bluuebunny/crossref_metadata_2025 huggingface dataset:
Atomic-level insights into metabolite recognition and specificity of the SAM-II riboswitch
Authors: Doshi Urmi , Kelley Jennifer M. , Hamelberg Donald
Published: December 2011

Although S-adenosylhomocysteine (SAH), a metabolic by-product of S-adenosylmethionine (SAM), differs from SAM only by a single methyl group and an overall positive charge, SAH binds the SAM-II riboswitch with more than 1000-fold less affinity than SAM. Using atomistic molecular dynamics simulations, we investigated the molecular basis of such high selectivity in ligand recognition by SAM-II riboswitch. The biosynthesis of SAM exclusively generates the (S,S) stereoisomer, and (S,S)-SAM can spontaneously convert to the (R,S) form. We, therefore, also examined the effects of (R,S)-SAM binding to SAM-II and its potential biological function. We find that the unfavorable loss in entropy in SAM-II binding is greater for (S,S)- and (R,S)-SAM than SAH, which is compensated by stabilizing electrostatic interactions with the riboswitch. The positively charged sulfonium moiety on SAM acts as the crucial anchor point responsible for the formation of key ionic interactions as it fits favorably in the negatively charged binding pocket. In contrast, SAH, with its lone pair of electrons on the sulfur, experiences repulsion in the binding pocket of SAM-II and is enthalpically destabilized. In the presence of SAH, similar to the unbound riboswitch, the pseudoknot structure of SAM-II is not completely formed, thus exposing the Shine-Dalgarno sequence. Unlike SAM, this may further facilitate ribosomal assembly and translation initiation. Our analysis of the conformational ensemble sampled by SAM-II in the absence of ligands and when bound to SAM or SAH reveals that ligand binding follows a combination of conformational selection and induced-fit mechanisms.
Common and distinct patterns of terminal modifications to mirtrons and canonical microRNAs
Authors: Westholm Jakub O. , Ladewig Erik , Okamura Katsutomo , Robine Nicolas , Lai Eric C.
Published: December 2011

Nucleotide modifications to microRNAs or their precursors can influence their processing and/or activity. A challenge to their analysis is the lack of independent references for the termini generated by primary processing; typically, these are empirically assigned as the most abundant mapped reads. Mirtrons offer such an independent measure since these microRNA hairpins are defined by splicing. Consequently, mirtron-derived reads that deviate from splice sites reflect modification following primary processing. Analysis in Drosophila revealed multiple modification patterns, including select alterations of 5′ termini, many 3′ resection events, and unexpectedly abundant 3′ untemplated monouridylation. Resections occur on mature AGO1-loaded species, whereas uridylation occurs on pre-miRNAs but is compatible with dicing and AGO1 loading. Strikingly, we found many mirtrons whose modified reads are more abundant than those produced by primary processing. In some cases, these abundant modified reads matched the genome owing to fortuitous uridines in downstream flanking exons, thus highlighting the value of an independent reference for the primary-processed sequence. We could further extend the principle of abundant and preferred uridylation of mirtrons, relative to canonical pre-miRNAs, to Caenorhabditis elegans, mouse, and human. Finally, we found that 3′ resection occurs broadly across AGO1-loaded canonical miRNA and star species. Altogether, these findings substantially broaden the complexity of terminal modification pathways acting upon small regulatory RNAs.
Broadening Focus: Spillovers, Complementarities, and Specialization in the Hospital Industry
Authors: Clark Jonathan R. , Huckman Robert S.
Published: December 2011

The long-standing argument that focused operations outperform others stands in contrast to claims about the benefits of broader operational scope. The performance benefits of focus are typically attributed to reduced complexity, lower uncertainty, and the development of specialized expertise; the benefits of greater breadth are linked to the economies of scope achieved by sharing common resources, such as advertising or production capacity, across activities. Within the literature on corporate strategy, this tension between focus and breadth is reconciled by the concept of related diversification (i.e., a firm with multiple operating units, each specializing in distinct but related activities). We consider whether there are similar benefits to related diversification within an operating unit and examine the mechanism that generates these benefits. Using the empirical context of cardiovascular care within hospitals, we first examine the relationship between a hospital's level of specialization in cardiovascular care and the quality of its clinical performance on cardiovascular patients. We find that, on average, focus has a positive effect on quality performance. We then distinguish between positive spillovers and complementarities to examine (1) the extent to which a hospital's specialization in areas related to cardiovascular care directly impacts performance on cardiovascular patients (positive spillovers) and (2) whether the marginal benefit of a hospital's focus in cardiovascular care depends on the degree to which the hospital “cospecializes” in related areas (complementarities). In our setting, we find evidence of such complementarities in specialization.

This paper was accepted by Christian Terwiesch, operations management.
Beyond the Glass Ceiling: Does Gender Matter?
Authors: Adams Renée B. , Funk Patricia
Published: December 2011

A large literature documents that women are different from men in their choices and preferences, but little is known about gender differences in the boardroom. If women must be like men to break the glass ceiling, we might expect gender differences to disappear among directors. Using a large survey of directors, we show that female and male directors differ systematically in their core values and risk attitudes, but in ways that differ from gender differences in the general population. These results are robust to controlling for differences in observable characteristics. Consistent with findings for the population, female directors are more benevolent and universally concerned but less power oriented than male directors. However, in contrast to findings for the population, they are less tradition and security oriented than their male counterparts. They are also more risk loving than male directors. Thus, having a woman on the board need not lead to more risk-averse decision making.

This paper was accepted by Brad Barber, Teck Ho, and Terrance Odean, special issue editors.
Railway Rolling Stock Planning: Robustness Against Large Disruptions
Authors: Cacchiani Valentina , Caprara Alberto , Galli Laura , Kroon Leo , Maróti Gábor , Toth Paolo
Published: December 2011

In this paper we describe a two-stage optimization model for determining robust rolling stock circulations for passenger trains. Here robustness means that the rolling stock circulations can better deal with large disruptions of the railway system. The two-stage optimization model is formulated as a large mixed-integer linear programming (MILP) model. We first use Benders decomposition to determine optimal solutions for the LP-relaxation of this model. Then we use the cuts that were generated by the Benders decomposition for computing heuristic robust solutions for the two-stage optimization model. We call our method Benders heuristic. We evaluate our approach on the real-life rolling stock-planning problem of Netherlands Railways, the main operator of passenger trains in the Netherlands. The computational results show that, thanks to Benders decomposition, the LP-relaxation of the two-stage optimization problem can be solved in a short time for a representative number of disruption scenarios. In addition, they demonstrate that the robust rolling stock circulation computed heuristically has total costs that are close to the LP lower bounds. Finally, we discuss the practical effectiveness of the robust rolling stock circulation: When a large number of disruption scenarios were applied to these robust circulations and to the nonrobust optimal circulations, the former appeared to be much more easily recoverable than the latter.
Indoor Allergen Surface Sampling Methods and Standards: A Review of the Theory and the Practice
Authors: Lewis Roger D. , Chen Daren
Published: December 2011

Understanding the relationship among allergies, asthma, and indoor air allergen triggers increasingly require use of standardized and evidence based exposure assessment methods. Exposure assessment for common indoor allergens, however, is often limited by use of surface in place of air sampling for a variety of reasons. Chief among them is that many indoor allergens settle to the ground quickly after being released. Another reason for the wide-spread use of surface over air sampling for indoor air allergens is that air sampling is typically performed over a limited time frame and plausibly cannot capture a composite of exposure that a surface sample can. Protocols have been developed to collect surface borne allergen in several US wide-national studies, and while these samplers may provide an adequate means to correlate composite dust mass or allergens to some specific health outcomes, there is still a lack of evidence to support their adoption on the basis of several criteria which stem from theoretical and evidence based considerations. To become more valuable tools to risk assessment, epidemiological studies, and environmental intervention, surface sampling methods should be constructed using basic principles of particle behavior on surfaces as well as in the air. Criteria need to be developed from these principles and studies that address these criteria should be used or developed to enable the creation of performance-based standards. This paper is a review of the literature, which highlights surface sampling methods that have taken this theory- or evidence-based approach. After the review, a discussion is then developed on the current state-of-the-art surface sampling for indoor allergens. Recommendations are suggested for both future theoretical or empirical work necessary for devising performance standards for sampling and collecting surface borne-allergens.
Improving the Confidence Level in Lead Clearance Examination Results through Modifications to Dust Sampling Protocols
Authors: Cox David C. , Dewalt F. Gary , White Kenneth T. , Schmehl Richard , Friedman Warren , Pinzer Eugene A.
Published: December 2011

Multiple pre-cleaned, four-room residential containments were each subjected to a single high-dust generating activity involving lead-based paint. After dust generation, a geometric wipe sampling grid was used, with a target of 8 interior and 8 perimeter samples in each room, to assess dust-lead on the floors. The containment was then cleaned using the “High Efficiency Particulate Air (HEPA) vacuum/3-bucket wet-mop/HEPA vacuum” procedure found in the U.S. Dept. of Housing and Urban Development Guidelines. Post-cleaning (clearance) floor wipe samples were then taken at side-by-side locations to the pre-cleaning samples. It was found that: [1] floor dust-lead along the perimeters of rooms was three times more difficult to clean than dust-lead from the interiors of the rooms; [2] post-cleaning dust-lead loadings tended to be higher along the perimeters of the rooms than in the interiors of the rooms such that clearance failure was much more likely for individual floor samples collected along the perimeters; and [3] four-wipe composite sampling within each room (two randomly selected from the perimeter and two randomly selected from the interior) provided a very reliable method for detecting clearance failure (99% or greater) versus a randomly selected single wipe sample per room (50% or less).
Pilot Evaluation for Lead-Based Paint Proficiency Testing of Field Portable XRF Instruments
Authors: White Kenneth T. , Dewalt F. Gary , Cox David C. , Schmehl Richard , Friedman Warren , Pinzer Eugene A.
Published: December 2011

A proficiency testing procedure for evaluating the accuracy of lead measurements taken by certified lead-based paint inspectors using portable X-ray fluorescence (XRF) instruments was developed and pilot tested. XRF instruments are widely used for inspection of housing units to determine the presence or absence of lead-based paint. Previous research showed variability between different XRF instruments when used to conduct lead-based paint inspections. Due to concerns over potential errors in inspection reports resulting from biased XRF measurements, a proficiency testing procedure was pilot tested to provide entities, such a state or federal regulators, a means of evaluating the instrumentation being used for lead-based paint inspections.
The Feasibility of Studying the Health Implications of Surface Beryllium Contamination: A Review of Eight Industries
Authors: McCawley M.
Published: December 2011

It has been suggested that beryllium can enter through either intact skin or breaks in the skin to initiate sensitization. Therefore, it is essential that all possible pathways of exposure be considered when assessing a work site for potential exposure to beryllium. A meta-analysis was done on the data from eight different industries that use beryllium or beryllium alloys, which were surveyed by Occupational Safety and Health Administration contractors, with reports being issued. During those visits, measurements were made to characterize worker exposure to skin and surface contamination levels of beryllium. Surface contamination evaluation followed the well-established protocol for lead surface contamination measurements using NIOSH Method 9100 and hand contamination using NIOSH Method 9102. It was found that both the arithmetic and geometric means of the surface samples were significantly higher in work areas as compared to administrative areas. Skin samples were also higher for individuals in production areas than for those in non-production areas. If skin contamination is a route of sensitization, these results would mean that past studies of beryllium exposure and subsequent disease might have been confounded by the lack of skin exposure data.
Application of ASTM Standard Practice D6602 in the Investigation of Outdoor Environmental Surface Particulate Including Darkening Agents
Authors: Millette James R. , Rook Harry L. , Compton Steven
Published: December 2011

ASTM D6602 “Standard Practice for Sampling and Testing of Possible Carbon Black Fugitive Emissions or Other Environmental Particulate, or Both” was developed for the investigation of outdoor sooty surface problems and distinguishing manufactured carbon black, in the N100 to N900 series, from other environmental particulates. It is a microscopy technique that is well suited for the study of darkening agent complaints. Samples are collected from surfaces with cotton balls, wipes, and tape-lifts. The particulate is then analyzed by light microscopy and electron microscopy. The practice is used as a means to differentiate between darkening caused by fungal growth (biofilms), soots, or other dark particles. Polarized light microscopy provides information about the relative amounts of the different types of particles present and some information about the type of biofilm, if present. Transmission electron microscopy provides confirmation of aciniform soot, if present, and some information about the possible source of the soot. An investigation of dark surface particulate in a city where both a carbon black manufacturing facility and an oil refinery were possible industrial sources provides an illustration of the use of the method.
Variants in KITLG predispose to testicular germ cell cancer independently from spermatogenic function
Authors: Ferlin Alberto , Pengo Manuel , Pizzol Damiano , Carraro Umberto , Frigo Anna Chiara , Foresta Carlo
Published: December 2011

Epidemiological data suggest an association and a common pathogenetic link between male infertility and testicular germ cell tumor (TGCT) development. Genome-wide studies identified that TGCT susceptibility is associated withKITLG(c-KIT ligand), which regulates the formation of primordial germ cells, from which TGCT is believed to arise and spermatogenesis develops. In this study, we analyzed the link betweenKITLG, TGCT, and spermatogenic disruption by performing an association study between theKITLGmarkers rs995030 and rs4471514 and 426 TGCT cases and 614 controls with normal and abnormal sperm count. We found that TGCT risk was increased more than twofold per copy of the major G allele and A allele inKITLGrs995030 and rs4471514 (odds ratio (OR)=2.38, 95% confidence interval (95% CI)=1.81–3.12; OR=2.43, 95% CI=1.86–3.17 respectively), and homozygotes for the risk allele had a sevenfold increased risk of TGCT.KITLGmarkers were strongly associated with seminoma subtype (per allele risk increased more than threefold, homozygote risk increased by 13- to 16-fold) and weakly with nonseminoma.KITLGmarkers were not associated with sperm production, as no difference was observed in men with normozoospermia and azoo–oligozoospermia, both in controls and in TGCT cases. In conclusion, this study provides evidence thatKITLGvariants are involved in TGCT development and they represent an independent and strong specific risk factor for TGCT independently from spermatogenic function. A shared genetic cause and a common pathogenetic link between TGCT development and impairment of spermatogenesis are not evident from this study.
Vitamin D Therapy in Chronic Kidney Disease and End Stage Renal Disease
Authors: Melamed Michal L. , Thadhani Ravi I.
Published: December 2011

Vitamin D has garnered much research and debate about supplementation in recent years, not only as it pertains to patients with kidney disease but also to those in the general population. This review discusses observational and available clinical trial evidence about the effects of both calcitriol and vitamin D analogs (active) and ergocalciferol and cholecalciferol (nutritional) vitamin D in patients with CKD and ESRD.
Attending Rounds
Authors: Clark William F. , Hildebrand Ainslie
Published: December 2011

The classification of thrombotic microangiopathy has evolved and expanded due to treatment and advances in understanding of the diseases associated with this clinical presentation. The three clinical forms of thrombotic microangiopathy—thrombotic thrombocytopenic purpura (TTP), hemolytic uremic syndrome (HUS), and disseminated intravascular coagulation—encompass a wide range of disorders that can be classified as either primary (idiopathic) or secondary to another identifiable disease or clinical context. Identification of an inhibitor to a disintegrin and metalloproteinase with a thrombospondin type 1 motif, member 13 (ADAMTS13) in the idiopathic and acute forms of TTP, recognition of the absence of ADAMTS13 inhibition in diarrheal HUS, identification of complement abnormalities in atypical HUS, and a better understanding of the role of plasma therapy, rituximab, and eculizumab therapy have all had a major effect on current understanding of the thrombotic microangiopathies. In this Attending Rounds, a patient with a thrombotic microangiopathy is presented, along with discussion highlighting the difficulty of differentiating TTP from HUS and disseminated intravascular coagulation, the need for a prompt diagnosis, and the role for plasma therapy in appropriately selected patients. The discussion attempts to provide a simple clinical approach to the diagnosis, treatment options, and future course of adults and children suffering from a thrombotic microangiopathy.
Dataset Preservation for the Long Term: Results of the DareLux Project
Authors: Dürr Eugène , Van der Meer Kees , Luxemburg Wim , Dekker Ronald
Published: December 2011

The purpose of the DareLux (Data Archiving River Environment Luxembourg) Project was the preservation of unique and irreplaceable datasets, for which we chose hydrology data that will be required to be used in future climatic models. The results are: an operational archive built with XML containers, the OAI-PMH protocol and an architecture based upon web services. Major conclusions are: quality control on ingest is important; digital rights management demands attention; and cost aspects of ingest and retrieval cannot be underestimated. We propose a new paradigm for information retrieval of this type of dataset. We recommend research into visualisation tools for the search and retrieval of this type of dataset.
Curation of Laboratory Experimental Data as Part of the Overall Data Lifecycle
Authors: Frey Jeremy
Published: December 2011

The explosion in the production of scientific data in recent years is placing strains upon conventional systems supporting integration, analysis, interpretation and dissemination of data and thus constraining the whole scientific process. Support for handling large quantities of diverse information can be provided by e-Science methodologies and the cyber-infrastructure that enables collaborative handling of such data. Regard needs to be taken of the whole process involved in scientific discovery. This includes the consideration of the requirements of the users and consumers further down the information chain and what they might ideally prefer to impose on the generators of those data. As the degree of digital capture in the laboratory increases, it is possible to improve the automatic acquisition of the ‘context of the data’ as well as the data themselves. This process provides an opportunity for the data creators to ensure that many of the problems they often encounter in later stages are avoided. We wish to elevate curation to an operation to be considered by the laboratory scientist as part of good laboratory practice, not a procedure of concern merely to the few specialising in archival processes. Designing curation into experiments is an effective solution to the provision of high-quality metadata that leads to better, more re-usable data and to better science.
Challenges and Issues Relating to the Use of Representation Information for the Digital Curation of Crystallography and Engineering Data
Authors: Patel Manjula , Ball Alexander
Published: December 2011

The OAIS concept of Representation Information (RI) is a potential strategy for the curation and preservation of all types of information. We share insights gained from our exploration of issues concerned with the capture of crystallography and engineering RI as well as its structuring, collection and curation. In addition, we discuss the supporting technical, IPR and globally collaborative infrastructures required to make such a strategy successful.
The DCC / Regional eScience Collaborative Workshop
Authors: Donnelly Martin
Published: December 2011

A report from the Digital Curation Centre (DCC) / Regional eScience Collaborative Workshop, held at the eScience Institute in Edinburgh on June 12, 2008. The DCC is committed to forging and strengthening links between the digital preservation and eScience communities via its eScience Liaison team. This event was the fifth in a series of workshops which are being arranged throughout the UK, with a view to helping the DCC learn more about the eScience perspective on data curation, and to giving eScience practitioners an opportunity to influence the current and future work of the DCC. The workshop took data sharing as its central theme.
Review: Scholarship in the Digital Age
Authors: Rusbridge Chris
Published: December 2011

A review of Scholarship in the Digital Age: Information, Infrastructure, and the Internet by Christine Borgman, MIT Press, 2007, hardback, 336 pp, ISBN-13: 978-0262026192.
SCOPE: A Scientific Compound Object Publishing and Editing System
Authors: Cheung Kwok , Hunter Jane , Lashtabeg Anna , Drennan John
Published: December 2011

This paper presents the SCOPE (Scientific Compound Object Publishing and Editing) system which is designed to enable scientists to easily author, publish and edit scientific compound objects. Scientific compound objects encapsulate the various datasets and resources generated or utilized during a scientific experiment or discovery process, within a single compound object, for publishing and exchange. The adoption of “named graphs” to represent these compound objects enables provenance information to be captured via the typed relationships between the components. This approach is also endorsed by the OAI-ORE initiative and hence ensures that we generate OAI-ORE-compliant Scientific Compound Objects. The SCOPE system is an extension of the Provenance Explorer tool – which supports access-controlled viewing of scientific provenance trails. Provenance Explorer provided dynamic rendering of RDF graphs of scientific discovery processes, showing the lineage from raw data to publication. Views of different granularity can be inferred automatically using SWRL (Semantic Web Rules Language) rules and an inferencing engine. SCOPE extends the Provenance Explorer tool and GUI by: 1) Adding an embedded web browser that can be used for incorporating objects discoverable via the Web; 2) Representing compound objects as Named Graphs, that can be saved in RDF, TriX, TriG or as an Atom syndication feed; 3) Enabling scientists to attach Creative Commons Licenses to the compound objects to specify how they may be re-used; 4) Enabling compound objects to be published as Fedora Object XML (FOXML) files within a Fedora digital library.
The Publication of Research Data: Researcher Attitudes and Behaviour
Authors: Griffiths Aaron
Published: December 2011

There is now widespread recognition that data are a valuable long-term resource and that making them publicly available is a way to realise their potential value - both as part of the scholarly record or for re-use by others. The Research Information Network (RIN) report, To share or not to share: Publication and quality assurance of research data outputs (June 2008), investigates whether or not researchers make their research data available to others and the issues they encounter when doing so. Importantly, it seeks to do this by seeking the perspectives of researchers themselves. This paper reflects on how this relates to the more top-down literature on the subject. The discussion of the significance of the RIN's main findings is correlated to the four themes of the RIN report. Firstly, it discusses some distinctions in the types of data that should be shared and preserved and what needs to done to do so effectively. Secondly, it reflects on the motivations for and constraints on researchers publishing their data, and how funders and publishers can address them. Thirdly, it reviews some issues around how data are discovered, accessed and re-used. Finally, it discusses the scholarly and technical quality of published data.
Curating Architectural 3D CAD Models
Authors: Smith MacKenzie
Published: December 2011

Increasing demand to manage and preserve 3-dimensional models for a variety of physical phenomena (e.g., building and engineering designs, computer games, or scientific visualizations) is creating new challenges for digital archives. Preserving 3D models requires identifying technical formats for the models that can be maintained over time, and the available formats offer different advantages and disadvantages depending on the intended future uses of the models. Additionally, the metadata required to manage 3D models is not yet standardized, and getting intellectual proposal rights for digital models is uncharted territory.Â  The FACADE Project at MIT is investigating these challenges in the architecture, engineering and construction (AEC) industry and has developed recommendations and systems to support digital archives in dealing with digital 3D models and related data. These results can also be generalized to other domains doing 3D modeling.
Embedding Metadata and Other Semantics in Word Processing Documents
Authors: Sefton Peter , Barnes Ian , Ward Ron , Downing Jim
Published: December 2011

This paper describes a technique for embedding document metadata, and potentially other semantic references inline in word processing documents, which the authors have implemented with the help of a software development team. Several assumptions underly the approach; It must be available across computing platforms and work with both Microsoft Word (because of its user base) and OpenOffice.org (because of its free availability). Further the application needs to be acceptable to and usable by users, so the initial implementation covers only small number of features, which will only be extended after user-testing. Within these constraints the system provides a mechanism for encoding not only simple metadata, but for inferring hierarchical relationships between metadata elements from a ‘flat’ word processing file.The paper includes links to open source code implementing the techniques as part of a broader suite of tools for academic writing. This addresses tools and software, semantic web and data curation, integrating curation into research workflows and will provide a platform for integrating work on ontologies, vocabularies and folksonomies into word processing tools.
Using the DCC Lifecycle Model to Curate a Gene Expression Database: A Case Study
Authors: Oâ€™Donoghue Jean , Van Hemert Jano I.
Published: December 2011

Developmental Gene Expression Map (DGEMap) is an EU-funded Design Study, which will accelerate an integrated European approach to gene expression in early human development. As part of this design study, we have had to address the challenges and issues raised by the long-term curation of such a resource. As this project is primarily one of data creators, learning about curation, we have been looking at some of the models and tools that are already available in the digital curation field in order to inform our thinking on how we should proceed with curating DGEMap. This has led us to uncover a wide range of resources for data creators and curators alike. Here we will discuss the future curation of DGEMap as a case study. We believe our experience could be instructive to other projects looking to improve the curation and management of their data.
Enduring Access to Digitized Books: Organizational and Technical Framework
Authors: Rieger Oya Y. , Kehoe William R.
Published: December 2011

The digitization of millions of books under corporate and non-profit programs is dramatically expanding our ability to search, discover, and retrieve published materials. Accompanying this progress are cultural heritage institutions’ concerns about the long-term management challenges associated with providing enduring access to a hlarge corpus of digitized materials, especially within the confinements of copyright laws. The goal of this presentation is to describe Cornell University Library’s program to illustrate a range of organizational and technical issues involved in planning and implementing a preservation infrastructure for digitized books.
Long-term Preservation of Earth Observation Data and Knowledge in ESA through CASPAR
Authors: Albani Sergio , Giaretta David
Published: December 2011

ESA-ESRIN, the European Space Agency Centre for Earth Observation (EO), is the largest European EO data provider and operates as the reference European centre for EO payload data exploitation. EO Space Missions provide global coverage of the Earth across both space and time generating on a routine continuous basis huge amounts of data (from a variety of sensors) that need to be acquired, processed, elaborated, appraised and archived by dedicated systems. Long-term Preservation of these data and of the ability to discover, access and process them is a fundamental issue and a major challenge at programmatic, technological and operational levels.Moreover these data are essential for scientists needing broad series of data covering long time periods and from many sources. They are used for many types of investigations including ones of international importance such as the study of the Global Change and the Global Monitoring for Environment and Security (GMES) Program. Therefore it is of primary importance not only to guarantee easy accessibility of historical data but also to ensure users are able to understand and use them; in fact data interpretation can be even more complicated given the fact that scientists may not have (or may not have access to) the right knowledge to interpret these data correctly.To satisfy these requirements, the European Space Agency (ESA), in addition to other internal initiatives, is participating in several EU-funded projects such as CASPAR (Cultural, Artistic, and Scientific knowledge for Preservation, Access and Retrieval), which is building a framework to support the end-to-end preservation lifecycle for digital information, based on the OAIS reference model, with a strong focus on the preservation of the knowledge associated with data.In the CASPAR Project ESA plays the role of both user and infrastructure provider for one of the scientific testbeds, putting into effect dedicated scenarios with the aim of validating the CASPAR solutions in the Earth Science domain. The other testbeds are in the domains of Cultural Heritage and of Contemporary Performing Arts; together they provide a severe test of preservation tools and techniques.In the context of the current ESA overall strategies carried out in collaboration with European EO data owners/providers, entities and institutions which have the objective of guaranteeing long-term preservation of EO data and knowledge, this paper will focus on the ESA participation and contribution to the CASPAR Project, describing in detail the implementation of the ESA scientific testbed.
Designing Digital Preservation Solutions: A Risk Management-Based Approach
Authors: Barateiro José , Antunes Gonçalo , Freitas Filipe , Borbinha José
Published: December 2011

Digital preservation aims to keep digital objects accessible over long periods of time, ensuring the authenticity and integrity of these digital objects. In such complex environments, Risk Management is a key factor in assuring the normal behaviour of systems over time. Currently, the digital preservation arena commonly uses Risk Management concepts to assess repositories. In this paper, we intend to go further and propose a perspective where Risk Management can be used not only to assess existing solutions, but also to conceive digital preservation environments. Thus, we propose a Risk Management-based approach to design and assess digital preservation environments, including:â€¢ the definition of context and identification of strategic objectives to determine specific requirements and characterize which consequences are acceptable within the identified context;â€¢ the identification, analysis and evaluation of threats and vulnerabilities that may affect the normal behaviour of a specific business or the achievement of the goals and conformance to the requirements identified in the context characterization; and, â€¢ definition of actions to deal with the risks associated with the identified threats and vulnerabilities.We generalize and survey the main requirements, threats, vulnerabilities and techniques that can be applied in the scope of digital preservation.
Chronopolis Digital Preservation Network
Authors: Minor David , Sutton Don , Kozbial Ardys , Westbrook Brad , Burek Michael , Smorul Michael
Published: December 2011

The Chronopolis Digital Preservation Initiative, one of the Library of Congress’ latest efforts to collect and preserve at-risk digital information, has completed its first year of service as a multi-member partnership to meet the archival needs of a wide range of domains.Chronopolis is a digital preservation data grid framework developed by the San Diego Supercomputer Center (SDSC) at UC San Diego, the UC San Diego Libraries (UCSDL), and their partners at the National Center for Atmospheric Research (NCAR) in Colorado and the University of Maryland's Institute for Advanced Computer Studies (UMIACS).Chronopolis addresses a critical problem by providing a comprehensive model for the cyberinfrastructure of collection management, in which preserved intellectual capital is easily accessible, and research results, education material, and new knowledge can be incorporated smoothly over the long term. Integrating digital library, data grid, and persistent archive technologies, Chronopolis has created trusted environments that span academic institutions and research projects, with the goal of long-term digital preservation.A key goal of the Chronopolis project is to provide cross-domain collection sharing for long-term preservation. Using existing high-speed educational and research networks and mass-scale storage infrastructure investments, the partnership is leveraging the data storage capabilities at SDSC, NCAR, and UMIACS to provide a preservation data grid that emphasizes heterogeneous and highly redundant data storage systems.In this paper we will explore the major themes within Chronopolis, including:a) The philosophy and theory behind a nationally federated data grid for preservation. b) The core tools and technologies used in Chronopolis. c) The metadata schema that is being developed within Chronopolis for all of the data elements. d) Lessons learned from the first year of the project.e) Next steps in digital preservation using Chronopolis: how we plan to strengthen and broaden our network with enhanced services and new customers.
Use of Ontologies for Data Integration and Curation
Authors: Gelernter Judith , Lesk Michael
Published: December 2011

Data curation includes the goal of facilitating the re-use and combination of datasets, which is often impeded by incompatible data schema. Can we use ontologies to help with data integration? We suggest a semi-automatic process that involves the use of automatic text searching to help identify overlaps in metadata that accompany data schemas, plus human validation of suggested data matches.Problems include different text used to describe the same concept, different forms of data recording and different organizations of data. Ontologies can help by focussing attention on important words, providing synonyms to assist matching, and indicating in what context words are used. Beyond ontologies, data on the statistical behavior of data can be used to decide which data elements appear to be compatible with which other data elements. When curating data which may have hundreds or even thousands of data labels, semi-automatic assistance with data fusion should be of great help.
Migrating Home Computer Audio Waveforms to Digital Objects: A Case Study on Digital Archaeology
Authors: Guttenbrunner Mark , Ghete Mihai , John Annu , Lederer Chrisanth , Rauber Andreas
Published: December 2011

Rescuing data from inaccessible or damaged storage media for the purpose of preserving the digital data for the long term is one of the dimensions of digital archaeology. With the current pace of technological development, any system can become obsolete in a matter of years and hence the data stored in a specific storage media might not be accessible anymore due to the unavailability of the system to access the media. In order to preserve digital records residing in such storage media, it is necessary to extract the data stored in those media by some means.One early storage medium for home computers in the 1980s was audio tape. The first home computer systems allowed the use of standard cassette players to record and replay data. Audio cassettes are more durable than old home computers when properly stored. Devices playing this medium (i.e. tape recorders) can be found in working condition or can be repaired, as they are usually made out of standard components. By re-engineering the format of the waveform and the file formats, the data on such media can then be extracted from a digitised audio stream and migrated to a non-obsolete format.In this paper we present a case study on extracting the data stored on an audio tape by an early home computer system, namely the Philips Videopac+ G7400. The original data formats were re-engineered and an application was written to support the migration of the data stored on tapes without using the original system. This eliminates the necessity of keeping an obsolete system alive for enabling access to the data on the storage media meant for this system. Two different methods to interpret the data and eliminate possible errors in the tape were implemented and evaluated on original tapes, which were recorded 20 years ago. Results show that with some error correction methods, parts of the tapes are still readable even without the original system. It also implies that it is easier to build solutions while original systems are still available in a working condition.
Open Science in Practice: Researcher Perspectives and Participation
Authors: Whyte Angus , Pryor Graham
Published: December 2011

