Implementing a Data Publishing Service via DSpace

4th International Conference on Open RepositoriesThis presentation was part of the session : DSpace User Group PresentationsDate: 2009-05-20 01:30 PM – 03:00 PMThe Indiana University Libraries and Digital Library Program offer a set of online scholarly communication services to IU scholars under the brand IUScholarWorks. Currently, these services include IUScholarWorks Repository, a DSpace-based institutional repository for dissemination and preservation of articles, papers, technical reports, and other scholarly products, and IUScholarWorks Journals, an Open Journal System-based online journal hosting service. To complement these two existing services, the Libraries and Digital Library Program are collaborating with the Research Technologies division of IU's central IT organization to implement a research data publishing service as a new feature of IUScholarWorks Repository. The idea of this service is to allow researchers to easily publish their datasets for online access at a stable web address, reference these datasets from publications, and assume at least bit-level preservation of the data. The intent is to develop a service that is generic enough to be used for everything from sensor data to statistical data to ethnographic field video. This service will leverage IU's existing Massive Data Storage System, which is an existing large scale centrally-funded distributed storage service offered by Research Technologies to IU faculty, staff, and graduate students for storage of their research data. Based on the consortium-developed High Performance Storage System (HPSS) software, MDSS offers over 2.8 petabytes of disk- and tape-based storage distributed between IU's Bloomington and Indianapolis campuses and supports replication of data between these two sites. Data may be transferred in and out of MDSS using a variety of interfaces, including SFTP, Parallel FTP, GridFTP, HSI, SMB/CIFS, and a simple Web-based user interface. We intend to initially support two data publishing scenarios: One in which a researcher submits a dataset by entering minimal metadata and uploading data files through DSpace's Configurable Submission Interface (which are then automatically placed in MDSS if they are over a specified filesize), and the other in which the researcher indicates as part of the submission process that the data to be published already resides in a personal or research group account in MDSS and should be copied into an IUScholarWorks-managed area of MDSS for availability through DSpace. In this presentation, we will discuss our conception of the service, its technical architecture and design, metadata requirements, and progress on implementation. We will also discuss the potential applicability of our approach and implementation to others who are interested in implementing similar services

Isolation and separation of inositol phosphates from hydrolysates of rat tissues

1. 1.An electrophoretic method for the rapid separation of the phosphate esters of inositol is presented.2. 2.It is used, together with ion-exchange chromatography, to establish the presence of inositol di- and triphosphates in hydrolysates of trichloroacetic acid residues of rat brain, liver, heart, kidney, and lung.3. 3.With the aid of a 32P marker, inositol di- and triphosphates were also found in hydrolysates of rat erythrocyte stroma.4. 4.Glycerol diphosphate was found in hydrolysates of rat liver.5. 5.Inositol tetraphosphate was not found in the hydrolysates of any of the tissues studied.6. 6.Residues remaining after extraction of rat brain by established lipid extraction procedures retained substantial amounts of bound inositol di- and triphosphates.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/32019/1/0000061.pd

Resolving the Radio Source Background: Deeper Understanding Through Confusion

We used the Karl G. Jansky Very Large Array (VLA) to image one primary beam area at 3 GHz with 8 arcsec FWHM resolution and 1.0 microJy/beam rms noise near the pointing center. The P(D) distribution from the central 10 arcmin of this confusion-limited image constrains the count of discrete sources in the 1 < S(microJy/beam) < 10 range. At this level the brightness-weighted differential count S^2 n(S) is converging rapidly, as predicted by evolutionary models in which the faintest radio sources are star-forming galaxies; and ~96$% of the background originating in galaxies has been resolved into discrete sources. About 63% of the radio background is produced by AGNs, and the remaining 37% comes from star-forming galaxies that obey the far-infrared (FIR) / radio correlation and account for most of the FIR background at lambda = 160 microns. Our new data confirm that radio sources powered by AGNs and star formation evolve at about the same rate, a result consistent with AGN feedback and the rough correlation of black hole and bulge stellar masses. The confusion at centimeter wavelengths is low enough that neither the planned SKA nor its pathfinder ASKAP EMU survey should be confusion limited, and the ultimate source detection limit imposed by "natural" confusion is < 0.01 microJy at 1.4 GHz. If discrete sources dominate the bright extragalactic background reported by ARCADE2 at 3.3 GHz, they cannot be located in or near galaxies and most are < 0.03 microJy at 1.4 GHz.Comment: 28 pages including 16 figures. ApJ accepted for publicatio

Nanorobotic investigation identifies novel visual, structural and functional correlates of autoimmune pathology in a blistering skin disease model

Copyright © 2014 Seiffert-Sinha et al. There remain major gaps in our knowledge regarding the detailed mechanisms by which autoantibodies mediate damage at the tissue level. We have undertaken novel strategies at the interface of engineering and clinical medicine to integrate nanoscale visual and structural data using nanorobotic atomic force microscopy with cell functional analyses to reveal previously unattainable details of autoimmune processes in real-time. Pemphigus vulgaris is a life-threatening autoimmune blistering skin condition in which there is disruption of desmosomal cell-cell adhesion structures that are associated with the presence of antibodies directed against specific epithelial proteins including Desmoglein (Dsg) 3. We demonstrate that pathogenic (blister-forming) anti-Dsg3 antibodies, distinct from non-pathogenic (non-blister forming) anti-Dsg3 antibodies, alter the structural and functional properties of keratinocytes in two sequential steps - an initial loss of cell adhesion and a later induction of apoptosis-related signaling pathways, but not full apoptotic cell death. We propose a ''2-Hit'' model for autoimmune disruption associated with skin-specific pathogenic autoantibodies. These data provide unprecedented details of autoimmune processes at the tissue level and offer a novel conceptual framework for understanding the action of selfreactive antibodies.published_or_final_versio

