75 FR 26788 - Public Land Order No. 7742; Withdrawal of Public Land for the Manning Canyon Tailings Repository; UT

Science.gov (United States)

2010-05-12

... 79765] Public Land Order No. 7742; Withdrawal of Public Land for the Manning Canyon Tailings Repository... period of 5 years to protect the integrity of the Manning Canyon Tailings Repository and surrounding... withdrawal is to protect public health and safety and the Federal investment in the Manning Canyon Tailings...

Compliance with minimum information guidelines in public metabolomics repositories.

Science.gov (United States)

Spicer, Rachel A; Salek, Reza; Steinbeck, Christoph

2017-09-26

The Metabolomics Standards Initiative (MSI) guidelines were first published in 2007. These guidelines provided reporting standards for all stages of metabolomics analysis: experimental design, biological context, chemical analysis and data processing. Since 2012, a series of public metabolomics databases and repositories, which accept the deposition of metabolomic datasets, have arisen. In this study, the compliance of 399 public data sets, from four major metabolomics data repositories, to the biological context MSI reporting standards was evaluated. None of the reporting standards were complied with in every publicly available study, although adherence rates varied greatly, from 0 to 97%. The plant minimum reporting standards were the most complied with and the microbial and in vitro were the least. Our results indicate the need for reassessment and revision of the existing MSI reporting standards.

Proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies

DEFF Research Database (Denmark)

Bennike, Tue Bjerg; Kastaniegaard, Kenneth; Padurariu, Simona

2016-01-01

Large repositories of well characterized RNAlater preserved samples and formalin-fixed, paraffin-embedded samples have been generated worldwide. However, the impact on the proteome of the preservation methods remain poorly described. Therefore, we analyzed the impact on the proteome of preserving...... throughput gel free quantitative proteomics. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PRIDE: PXD002029....

Personal Spaces in Public Repositories as a Facilitator for Open Educational Resource Usage

Science.gov (United States)

Cohen, Anat; Reisman, Sorel; Sperling, Barbra Bied

2015-01-01

Learning object repositories are a shared, open and public space; however, the possibility and ability of personal expression in an open, global, public space is crucial. The aim of this study is to explore personal spaces in a big learning object repository as a facilitator for adoption of Open Educational Resources (OER) into teaching practices…

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.

Science.gov (United States)

Perez-Riverol, Yasset; Xu, Qing-Wei; Wang, Rui; Uszkoreit, Julian; Griss, Johannes; Sanchez, Aniel; Reisinger, Florian; Csordas, Attila; Ternent, Tobias; Del-Toro, Noemi; Dianes, Jose A; Eisenacher, Martin; Hermjakob, Henning; Vizcaíno, Juan Antonio

2016-01-01

The original PRIDE Inspector tool was developed as an open source standalone tool to enable the visualization and validation of mass-spectrometry (MS)-based proteomics data before data submission or already publicly available in the Proteomics Identifications (PRIDE) database. The initial implementation of the tool focused on visualizing PRIDE data by supporting the PRIDE XML format and a direct access to private (password protected) and public experiments in PRIDE.The ProteomeXchange (PX) Consortium has been set up to enable a better integration of existing public proteomics repositories, maximizing its benefit to the scientific community through the implementation of standard submission and dissemination pipelines. Within the Consortium, PRIDE is focused on supporting submissions of tandem MS data. The increasing use and popularity of the new Proteomics Standards Initiative (PSI) data standards such as mzIdentML and mzTab, and the diversity of workflows supported by the PX resources, prompted us to design and implement a new suite of algorithms and libraries that would build upon the success of the original PRIDE Inspector and would enable users to visualize and validate PX "complete" submissions. The PRIDE Inspector Toolsuite supports the handling and visualization of different experimental output files, ranging from spectra (mzML, mzXML, and the most popular peak lists formats) and peptide and protein identification results (mzIdentML, PRIDE XML, mzTab) to quantification data (mzTab, PRIDE XML), using a modular and extensible set of open-source, cross-platform libraries. We believe that the PRIDE Inspector Toolsuite represents a milestone in the visualization and quality assessment of proteomics data. It is freely available at http://github.com/PRIDE-Toolsuite/. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Towards a Comprehensive and Up-To-Date Institutional Repository: Development of a Publications Tracking Process

KAUST Repository

Baessa, Mohamed

2016-06-15

As our repository matured we found that a concerted effort was needed to establish it as a resource that institutional stakeholders knew they could turn to for reliable information about the research outputs produced by researchers affiliated with or funded by our institution. The initial impetus for this project was the adoption of an institutional open access policy, which necessitated a process to track the publications of institutional authors, deposit items with applicable open access licenses, and notify authors when an accepted manuscript was needed. To support this process we developed a local publications tracking system independent of our hosted DSpace repository that regularly queries publisher and indexer APIs for new publications, checks for relevant permissions policies, identifies institutional authors and helps us send manuscript request emails. We also harvested records for past items and modified our repository to accommodate metadata-only records. The success of these tracking and harvesting services in making our repository comprehensive and up-to-date has allowed us to rely on our repository as the key source of publications information for additional integrations that update ORCID records with publication information, populate a PlumX metrics dashboard and, most recently, support the implementation of a current research information system (CRIS).

Towards a Comprehensive and Up-To-Date Institutional Repository: Development of a Publications Tracking Process

KAUST Repository

Baessa, Mohamed A.; Grenz, Daryl M.; Wang, Han

2016-01-01

As our repository matured we found that a concerted effort was needed to establish it as a resource that institutional stakeholders knew they could turn to for reliable information about the research outputs produced by researchers affiliated with or funded by our institution. The initial impetus for this project was the adoption of an institutional open access policy, which necessitated a process to track the publications of institutional authors, deposit items with applicable open access licenses, and notify authors when an accepted manuscript was needed. To support this process we developed a local publications tracking system independent of our hosted DSpace repository that regularly queries publisher and indexer APIs for new publications, checks for relevant permissions policies, identifies institutional authors and helps us send manuscript request emails. We also harvested records for past items and modified our repository to accommodate metadata-only records. The success of these tracking and harvesting services in making our repository comprehensive and up-to-date has allowed us to rely on our repository as the key source of publications information for additional integrations that update ORCID records with publication information, populate a PlumX metrics dashboard and, most recently, support the implementation of a current research information system (CRIS).

Public opposition to the siting of the high-level nuclear waste repository: The importance of trust

International Nuclear Information System (INIS)

Pijawka, K.D.; Mushkatel, A.H.

1991-01-01

This paper examines several dimensions of public opposition to the proposed siting of the high-level nuclear waste repository at Yucca Mountain. In order to provide a context for the public's views of the repository in metropolitan Clark County, both governmental studies of the repository siting process are analyzed, as well as elements of the Nuclear Waste Policy Act. This analysis suggests that one potentially key component of the public's opposition to the siting, as well as their perceptions of risk of the facility, may be the result of a lack of trust in the Department of Energy. Empirical analysis of survey data collected in Nevada in 1988 confirms the strong relationship between political trust and repository risk perceptions

Assessment of Public Acceptability in LILW Repository Site Selection Process in Slovenia

International Nuclear Information System (INIS)

Zeleznik, N.; Kralj, M.; Polic, M.; Kos, D.

2006-01-01

Slovenian national agency for radioactive waste management ARAO has after longer period of preparation activities started with the more direct work on the site selection process for low and intermediate level waste (LILW) repository. In November 2004, the official administrative procedure for the siting of the repository started with the First public conference on spatial planning issues carried out by the Ministry of Environment and Spatial Planning together with ARAO. Just after the conference the Program for the preparation of the Detailed plan of national importance for the LILW repository was accepted by the Ministry. ARAO invited in the beginning of December 2004 all local communities in Slovenia (except 3 of them which have already refused to cooperate) to participate and volunteer a site or area in their local community for further investigation. The invitation for the application of local communities provided clear instructions on how to participate in further determination of potentially suitable sites and under what conditions. By the beginning of April 2005 ARAO finished the bidding process with 8 applications of local communities which decided to participate in the further site selection for LILW repository. Due to the financial and other limitations (human resources, spatial planning procedure, etc.) only in maximum three local communities further characterization could be performed. Therefore prefeasibility study of all volunteer local communities was conducted in which besides technical, environmental and spatial availability also public acceptability should be assessed. For assessment of public acceptability the methodology has been prepared which includes objective parameters of local environment (such as demographic data, economy, infrastructure and social issues in relation to the repository) as well as subjective values (attitudes of individual groups - opinion makers, politicians and all residents - to the sitting and construction of LILW

Radioactive wastes repository in Temascalapa, State of Mexico, public opinion. Determination of health effects

International Nuclear Information System (INIS)

Solis Tinoco, E.

1998-01-01

Nuclear waste usually concerns public about the impact on public health and the environment. In Mexico, such interest exists, particularly in the Temascalapa Municipality, Mexico where a low level waste repository recognized by the IAEA, has been functioning since 1972. Maquixco repository is located at 42 Kilometers northeast of Mexico City. Although the environmental radiological monitoring records have demonstrated negligible impact on the environment, in 1998 an unusual public polemic on radioactive health effects appeared among Temascalapa residents. This paper presents a research performed during 1998 with the participation of the National Nuclear Research Institute of Mexico and the National Autonomous University of Mexico. The research design allowed the involvement of local authorities, as a way of stimulate public participation. The research was performed in nine locations of the Temascalapa Municipality, it was focused on public polemics, associated to Maquixco repository as well as trying to identify demographic factors that exert influence on public attitudes. There are also presented the results of personal dosimetry analysis performed on a four hundred residents sample of this Municipality. (Author)

Characterization of the porcine synovial fluid proteome and a comparison to the plasma proteome

DEFF Research Database (Denmark)

Bennike, Tue Bjerg; Barnaby, Omar; Steen, Hanno

2015-01-01

Synovial fluid is present in all joint cavities, and protects the articular cartilage surfaces in large by lubricating the joint, thus reducing friction. Several studies have described changes in the protein composition of synovial fluid in patients with joint disease. However, the protein concen...... data used in the method optimization, human plasma proteomics data, and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD000935....

Public acceptance for centralized storage and repositories of low-level waste session (Panel)

Energy Technology Data Exchange (ETDEWEB)

Lutz, H.R.

1995-12-31

Participants from various parts of the world will provide a summary of their particular country`s approach to low-level waste management and the cost of public acceptance for low-level waste management facilities. Participants will discuss the number, geographic location, and type of low-level waste repositories and centralized storage facilities located in their countries. Each will discuss the amount, distribution, and duration of funds to gain public acceptance of these facilities. Participants will provide an estimated $/meter for centralized storage facilities and repositories. The panel will include a brief discussion about the ethical aspects of public acceptance costs, approaches for negotiating acceptance, and lessons learned in each country. The audience is invited to participate in the discussion.

The Centre de l'Aube repository. The Public Information Center

International Nuclear Information System (INIS)

Fernique, J.C.

1993-01-01

The Centre de l'Aube repository, second French final disposal site for low activity short lived wastes, started operating in january 1992. Since the beginning of the Project public reception and information were among ANDRA's main concern. Open to public one year before disposal operations, the Public Information Center received many visitors coming as well from the regional as from national and international origin. The two years experience will be presented as well as the modifications of the information center taking into account ANDRA's evolution. (author)

Presentation of the paper “Open access repositories as channel of publication scientific grey literature”

OpenAIRE

Ferreras Fernández, Tránsito; García-Peñalvo, Francisco José; Merlo Vega, José Antonio

2015-01-01

This is the presentation of the paper entitled “Open access repositories as channel of publication scientific grey literature” in the TEEM 2015 International Conference held in Porto (Portugal) in October 7-9, 2015. In this paper we describe how the open access repositories are valid channels for the publication of scientific grey literature. Technological development facilitates the communication of scientific knowledge, allowing expand distribution channels and significantly reducing tra...

Assessing the demographic and public service impacts of repository siting

International Nuclear Information System (INIS)

Murdock, S.H.; Hamm, R.R.

1983-01-01

Demographic and public service impacts are likely to be among the most evident of those changes resulting from nuclear waste repository development. Knowledge of the characteristics of such impacts and of the means to assess them is critical. The first section of this chapter examines those likely to be unique to repositories. The second section describes the alternatives for assessing such impacts and the particular difficulties likely to affect the assessments. Given the state of development of techniques for assessing impacts and the range of factors that must be considered, perhaps their best use is as a means of sensitizing decision makers to the potential implications of their decisions. 2 tables

Low and intermediate level waste repositories: Socioeconomic aspects and public involvement. Proceedings of a workshop

International Nuclear Information System (INIS)

2007-06-01

Waste management facilities are needed to protect the environment and improve public health for the long term future. One significant challenge is to inform the public on the relative hazards of radioactive waste compared to other hazards in our modern society and to get the acceptance of the appropriate members of the public for these necessary facilities. Over the entire life cycle of these facilities, the projects must be managed without expending a disproportionate share of the collective resources. Public involvement plays a key role and the sophisticated and extensive public education systems that exist provide a vital service to gain public acceptance. There is a full range of compensation and benefit programmes used as incentives for hosting a LILW facility. Even if exemptions exist the experience in most countries indicate the direct/indirect incentives as a necessary part of gaining public acceptance. The countries, regions and local communities have their own established processes to make public decisions. Each organization developing a site must select and implement the methods that are acceptable within their framework of laws and regulations. A three day workshop on socio-economic issues and public involvement practices and approaches for developing and operating repositories for low and intermediate level waste took place in the IAEA headquarters on 9-11 November 2005. The workshop provided a forum where experts from Member States shared their experiences in non-technical aspects of planning, licensing and operating LILW disposal facilities. Description of both principles and practices applied in particular countries provides a useful overview of potential approaches in application of non-technical issues during a repository lifecycle. Participants presented approaches and practices applied in their countries, established new contacts and were able to take advantage of activities and experiences from abroad. There were 25 interesting presentations

Designing a Secure Storage Repository for Sharing Scientific Datasets using Public Clouds

Energy Technology Data Exchange (ETDEWEB)

Kumbhare, Alok [Univ. of Southern California, Los Angeles, CA (United States); Simmhan, Yogesth [Univ. of Southern California, Los Angeles, CA (United States); Prasanna, Viktor [Univ. of Southern California, Los Angeles, CA (United States)

2011-11-14

As Cloud platforms gain increasing traction among scientific and business communities for outsourcing storage, computing and content delivery, there is also growing concern about the associated loss of control over private data hosted in the Cloud. In this paper, we present an architecture for a secure data repository service designed on top of a public Cloud infrastructure to support multi-disciplinary scientific communities dealing with personal and human subject data, motivated by the smart power grid domain. Our repository model allows users to securely store and share their data in the Cloud without revealing the plain text to unauthorized users, the Cloud storage provider or the repository itself. The system masks file names, user permissions and access patterns while providing auditing capabilities with provable data updates.

National radioactive waste repository site selection study. Phase 2. A report on public comment

International Nuclear Information System (INIS)

1995-11-01

Agreement was reached in principle between State/Territory and the Commonwealth of Australia Governments that a suitable site for a radioactive wastes repository must be found. The discussion papers resulting from the Phase 1 and Phase 2 of the site selection study were released for public comment. The national repository will be for disposal of low level and short-lived intermediate level radioactive wastes streaming from the medical, research and industrial use of radioisotopes in Australia. The purpose of this report is to summarise and respond in general terms to comment received on the discussion paper -Phase 2 of the study. Forty five submissions were received. Of these: 18 supported the Phase 2 study approach and the concept of a national repository; 13 did not state a clear position but either requested more information or provided constructive comment on the siting process; 7 supported the site selection approach and the repository concept but suggested that the repository should not be sited in a particular area; 3 opposed the siting of the repository in their vicinity but not necessarily the repository concept and site selection approach; 4 opposed the concept of a national repository. This compares with 124 submissions on Phase 1 of the study, of which 57 opposed the national repository concept (52 of these were from letters elicited by Greenpeace) and 48 supported the establishment of a national repository and the site selection approach proposed. 3 figs

Repository Safety Strategy: Strategy for Protecting Public Health and Safety after Closure of a Yucca Mountain Repository, Rev. 1

Energy Technology Data Exchange (ETDEWEB)

DOE

1998-01-01

The updated Strategy to Protect Public Health and Safety explains the roles that the natural and engineered systems are expected to play in achieving the objectives of a potential repository system at Yucca Mountain. These objectives are to contain the radionuclides within the waste packages for thousands of years, and to ensure that annual doses to a person living near the site will be acceptably low. This strategy maintains the key assumption of the Site Characterization Plan (DOE 1988) strategy that the potential repository level (horizon) will remain unsaturated. Thus, the strategy continues to rely on the natural attributes of the unsaturated zone for primary protection by providing a setting where waste packages assisted by other engineered barriers are expected to contain wastes for thousands of years. As in the Site Characterization Plan (DOE 1988) strategy, the natural system from the walls of the underground openings (drifts) to the human environment is expected to provide additional defense by reducing the concentrations of any radionuclides released from the waste packages. The updated Strategy to Protect Public Health and Safety is the framework for the integration of site information, repository design and assessment of postclosure performance to develop a safety case for the viability assessment and a subsequent license application. Current site information and a reference design are used to develop a quantitative assessment of performance to be compared with a performance measure. Four key attributes of an unsaturated repository system that are critical to meeting the objectives: (1) Limited water contacting the waste packages; (2) Long waste package lifetime; (3) Slow rate of release of radionuclides from the waste form; and (4) Concentration reduction during transport through engineered and natural barriers.

