level phylogeny of Archosauria (Tetrapoda:Diapsida)

Crown group Archosauria, which includes birds, dinosaurs, crocodylomorphs, and several extinct Mesozoic groups, is a primary division of the vertebrate tree of life. However, the higher-level phylogenetic relationships within Archosauria are poorly resolved and controversial, despite years of study. The phylogeny of crocodile-line archosaurs (Crurotarsi) is particularly contentious, and has been plagued by problematic taxon and character sampling. Recent discoveries and renewed focus on archosaur anatomy enable the compilation of a new dataset, which assimilates and standardizes character data pertinent to higher-level archosaur phylogeny, and is scored across the largest group of taxa yet analysed. This dataset includes 47 new characters (25% of total) and eight taxa that have yet to be included in an analysis, and total taxonomic sampling is more than twice that of any previous study. This analysis produces a well-resolved phylogeny, which recovers mostly traditional relationships within Avemetatarsalia, places Phytosauria as a basal crurotarsan clade, finds a close relationship between Aetosauria and Crocodylomorpha, and recovers a monophyletic Rauisuchia comprised of two major subclades. Support values are low, suggesting rampant homoplasy and missing data within Archosauria, but the phylogeny is highly congruent with stratigraphy. Comparison with alternative analyses identifies numerous scoring differences, but indicates that character sampling is the main source of incongruence. The phylogeny implies major missing lineages in the Early Triassic and may support a Carnian-Norian extinction event.Marshall Scholarship for study in the United KingdomJurassic FoundationUniversity of BristolPaleontological Societ

Evolution of the Toarcian (Early Jurassic) carbon-cycle and global climatic controls on local sedimentary processes (Cardigan Bay Basin, UK)

The late Early Jurassic Toarcian Stage represents the warmest interval of the Jurassic Period, with an abrupt rise in global temperatures of up to ∼7 °C in mid-latitudes at the onset of the early Toarcian Oceanic Anoxic Event (T-OAE; ∼183 Ma). The T-OAE, which has been extensively studied in marine and continental successions from both hemispheres, was marked by the widespread expansion of anoxic and euxinic waters, geographically extensive deposition of organic-rich black shales, and climatic and environmental perturbations. Climatic and environmental processes following the T-OAE are, however, poorly known, largely due to a lack of study of stratigraphically well-constrained and complete sedimentary archives. Here, we present integrated geochemical and physical proxy data (high-resolution carbon-isotope data (δ13C), bulk and molecular organic geochemistry, inorganic petrology, mineral characterisation, and major- and trace-element concentrations) from the biostratigraphically complete and expanded entire Toarcian succession in the Llanbedr (Mochras Farm) Borehole, Cardigan Bay Basin, Wales, UK. With these data, we (1) construct the first high-resolution biostratigraphically calibrated chemostratigraphic reference record for nearly the complete Toarcian Stage, (2) establish palaeoceanographic and depositional conditions in the Cardigan Bay Basin, (3) show that the T-OAE in the hemipelagic Cardigan Bay Basin was marked by the occurrence of gravity-flow deposits that were likely linked to globally enhanced sediment fluxes to continental margins and deeper marine (shelf) basins, and (4) explore how early Toarcian (tenuicostatum and serpentinum zones) siderite formation in the Cardigan Bay Basin may have been linked to low global oceanic sulphate concentrations and elevated supply of iron (Fe) from the hinterland, in response to climatically induced changes in hydrological cycling, global weathering rates and large-scale sulphide and evaporite deposition

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice