Evaluation of effects caused by differentially spliced Ets-1 transcripts in fibroblasts

The transcription factor Ets-1 is known to be involved in a broad variety of cellular functions such as cell proliferation, migration, invasion, apoptosis and angiogenesis. In nearly all these reports, the full-length Ets-1 (p51) is commonly considered to be the active form and the role of the Ets-1?VII splice variant (p42) has not been addressed. Therefore, we studied the functional effects of p42 Ets-1 in comparison to p51 Ets-1 expression in a well-characterized mouse fibroblast cell line. Furthermore, the specific role of Ets-1 was evaluated using mouse fibroblasts with a reduced Ets-1 expression caused by RNAi and compared to fibroblasts with a binding inhibition of the whole ETS transcription factor family by stably overexpressing the ETS DNA binding domain as transdominant-negative mutant. Our results demonstrate that p42 Ets-1 has quite different functions and target genes compared to p51 Ets-1 (e.g. TIMP-4, MMP-3, MMP-9, MMP-13). In some cases (e.g. in cytokine expression) p42 Ets-1 is a functional transcription factor which acts in the same manner as a transdominant-negative approach

Results of 2013 Survey of Parallel Computing Needs Focusing on NSF-funded Researchers

The field of supercomputing is experiencing a rapid change in system structure, programming models, and software environments in response to advances in application requirements and in underlying enabling technologies. Traditional parallel programming approaches have relied on static resource allocation and task scheduling through programming interfaces such as MPI and OpenMP. These methods are reaching their efficiency and scalability limits on the new emerging classes of systems, spurring the creation of innovative dynamic strategies and software tools, including advanced runtime system software and programming interfaces that use them. To accelerate adoption of these next-generation methods, Indiana University is investigating the creation of a single supported Reconfigurable Execution Framework Testbed (REFT) to be used by parallel application algorithm developers as well as researchers in advanced tools for parallel computing. These investigations are funded by the National Science Foundation Award Number 1205518 to Indiana University with Thomas Sterling as Principal Investigator, and Maciej Brodowicz, Matthew R. Link, Andrew Lumsdaine, and Craig Stewart as Co-Principal Investigators. As a starting point in this research we proposed to assess needs in parallel computing in general and needs for software tools and testbeds in particular within the NSF-funded research community. As one set of data toward understanding these needs, we conducted a survey of researchers funded by the National Science Foundation. Because of the strong possibility of distinct needs of researchers funded by what is now the Division of Advanced Cyberinfrastructure, researchers funded by the other divisions of the Computer and Information Sciences and Engineering Directorate, and researchers funded by the remainder of the NSF, we surveyed these populations separately. The report states the methods and summarize survey results. The data sets and copies of SPSS descriptive statistics describing the data are available online at http://hdl.handle.net/2022/19924.National Science Foundation Award Number 120551

Information technology in support of research, scholarship, and creative activities: A strategic plan for Research Technologies – a division of UITS and a PTI Service and Cyberinfrastructure Center

Stewart, C.A., M.R. Link, E. Wernert, W.K. Barnett, T.M. Miller. 2012. Information technology in support of research, scholarship, and creative activities: A strategic plan for Research Technologies – a division of UITS and a PTI Service and Cyberinfrastructure Center. Indiana University, Bloomington, IN. PTI Technical Report PTI-TR12-007.IU is currently executing its second information technology strategic plan – Empowering People: Indiana University's Strategic Plan for Information Technology 2009 (hereafter referred to as Empowering People). In this document, we set out long-term goals for the Research Technologies (RT) division of UITS, reaffirm specific goals set for RT for 2019, describe Actions within Empowering People for which RT is responsible, and describe the new internal structure of Research Technologies. The mission of the Research Technologies division of UITS is to develop, deliver, and support advanced technology solutions that improve productivity of and enable new possibilities in research, scholarly endeavors, and creative activity at Indiana University and beyond; and to complement this with education and technology translation activities to improve the quality of life of people in Indiana, the nation, and the world