Proteome identification of the silkworm middle silk gland

Directory of Open Access Journals (Sweden)

Jian-ying Li

2016-03-01

Full Text Available To investigate the functional differentiation among the anterior (A, middle (M, and posterior (P regions of silkworm middle silk gland (MSG, their proteomes were characterized by shotgun LC–MS/MS analysis with a LTQ-Orbitrap mass spectrometer. To get better proteome identification and quantification, triplicate replicates of mass spectrometry analysis were performed for each sample. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Vizcaíno et al., 2014 [1] via the PRIDE partner repository (Vizcaino, 2013 [2] with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD003371. The peptide identifications that were further processed by PeptideProphet program in Trans-Proteomic Pipeline (TPP after database search with Mascot software were also available in .XML format files. Data presented here are related to a research article published in Journal of Proteomics by Li et al. (2015 [3]. Keywords: Bombyx mori, Middle silk gland, Silk protein synthesis, Shotgun proteomics, Label-free

A Digital Repository and Execution Platform for Interactive Scholarly Publications in Neuroscience.

Science.gov (United States)

Hodge, Victoria; Jessop, Mark; Fletcher, Martyn; Weeks, Michael; Turner, Aaron; Jackson, Tom; Ingram, Colin; Smith, Leslie; Austin, Jim

2016-01-01

The CARMEN Virtual Laboratory (VL) is a cloud-based platform which allows neuroscientists to store, share, develop, execute, reproduce and publicise their work. This paper describes new functionality in the CARMEN VL: an interactive publications repository. This new facility allows users to link data and software to publications. This enables other users to examine data and software associated with the publication and execute the associated software within the VL using the same data as the authors used in the publication. The cloud-based architecture and SaaS (Software as a Service) framework allows vast data sets to be uploaded and analysed using software services. Thus, this new interactive publications facility allows others to build on research results through reuse. This aligns with recent developments by funding agencies, institutions, and publishers with a move to open access research. Open access provides reproducibility and verification of research resources and results. Publications and their associated data and software will be assured of long-term preservation and curation in the repository. Further, analysing research data and the evaluations described in publications frequently requires a number of execution stages many of which are iterative. The VL provides a scientific workflow environment to combine software services into a processing tree. These workflows can also be associated with publications and executed by users. The VL also provides a secure environment where users can decide the access rights for each resource to ensure copyright and privacy restrictions are met.

Kincardine deep geologic repository proposal and the public

International Nuclear Information System (INIS)

Squire, T.

2005-01-01

'Full text:' In 2002, the Municipality of Kincardine and OPG signed a Memorandum of Understanding (MOU) regarding the long-term management of low and intermediate level radioactive wastes. The purpose of the MOU was for OPG, in consultation with Kincardine, to develop a plan for the long-term management of low and intermediate level waste at OPG's Western Waste Management Facility (WWMF) located on the Bruce site. An independent assessment, which included geotechnical feasibility and safety analyses, a community attitude survey and interviews with local residents, businesses and tourists, and economic modeling to determine the potential benefits and impacts, was completed in February 2004. Ultimately, Kincardine Council endorsed a resolution (Kincardine Council no. 2004-232) to: 'endorse the opinion of the Nuclear Waste Steering Committee and select the 'Deep Rock Vault' option as the preferred course of study in regards to the management of low and intermediate level radioactive waste'. The surrounding municipalities of Saugeen Shores, Brockton, Arran-Elderslie, and Huron-Kinloss expressed their support for the Deep Geologic Repository proposal. This presentation discusses the history, major steps and public processes surrounding the Kincardine Deep Geologic Repository proposal. (author)

CGPD: Cancer Genetics and Proteomics Database - A Dataset for Computational Analysis and Online Cancer Diagnostic Centre

Directory of Open Access Journals (Sweden)

Muhammad Rizwan Riaz

2014-06-01

Full Text Available Cancer Genetics and Proteomics Database (CGPD is a repository for genetics and proteomics data of those Homo sapiens genes which are involved in Cancer. These genes are categorized in the database on the basis of cancer type. 72 genes of 13 types of cancers are considered in this database yet. Primers, promoters and peptides of these genes are also made available. Primers provided for each gene, with their features and conditions given to facilitate the researchers, are useful in PCR amplification, especially in cloning experiments. CGPD also contains Online Cancer Diagnostic Center (OCDC. It also contains transcription and translation tools to assist research work in progressive manner. The database is publicly available at http://www.cgpd.comyr.com.

The HUPO proteomics standards initiative--overcoming the fragmentation of proteomics data.

Science.gov (United States)

Hermjakob, Henning

2006-09-01

Proteomics is a key field of modern biomolecular research, with many small and large scale efforts producing a wealth of proteomics data. However, the vast majority of this data is never exploited to its full potential. Even in publicly funded projects, often the raw data generated in a specific context is analysed, conclusions are drawn and published, but little attention is paid to systematic documentation, archiving, and public access to the data supporting the scientific results. It is often difficult to validate the results stated in a particular publication, and even simple global questions like "In which cellular contexts has my protein of interest been observed?" can currently not be answered with realistic effort, due to a lack of standardised reporting and collection of proteomics data. The Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organisation (HUPO), defines community standards for data representation in proteomics to facilitate systematic data capture, comparison, exchange and verification. In this article we provide an overview of PSI organisational structure, activities, and current results, as well as ways to get involved in the broad-based, open PSI process.

Desiderata for healthcare integrated data repositories based on architectural comparison of three public repositories.

Science.gov (United States)

Huser, Vojtech; Cimino, James J

2013-01-01

Integrated data repositories (IDRs) are indispensable tools for numerous biomedical research studies. We compare three large IDRs (Informatics for Integrating Biology and the Bedside (i2b2), HMO Research Network's Virtual Data Warehouse (VDW) and Observational Medical Outcomes Partnership (OMOP) repository) in order to identify common architectural features that enable efficient storage and organization of large amounts of clinical data. We define three high-level classes of underlying data storage models and we analyze each repository using this classification. We look at how a set of sample facts is represented in each repository and conclude with a list of desiderata for IDRs that deal with the information storage model, terminology model, data integration and value-sets management.

Proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies

Directory of Open Access Journals (Sweden)

Tue Bjerg Bennike

2016-03-01

Full Text Available Large repositories of well characterized RNAlater preserved samples and formalin-fixed, paraffin-embedded samples have been generated worldwide. However, the impact on the proteome of the preservation methods remain poorly described. Therefore, we analyzed the impact on the proteome of preserving samples in RNAlater, and by formalin-fixation, paraffin-embedding on human soft tissue, using directly frozen samples as a control (“Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples” [1]. We here report the data from the analysis. The comparative analysis was performed on 24 colon mucosa biopsies, extracted from the sigmoideum of two gastroenterologically healthy participants for the purpose of this study. A set of biopsies were additionally stored for 30 min at room temperature prior to formalin-fixation. The samples were analyzed by high throughput gel free quantitative proteomics. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002029. Keywords: Human, Colon, Mucosa, RNAlater, FFPE, Snap-frozen, Stability, LC–MS, Proteomics

Towards Establishing an Open Access Repository of Indian Publications in Astronomy -- a Case Study of Indian Institute of Astrophysics Repository

Science.gov (United States)

Birdie, C.; Vagiswari, A.

2007-10-01

The continued escalation of journal prices, and inadequate access to scholarly journals along with a consistent reduction in library resources and the advent of new technologies have all contributed to a change in the present scholarly communication. The initiative towards establishing Open Access communication has been advocated among scholars and researchers. An Institutional Archive for holding pre- and post-prints of articles written by academic and research staff increases the accessibility, visibility and impact of research output. The Indian Institute of Astrophysics (IIA) is one of the astronomical research institutes in India pioneering the Open Access movement. The institute has set up a pilot project to store the institute's publications in an institutional repository (IR). The library at IIA plays an important role in setting up this archive. While the authors and publishers are the key players in this endeavor, the role of librarians needs to be redefined in the present paradigm shift of publishing. When the Institutes decide to develop their own repositories, the skills and expertise of librarians are needed to design, develop, manage and maintain a successful repository. These and the knowledge of copyright issues relevant to the digital content of IRs are highlighted in this paper. This paper also discusses the various opportunities and tools available for librarians to learn the procedures and involve themselves in establishing their institutional repositories.

Qualified public involvement in the decision making process of siting a waste repository

International Nuclear Information System (INIS)

Rodrigues, Danielle Monegalha; Almeida, Ivan Pedro Salati de

2009-01-01

The main objective of this paper is to identify the most important characteristics required for the qualification of local communities for participating in the process of defining a specific site for a radioactive waste repository. It also compares the strategies used by Hungary, United Kingdom and Belgium to stimulate the public participation in the decision-making process of building and operating a radioactive waste repository, considering both the stepwise process and the spontaneous candidacy. Two main aspects are discussed as prerequisites to constitute a qualified public. The first aspect is how well the person or entity can be considered an effective representative of the community affected by the repository. This means the conditions the representative has to speak on behalf of the community and participate in the decision making process as its voice. The second characteristic is the level and quality of the information that the community and its representatives must have to participate actively in the decision-making process and what can be done to improve this status. Referring to the strategy to public involvement, this paper discusses the importance of transparency in the process, aiming the credibility of the entrepreneur as the first pace to gaining the confidence of the public affected by the project. Implementing an open dialog and listening to the needs and claims of the population are the first steps to being accepted as a true partner of the community. Preliminary discussions and explanations are important to introduce the subject and to reduce beliefs of false threats in the affected community. The constitution of a local committee is suggested, to act as a legal and formal channel to facilitate the partnership between local community, neighbors and the entrepreneur in order to achieve a positive result in the whole process. (author)

Final repository search together with the citizens. Information, consultation, dialogue, participation

International Nuclear Information System (INIS)

Mueller, Monika C.M.

2013-01-01

The documentation on the Loccum meeting 2013 includes contributions on the following topics: Public participation for the final repository search; Lessons learned from the past; Public participation: what is expected? Experiences of repository operators on public participation; The TRIPLEX concept; From Gorleben to the law on final repository search: a long and a short story; Public participation concerning radioactive waste storage; The public has to be informed on the radioactive waste problem and the possible solutions; After consensus is before consensus - German final repository conflict between legislation and simulated public participation; Political concept of public participation; A fast final repository law will not bring about social peace; Good public participation on final repository search - requirements, challenges, questions and approaches.

Repositories; Repositorios

Energy Technology Data Exchange (ETDEWEB)

Freire, Carolina Braccini; Tello, Cledola Cassia Oliveira de [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil)]. E-mails: cbf@cdtn.br; tellocc@cdtn.br

2007-11-15

The use of the nuclear energy is increasing in all areas. Then the radioactive waste management is in continuous development to comply the national and international established requirements. The final objective is to assure that it will not have any contamination of the public or the environmental, and that the exposition doses will be lower than the radiological protection limits. The multi barrier concept for the repository is internationally recognized. Among the repository types, the most used are: near surface, geological formations and of deposition in rock cavities. This article explains the concept and the types of repository and gives some examples of them. (author)

Publishing descriptions of non-public clinical datasets: proposed guidance for researchers, repositories, editors and funding organisations.

Science.gov (United States)

Hrynaszkiewicz, Iain; Khodiyar, Varsha; Hufton, Andrew L; Sansone, Susanna-Assunta

2016-01-01

Sharing of experimental clinical research data usually happens between individuals or research groups rather than via public repositories, in part due to the need to protect research participant privacy. This approach to data sharing makes it difficult to connect journal articles with their underlying datasets and is often insufficient for ensuring access to data in the long term. Voluntary data sharing services such as the Yale Open Data Access (YODA) and Clinical Study Data Request (CSDR) projects have increased accessibility to clinical datasets for secondary uses while protecting patient privacy and the legitimacy of secondary analyses but these resources are generally disconnected from journal articles-where researchers typically search for reliable information to inform future research. New scholarly journal and article types dedicated to increasing accessibility of research data have emerged in recent years and, in general, journals are developing stronger links with data repositories. There is a need for increased collaboration between journals, data repositories, researchers, funders, and voluntary data sharing services to increase the visibility and reliability of clinical research. Using the journal Scientific Data as a case study, we propose and show examples of changes to the format and peer-review process for journal articles to more robustly link them to data that are only available on request. We also propose additional features for data repositories to better accommodate non-public clinical datasets, including Data Use Agreements (DUAs).

Analysis of high accuracy, quantitative proteomics data in the MaxQB database.

Science.gov (United States)

Schaab, Christoph; Geiger, Tamar; Stoehr, Gabriele; Cox, Juergen; Mann, Matthias

2012-03-01

MS-based proteomics generates rapidly increasing amounts of precise and quantitative information. Analysis of individual proteomic experiments has made great strides, but the crucial ability to compare and store information across different proteome measurements still presents many challenges. For example, it has been difficult to avoid contamination of databases with low quality peptide identifications, to control for the inflation in false positive identifications when combining data sets, and to integrate quantitative data. Although, for example, the contamination with low quality identifications has been addressed by joint analysis of deposited raw data in some public repositories, we reasoned that there should be a role for a database specifically designed for high resolution and quantitative data. Here we describe a novel database termed MaxQB that stores and displays collections of large proteomics projects and allows joint analysis and comparison. We demonstrate the analysis tools of MaxQB using proteome data of 11 different human cell lines and 28 mouse tissues. The database-wide false discovery rate is controlled by adjusting the project specific cutoff scores for the combined data sets. The 11 cell line proteomes together identify proteins expressed from more than half of all human genes. For each protein of interest, expression levels estimated by label-free quantification can be visualized across the cell lines. Similarly, the expression rank order and estimated amount of each protein within each proteome are plotted. We used MaxQB to calculate the signal reproducibility of the detected peptides for the same proteins across different proteomes. Spearman rank correlation between peptide intensity and detection probability of identified proteins was greater than 0.8 for 64% of the proteome, whereas a minority of proteins have negative correlation. This information can be used to pinpoint false protein identifications, independently of peptide database

Environmental impact statements and public consultations on the repository. An outline of SKB's planning

International Nuclear Information System (INIS)

2001-09-01

In December 2000 SKB selected three locations for further investigations as possible sites for the Swedish repository for spent nuclear fuels, Simpevarp at Oskarshamn, Forsmark at Oesthammar and Tierp. Site investigations will be performed during 5-6 years, and will provide data for a site selection. In the application for the repository commission an environmental impact statement should be included, that has been object for consultations with authorities, local communities, other organizations and the public. These consultations will take place during the whole investigation period, and will give ample possibilities for all parties to give their views and to exert an influence on the EIS

EEI/UWASTE oversight of the DOE Repository Program by the Repository Information Exchange Team

International Nuclear Information System (INIS)

Henkel, C.J.; Supko, E.M.; Schwartz, M.H.