We report on an exploratory study consisting of brief case studies in selected disciplines, examining what motivates researchers to work (or want to work) in an open manner with regard to their data, results and protocols, and whether advantages are delivered by working in this way. We review the policy background to open science, and literature on the benefits attributed to open data, considering how these relate to curation and to questions of who participates in science. The case studies investigate the perceived benefits to researchers, research institutions and funding bodies of utilising open scientific methods, the disincentives and barriers, and the degree to which there is evidence to support these perceptions. Six case study groups were selected in astronomy, bioinformatics, chemistry, epidemiology, language technology and neuroimaging. The studies identify relevant examples and issues through qualitative analysis of interview transcripts. We provide a typology of degrees of open working across the research lifecycle, and conclude that better support for open working, through guidelines to assist research groups in identifying the value and costs of working more openly, and further research to assess the risks, incentives and shifts in responsibility entailed by opening up the research process are needed.
Educating Digital Curators: Challenges and Opportunities
Authors: Botticelli Peter , Fulton Bruce , Pearce-Moses Richard , Szuter Christine , Watters Pete
Published: December 2011

This paper describes a number of critical challenges faced by digital curation educators and suggests how the choices we make in building educational programs may impact the development of curation as a professional discipline. We focus on curriculum and program building as key steps in defining the educational needs of curators, and we argue for greater collaboration among educators, researchers and practitioners in the field, as a way to speed the emergence of curation as a discipline and to foster the integration of curation programs within libraries and archives.
A Practice and Value Proposal for Doctoral Dissertation Data Curation
Authors: Collie W. Aaron , Witt Michael
Published: December 2011

The preparation and publication of dissertations can be viewed as a subsystem of scholarly communication, and the treatment of data that support doctoral research can be mapped in a very controlled manner to the data curation lifecycle. Dissertation datasets represent “low-hanging fruit” for universities who are developing institutional data collections. The current workflow for processing electronic theses and dissertations (ETD) at a typical American university is presented, and a new practice is proposed that includes datasets in the process of formulating, awarding, and disseminating dissertations in a way that enables them to be linked and curated together. The value proposition and new roles for the university and its student-authors, faculty, graduate programs and librarians are explored.
Digital Curation Education in Practice: Catching up with Two Former Fellows
Authors: Gregory Lisa , Guss Samantha
Published: December 2011

From 2008-2010, as part of the grant: ‘DigCCurr I: Preserving Access to Our Digital Future: Building an International Digital Curation Curriculum’ (DigCCurr I) funded through the Institute of Museum and Library Services, a number of fellows at the School of Information and Library Science (SILS) at the University of North Carolina at Chapel Hill (UNC-CH) were comprehensively trained by library and archive professionals in digital curation theory and practice. This paper examines the curriculum skill areas matrix of the DigCCurr I program from the perspective of two former fellows, now employed in professional positions that utilize digital curation principles. Each fellow offers an analysis of digital curation functions and subfunctions as they relate to her current position, deriving suggestions for future iterations of the DigCCurr program and other graduate programs meant to prepare digital curators. While DigCCurr has been reported by its creators, a group of seasoned digital curation professionals and educators from around the world, this paper provides a fresh perspective from graduates of the program who are applying their newly learned digital curation skills and knowledge in the workforce.
TextGrid – Virtual Research Environment for the Humanities
Authors: Neuroth Heike , Lohmeier Felix , Smith Kathleen Marie
Published: December 2011

The TextGrid research group, a consortium of 10 research institutions in Germany, is developing a virtual research environment for researchers in the arts and humanities that provides services and tools for the analysis of text data and supports the curation of research data by means of grid technology. The TextGrid virtual research environment consists of two main components: the TextGrid Laboratory (TextGridLab), which serves as the entry point to the virtual research environment, and the TextGrid Repository (TextGridRep), which is a long-term humanities data archive ensuring sustainability, interoperability and long-term access to research data. To support all stages of the research lifecycle, preserve and maintain research data, and ensure its long-term usefulness, existing research practices must be supported. Therefore the TextGridLab provides common functionalities in a sustainable environment to intensify re-use of data, tools, and services, and the TextGridRep enables researchers to publish and share their data in a way that supports long-term availability and re-usability.
Citation and Peer Review of Data: Moving Towards Formal Data Publication
Authors: Lawrence Bryan , Jones Catherine , Matthews Brian , Pepler Sam , Callaghan Sarah
Published: December 2011

This paper discusses many of the issues associated with formally publishing data in academia, focusing primarily on the structures that need to be put in place for peer review and formal citation of datasets. Data publication is becoming increasingly important to the scientific community, as it will provide a mechanism for those who create data to receive academic credit for their work and will allow the conclusions arising from an analysis to be more readily verifiable, thus promoting transparency in the scientific process. Peer review of data will also provide a mechanism for ensuring the quality of datasets, and we provide suggestions on the types of activities one expects to see in the peer review of data. A simple taxonomy of data publication methodologies is presented and evaluated, and the paper concludes with a discussion of dataset granularity, transience and semantics, along with a recommended human-readable citation syntax.