Orchestration of signaling by structural disorder in class 1 cytokine receptors

Background:Class 1 cytokine receptors (C1CRs) are single-pass transmembrane proteins responsible for transmitting signals between the outside and the inside of cells. Remarkably, they orchestrate key biological processes such as proliferation, differentiation, immunity and growth through long disordered intracellular domains (ICDs), but without having intrinsic kinase activity. Despite these key roles, their characteristics remain rudimentarily understood.Methods:The current paper asks the question of why disorder has evolved to govern signaling of C1CRs by reviewing the literature in combination with new sequence and biophysical analyses of chain properties across the family.Results:We uncover that the C1CR-ICDs are fully disordered and brimming with SLiMs. Many of these short linear motifs (SLiMs) are overlapping, jointly signifying a complex regulation of interactions, including network rewiring by isoforms. The C1CR-ICDs have unique properties that distinguish them from most IDPs and we forward the perception that the C1CR-ICDs are far from simple strings with constitutively bound kinases. Rather, they carry both organizational and operational features left uncovered within their disorder, including mechanisms and complexities of regulatory functions.Conclusions:Critically, the understanding of the fascinating ability of these long, completely disordered chains to orchestrate complex cellular signaling pathways is still in its infancy, and we urge a perceptional shift away from the current simplistic view towards uncovering their full functionalities and potential

Attosecond physics at the nanoscale

Recently two emerging areas of research, attosecond and nanoscale physics, have started to come together. Attosecond physics deals with phenomena occurring when ultrashort laser pulses, with duration on the femto- and sub-femtosecond time scales, interact with atoms, molecules or solids. The laser-induced electron dynamics occurs natively on a timescale down to a few hundred or even tens of attoseconds, which is comparable with the optical field. On the other hand, the second branch involves the manipulation and engineering of mesoscopic systems, such as solids, metals and dielectrics, with nanometric precision. Although nano-engineering is a vast and well-established research field on its own, the merger with intense laser physics is relatively recent. In this article we present a comprehensive experimental and theoretical overview of physics that takes place when short and intense laser pulses interact with nanosystems, such as metallic and dielectric nanostructures. In particular we elucidate how the spatially inhomogeneous laser induced fields at a nanometer scale modify the laser-driven electron dynamics. Consequently, this has important impact on pivotal processes such as ATI and HHG. The deep understanding of the coupled dynamics between these spatially inhomogeneous fields and matter configures a promising way to new avenues of research and applications. Thanks to the maturity that attosecond physics has reached, together with the tremendous advance in material engineering and manipulation techniques, the age of atto-nano physics has begun, but it is in the initial stage. We present thus some of the open questions, challenges and prospects for experimental confirmation of theoretical predictions, as well as experiments aimed at characterizing the induced fields and the unique electron dynamics initiated by them with high temporal and spatial resolution

HI intensity mapping : a single dish approach

We discuss the detection of large scale HI intensity fluctuations using a single dish approach with the ultimate objective of measuring the Baryonic Acoustic Oscillations and constraining the properties of dark energy. We present 3D power spectra, 2D angular power spectra for individual redshift slices, and also individual line-of-sight spectra, computed using the S^3 simulated HI catalogue which is based on the Millennium Simulation. We consider optimal instrument design and survey strategies for a single dish observation at low and high redshift for a fixed sensitivity. For a survey corresponding to an instrument with T_sys=50 K, 50 feed horns and 1 year of observations, we find that at low redshift (z \approx 0.3), a resolution of 40 arc min and a survey of 5000 deg^2 is close to optimal, whereas at higher redshift (z \approx 0.9) a resolution of 10 arcmin and 500 deg^2 would be necessary. Continuum foreground emission from the Galaxy and extragalactic radio sources are potentially a problem. We suggest that it could be that the dominant extragalactic foreground comes from the clustering of very weak sources. We assess its amplitude and discuss ways by which it might be mitigated. We then introduce our concept for a single dish telescope designed to detect BAO at low redshifts. It involves an under-illumintated static 40 m dish and a 60 element receiver array held 90 m above the under-illuminated dish. Correlation receivers will be used with each main science beam referenced against an antenna pointing at one of the Celestial Poles for stability and control of systematics. We make sensitivity estimates for our proposed system and projections for the uncertainties on the power spectrum after 1 year of observations. We find that it is possible to measure the acoustic scale at z\approx 0.3 with an accuracy 2.4% and that w can be measured to an accuracy of 16%.Comment: 20 pages, 20 figures, submitted to MNRA

Influence of supramolecular forces on the linear viscoelasticity of gluten

Stress relaxation behavior of hydrated gluten networks was investigated by means of rheometry combined with μ-computed tomography (μ-CT) imaging. Stress relaxation behavior was followed over a wide temperature range (0–70 °C). Modulation of intermolecular bonds was achieved with urea or ascorbic acid in an effort to elucidate the presiding intermolecular interactions over gluten network relaxation. Master curves of viscoelasticity were constructed, and relaxation spectra were computed revealing three relaxation regimes for all samples. Relaxation commences with a well-defined short-time regime where Rouse-like modes dominate, followed by a power law region displaying continuous relaxation concluding in a terminal zone. In the latter zone, poroelastic relaxation due to water migration in the nanoporous structure of the network also contributes to the stress relief in the material. Hydrogen bonding between adjacent protein chains was identified as the determinant force that influences the relaxation of the networks. Changes in intermolecular interactions also resulted in changes in microstructure of the material that was also linked to the relaxation behavior of the networks