1993-01-01

The Utility Nuclear Waste and Transportation Program of the Edison Electric Institute (EEI/UWASTE) has conducted reviews of the US DOE's repository program through its Repository Information Exchange Team (RIET or Team). Eight such reviews have been conducted since 1985 covering topics that include repository program management and control; repository schedule; repository budget; quality assurance; site characterization; repository licensing; environmental issues; and institutional and public information activities. The utility industry has used these repository program reviews as a forum for providing DOE's Office of Civilian Radioactive Waste Management (OCRWM) with comments on the direction of the repository program, advice for future actions regarding quality assurance activities and repository licensing, and suggestions for management and control of the Repository Program. The most significant recommendations made by the utility industry through the RIET are discussed along with any subsequent action by OCRWM in response to or subsequent to utility industry recommendations. The process used by the RIET to develop its recommendations to OCRWM regarding the repository program is also discussed

CRIS and Institutional Repositories

Directory of Open Access Journals (Sweden)

A Asserson

2010-04-01

Full Text Available CRIS (Current Research Information Systems provide researchers, research managers, innovators, and others with a view over the research activity of a domain. IRs (institutional repositories provide a mechanism for an organisation to showcase through OA (open access its intellectual property. Increasingly, organizations are mandating that their employed researchers deposit peer-reviewed published material in the IR. Research funders are increasingly mandating that publications be deposited in an open access repository: some mandate a central (or subject-based repository, some an IR. In parallel, publishers are offering OA but replacing subscription-based access with author (or author institution payment for publishing. However, many OA repositories have metadata based on DC (Dublin Core which is inadequate; a CERIF (Common-European Research Information Format CRIS provides metadata describing publications with formal syntax and declared semantics thus facilitating interoperation or homogeneous access over heterogeneous sources. The formality is essential for research output metrics, which are increasingly being used to determine future funding for research organizations.

CPTC and NIST-sponsored Yeast Reference Material Now Publicly Available | Office of Cancer Clinical Proteomics Research

Science.gov (United States)

The yeast protein extract (RM8323) developed by National Institute of Standards and Technology (NIST) under the auspices of NCI's CPTC initiative is currently available to the public at https://www-s.nist.gov/srmors/view_detail.cfm?srm=8323. The yeast proteome offers researchers a unique biological reference material. RM8323 is the most extensively characterized complex biological proteome and the only one associated with several large-scale studies to estimate protein abundance across a wide concentration range.

Effects of High-Pressure Treatment on the Muscle Proteome of Hake by Bottom-Up Proteomics.

Science.gov (United States)

Carrera, Mónica; Fidalgo, Liliana G; Saraiva, Jorge A; Aubourg, Santiago P

2018-05-02

A bottom-up proteomics approach was applied for the study of the effects of high-pressure (HP) treatment on the muscle proteome of fish. The performance of the approach was established for a previous HP treatment (150-450 MPa for 2 min) on frozen (up to 5 months at -10 °C) European hake ( Merluccius merluccius). Concerning possible protein biomarkers of quality changes, a significant degradation after applying a pressure ≥430 MPa could be observed for phosphoglycerate mutase-1, enolase, creatine kinase, fructose bisphosphate aldolase, triosephosphate isomerase, and nucleoside diphosphate kinase; contrary, electrophoretic bands assigned to tropomyosin, glyceraldehyde-3-phosphate dehydrogenase, and beta parvalbumin increased their intensity after applying a pressure ≥430 MPa. This repository of potential protein biomarkers may be very useful for further HP investigations related to fish quality.

Data in support of quantitative proteomics to identify potential virulence regulators in Paracoccidioides brasiliensis isolates

Directory of Open Access Journals (Sweden)

Alexandre Keiji Tashima

2015-12-01

Full Text Available Paracoccidioides genus are the etiologic agents of paracoccidioidomycosis (PCM, a systemic mycosis endemic in Latin America. Few virulence factors have been identified in these fungi. This paper describes support data from the quantitative proteomics of Paracoccidioides brasiliensis attenuated and virulent isolates [1]. The protein compositions of two isolates of the Pb18 strain showing distinct infection profiles were quantitatively assessed by stable isotopic dimethyl labeling and proteomic analysis. The mass spectrometry and the analysis dataset have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with identifier PXD000804.

Development of a central final repository management for the coordination of the waste for Schacht Konrad from public authorities

International Nuclear Information System (INIS)

Graffunder, Iris; Dominke-Bendix, Carola; Waldek, Achim

2012-01-01

The central final repository management is supposed to fulfill the following tasks: active collaboration of Konrad contract draft, signing of internal contracts and agreements, cooperation contract with GNS, cooperation with coordination authorities, inventory taking of wastes (existing inventory and prognosis) and interim storage capacities of public authorities, development of planning and management software, optimization of the final repository documentation, container management, logistics concept, long-term disposal planning and prognosis, planning and coordination of the annual waste amount, management and documentation of disposed waste allocation, coordination of transport schedules, consulting service for waste obligations (final repository requirements, product control, documentation).

Extensive mass spectrometry proteomics data of Persicaria minor herb upon methyl jasmonate treatment

Directory of Open Access Journals (Sweden)

Wan Mohd Aizat

2018-02-01

Full Text Available Proteomics is often hindered by the lack of protein sequence database particularly for non-model species such as Persicaria minor herbs. An integrative approach called proteomics informed by transcriptomics is possible [1], in which translated transcriptome sequence database is used as the protein sequence database. In this current study, the proteome profile were profiled using SWATH-MS technology complemented with documented transcriptome profiling [2], the first such report in this tropical herb. The plant was also elicited using a phytohormone, methyl jasmonate (MeJA and protein changes were elucidated using label-free quantification of SWATH-MS to understand the role of such signal molecule in this herbal species. The mass spectrometry proteomics data was deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD005749. This data article refers to the article entitled “Proteomics (SWATH-MS-informed by transcriptomics approach of Persicaria minor leaves upon methyl jasmonate elicitation” [3].

Scientific, institutional, regulatory, political, and public acceptance of the waste isolation pilot plant transuranic waste repository

International Nuclear Information System (INIS)

Eriksson, L.G.

2000-01-01

The recent successful certification and opening of a first-of-a-kind, deep geological repository for safe disposal of long-lived, transuranic radioactive waste (TRUW) at the Waste Isolation Pilot Plant (WIPP) site, New Mexico, United States of America (USA), embody both long-standing local and wide-spread, gradually achieved, scientific, institutional, regulatory, political, and public acceptance. The related historical background and development are outlined and the main contributors to the successful siting, certification, and acceptance of the WIPP TRUW repository, which may also serve as a model to success for other radioactive waste disposal programs, are described. (author)

The Pig PeptideAtlas

DEFF Research Database (Denmark)

Hesselager, Marianne Overgaard; Codrea, Marius; Sun, Zhi

2016-01-01

Biological research of Sus scrofa, the domestic pig, is of immediate relevance for food production sciences, and for developing pig as a model organism for human biomedical research. Publicly available data repositories play a fundamental role for all biological sciences, and protein data...... repositories are in particular essential for the successful development of new proteomic methods. Cumulative proteome data repositories, including the PeptideAtlas, provide the means for targeted proteomics, system-wide observations, and cross-species observational studies, but pigs have so far been...... underrepresented in existing repositories. We here present a significantly improved build of the Pig PeptideAtlas, which includes pig proteome data from 25 tissues and three body fluid types mapped to 7139 canonical proteins. The content of the Pig PeptideAtlas reflects actively ongoing research within...

Proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies

DEFF Research Database (Denmark)

Bjerg Bennike, Tue; Kastaniegaard, Kenneth; Padurariu, Simona

2016-01-01

Large repositories of well characterized RNAlater preserved samples and formalin-fixed, paraffin-embedded samples have been generated worldwide. However, the impact on the proteome of the preservation methods remain poorly described. Therefore, we analyzed the impact on the proteome of preserving...... samples in RNAlater, and by formalin-fixation, paraffin-embedding on human soft tissue, using directly frozen samples as a control ("Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples" [1]). We here report the data from the analysis...

ProteomicsDB.

Science.gov (United States)

Schmidt, Tobias; Samaras, Patroklos; Frejno, Martin; Gessulat, Siegfried; Barnert, Maximilian; Kienegger, Harald; Krcmar, Helmut; Schlegl, Judith; Ehrlich, Hans-Christian; Aiche, Stephan; Kuster, Bernhard; Wilhelm, Mathias

2018-01-04

ProteomicsDB (https://www.ProteomicsDB.org) is a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. ProteomicsDB was first released in 2014 to enable the interactive exploration of the first draft of the human proteome. To date, it contains quantitative data from 78 projects totalling over 19k LC-MS/MS experiments. A standardized analysis pipeline enables comparisons between multiple datasets to facilitate the exploration of protein expression across hundreds of tissues, body fluids and cell lines. We recently extended the data model to enable the storage and integrated visualization of other quantitative omics data. This includes transcriptomics data from e.g. NCBI GEO, protein-protein interaction information from STRING, functional annotations from KEGG, drug-sensitivity/selectivity data from several public sources and reference mass spectra from the ProteomeTools project. The extended functionality transforms ProteomicsDB into a multi-purpose resource connecting quantification and meta-data for each protein. The rich user interface helps researchers to navigate all data sources in either a protein-centric or multi-protein-centric manner. Several options are available to download data manually, while our application programming interface enables accessing quantitative data systematically. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Rock support for nuclear waste repositories

International Nuclear Information System (INIS)

Abramson, L.W.; Schmidt, B.

1984-01-01

The design of rock support for underground nuclear waste repositories requires consideration of special construction and operation requirements, and of the adverse environmental conditions in which some of the support is placed. While repository layouts resemble mines, design, construction and operation are subject to quality assurance and public scrutiny similar to what is experienced for nuclear power plants. Exploration, design, construction and operation go through phases of review and licensing by government agencies as repositories evolve. This paper discusses (1) the various stages of repository development; (2) the environment that supports must be designed for; (3) the environmental effects on support materials; and (4) alternative types of repository rock support

Integral Public Activities as a Support to the Site Selection Process for LILW Repository

International Nuclear Information System (INIS)

Zeleznik, N.; Kralj, M.

2008-01-01

The first site selection process for low and intermediate level radioactive waste (LILW) repository took place between 1990 and 1993 in Slovenia was stopped unsuccessfully with very strong public opposition at local level, followed by political withdrawal on national level. As one of the consequences ARAO started to develop new approach to the site selection based also on the findings from sociology, psychology and other human sciences. The recommendations on public involvement and transparency were so strong that ARAO started with first limited public relation (PR) activities which later grew to the PR process which supports all technical activities in ARAO. Presently the PR process covers communication, information and research activities and assures careful planning, prompt responds and involvement of the highest responsible persons at ARAO. Integral public relation activities are divided in several parts. Majority of activities support the on-going site selection process where activities are presently focused on functioning of local partnerships developed as a basic communication tool to involve as much citizens and public as possible on local level. Presently two local partnerships are working in Krsko and Brezice community with clear role to enhance public involvement according to Aarchus convention. Each of the partnerships is organized in a specific way adjusted to the local needs. Communication activities are organized also for different other projects and are preparing the necessary basis for the work with different groups of stake holders and in different situations. As a foundation very broad information material, such as books, leaflets, reports, magazines, video cassettes, CD and DVD on the radioactive waste management is prepared and used for different purposes. We also try to be proactive with web pages and have a well organized visitors' center. Improvement of public relation process is achieved through constant survey and feed-back information

MASCP Gator: An overview of the Arabidopsis proteomic aggregation portal

Directory of Open Access Journals (Sweden)

Gregory W Mann

2013-10-01

Full Text Available A key challenge in the area of bioinformatics in the coming decades is the ability to manage the wealth of information that is being generated from the variety of high throughput methodologies currently being undertaken in laboratories across the world. While these approaches have made available large volumes of data to the research community, less attention has been given to the problem of how to intuitively present the data to enable greater biological insights. Recently, an attempt was made to tackle this problem in the area of Arabidopsis proteomics. The model plant has been the target of countless proteomics surveys producing an exhaustive array of data and online repositories. The MASCP Gator is an aggregation portal for proteomic data currently being produced by the community and unites a large collection of specialized resources to a single portal (http://gator.masc-proteomics.org/. Here we describe the latest additions, upgrades and features to this resource further expanding its role into protein modifications and genome sequence variations.

Analysis of the variability of human normal urine by 2D-GE reveals a "public" and a "private" proteome.

Science.gov (United States)

Molina, Laurence; Salvetat, Nicolas; Ameur, Randa Ben; Peres, Sabine; Sommerer, Nicolas; Jarraya, Fayçal; Ayadi, Hammadi; Molina, Franck; Granier, Claude

2011-12-10

The characterization of the normal urinary proteome is steadily progressing and represents a major interest in the assessment of clinical urinary biomarkers. To estimate quantitatively the variability of the normal urinary proteome, urines of 20 healthy people were collected. We first evaluated the impact of the sample conservation temperature on urine proteome integrity. Keeping the urine sample at RT or at +4°C until storage at -80°C seems the best way for long-term storage of samples for 2D-GE analysis. The quantitative variability of the normal urinary proteome was estimated on the 20 urines mapped by 2D-GE. The occurrence of the 910 identified spots was analysed throughout the gels and represented in a virtual 2D gel. Sixteen percent of the spots were found to occur in all samples and 23% occurred in at least 90% of urines. About 13% of the protein spots were present only in 10% or less of the samples, thus representing the most variable part of the normal urinary proteome. Twenty proteins corresponding to a fraction of the fully conserved spots were identified by mass spectrometry. In conclusion, a "public" urinary proteome, common to healthy individuals, seems to coexist with a "private" urinary proteome, which is more specific to each individual. Copyright © 2011 Elsevier B.V. All rights reserved.

Proteome-wide dataset supporting functional study of tyrosine kinases in breast cancer

Directory of Open Access Journals (Sweden)

Nicos Angelopoulos

2016-06-01

Full Text Available Tyrosine kinases (TKs play an essential role in regulating various cellular activities and dysregulation of TK signaling contributes to oncogenesis. However, less than half of the TKs have been thoroughly studied. Through a combined use of RNAi and stable isotope labeling with amino acids in cell culture (SILAC-based quantitative proteomics, a global functional proteomic landscape of TKs in breast cancer was recently revealed highlighting a comprehensive and highly integrated signaling network regulated by TKs (Stebbing et al., 2015 [1]. We collate the enormous amount of the proteomic data in an open access platform, providing a valuable resource for studying the function of TKs in cancer and benefiting the science community. Here we present a detailed description related to this study (Stebbing et al., 2015 [1] and the raw data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the identifier http://www.ebi.ac.uk/pride/archive/projects/PXD002065.

Knowledge Translation: Moving Proteomics Science to Innovation in Society.

Science.gov (United States)

Holmes, Christina; McDonald, Fiona; Jones, Mavis; Graham, Janice

2016-06-01

Proteomics is one of the pivotal next-generation biotechnologies in the current "postgenomics" era. Little is known about the ways in which innovative proteomics science is navigating the complex socio-political space between laboratory and society. It cannot be assumed that the trajectory between proteomics laboratory and society is linear and unidirectional. Concerned about public accountability and hopes for knowledge-based innovations, funding agencies and citizens increasingly expect that emerging science and technologies, such as proteomics, are effectively translated and disseminated as innovation in society. Here, we describe translation strategies promoted in the knowledge translation (KT) and science communication literatures and examine the use of these strategies within the field of proteomics. Drawing on data generated from qualitative interviews with proteomics scientists and ethnographic observation of international proteomics conferences over a 5-year period, we found that proteomics science incorporates a variety of KT strategies to reach knowledge users outside the field. To attain the full benefit of KT, however, proteomics scientists must challenge their own normative assumptions and approaches to innovation dissemination-beyond the current paradigm relying primarily on publication for one's scientific peers within one's field-and embrace the value of broader (interdisciplinary) KT strategies in promoting the uptake of their research. Notably, the Human Proteome Organization (HUPO) is paying increasing attention to a broader range of KT strategies, including targeted dissemination, integrated KT, and public outreach. We suggest that increasing the variety of KT strategies employed by proteomics scientists is timely and would serve well the omics system sciences community.

Radioactive Waste Repositories and Incentives to Local Communities

International Nuclear Information System (INIS)

Knapp, A.; Medakovic, S.

2008-01-01

Public acceptance of radioactive waste (RW) repository depends on various and often community-specific factors. Although radiological risk from a properly constructed low and intermediate level waste (LILW) repository is practically negligible, routine safety considerations will favor low populated areas and therefore probably underdeveloped communities. Repository acceptance in such communities is more likely to be facilitated by prospective benefits to local economy, such as infrastructure development and increased employment, as well as by dedicated financial incentives to the community. Direct financial compensation to the local community for acceptance of the repository has been considered in some documents in countries experienced in RW management, but it has not become a widely accepted practice. In Croatia, a possibility for such compensation is mentioned in the land use plan in conjunction with the prospective RW repository site. In Slovenia, the government has already specified the annual amount of 2.33 million euro as a compensation for 'limited land use' to be shared by local communities in the vicinity of the planned LILW repository during its operation. Applicability of the Slovenian compensations to the prospective joint Slovenian-Croatian repository is not yet clear, at least in the aspect of joint funding. The joint Slovenian-Croatian Decommissioning and LILW and SF management program for NPP Krsko from 2004 did conservatively include the compensations into the repository cost estimates, but that might not be retained in subsequent revisions of the Program. According to the agreement between governments of Slovenia and Croatia on the Nuclear power plant Krsko, Croatian side has no obligations to participate in 'public expenditures' introduced after the agreement, as would be the case of community compensations for LILW repository in Slovenia. Before further decisions on joint NPP Krsko waste management are made, including the issue of LILW

Cultural text mining: using text mining to map the emergence of transnational reference cultures in public media repositories

NARCIS (Netherlands)

Pieters, Toine; Verheul, Jaap

2014-01-01

This paper discusses the research project Translantis, which uses innovative technologies for cultural text mining to analyze large repositories of digitized public media, such as newspapers and journals.1 The Translantis research team uses and develops the text mining tool Texcavator, which is

Data Collection, Collaboration, Analysis, and Publication Using the Open Data Repository's (ODR) Data Publisher

Science.gov (United States)

Lafuente, B.; Stone, N.; Bristow, T.; Keller, R. M.; Blake, D. F.; Downs, R. T.; Pires, A.; Dateo, C. E.; Fonda, M.

2017-12-01

In development for nearly four years, the Open Data Repository's (ODR) Data Publisher software has become a useful tool for researchers' data needs. Data Publisher facilitates the creation of customized databases with flexible permission sets that allow researchers to share data collaboratively while improving data discovery and maintaining ownership rights. The open source software provides an end-to-end solution from collection to final repository publication. A web-based interface allows researchers to enter data, view data, and conduct analysis using any programming language supported by JupyterHub (http://www.jupyterhub.org). This toolset makes it possible for a researcher to store and manipulate their data in the cloud from any internet capable device. Data can be embargoed in the system until a date selected by the researcher. For instance, open publication can be set to a date that coincides with publication of data analysis in a third party journal. In conjunction with teams at NASA Ames and the University of Arizona, a number of pilot studies are being conducted to guide the software development so that it allows them to publish and share their data. These pilots include (1) the Astrobiology Habitable Environments Database (AHED), a central searchable repository designed to promote and facilitate the integration and sharing of all the data generated by the diverse disciplines in astrobiology; (2) a database containing the raw and derived data products from the CheMin instrument on the MSL rover Curiosity (http://odr.io/CheMin), featuring a versatile graphing system, instructions and analytical tools to process the data, and a capability to download data in different formats; and (3) the Mineral Evolution project, which by correlating the diversity of mineral species with their ages, localities, and other measurable properties aims to understand how the episodes of planetary accretion and differentiation, plate tectonics, and origin of life lead to a

Influence analysis of Github repositories.

Science.gov (United States)

Hu, Yan; Zhang, Jun; Bai, Xiaomei; Yu, Shuo; Yang, Zhuo

2016-01-01

With the support of cloud computing techniques, social coding platforms have changed the style of software development. Github is now the most popular social coding platform and project hosting service. Software developers of various levels keep entering Github, and use Github to save their public and private software projects. The large amounts of software developers and software repositories on Github are posing new challenges to the world of software engineering. This paper tries to tackle one of the important problems: analyzing the importance and influence of Github repositories. We proposed a HITS based influence analysis on graphs that represent the star relationship between Github users and repositories. A weighted version of HITS is applied to the overall star graph, and generates a different set of top influential repositories other than the results from standard version of HITS algorithm. We also conduct the influential analysis on per-month star graph, and study the monthly influence ranking of top repositories.

An update on sORFs.org: a repository of small ORFs identified by ribosome profiling.

Science.gov (United States)

Olexiouk, Volodimir; Van Criekinge, Wim; Menschaert, Gerben

2018-01-04

sORFs.org (http://www.sorfs.org) is a public repository of small open reading frames (sORFs) identified by ribosome profiling (RIBO-seq). This update elaborates on the major improvements implemented since its initial release. sORFs.org now additionally supports three more species (zebrafish, rat and Caenorhabditis elegans) and currently includes 78 RIBO-seq datasets, a vast increase compared to the three that were processed in the initial release. Therefore, a novel pipeline was constructed that also enables sORF detection in RIBO-seq datasets comprising solely elongating RIBO-seq data while previously, matching initiating RIBO-seq data was necessary to delineate the sORFs. Furthermore, a novel noise filtering algorithm was designed, able to distinguish sORFs with true ribosomal activity from simulated noise, consequently reducing the false positive identification rate. The inclusion of other species also led to the development of an inner BLAST pipeline, assessing sequence similarity between sORFs in the repository. Building on the proof of concept model in the initial release of sORFs.org, a full PRIDE-ReSpin pipeline was now released, reprocessing publicly available MS-based proteomics PRIDE datasets, reporting on true translation events. Next to reporting those identified peptides, sORFs.org allows visual inspection of the annotated spectra within the Lorikeet MS/MS viewer, thus enabling detailed manual inspection and interpretation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

People's perception of LILW repository

International Nuclear Information System (INIS)

Zeleznik, Nadja; Polic, Marko

2002-01-01

Full text: Social acceptability of the radioactive waste repository presents a great problem in every country with such a waste. Even if people agree with the need for its construction, the chosen location should be far from their homes (NIMBY). The reasons for such attitudes were attributed to different causes: uneducated public, differences in understanding of radioactivity and risk by experts and lay public, risk communication problems, lack of credibility and social trust, etc. While in earlier days public was blamed for its irrationality, and need for education and information was emphasized, today it is realized that public trust is extremely important if effective risk communication is to be achieved. It is also recognized that it is not so much the content of the risk message itself, as the lack of trust to those responsible for provision of information that is behind this opposition. Perhaps we could apply here Petty and Caciopo's elaboration likelihood model of persuasion, with credibility as a factor in peripheral route of persuasion. Nevertheless also general lowering of social trust should explain social non-agreement. This lack of trust in experts and political institutions is perhaps caused by outwitting public in earlier years, its bad experiences with responsible officials, dangerous accidents (e.g. TMI, Chernobyl), increased influence that professions have over people's welfare, a greater value placed on equality and better educated public, etc. In 1996 the ARAO re-initiated the search for a LILW repository location with a new, so-called combined approach to the site selection, where the technical, geologically led process is combined with participation of local community. In order to get information on people's perception of the LILW repository construction, their willingness to accept it and factors that influence the acceptability, several surveys have been conducted. Groups of experts and lay persons answered the questionnaires. The results of

The role of weapons production and military waste in the repository selection process

International Nuclear Information System (INIS)

Nelson, D.; Hope, J.; Power, W.; Hunter, T.

1987-01-01

The decision to commingle defense waste with commercial waste in the nuclear waste repository program has many impacts on that program. There will be more waste to place in the two repositories authorized under the Nuclear Waste Policy Act, more transport miles to get the waste to a repository, and more costs associated with environmental and socio-economic impact mitigation. This paper explores the links between weapons production and military waste, and the repository selection process. The paper first describes the importance of state, tribe and public participation to the acceptance of a repository site selection. The paper then examines the various estimates of amounts of existing and future military nuclear wastes, and how these estimates affect repository siting decisions. The final section addresses the public policy questions which surround this issue. Repository siting may be jeopardized unless there is open public discussion about existing radioactive contamination at military production sites and about future nuclear weapons production. Cost-sharing is considered within this context

Proteomics in Argentina - limitations and future perspectives: A special emphasis on meat proteomics.

Science.gov (United States)

Fadda, Silvina; Almeida, André M

2015-11-01

Argentina is one of the most relevant countries in Latin America, playing a major role in regional economics, culture and science. Over the last 80 years, Argentinean history has been characterized by several upward and downward phases that had major consequences on the development of science in the country and most recently on proteomics. In this article, we characterize the evolution of Proteomics sciences in Argentina over the last decade and a half. We describe the proteomics publication output of the country in the framework of the regional and international contexts, demonstrating that Argentina is solidly anchored in a regional context, showing results similar to other emergent and Latin American countries, albeit still far from the European, American or Australian realities. We also provide a case-study on the importance of Proteomics to a specific sector in the area of food science: the use of bacteria of technological interest, highlighting major achievements obtained by Argentinean proteomics scientists. Finally, we provide a general picture of the endeavors being undertaken by Argentinean Proteomics scientists and their international collaborators to promote the Proteomics-based research with the new generation of scientists and PhD students in both Argentina and other countries in the Southern cone. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Digital repository service (DRS) at National Institute of Oceanography: A case study

Digital Repository Service at National Institute of Oceanography (India)

Sahu, S.R.

Open access to the publications over Internet has become a reality. The software likes DSpace help in creating institutional repositories to place the publications on Internet. Implementation of an institutional repository at National Institute...

Public involvement in the siting of contentious facilities; Lessons from the radioactive waste repository siting programmes in Canada and the United States, with special reference to the Swedish repository siting process

International Nuclear Information System (INIS)

Richardson, P.J.

1997-08-01

This report describes the conclusion of a two-part programme, begun in 1994 with the overall aim of assisting in the development of an acceptable public participation strategy for use in Sweden for the siting of contentious facilities, with particular reference to the ongoing siting programme for a deep repository for spent nuclear fuel. The first part of the work programme, a global review of siting practice, was reported as SSI Rapport 94-15, in November 1994. This recommended further detailed studies of at least two individual programmes, which have now been carried out in Canada and the United States, and are reported on here. They involved face to face meetings with many of the main stake holders in the two programmes and enabled valuable insight to be gained into the potential problems associated with increased public participation, as well as identifying good practice where it exists. The lessons learned have then been applied to the evolving repository siting process in Sweden. 35 refs

Public involvement in the siting of contentious facilities; Lessons from the radioactive waste repository siting programmes in Canada and the United States, with special reference to the Swedish repository siting process

Energy Technology Data Exchange (ETDEWEB)

Richardson, P J [Geosciences for Development and the Environment (United Kingdom)

1997-08-01

This report describes the conclusion of a two-part programme, begun in 1994 with the overall aim of assisting in the development of an acceptable public participation strategy for use in Sweden for the siting of contentious facilities, with particular reference to the ongoing siting programme for a deep repository for spent nuclear fuel. The first part of the work programme, a global review of siting practice, was reported as SSI Rapport 94-15, in November 1994. This recommended further detailed studies of at least two individual programmes, which have now been carried out in Canada and the United States, and are reported on here. They involved face to face meetings with many of the main stake holders in the two programmes and enabled valuable insight to be gained into the potential problems associated with increased public participation, as well as identifying good practice where it exists. The lessons learned have then been applied to the evolving repository siting process in Sweden. 35 refs.

Experimental Peptide Identification Repository (EPIR): an integrated peptide-centric platform for validation and mining of tandem mass spectrometry data

DEFF Research Database (Denmark)

Kristensen, Dan Bach; Brønd, Jan Christian; Nielsen, Peter Aagaard

2004-01-01

LC MS/MS has become an established technology in proteomic studies, and with the maturation of the technology the bottleneck has shifted from data generation to data validation and mining. To address this bottleneck we developed Experimental Peptide Identification Repository (EPIR), which...... is an integrated software platform for storage, validation, and mining of LC MS/MS-derived peptide evidence. EPIR is a cumulative data repository where precursor ions are linked to peptide assignments and protein associations returned by a search engine (e.g. Mascot, Sequest, or PepSea). Any number of datasets can...

Data mining in newt-omics, the repository for omics data from the newt.

Science.gov (United States)

Looso, Mario; Braun, Thomas

2015-01-01

Salamanders are an excellent model organism to study regenerative processes due to their unique ability to regenerate lost appendages or organs. Straightforward bioinformatics tools to analyze and take advantage of the growing number of "omics" studies performed in salamanders were lacking so far. To overcome this limitation, we have generated a comprehensive data repository for the red-spotted newt Notophthalmus viridescens, named newt-omics, merging omics style datasets on the transcriptome and proteome level including expression values and annotations. The resource is freely available via a user-friendly Web-based graphical user interface ( http://newt-omics.mpi-bn.mpg.de) that allows access and queries to the database without prior bioinformatical expertise. The repository is updated regularly, incorporating new published datasets from omics technologies.

Final repository search together with the citizens. Information, consultation, dialogue, participation; Endlagersuche - gemeinsam mit den Buergern. Information, Konsultation, Dialog, Beteiligung

Energy Technology Data Exchange (ETDEWEB)

Mueller, Monika C.M. (ed.)

2013-07-01

The documentation on the Loccum meeting 2013 includes contributions on the following topics: Public participation for the final repository search; Lessons learned from the past; Public participation: what is expected? Experiences of repository operators on public participation; The TRIPLEX concept; From Gorleben to the law on final repository search: a long and a short story; Public participation concerning radioactive waste storage; The public has to be informed on the radioactive waste problem and the possible solutions; After consensus is before consensus - German final repository conflict between legislation and simulated public participation; Political concept of public participation; A fast final repository law will not bring about social peace; Good public participation on final repository search - requirements, challenges, questions and approaches.

The Swedish approach to siting of a deep geological repository and interaction with the public

International Nuclear Information System (INIS)

Thegerstroem, C.

1993-01-01

The planned process for siting of a deep geological repository for encapsulated spent nuclear fuel in Sweden was presented in the 1992 SKB R and D programme. A first phase of the repository operation will be limited to disposal of a small amount of encapsulated spent nuclear fuel (approximately 800 tons). This phase will be followed by an evaluation of experiences as well as alternative options before deciding if, when and how to proceed with disposal of the remaining amounts of spent fuel. During the first phase it will be possible to retrieve the waste. Siting is planned to be done in stages. The field studies and safety assessments performed strongly indicate that it is possible to find geological suitable sites within many regions of Sweden. The potential for fulfilling safety requirements will be a crucial factor in site-selection. Local interest in, and attitude to a repository siting will play an important role in the siting process. It is important that an atmosphere of trust and openness can be established. Extensive geological site characterization work will be carried out at the sites selected and studies of other technical, social, economical or political matters will be equally important. Public communication and local participation will form an essential part of the siting programme from the outset. 3 refs., 3 figs

Estimating and coping with public response to radioactive waste repository siting

International Nuclear Information System (INIS)

Payne, B.A.

1984-01-01

The siting, construction, and operation of a radioactive waste repository is likely to be controversial in the communities being considered and at the state and national levels as well. Public response can be conceptualized at two levels: individual and group or organizational. At the individual level, public response is the behavior of people motivated by their attitudes, knowledge, and perceptions of radioactive waste and its hazards and risks. Groups or organizations provide a structure to public response through which to pool resources and talents, set up a division of labor, hire experts, develop a skilled leadership, take legal action, and so on. A broad range of organizations is possible: ad hoc, existing community groups with an added purpose, nationally-recognized organizations, or government offices and agencies. Two cases of response to radioactive waste disposal sites illustrate these sources and kinds of response and suggest indicators to estimate the nature and level of response. Specific coping strategies take different forms, depending on the nature and level of response (either supporting or opposing) to the proposed siting, the past experience of community members with similar projects, with federal agencies, and with citizens' action groups, and sources and accuracy of information individuals and groups have. All strategies are based on a policy of honesty and straight-forwardness, with a sincere effort on the part of site evaluators and decision-makers to be attentive and responsive to the public's concerns

Proteomic data set of the organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates

Directory of Open Access Journals (Sweden)

Tobias Goris

2016-09-01

Full Text Available Sulfurospirillum multivorans is a free-living, physiologically versatile Epsilonproteobacterium able to couple the reductive dehalogenation of chlorinated and brominated ethenes to growth (organohalide respiration. We present proteomic data of S. multivorans grown with different electron donors (formate or pyruvate and electron acceptors (fumarate, nitrate, or tetrachloroethene [PCE]. To obtain information on the cellular localization of proteins, membrane extracts and soluble fractions were separated before data collection from both fractions. The proteome analysis of S. multivorans was performed by mass spectrometry (nanoLC-MS/MS. Raw data have been deposited at ProteomeXchange, “ProteomeXchange provides globally coordinated proteomics data submission and dissemination” [1], via the PRIDE partner repository with the dataset identifier PRIDE: PXD004011. The data might support further research in organohalide respiration and in the general metabolism of free-living Epsilonproteobacteria. The dataset is associated with a previously published study “Proteomics of the organohalide-respiring Epsilonproteobacterium S. multivorans adapted to tetrachloroethene and other energy substrates” [2]. Keywords: Anaerobic respiration, Epsilonproteobacteria, Nitrate respiration, Reductive dechlorination, Reductive dehalogenase

Enlargement of the Baldone near-surface radioactive waste repository

International Nuclear Information System (INIS)

Dreimanis, A.