Cyberinfrastructure, Science Gateways, Campus Bridging, and Cloud Computing

Computers accelerate our ability to achieve scientific breakthroughs. As technology evolves and new research needs come to light, the role for cyberinfrastructure as “knowledge” infrastructure continues to expand. This article defines and discusses cyberinfrastructure and the related topics of science gateways and campus bridging; identifies future challenges in cyberinfrastructure; and discusses challenges and opportunities related to the evolution of cyberinfrastructure, “big data” (datacentric, data-enabled, and data-intensive research and data analytics), and cloud computing.This material is based upon work supported by the National Science Foundation under grants 0504075, 0451237, 0723054, 1062432, 0116050, 0521433, 0503697, and 1053575, and several IBM Shared University Research grants and support provided by Lilly Endowment, Inc. for the Indiana University Pervasive Technology Institute. Any opinions, findings and conclusions or recommendations expressed herein are those of the authors and do not necessarily reflect the views of the supporting agencies

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

Pathogen burden, inflammation, proliferation and apoptosis in human in-stent restenosis - Tissue characteristics compared to primary atherosclerosis

Pathogenic events leading to in-stent restenosis (ISR) are still incompletely understood. Among others, inflammation, immune reactions, deregulated cell death and growth have been suggested. Therefore, atherectomy probes from 21 patients with symptomatic ISR were analyzed by immunohistochemistry for pathogen burden and compared to primary target lesions from 20 stable angina patients. While cytomegalovirus, herpes simplex virus, Epstein-Barr virus and Helicobacter pylori were not found in ISR, acute and/or persistent chlamydial infection were present in 6/21 of these lesions (29%). Expression of human heat shock protein 60 was found in 8/21 of probes (38%). Indicated by distinct signals of CD68, CD40 and CRP, inflammation was present in 5/21 (24%), 3/21 (14%) and 2/21 (10%) of ISR cases. Cell density of ISR was significantly higher than that of primary lesions ( 977 +/- 315 vs. 431 +/- 148 cells/mm(2); p < 0.001). There was no replicating cell as shown by Ki67 or PCNA. TUNEL+ cells indicating apoptosis were seen in 6/21 of ISR specimens (29%). Quantitative analysis revealed lower expression levels for each intimal determinant in ISR compared to primary atheroma (all p < 0.05). In summary, human ISR at the time of clinical presentation is characterized by low frequency of pathogen burden and inflammation, but pronounced hypercellularity, low apoptosis and absence of proliferation. Copyright (C) 2004 S. Karger AG, Basel

Services and support for IU School of Medicine and Clinical Affairs Schools by the UITS/PTI Advanced Biomedical Information Technology Core and Research Technologies Division in FY 2013 - Extended Version

The report presents information on services delivered in FY 2013 by ABITC and RT to the IU School of Medicine and the other Clinical Affairs schools that include the Schools of Nursing, Dentistry, Health and Rehabilitation Sciences, and Optometry; the Fairbanks School of Public Health at IUPUI; the School of Public Health at IU Bloomington; and the School of Social Work

2012 Annual Report - Advanced Biomedical Information Technology Core

This material is based upon work supported in part by the following funding agencies and grant awards: • Lilly Endowment, for its support of the Indiana Genomics Initiative (INGEN) – 2000; Indiana Metabolomics and Cytomics Initiative (METACyt); Indiana Pervasive Computing Research (IPCRES) initiative and Pervasive Technology Institute (1999 and 2008 respectively) • National Science Foundation under grants 01116050 MRI: Creation of the AVIDD Data Facility: A Distributed Facility for Managing, Analyzing and Visualizing Instrument-Driven Data (Michael A. McRobbie, PI); 0521433 MRI: Acquisition of a High-Speed, High Capacity Storage System to Support Scientific Computing: The Data Capacitor (Craig A. Stewart, PI); 0521433 ABI Development: National Center for Genome Analysis Support (Craig A. Stewart, PI) • National Institutes of Health NIAAA awards U24 AA014818-01 (Craig A. Stewart, PI) and U24 AA014818-04 (William K. Barnett, PI) Informatics Core for the Collaborative Initiative on Fetal Alcohol Spectrum Disorder • Subcontracts through the following NIH grant awards: 5P40RR024928 (Kenneth Cornetta, PI), 2U01AA014809 (Tatiana Foroud, PI), 1DP2OD007363-01 (Alexander Niculescu, PI), UL1RR025761-01 (Anantha Shekhar, PI), 3UL1RR025761-04S2 (Anantha Shekhar, PI), and 3UL1RR025761-04S3 (Anantha Shekhar, PI) • Funding from the general funds of Indiana University Any opinions expressed in this document are those of the authors and do not necessarily reflect the views of the funding agencies above