2007-01-01

A unified analysis of the enlargement of the Baldone near-surface radioactive waste (RW) repository RADONS considers the interplay of the existing engineering, safety and infrastructure premises, with the foreseen newly socio-technical features. This enlargement consists in construction of two additional RW disposal vaults and in building a long-term storage facility for spent sealed sources at the RADONS territory. Our approach is based on consecutive analysis of following basic elements: - the origin of enlargement - the RADONS safety analysis and a set of optimal socio-technical solutions of Salaspils research reactor decommissioning waste management; - the enlargement - a keystone of the national RW management concept, including the long-term approach; - the enlargement concept - the result of international co-operation and obligations; - arrangement optimization of new disposal and storage space; - environmental impact assessment for the repository enlargement - the update of socio-technical studies. The study of the public opinion revealed: negative attitude to repository enlargement is caused mainly due to missing information on radiation level and on the RADONS previous operations. These results indicate: basic measures to improve the public attitude to repository enlargement: the safety upgrade, public education and compensation mechanisms. A detailed stakeholders engagement and public education plan is elaborated. (author)

Multinational repositories: Ethical, legal and political/public aspects

International Nuclear Information System (INIS)

Boutellier, C.; McCombie, C.; Mele, I.

2006-01-01

Concepts for shared multinational repositories face a great challenge in achieving acceptance, despite the fact that they promise advantages in safety, security, environmental protection and costs. When considering advantages of shared multinational repositories, it is instructive to examine which are the ethical, legal and political issues that mostly affect the feasibility of implementing such facilities. This paper addresses the key questions from two opposite sides. The early part takes a 'top-down' view, looking at the international debate on ethical issues, summarising a wide range of national political attitudes and identifying relevant international legislation and treaties. The latter looks 'bottom-up' at the problem, by discussing the situation of a small country, Slovenia. Slovenia has limited financial resources for implementing disposal - but it has a firm commitment to fulfilling its responsibilities for safely managing all Radioactive Wastes (RAW) arising in the country. Strategies considered to do so are laid out in this paper. (author)

ROSA P : The National Transportation Library’s Repository and Open Science Access Portal

Science.gov (United States)

2018-01-01

The National Transportation Library (NTL) was founded as an all-digital repository of US DOT research reports, technical publications and data products. NTLs primary public offering is ROSA P, the Repository and Open Science Access Portal. An open...

Prestudy Oskarshamn. Tourism in Oskarshamn with or without a repository

International Nuclear Information System (INIS)

Nordblom, C.J.; Foghagen, C.

1998-11-01

Consequences for the tourism at Oskarshamn from siting a spent fuel repository in the community are studied. Four questionnaire/interview enquires were performed, and the analysis of the results show that no noticeable effects are expected. Still, an uncertainty about the impact of a repository is felt by the public, and more thorough information about the repository and its components is needed

Geological repositories: The last nuclear frontier. International Conference on Geological Repositories: Political and Technical Progress, 8-10 December 2003, Stockholm, Sweden

International Nuclear Information System (INIS)

ElBaradei, M.

2003-01-01

Few issues play so central a role in the public acceptance of nuclear technologies as the management and disposal of spent fuel and radioactive waste. In the current climate, geological repositories have come to be viewed not as one option among many for completing the nuclear fuel cycle, but as the only sustainable solution achievable in the near term. But despite a longstanding agreement among experts that geological disposal can be safe, technologically feasible and environmentally sound, a large part of the general public remains skeptical. This statement deals with the challenges that IAEA is facing to build public confidence related to spent fuel repositories

Comparative leaf proteomic profiling of salt-treated natural variants of Imperata cylindrica

Directory of Open Access Journals (Sweden)

Yun-Jhih Shih

2018-06-01

Full Text Available Cogon grass (Imperata cylindrica (L. Beauv. var. major (Nees Hubb. is one of the top-ten weeds worldwide. It is also a C4 medicinal plant. In particular, an ecotype from Chuwei (CW mangrove forest was found to be salt tolerant. Comparative proteomic analysis using two-dimensional (2D-difference in gel electrophoresis coupled with liquid chromatography-mass spectrometry (LC-MS was carried out to identify responsive leaf proteins in the CW ecotype and salt-intolerant Sarlun (SL population following three days of 150 mM sodium chloride salt stress treatment. We identified five photosynthesis proteins including Rubisco small subunit, uncharacterized protein LOC100194054, Cyt b6-f, oxygen-evolving enhancer 2, and photosystem I reaction center subunit IV which were significantly up- or down-regulated by salt stress in CW ecotype but not SL population. Gene ontology enrichment analysis showed that photosynthesis was over-represented. The mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD008482. Taken together, our proteomic study identified differentially accumulated proteins which provide additional evidence of ecophysiological variation in two natural variants of I. cylindrica.

Ethical considerations surrounding nuclear waste repository siting and mitigation

International Nuclear Information System (INIS)

Peters, T.F.

1983-01-01

The potential long-term health and safety effects of the nuclear materials stored in repositories, the extremely long periods of time over which such materials may be dangerous, and the equity implications of the siting of a repository in any given area are unlike the issues involved in other large-scale projects. They involve major philosophical issues basic to human perspectives on social relationships and on insuring the future of mankind. Safety and permanence are the two basic criteria for determining whether a waste proposal is satisfactory. This chapter takes the approach of public (or micro) ethics, whose task is to 1) articulate and clarify public values relevant to a problem, 2) identify and evaluate public options, and 3) rank alternatives in some order of ethical preferability. It addresses the four major repository-related issues: uncertainty and risks, geographic equity, intergenerational ethics, and implementation ethics

Development of local partnership for siting of LILW repository in Slovenia

International Nuclear Information System (INIS)

Kralj, Metka; Zeleznik, Nadja

2007-01-01

Available in abstract form only. Full text of publication follows: Slovenia has only temporary storage facilities for radioactive waste. According to the legislation, a permanent LILW repository site should be authorized by 2008, and the repository has to acquire the operating licence by 2013. In 2006, ARAO, the general public and three municipalities established local partnerships in order to increase public acceptability of the LILW repository. Civil initiative groups opposed to the siting appeared in all three local communities. In one case they forced the municipality to withdraw, in one case they changed the siting location, and in one case they were integrated to local partnership. In the municipality of Krsko, the program of local partnership was publicly discussed. There is an NPP in Krsko, so the local partnership also demanded to discuss the power plant issues. Thematic committees were established that worked separately. They also discussed the issues of the spatial plan for the repository. In the municipality of Brezice, a steering committee was established to promote local partnership activities and organization of thematic committees. There was only one active thematic committee, but many activities for the general public were organised. In the municipality of Sevnica, the local partnership was soon cancelled. (authors)

Radioactive wastes repository in Temascalapa, State of Mexico, public opinion. Determination of health effects; Repositorio de residuos radiactivos en Temascalapa Estado de Mexico, Opinion publica. Determinacion de efectos en la salud

Energy Technology Data Exchange (ETDEWEB)

Solis Tinoco, E

1998-12-31

Nuclear waste usually concerns public about the impact on public health and the environment. In Mexico, such interest exists, particularly in the Temascalapa Municipality, Mexico where a low level waste repository recognized by the IAEA, has been functioning since 1972. Maquixco repository is located at 42 Kilometers northeast of Mexico City. Although the environmental radiological monitoring records have demonstrated negligible impact on the environment, in 1998 an unusual public polemic on radioactive health effects appeared among Temascalapa residents. This paper presents a research performed during 1998 with the participation of the National Nuclear Research Institute of Mexico and the National Autonomous University of Mexico. The research design allowed the involvement of local authorities, as a way of stimulate public participation. The research was performed in nine locations of the Temascalapa Municipality, it was focused on public polemics, associated to Maquixco repository as well as trying to identify demographic factors that exert influence on public attitudes. There are also presented the results of personal dosimetry analysis performed on a four hundred residents sample of this Municipality. (Author)

Radioactive wastes repository in Temascalapa, State of Mexico, public opinion. Determination of health effects; Repositorio de residuos radiactivos en Temascalapa Estado de Mexico, Opinion publica. Determinacion de efectos en la salud

Energy Technology Data Exchange (ETDEWEB)

Solis Tinoco, E

1999-12-31

Nuclear waste usually concerns public about the impact on public health and the environment. In Mexico, such interest exists, particularly in the Temascalapa Municipality, Mexico where a low level waste repository recognized by the IAEA, has been functioning since 1972. Maquixco repository is located at 42 Kilometers northeast of Mexico City. Although the environmental radiological monitoring records have demonstrated negligible impact on the environment, in 1998 an unusual public polemic on radioactive health effects appeared among Temascalapa residents. This paper presents a research performed during 1998 with the participation of the National Nuclear Research Institute of Mexico and the National Autonomous University of Mexico. The research design allowed the involvement of local authorities, as a way of stimulate public participation. The research was performed in nine locations of the Temascalapa Municipality, it was focused on public polemics, associated to Maquixco repository as well as trying to identify demographic factors that exert influence on public attitudes. There are also presented the results of personal dosimetry analysis performed on a four hundred residents sample of this Municipality. (Author)

Digital Libraries and Repositories in India: An Evaluative Study

Science.gov (United States)

Mittal, Rekha; Mahesh, G.

2008-01-01

Purpose: The purpose of this research is to identify and evaluate the collections within digital libraries and repositories in India available in the public domain. Design/methodology/approach: The digital libraries and repositories were identified through a study of the literature, as well as internet searching and browsing. The resulting digital…

Low and medium level radioactive waste repository: risk perception

International Nuclear Information System (INIS)

Aquino, Afonso Rodrigues de; Bueno, Lilian de Oliveira; Vieira, Martha Marques Ferreira; Fonseca, Edvaldo Roberto Paiva da; Bellintani, Sandra Aparecida

2009-01-01

This paper focuses on the risk perception associated to the installation of low and intermediate level radioactive waste (LLRW and ILRW) disposal facilities. The purpose is to give support for the implementation of a repository in Brazil. Public acceptance results from a long term work and trust is vital for the process as it takes long to be conquered but might be shortly lost. Therefore, it is essential to care about the way each step is conducted. The knowledge about the system and the risks, the comprehension about these risks, the commitment with safety, adequate support systems for the project (legislation, involved institutions) and the excellence as a goal to be reached are extremely important parameters. The involvement of all interested parties in the decision-making process is condition for a successful and publicly acceptable implementation of such project. The steps for public acceptance of a repository are summarized as follow: Risk perception: to verify how the local population understand and feel the installation of a repository in the region. Media observatory: to continuously follow the news reaching the region where the repository will be installed, including different media. Local population social/economical/cultural profile identification: to determine the local population social/economical/cultural profile; to conduct a survey to know their expectations, allowing the proposal of compensation and incentives to fully account for their expectations. Finally, the philosophy governing this Project is: on doubt, the public must be heard and only after this public hearing the policies concerning the project shall be formulated. (author)

Low and medium level radioactive waste repository: risk perception

Energy Technology Data Exchange (ETDEWEB)

Aquino, Afonso Rodrigues de; Bueno, Lilian de Oliveira; Vieira, Martha Marques Ferreira; Fonseca, Edvaldo Roberto Paiva da; Bellintani, Sandra Aparecida [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)], e-mail: araquino@ipen.br, e-mail: lbueno@ipen.br, e-mail: mmvieira@ipen.br, e-mail: efonseca@ipen.br, e-mail: sbellint@ipen.br

2009-07-01

This paper focuses on the risk perception associated to the installation of low and intermediate level radioactive waste (LLRW and ILRW) disposal facilities. The purpose is to give support for the implementation of a repository in Brazil. Public acceptance results from a long term work and trust is vital for the process as it takes long to be conquered but might be shortly lost. Therefore, it is essential to care about the way each step is conducted. The knowledge about the system and the risks, the comprehension about these risks, the commitment with safety, adequate support systems for the project (legislation, involved institutions) and the excellence as a goal to be reached are extremely important parameters. The involvement of all interested parties in the decision-making process is condition for a successful and publicly acceptable implementation of such project. The steps for public acceptance of a repository are summarized as follow: Risk perception: to verify how the local population understand and feel the installation of a repository in the region. Media observatory: to continuously follow the news reaching the region where the repository will be installed, including different media. Local population social/economical/cultural profile identification: to determine the local population social/economical/cultural profile; to conduct a survey to know their expectations, allowing the proposal of compensation and incentives to fully account for their expectations. Finally, the philosophy governing this Project is: on doubt, the public must be heard and only after this public hearing the policies concerning the project shall be formulated. (author)

Public involvement on closure of Asse II radioactive waste repository in Germany

Energy Technology Data Exchange (ETDEWEB)

Kallenbach-Herbert, Beate [Oko-Institut e.V., Darmstadt (Germany)

2013-07-01

From 1967 to 1978, about 125,800 barrels of low- and intermediate level waste were disposed of - nominally for research purposes - in the former 'Asse' salt mine which had before been used for the production of potash for many years. Since 1988 an inflow of brine is being observed which will cause dangers of flooding and of a collapse due to salt weakening and dissolution if it should increase. Since several years the closure of the Asse repository is planned with the objective to prevent the flooding and collapse of the mine and the release of radioactive substances to the biosphere. The first concept that was presented by the former operator, however, seemed completely unacceptable to regional representatives from politics and NGOs. Their activities against these plans made the project a top issue on the political agenda from the federal to the local level. The paper traces the main reasons which lead to the severe safety problems in the past as well as relevant changes in the governance system today. A focus is put on the process for public involvement in which the Citizens' Advisory Group 'A2B' forms the core measure. Its structure and framework, experience and results, expectations from inside and outside perspectives are presented. Furthermore the question is tackled how far this process can serve as an example for a participatory approach in a siting process for a geological repository for high active waste which can be expected to be highly contested in the affected regions. (authors)

Public involvement on closure of Asse II radioactive waste repository in Germany

International Nuclear Information System (INIS)

Kallenbach-Herbert, Beate

2013-01-01

From 1967 to 1978, about 125,800 barrels of low- and intermediate level waste were disposed of - nominally for research purposes - in the former 'Asse' salt mine which had before been used for the production of potash for many years. Since 1988 an inflow of brine is being observed which will cause dangers of flooding and of a collapse due to salt weakening and dissolution if it should increase. Since several years the closure of the Asse repository is planned with the objective to prevent the flooding and collapse of the mine and the release of radioactive substances to the biosphere. The first concept that was presented by the former operator, however, seemed completely unacceptable to regional representatives from politics and NGOs. Their activities against these plans made the project a top issue on the political agenda from the federal to the local level. The paper traces the main reasons which lead to the severe safety problems in the past as well as relevant changes in the governance system today. A focus is put on the process for public involvement in which the Citizens' Advisory Group 'A2B' forms the core measure. Its structure and framework, experience and results, expectations from inside and outside perspectives are presented. Furthermore the question is tackled how far this process can serve as an example for a participatory approach in a siting process for a geological repository for high active waste which can be expected to be highly contested in the affected regions. (authors)

Analysis of computational vulnerabilities in digital repositories

Directory of Open Access Journals (Sweden)

Valdete Fernandes Belarmino

2015-04-01

Full Text Available Objective. Demonstrates the results of research that aimed to analyze the computational vulnerabilities of digital directories in public Universities. Argues the relevance of information in contemporary societies like an invaluable resource, emphasizing scientific information as an essential element to constitute scientific progress. Characterizes the emergence of Digital Repositories and highlights its use in academic environment to preserve, promote, disseminate and encourage the scientific production. Describes the main software for the construction of digital repositories. Method. The investigation identified and analyzed the vulnerabilities that are exposed the digital repositories using Penetration Testing running. Discriminating the levels of risk and the types of vulnerabilities. Results. From a sample of 30 repositories, we could examine 20, identified that: 5% of the repositories have critical vulnerabilities, 85% high, 25% medium and 100% lowers. Conclusions. Which demonstrates the necessity to adapt actions for these environments that promote informational security to minimizing the incidence of external and / or internal systems attacks.Abstract Grey Text – use bold for subheadings when needed.

YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research.

Science.gov (United States)

Colangelo, Christopher M; Shifman, Mark; Cheung, Kei-Hoi; Stone, Kathryn L; Carriero, Nicholas J; Gulcicek, Erol E; Lam, TuKiet T; Wu, Terence; Bjornson, Robert D; Bruce, Can; Nairn, Angus C; Rinehart, Jesse; Miller, Perry L; Williams, Kenneth R

2015-02-01

We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography-tandem mass spectrometry (LC-MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

Natural analogues, paradigm for manmade repositories for radioactive wastes

International Nuclear Information System (INIS)

Pavelescu, M.; Pavelescu, A.

2004-01-01

Natural analogues are given by nature. They show the results of natural processes which have lasted thousands or millions of years. They provide an excellent example of what could happen in an underground site, offering in the same time the opportunity to test by observation and measurement, many of the geochemical processes that are expected to influence in a realistic and appropriate way, the predicted reliability of the radioactive waste repository over long periods of geological time. The natural analogue studies attempt to understand the multiprocessing complexity of the natural system, which contrasts with the limitations of the laboratory experiments and bring arguments to overcome the difficult time scale issue. By this the natural analogues are a useful paradigm for manmade repository for radioactive wastes. The paper discusses the implicit link in the public mind between natural analogues and manmade waste repository with an accent of the positive impact on public acceptance. It is also discussed the decisive qualities of the natural analogues concerning providing valid long term data and increasing the confidence of the public for manmade repositories. The debate is conducting in terms of sustainable development, having at base high-level principles in order to protect humans and their environment, both now and in the future, from potential hazards arising from such wastes. Safe radwaste management involves the application of technology and resources in a regulated manner so that the public, workers and the environment are protected in accordance with the accepted national and international standards. There are at least seven high-level principles which are mentioned in the paper. It is presented the general concept of the deep geological repository, very important for an acceptable solution for the management of nuclear waste, what is a prerequisite for a renewal of nuclear power. Further are introduced natural and archaeological (manufactured) analogue

Genomes to Proteomes

Energy Technology Data Exchange (ETDEWEB)

Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2009-03-01

Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

A Socio-Technical Perspective on Repository Monitoring - 12229

Energy Technology Data Exchange (ETDEWEB)

Bergmans, Anne [University of Antwerp, Faculty of Political and Social Sciences, Sint-Jacobstraat 2, 2000 Antwerpen (Belgium); Elam, Mark; Sundqvist, Goeran [University of Gothenburg, Department of Sociology, Box 720, 40530 Gothenburg (Sweden); Simmons, Peter [University of East Anglia, School of Environmental Sciences, Norwich NR4 7TJ (United Kingdom)

2012-07-01

Monitoring geological repositories for high-activity radioactive wastes has both technical and social dimensions, which are closely interrelated. To investigate the implications of this for geological disposal, data on experts' expectations of repository monitoring and the functions that it is expected to serve were analysed. The analysis drew on strategic and technical documents on monitoring produced by national agencies and by international organisations or projects; interviews with specialists in radioactive waste management organisations on monitoring and on their perceptions of societal concerns and expectations; and observations from technical workshops on repository monitoring. Three main rationales for monitoring were found: performance confirmation; decision support in a step-wise process; and public and stakeholder confidence building. The expectation that monitoring will enhance public confidence is then examined from a social scientific perspective and the potential for and challenges to using monitoring in this way are reviewed. In conclusion, implications for stakeholder engagement in the development of monitoring objectives and strategies are discussed. (authors)

Ventilation System Strategy for a Prospective Korean Radioactive Waste Repository

International Nuclear Information System (INIS)

Kim, Jin; Kwon, Sang Ki

2005-01-01

In the stage of conceptual design for the construction and operation of the geologic repository for radioactive wastes, it is important to consider a repository ventilation system which serves the repository working environment, hygiene and safety of the public at large, and will allow safe maintenance like moisture content elimination in repository for the duration of the repositories life, construction/operation/closure, also allowing safe waste transportation and emplacement. This paper describes the possible ventilation system design criteria and requirements for the prospective Korean radioactive waste repositories with emphasis on the underground rock cavity disposal method in the both cases of low and medium-level and high-level wastes. It was found that the most important concept is separate ventilation systems for the construction (development) and waste emplacement (storage) activities. In addition, ventilation network system modeling, natural ventilation, ventilation monitoring systems and real time ventilation simulation, and fire simulation and emergency system in the repository are briefly discussed.

Exploring Characterizations of Learning Object Repositories Using Data Mining Techniques

Science.gov (United States)

Segura, Alejandra; Vidal, Christian; Menendez, Victor; Zapata, Alfredo; Prieto, Manuel

Learning object repositories provide a platform for the sharing of Web-based educational resources. As these repositories evolve independently, it is difficult for users to have a clear picture of the kind of contents they give access to. Metadata can be used to automatically extract a characterization of these resources by using machine learning techniques. This paper presents an exploratory study carried out in the contents of four public repositories that uses clustering and association rule mining algorithms to extract characterizations of repository contents. The results of the analysis include potential relationships between different attributes of learning objects that may be useful to gain an understanding of the kind of resources available and eventually develop search mechanisms that consider repository descriptions as a criteria in federated search.

BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication.

Science.gov (United States)

Turewicz, Michael; Kohl, Michael; Ahrens, Maike; Mayer, Gerhard; Uszkoreit, Julian; Naboulsi, Wael; Bracht, Thilo; Megger, Dominik A; Sitek, Barbara; Marcus, Katrin; Eisenacher, Martin

2017-11-10

The analysis of high-throughput mass spectrometry-based proteomics data must address the specific challenges of this technology. To this end, the comprehensive proteomics workflow offered by the de.NBI service center BioInfra.Prot provides indispensable components for the computational and statistical analysis of this kind of data. These components include tools and methods for spectrum identification and protein inference, protein quantification, expression analysis as well as data standardization and data publication. All particular methods of the workflow which address these tasks are state-of-the-art or cutting edge. As has been shown in previous publications, each of these methods is adequate to solve its specific task and gives competitive results. However, the methods included in the workflow are continuously reviewed, updated and improved to adapt to new scientific developments. All of these particular components and methods are available as stand-alone BioInfra.Prot services or as a complete workflow. Since BioInfra.Prot provides manifold fast communication channels to get access to all components of the workflow (e.g., via the BioInfra.Prot ticket system: bioinfraprot@rub.de) users can easily benefit from this service and get support by experts. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Harvesting NASA's Common Metadata Repository

Science.gov (United States)

Shum, D.; Mitchell, A. E.; Durbin, C.; Norton, J.

2017-12-01

As part of NASA's Earth Observing System Data and Information System (EOSDIS), the Common Metadata Repository (CMR) stores metadata for over 30,000 datasets from both NASA and international providers along with over 300M granules. This metadata enables sub-second discovery and facilitates data access. While the CMR offers a robust temporal, spatial and keyword search functionality to the general public and international community, it is sometimes more desirable for international partners to harvest the CMR metadata and merge the CMR metadata into a partner's existing metadata repository. This poster will focus on best practices to follow when harvesting CMR metadata to ensure that any changes made to the CMR can also be updated in a partner's own repository. Additionally, since each partner has distinct metadata formats they are able to consume, the best practices will also include guidance on retrieving the metadata in the desired metadata format using CMR's Unified Metadata Model translation software.

INIS: Nuclear Grey Literature Repository

International Nuclear Information System (INIS)

Savić, Dobrica

2016-01-01

As one of the world's largest collections of published information on the peaceful uses of nuclear science and technology, INIS represents an extraordinary example of world cooperation. Currently, as INIS members, 130 countries and 24 international organizations share and allow access to their valuable nuclear information resources, preserving them for future generations and offering a freely available nuclear knowledge repository. Since its creation in 1970, INIS has collected and provided access to more than 3.8 million bibliographic references to publications, documents, technical reports, non-copyrighted documentation, and other grey literature, as well as over a million full texts. Public interest throughout the years in accessing the INIS Collection has been remarkable. This paper deals with the challenges faced by INIS in its endeavour to increase the use, accessibility, usability and expandability of its on-line repository. It also describes document collection, the features and characteristics of implementing a new search engine, as well as the lessons learned. (author)

PRIDE and "Database on Demand" as valuable tools for computational proteomics.

Science.gov (United States)

Vizcaíno, Juan Antonio; Reisinger, Florian; Côté, Richard; Martens, Lennart

2011-01-01

The Proteomics Identifications Database (PRIDE, http://www.ebi.ac.uk/pride ) provides users with the ability to explore and compare mass spectrometry-based proteomics experiments that reveal details of the protein expression found in a broad range of taxonomic groups, tissues, and disease states. A PRIDE experiment typically includes identifications of proteins, peptides, and protein modifications. Additionally, many of the submitted experiments also include the mass spectra that provide the evidence for these identifications. Finally, one of the strongest advantages of PRIDE in comparison with other proteomics repositories is the amount of metadata it contains, a key point to put the above-mentioned data in biological and/or technical context. Several informatics tools have been developed in support of the PRIDE database. The most recent one is called "Database on Demand" (DoD), which allows custom sequence databases to be built in order to optimize the results from search engines. We describe the use of DoD in this chapter. Additionally, in order to show the potential of PRIDE as a source for data mining, we also explore complex queries using federated BioMart queries to integrate PRIDE data with other resources, such as Ensembl, Reactome, or UniProt.

Displays for promotion of public understanding of geological repository concept and the spatial scale

International Nuclear Information System (INIS)

Shobu, Nobuhiro; Kashiwazaki, Hiroshi

2003-05-01

Japan Nuclear Cycle Development Institutes (JNC) has a few thousands of short term visitors to Geological Isolation Basic Research Facility of Tokai works in every year. From the viewpoint of promotion of the visitor's understanding and also smooth communication between researchers and visitors, the explanation of the technical information on geological disposal should be carried out in more easily understandable methods, as well as conventional tour to the engineering-scale test facility (ENTRY). This paper reports on the background information and the appearance of displays, which were installed at ENTRY, to promote public understanding of geological repository concept and the spatial scale. They have been practically used as one of the explanation tools to support visitor's understanding. (author)

Data set of Aspergillus flavus induced alterations in tear proteome: Understanding the pathogen-induced host response to fungal infection

Directory of Open Access Journals (Sweden)

Jeyalakshmi Kandhavelu

2016-12-01

Full Text Available Fungal keratitis is one of the leading causes of blindness in the tropical countries affecting individuals in their most productive age. The host immune response during this infection is poorly understood. We carried out comparative tear proteome analysis of Aspergillus flavus keratitis patients and uninfected controls. Proteome was separated into glycosylated and non-glycosylated fractions using lectin column chromatography before mass spectrometry. The data revealed the major processes activated in the human host in response to fungal infection and reflected in the tear. Extended analysis of this dataset presented here complements the research article entitled “Aspergillus flavus induced alterations in tear protein profile reveal pathogen-induced host response to fungal infection [1]” (Jeyalakhsmi Kandhavelu, Naveen Luke Demonte, Venkatesh Prajna Namperumalsamy, Lalitha Prajna, Chitra Thangavel, Jeya Maheshwari Jayapal, Dharmalingam Kuppamuthu, 2016. The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PRIDE:PXD003825.

International Conference on Geological Repositories 2016. Conference Synthesis, 7-9 December 2016, Paris, France

International Nuclear Information System (INIS)

Walke, Russell; Kwong, Gloria; )

2017-01-01

Worldwide consensus exists within the international community that geological repositories can provide the necessary long-term safety and security to isolate long-lived radioactive waste from the human environment over long timescales. Such repositories are also feasible to construct using current technologies. However, proving the technical merits and safety of repositories, while satisfying societal and political requirements, has been a challenge in many countries. Building upon the success of previous conferences held in Denver (1999), Stockholm (2003), Berne (2007) and Toronto (2012), the ICGR 2016 brought together high-level decision makers from regulatory and local government bodies, waste management organisations and public stakeholder communities to review current perspectives of geological repository development. This publication provides a synthesis of the 2016 conference on continued engagement and safe implementation of repositories, which was designed to promote information and experience sharing, particularly in the development of polices and regulatory frameworks. Repository safety, and the planning and implementation of repository programs with societal involvement, as well as ongoing work within different international organisations, were also addressed at the conference. (authors)

Building Connections, Collections, and Communities: Increasing the Visibility and Impact of Extension through Institutional Repositories

Science.gov (United States)

Inefuku, Harrison W.; Franz, Nancy K.

2015-01-01

Over the past 20 years, university libraries have developed and manage institutional repositories--digital libraries that provide free, public access to the research, scholarship, and publications of their university's faculty, staff, and students. Although underused by Extension professionals, institutional repositories are powerful tools that…

Fair rules for siting a high-level nuclear waste repository

International Nuclear Information System (INIS)

Easterling, D.

1992-01-01

Geologic repositories are designed to resolve the ever-growing problem of high-level nuclear waste, but these facilities invite intense local opposition due to the perceived severity of the risks and the possibility of stigma effects. This analysis examines whether the perceived fairness of the siting process affects local residents' support for hosting a repository. In particular, a survey of 1,001 Nevada residents is used to test the hypothesis that an individual's willingness to accept a local repository will increase if he or she is convinced that this is the safest disposal option available. A logistic analysis indicates that beliefs regarding relative suitability have an independent effect on the acceptability of a local repository (i.e., Yucca Mountain). The article then considers the question of how to implement an optimizing strategy for siting facilities, comparing an idealized strategy against the original Nuclear Waste Policy Act (NWPA) of 1982 and the Amendments Act of 1987. Although choosing the safest site seems as if it could enhance public acceptance of the repository program, there is currently little prospect of identifying the best option to the high-level waste problem and, as a results, little chance of gaining the public support that is necessary to promote a successful siting outcome. 81 refs., 1 fig., 5 tabs

Proteomics methods applied to malaria: Plasmodium falciparum

International Nuclear Information System (INIS)

Cuesta Astroz, Yesid; Segura Latorre, Cesar

2012-01-01

Malaria is a parasitic disease that has a high impact on public health in developing countries. The sequencing of the plasmodium falciparum genome and the development of proteomics have enabled a breakthrough in understanding the biology of the parasite. Proteomics have allowed to characterize qualitatively and quantitatively the parasite s expression of proteins and has provided information on protein expression under conditions of stress induced by antimalarial. Given the complexity of their life cycle, this takes place in the vertebrate host and mosquito vector. It has proven difficult to characterize the protein expression during each stage throughout the infection process in order to determine the proteome that mediates several metabolic, physiological and energetic processes. Two dimensional electrophoresis, liquid chromatography and mass spectrometry have been useful to assess the effects of antimalarial on parasite protein expression and to characterize the proteomic profile of different p. falciparum stages and organelles. The purpose of this review is to present state of the art tools and advances in proteomics applied to the study of malaria, and to present different experimental strategies used to study the parasite's proteome in order to show the advantages and disadvantages of each one.

University digital repositories and authors.

Directory of Open Access Journals (Sweden)

Alice Keefer

2008-02-01

Full Text Available The Open Access movement offers two strategies for making scientific information available without economic, technical or legal obstacles: the publication of articles in OA journals and the deposit by authors of their Works in stable institutional or discipline-based repositories. This article explores the implementation of the second “route” on the part of authors, because it is the strategy that offers the greatest possibility of attaining OA in the short term. However, it does require repositories to exert great effort in informing the authors of the advantages of self-archiving and of the procedures for depositing their work and, even helping them to do so – through services and promotional activities.

Staged Repository Development Programmes

International Nuclear Information System (INIS)

Isaacs, T

2003-01-01

Programs to manage and ultimately dispose of high-level radioactive wastes are unique from scientific and technological as well as socio-political aspects. From a scientific and technological perspective, high-level radioactive wastes remain potentially hazardous for geological time periods-many millennia-and scientific and technological programs must be put in place that result in a system that provides high confidence that the wastes will be isolated from the accessible environment for these many thousands of years. Of course, ''proof'' in the classical sense is not possible at the outset, since the performance of the system can only be known with assurance, if ever, after the waste has been emplaced for those geological time periods. Adding to this challenge, many uncertainties exist in both the natural and engineered systems that are intended to isolate the wastes, and some of the uncertainties will remain regardless of the time and expense in attempting to characterize the system and assess its performance. What was perhaps underappreciated in the early days of waste management and repository program development were the unique and intense reactions that the institutional, political, and public bodies would have to repository program development, particularly in programs attempting to identify and then select sites for characterization, design, licensing, and ultimate development. Reactions in most nations were strong, focused, unrelenting, and often successful in hindering, derailing, and even stopping national repository programs. The reasons for such reactions and the measures to successfully respond to them are still evolving and continue to be the focus of many national program and political leaders. Adaptive Staging suggests an approach to repository program development that reflects the unique challenges associated with the disposal of high-level radioactive waste. The step-wise, incremental, learn-as-you-go approach is intended to maximize the

Implementation of the Brazilian national repository

International Nuclear Information System (INIS)

Tello, Cledola Cassia Oliveira de

2013-01-01

Ionizing radiation in Brazil is used in electricity generation, medicine, industry, agriculture and for research and development purposes. All these activities can generate radioactive waste. At this point, in Brazil, the use of nuclear energy and radioisotopes justifies the construction of a national repository for radioactive wastes of low and intermediate-level. According to Federal Law No. 10308, Brazilian National Commission for Nuclear Energy (CNEN) is responsible for designing and constructing the intermediate and final storages for radioactive wastes. Additionally, a restriction on the construction of Angra 3 is that the repository is under construction until its operation start, attaining some requirements of the Brazilian Environmental Regulator (IBAMA). The RBMN Project (Repository for Low and Intermediate-Level Radioactive Wastes) aims at the implantation of a National Repository for disposal of low and intermediate-level of radiation wastes. This Project has some aspects that are unique in the Brazilian context, especially referring to the time between its construction and the end of its institutional period. This time is about 360 years, when the area will be released for unrestricted uses. It means that the Repository must be safe and secure for more than three hundred years, which is longer than half of the whole of Brazilian history. This aspect is very new for the Brazilian people, bringing a new dimension to public acceptance. Another point is this will be the first repository in South America, bringing a real challenge for the continent. The current status of the Project is summarized. (author)

The Morsleben radwaste repository. Preparing for decommissioning

International Nuclear Information System (INIS)

Mehnert, M.; Schmitt, R.

2001-06-01

The publication is intended to illustrate with a brief chronology the history and the present situation of the Morsleben radwaste repository, including specific aspects such as the geology of the site and construction and engineering activities, the particulars of waste form emplacement and log-term storage conditions, topical issues relating to radiological safety during operation and after decommissioning. The brochure is designed for the general audience interested in background information on all aspects of the uses, operation and decommissioning of a radwaste repository in Germany. (orig./CB) [de

Integrating repositories with fuel cycles: The airport authority model

Energy Technology Data Exchange (ETDEWEB)

Forsberg, C. [Massachusetts Inst. of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139-4307 (United States)

2012-07-01

The organization of the fuel cycle is a legacy of World War II and the cold war. Fuel cycle facilities were developed and deployed without consideration of the waste management implications. This led to the fuel cycle model of a geological repository site with a single owner, a single function (disposal), and no other facilities on site. Recent studies indicate large economic, safety, repository performance, nonproliferation, and institutional incentives to collocate and integrate all back-end facilities. Site functions could include geological disposal of spent nuclear fuel (SNF) with the option for future retrievability, disposal of other wastes, reprocessing with fuel fabrication, radioisotope production, other facilities that generate significant radioactive wastes, SNF inspection (navy and commercial), and related services such as SNF safeguards equipment testing and training. This implies a site with multiple facilities with different owners sharing some facilities and using common facilities - the repository and SNF receiving. This requires a different repository site institutional structure. We propose development of repository site authorities modeled after airport authorities. Airport authorities manage airports with government-owned runways, collocated or shared public and private airline terminals, commercial and federal military facilities, aircraft maintenance bases, and related operations - all enabled and benefiting the high-value runway asset and access to it via taxi ways. With a repository site authority the high value asset is the repository. The SNF and HLW receiving and storage facilities (equivalent to the airport terminal) serve the repository, any future reprocessing plants, and others with needs for access to SNF and other wastes. Non-public special-built roadways and on-site rail lines (equivalent to taxi ways) connect facilities. Airport authorities are typically chartered by state governments and managed by commissions with members

Integrating repositories with fuel cycles: The airport authority model

International Nuclear Information System (INIS)

Forsberg, C.

2012-01-01

The organization of the fuel cycle is a legacy of World War II and the cold war. Fuel cycle facilities were developed and deployed without consideration of the waste management implications. This led to the fuel cycle model of a geological repository site with a single owner, a single function (disposal), and no other facilities on site. Recent studies indicate large economic, safety, repository performance, nonproliferation, and institutional incentives to collocate and integrate all back-end facilities. Site functions could include geological disposal of spent nuclear fuel (SNF) with the option for future retrievability, disposal of other wastes, reprocessing with fuel fabrication, radioisotope production, other facilities that generate significant radioactive wastes, SNF inspection (navy and commercial), and related services such as SNF safeguards equipment testing and training. This implies a site with multiple facilities with different owners sharing some facilities and using common facilities - the repository and SNF receiving. This requires a different repository site institutional structure. We propose development of repository site authorities modeled after airport authorities. Airport authorities manage airports with government-owned runways, collocated or shared public and private airline terminals, commercial and federal military facilities, aircraft maintenance bases, and related operations - all enabled and benefiting the high-value runway asset and access to it via taxi ways. With a repository site authority the high value asset is the repository. The SNF and HLW receiving and storage facilities (equivalent to the airport terminal) serve the repository, any future reprocessing plants, and others with needs for access to SNF and other wastes. Non-public special-built roadways and on-site rail lines (equivalent to taxi ways) connect facilities. Airport authorities are typically chartered by state governments and managed by commissions with members

Data in support of proteomic analysis of pneumococcal pediatric clinical isolates to construct a protein array

Directory of Open Access Journals (Sweden)

Alfonso Olaya-Abril

2016-03-01

Full Text Available Surface proteins play key roles in the interaction between cells and their environment, and in pathogenic microorganisms they are the best targets for drug or vaccine discovery and/or development. In addition, surface proteins can be the basis for serodiagnostic tools aiming at developing more affordable techniques for early diagnosis of infection in patients. We carried out a proteomic analysis of a collection of pediatric clinical isolates of Streptococcus pneumoniae, an important human pathogen responsible for more than 1.5 million child deaths worldwide. For that, cultured live bacterial cells were “shaved” with trypsin, and the recovered peptides were analyzed by LC/MS/MS. We selected 95 proteins to be produced as recombinant polypeptides, and printed them on an array. We probed the protein array with a collection of patient sera to define serodiagnostic antigens. The mass spectrometry proteomics data correspond to those published in [1] and have been deposited to the ProteomeXchange Consortium [2] via the PRIDE partner repository [3] with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD001740. The protein array raw data are provided as supplemental material in this article. Keywords: Pneumococcus, Protein arrays, Proteomics, Diagnostics

Proteomic and metabolomic approaches to biomarker discovery

CERN Document Server

Issaq, Haleem J

2013-01-01

Proteomic and Metabolomic Approaches to Biomarker Discovery demonstrates how to leverage biomarkers to improve accuracy and reduce errors in research. Disease biomarker discovery is one of the most vibrant and important areas of research today, as the identification of reliable biomarkers has an enormous impact on disease diagnosis, selection of treatment regimens, and therapeutic monitoring. Various techniques are used in the biomarker discovery process, including techniques used in proteomics, the study of the proteins that make up an organism, and metabolomics, the study of chemical fingerprints created from cellular processes. Proteomic and Metabolomic Approaches to Biomarker Discovery is the only publication that covers techniques from both proteomics and metabolomics and includes all steps involved in biomarker discovery, from study design to study execution.  The book describes methods, and presents a standard operating procedure for sample selection, preparation, and storage, as well as data analysis...

A method and software framework for enriching private biomedical sources with data from public online repositories.

Science.gov (United States)

Anguita, Alberto; García-Remesal, Miguel; Graf, Norbert; Maojo, Victor

2016-04-01

Modern biomedical research relies on the semantic integration of heterogeneous data sources to find data correlations. Researchers access multiple datasets of disparate origin, and identify elements-e.g. genes, compounds, pathways-that lead to interesting correlations. Normally, they must refer to additional public databases in order to enrich the information about the identified entities-e.g. scientific literature, published clinical trial results, etc. While semantic integration techniques have traditionally focused on providing homogeneous access to private datasets-thus helping automate the first part of the research, and there exist different solutions for browsing public data, there is still a need for tools that facilitate merging public repositories with private datasets. This paper presents a framework that automatically locates public data of interest to the researcher and semantically integrates it with existing private datasets. The framework has been designed as an extension of traditional data integration systems, and has been validated with an existing data integration platform from a European research project by integrating a private biological dataset with data from the National Center for Biotechnology Information (NCBI). Copyright © 2016 Elsevier Inc. All rights reserved.

N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana.

Science.gov (United States)

Willems, Patrick; Ndah, Elvis; Jonckheere, Veronique; Stael, Simon; Sticker, Adriaan; Martens, Lennart; Van Breusegem, Frank; Gevaert, Kris; Van Damme, Petra

2017-06-01

Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N termini encoded in the Arabidopsis thaliana genome. After a stringent false discovery rate filtering, 117 protein N termini compliant with N-terminal methionine excision specificity and indicative of translation initiation were found. These include N-terminal protein extensions and translation from transposable elements and pseudogenes. Gene prediction provided supporting protein-coding models for approximately half of the protein N termini. Besides the prediction of functional domains (partially) contained within the newly predicted ORFs, further supporting evidence of translation was found in the recently released Araport11 genome re-annotation of Arabidopsis and computational translations of sequences stored in public repositories. Most interestingly, complementary evidence by ribosome profiling was found for 23 protein N termini. Finally, by analyzing protein N-terminal peptides, an in silico analysis demonstrates the applicability of our N-terminal proteogenomics strategy in revealing protein-coding potential in species with well- and poorly-annotated genomes. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Record of responses to public comments on proposed general guidelines for recommendation of sites for nuclear waste repositories

International Nuclear Information System (INIS)

1983-01-01

The Nuclear Waste Policy Act of 1982 (Public Law 97-425, referred to in this document as the Act) assigned to the US Department of Energy (DOE) the authority for the disposal of high-level radioactive waste and spent nuclear fuel. Among other provisions, the Act specifies a process and schedule for the siting of two geologic repositories for this purpose. The Act requires that the DOE issue general guidelines for the recommendation of sites for repositories. The guidelines are to be developed in consultation with three Federal agencies (the Council on Environmental Quality, the US Environmental Protection Agency, and the US Geological Survey) and with interested Governors and issued with the concurrence of the US Nuclear Regulatory Commission. To meet this directive, the DOE convened a task force of program experts to develop proposed guidelines, issued the proposed guidelines on February 7, 1983, and invited comments from the specified Federal agencies, interested Governors, and the general public. Public hearings on the proposed guidelines were held in March at the following locations: Chicago, New Orleans, Washington, DC, Salt Lake City, and Seattle. After considering the resulting comments and preparing responses to them, the task force prepared a draft of this comment-response document and a set of alternative guidelines; these documents were issued on May 27, 1983. This document summarizes the record of comments that directly led to the alternative guidelines of May 27, 1983. It contains synopses of comments, presents the responses of the task force to the comments, and briefly describes how the proposed guidelines of February 7, 1983, were revised to produce the alternative guidelines of May 27, 1983. 13 references

Planning and Design Considerations for Geological Repository Programmes of Radioactive Waste

International Nuclear Information System (INIS)

2014-11-01

Disposal in a geological repository is the generally accepted solution for the long term management of high level and/or long lived radioactive wastes, in line with the general principles defined in the IAEA Safety Fundamentals. This publication presents practical information on the way a geological repository programme for radioactive waste could be defined and planned, with special attention to all aspects having an impact on the timing. Country specific examples for repository development phases are provided, based on actual experiences from Member States

SpirPro: A Spirulina proteome database and web-based tools for the analysis of protein-protein interactions at the metabolic level in Spirulina (Arthrospira) platensis C1.

Science.gov (United States)

Senachak, Jittisak; Cheevadhanarak, Supapon; Hongsthong, Apiradee

2015-07-29

Spirulina (Arthrospira) platensis is the only cyanobacterium that in addition to being studied at the molecular level and subjected to gene manipulation, can also be mass cultivated in outdoor ponds for commercial use as a food supplement. Thus, encountering environmental changes, including temperature stresses, is common during the mass production of Spirulina. The use of cyanobacteria as an experimental platform, especially for photosynthetic gene manipulation in plants and bacteria, is becoming increasingly important. Understanding the mechanisms and protein-protein interaction networks that underlie low- and high-temperature responses is relevant to Spirulina mass production. To accomplish this goal, high-throughput techniques such as OMICs analyses are used. Thus, large datasets must be collected, managed and subjected to information extraction. Therefore, databases including (i) proteomic analysis and protein-protein interaction (PPI) data and (ii) domain/motif visualization tools are required for potential use in temperature response models for plant chloroplasts and photosynthetic bacteria. A web-based repository was developed including an embedded database, SpirPro, and tools for network visualization. Proteome data were analyzed integrated with protein-protein interactions and/or metabolic pathways from KEGG. The repository provides various information, ranging from raw data (2D-gel images) to associated results, such as data from interaction and/or pathway analyses. This integration allows in silico analyses of protein-protein interactions affected at the metabolic level and, particularly, analyses of interactions between and within the affected metabolic pathways under temperature stresses for comparative proteomic analysis. The developed tool, which is coded in HTML with CSS/JavaScript and depicted in Scalable Vector Graphics (SVG), is designed for interactive analysis and exploration of the constructed network. SpirPro is publicly available on the web

National Geoscience Data Repository System: Phase 2 final report

Energy Technology Data Exchange (ETDEWEB)

NONE

1997-07-01

The American Geological Institute (AGI) has completed Phase 2 of a project to establish a National Geoscience Data Repository System (NGDRS). The project`s primary objectives are to preserve geoscience data in jeopardy of being destroyed and to make that data available to those who have a need to use it in future investigations. These data are available for donation to the public as a result of the downsizing that has occurred in the major petroleum and mining companies in the US for the past decade. In recent years, these companies have consolidated domestic operations, sold many of their domestic properties and relinquished many of their leases. The scientific data associated with those properties are no longer considered to be useful assets and are consequently in danger of being lost forever. The national repository project will make many of these data available to the geoscience community for the first time. Phase 2 encompasses the establishment of standards for indexing and cataloging of geoscience data and determination of the costs of transferring data from the private sector to public-sector data repositories. Pilot projects evaluated the feasibility of the project for transfer of different data types and creation of a Web-based metadata supercatalog and browser. Also as part of the project, a national directory of geoscience data repositories was compiled to assess what data are currently available in existing facilities. The next step, Phase 3, will focus on the initiation of transfer of geoscience data from the private sector to the public domain and development of the web-based Geotrek metadata supercatalog.

Glyco-centric lectin magnetic bead array (LeMBA − proteomics dataset of human serum samples from healthy, Barrett׳s esophagus and esophageal adenocarcinoma individuals

Directory of Open Access Journals (Sweden)

Alok K. Shah

2016-06-01

Full Text Available This data article describes serum glycoprotein biomarker discovery and qualification datasets generated using lectin magnetic bead array (LeMBA – mass spectrometry techniques, “Serum glycoprotein biomarker discovery and qualification pipeline reveals novel diagnostic biomarker candidates for esophageal adenocarcinoma” [1]. Serum samples collected from healthy, metaplastic Barrett׳s esophagus (BE and esophageal adenocarcinoma (EAC individuals were profiled for glycoprotein subsets via differential lectin binding. The biomarker discovery proteomics dataset consisting of 20 individual lectin pull-downs for 29 serum samples with a spiked-in internal standard chicken ovalbumin protein has been deposited in the PRIDE partner repository of the ProteomeXchange Consortium with the data set identifier PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002442. Annotated MS/MS spectra for the peptide identifications can be viewed using MS-Viewer (〈http://prospector2.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msviewer〉 using search key “jn7qafftux”. The qualification dataset contained 6-lectin pulldown-coupled multiple reaction monitoring-mass spectrometry (MRM-MS data for 41 protein candidates, from 60 serum samples. This dataset is available as a supplemental files with the original publication [1].

Mining knowledge from text repositories using information extraction ...

Indian Academy of Sciences (India)

Information extraction (IE); text mining; text repositories; knowledge discovery from .... general purpose English words. However ... of precision and recall, as extensive experimentation is required due to lack of public tagged corpora. 4. Mining ...

Progress towards developing an international repository for radioactive waste

International Nuclear Information System (INIS)

Kurzeme, M.

2001-01-01

Pangea Resources was established to develop and promote the concept of international repositories. The concept was based on repositories located in geologically stable, flat, arid environments meeting the 'high isolation' criteria developed by Pangea Resources. The high isolation concept of Pangea Resources can be applied in various regions of the world, and these have been made public. The pilot project chosen for exploring feasibility was for an international repository in Australia. This study was in preparation for public release, when the existence of the proposal was prematurely revealed to the media. The general media and public reaction to the concept was understandably negative. However, there were also some opinion pieces reported suggesting that the concept of an international repository should be thought about seriously, before it is accepted or rejected. In addition, thoughtful reactions were received from the business and scientific communities. In particular a group of very eminent scientists, the Scientific Review Group, undertook to review independently the quality of the work done. Nevertheless, the reaction from the state and federal governments, was also negative. The Australian Government stated its policy not to permit importation or disposal of foreign nuclear waste. During the last two years Pangea Resources has been developing the technical aspects of the concept and has produced and published several scientific reports on transport, storage and disposal of radioactive materials. All the scientific studies of Pangea Resources have been reviewed by the Scientific Review Group. The work has also been presented in scientific conferences, to the media (including a dedicated television documentary) and to the public. The technical work is generic or is based on diverse potential siting areas around the world and the disposal and storage technologies studied are being broadened beyond the specific high-isolation concept. Most importantly, it has

Birth of plant proteomics in India: a new horizon.

Science.gov (United States)

Narula, Kanika; Pandey, Aarti; Gayali, Saurabh; Chakraborty, Niranjan; Chakraborty, Subhra

2015-09-08

In the post-genomic era, proteomics is acknowledged as the next frontier for biological research. Although India has a long and distinguished tradition in protein research, the initiation of proteomics studies was a new horizon. Protein research witnessed enormous progress in protein separation, high-resolution refinements, biochemical identification of the proteins, protein-protein interaction, and structure-function analysis. Plant proteomics research, in India, began its journey on investigation of the proteome profiling, complexity analysis, protein trafficking, and biochemical modeling. The research article by Bhushan et al. in 2006 marked the birth of the plant proteomics research in India. Since then plant proteomics studies expanded progressively and are now being carried out in various institutions spread across the country. The compilation presented here seeks to trace the history of development in the area during the past decade based on publications till date. In this review, we emphasize on outcomes of the field providing prospects on proteomic pathway analyses. Finally, we discuss the connotation of strategies and the potential that would provide the framework of plant proteome research. The past decades have seen rapidly growing number of sequenced plant genomes and associated genomic resources. To keep pace with this increasing body of data, India is in the provisional phase of proteomics research to develop a comparative hub for plant proteomes and protein families, but it requires a strong impetus from intellectuals, entrepreneurs, and government agencies. Here, we aim to provide an overview of past, present and future of Indian plant proteomics, which would serve as an evaluation platform for those seeking to incorporate proteomics into their research programs. This article is part of a Special Issue entitled: Proteomics in India. Copyright © 2015 Elsevier B.V. All rights reserved.

NWTS program criteria for mined geologic disposal of nuclear waste: repository performance and development criteria. Public draft

Energy Technology Data Exchange (ETDEWEB)

None

1982-07-01

This document, DOE/NWTS-33(3) is one of a series of documents to establish the National Waste Terminal Storage (NWTS) program criteria for mined geologic disposal of high-level radioactive waste. For both repository performance and repository development it delineates the criteria for design performance, radiological safety, mining safety, long-term containment and isolation, operations, and decommissioning. The US Department of Energy will use these criteria to guide the development of repositories to assist in achieving performance and will reevaluate their use when the US Nuclear Regulatory Commission issues radioactive waste repository rules.

NWTS program criteria for mined geologic disposal of nuclear waste: repository performance and development criteria. Public draft

International Nuclear Information System (INIS)

1982-07-01

This document, DOE/NWTS-33(3) is one of a series of documents to establish the National Waste Terminal Storage (NWTS) program criteria for mined geologic disposal of high-level radioactive waste. For both repository performance and repository development it delineates the criteria for design performance, radiological safety, mining safety, long-term containment and isolation, operations, and decommissioning. The US Department of Energy will use these criteria to guide the development of repositories to assist in achieving performance and will reevaluate their use when the US Nuclear Regulatory Commission issues radioactive waste repository rules

Proposed nomination of Yucca Mountain as a potential high-level radioactive waste repository. Correspondence and request for oral presentations for US Department of Energy public hearings

International Nuclear Information System (INIS)

1983-01-01

This volume contains correspondence and requests by the public citizens for oral presentation at the public hearings for the proposed nomination of Yucca Mountain as a potential high-level radioactive waste repository. Written comments are also included on: the proposed nomination; the issues to be addressed in the Environmental Assessment; and the issues to be addressed by any Site Characterization Plan, if developed

An OAI repository centric peer-review model

CERN Multimedia

CERN. Geneva

2005-01-01

Pre-print repositories have seen a significant increase in use over the past fifteen years across multiple research domains. Researchers are beginning to develop applications capable of using these repositories to assist the scientific community above and beyond the pure dissemination of information. The contributions set forth by this paper emphasize a deconstructed publication model where in which the peer-review certification phase of a pre-print is mediated by an OAI-compliant peer-review service. This peer-review service uses a social-network algorithm for determining potential reviewers for a submitted manuscript and for weighting the influence of each participating reviewer’s evaluations. The paper also provides a set of peer-review specific metadata tags that can accompany a pre-prints existing metadata record. The combinations of these contributions provide a unique repository-centric peer-review model within the framework of the current OAI standards existing today.

Proteomics Core

Data.gov (United States)

Federal Laboratory Consortium — Proteomics Core is the central resource for mass spectrometry based proteomics within the NHLBI. The Core staff help collaborators design proteomics experiments in a...

DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Ashland Public High School, Ashland, Wisconsin: Session 2, April 9, 1986: Transcript of proceedings

International Nuclear Information System (INIS)

1986-01-01

This document contains a transcript of the comments of 111 witnesses. These meetings were held to hear the public's comments regarding the selection of a site for a second high-level radioactive waste repository

The Open Data Repositorys Data Publisher

Science.gov (United States)

Stone, N.; Lafuente, B.; Downs, R. T.; Blake, D.; Bristow, T.; Fonda, M.; Pires, A.

2015-01-01

Data management and data publication are becoming increasingly important components of researcher's workflows. The complexity of managing data, publishing data online, and archiving data has not decreased significantly even as computing access and power has greatly increased. The Open Data Repository's Data Publisher software strives to make data archiving, management, and publication a standard part of a researcher's workflow using simple, web-based tools and commodity server hardware. The publication engine allows for uploading, searching, and display of data with graphing capabilities and downloadable files. Access is controlled through a robust permissions system that can control publication at the field level and can be granted to the general public or protected so that only registered users at various permission levels receive access. Data Publisher also allows researchers to subscribe to meta-data standards through a plugin system, embargo data publication at their discretion, and collaborate with other researchers through various levels of data sharing. As the software matures, semantic data standards will be implemented to facilitate machine reading of data and each database will provide a REST application programming interface for programmatic access. Additionally, a citation system will allow snapshots of any data set to be archived and cited for publication while the data itself can remain living and continuously evolve beyond the snapshot date. The software runs on a traditional LAMP (Linux, Apache, MySQL, PHP) server and is available on GitHub (http://github.com/opendatarepository) under a GPLv2 open source license. The goal of the Open Data Repository is to lower the cost and training barrier to entry so that any researcher can easily publish their data and ensure it is archived for posterity.

Learning Object Repositories

Science.gov (United States)

Lehman, Rosemary

2007-01-01

This chapter looks at the development and nature of learning objects, meta-tagging standards and taxonomies, learning object repositories, learning object repository characteristics, and types of learning object repositories, with type examples. (Contains 1 table.)

Citizen participation in nuclear waste repository siting

International Nuclear Information System (INIS)

Howell, R.E.; Olsen, D.

1982-12-01

The following study presents a proposed strategy for citizen participation during the planning stages of nuclear waste repository siting. It discusses the issue from the general perspective of citizen participation in controversial issues and in community development. Second, rural institutions and attitudes toward energy development as the context for developing a citizen participation program are examined. Third, major citizen participation techniques and the advantages and disadvantages of each approach for resolving public policy issues are evaluated. Fourth, principles of successful citizen participation are presented. Finally, a proposal for stimulating and sustaining effective responsible citizen participation in nuclear waste repository siting and management is developed

Siting Process for HLW Repository in Japan

International Nuclear Information System (INIS)

Masuda, S.; Kitayama, K.; Umeki, H.; Naito, M.

2002-01-01

In the year 2000, the geological disposal program for high-level radioactive waste in Japan moved from the phase of generic research and development (R and D) into the phase of implementation. Following legislation entitled the ''Specified Radioactive Waste Final Disposal Act'', the Nuclear Waste Management Organization of Japan (NUMO) was established as the implementing organization. The assigned activities of NUMO include selection of the repository site, demonstration of disposal technology at the site, developing relevant licensing applications and construction, operation and closure of the repository. As the first milestone of siting process, NUMO announced to the public an overall procedure for selection of preliminary investigation areas for potential candidate sites on October 29, 2001. The procedure specifies that NUMO will solicit volunteer municipalities for preliminary investigation areas with publishing four documents as an information package. These documents are tentatively entitled ''Instructions for Application'', ''Siting Factors for the Preliminary Investigation Areas'', a ''Repository Concepts'' as well as an ''Site Investigation Community Outreach Scheme''

Effective summary evaluators for deep nuclear waste repositories: geohydrologic response function

International Nuclear Information System (INIS)

Nelson, R.W.; Dove, F.H.

1981-03-01

Useful insight has been gained over the past four years as hydrologic system modeling has been applied to evaluate hypothetical, waste-repository sites in various geologic media. The Geohydrologic Response Functions, described in this paper, are shown to: blend extensive results of technical analysis into simple summary relationships, and to potentially help the public and decision makers to evaluate the magnitude of any loss in repository integrity

Reference design description for a geologic repository: Revision 01

International Nuclear Information System (INIS)

1997-09-01

This document describes the current design expectations for a potential geologic repository that could be located at Yucca Mountain in Nevada. This Reference Design Description (RDD) looks at the surface and subsurface repository and disposal container design. Additionally, it reviews the expected long-term performance of the potential repository. In accordance with current legislation, the reference design for the potential repository does not include an interim storage option. The reference design presented allows the disposal of highly radioactive material received from government-owned spent fuel custodian sites; produces high-level waste sites, and commercial spent fuel sites. All design elements meet current federal, state, and local regulations governing the disposal of high-level radioactive waste and protection of the public and the environment. Due to the complex nature of developing a repository, the design will be created in three phases to support Viability Assessment, License Application, and construction. This document presents the current reference design. It will be updated periodically as the design progresses. Some of the details presented here may change significantly as more cost-effective solutions, technical advancements, or changes to requirements are identified

Global Proteome Analysis of the NCI-60 Cell Line Panel

Directory of Open Access Journals (Sweden)

Amin Moghaddas Gholami

2013-08-01

Full Text Available The NCI-60 cell line collection is a very widely used panel for the study of cellular mechanisms of cancer in general and in vitro drug action in particular. It is a model system for the tissue types and genetic diversity of human cancers and has been extensively molecularly characterized. Here, we present a quantitative proteome and kinome profile of the NCI-60 panel covering, in total, 10,350 proteins (including 375 protein kinases and including a core cancer proteome of 5,578 proteins that were consistently quantified across all tissue types. Bioinformatic analysis revealed strong cell line clusters according to tissue type and disclosed hundreds of differentially regulated proteins representing potential biomarkers for numerous tumor properties. Integration with public transcriptome data showed considerable similarity between mRNA and protein expression. Modeling of proteome and drug-response profiles for 108 FDA-approved drugs identified known and potential protein markers for drug sensitivity and resistance. To enable community access to this unique resource, we incorporated it into a public database for comparative and integrative analysis (http://wzw.tum.de/proteomics/nci60.

Socioeconomic impacts of large-scale developments: implications for high-level nuclear waste repositories

International Nuclear Information System (INIS)

Murdock, S.H.; Leistritz, F.L.; Hamm, R.R.

1983-01-01

High-level nuclear waste repositories will likely be located in sparsely settled rural areas in the US. These projects will significantly affect the economic, demographic, public service, fiscal, and social (the socioeconomic) dimensions of those rural areas. The impacts and means of mitigating them thus require careful analysis. This paper examines some of the potential socioeconomic impacts likely to occur in rural areas as a result of repository siting and development, and it describes some of the characteristics of mitigation programs that are likely to be necessary, if the impacts are to be addressed. Both (1) standard impacts, those resulting from the fact that, like many other large-scale developments, repositories will involve a substantial number of new workers and residents (relative to the size of existing communities), and (2) special impacts, those resulting from the fact that repositories store radioactive materials, are examined. The discussion indicates that economic, demographic, public service, fiscal, and social impacts (standard and special) of these repositories will be substantial and problematic in many cases. Unless the impacts are effectively addressed with carefully planned and well financed mitigation efforts that insure that high-quality planning information is provided to local residents, and that local residents are involved in impact planning and management throughout the siting and development process, repository siting is unlikely to be effectively and equitably achieved. 44 references

A strategy to establish Food Safety Model Repositories.

Science.gov (United States)

Plaza-Rodríguez, C; Thoens, C; Falenski, A; Weiser, A A; Appel, B; Kaesbohrer, A; Filter, M

2015-07-02

Transferring the knowledge of predictive microbiology into real world food manufacturing applications is still a major challenge for the whole food safety modelling community. To facilitate this process, a strategy for creating open, community driven and web-based predictive microbial model repositories is proposed. These collaborative model resources could significantly improve the transfer of knowledge from research into commercial and governmental applications and also increase efficiency, transparency and usability of predictive models. To demonstrate the feasibility, predictive models of Salmonella in beef previously published in the scientific literature were re-implemented using an open source software tool called PMM-Lab. The models were made publicly available in a Food Safety Model Repository within the OpenML for Predictive Modelling in Food community project. Three different approaches were used to create new models in the model repositories: (1) all information relevant for model re-implementation is available in a scientific publication, (2) model parameters can be imported from tabular parameter collections and (3) models have to be generated from experimental data or primary model parameters. All three approaches were demonstrated in the paper. The sample Food Safety Model Repository is available via: http://sourceforge.net/projects/microbialmodelingexchange/files/models and the PMM-Lab software can be downloaded from http://sourceforge.net/projects/pmmlab/. This work also illustrates that a standardized information exchange format for predictive microbial models, as the key component of this strategy, could be established by adoption of resources from the Systems Biology domain. Copyright © 2015. Published by Elsevier B.V.

Developing multinational radioactive waste repositories: Infrastructural framework and scenarios of cooperation

International Nuclear Information System (INIS)

2004-10-01

Currently the management of radioactive wastes centres on national strategies for collection, treatment, interim storage and disposal. This tendency to focus exclusively on national strategies reflects the fact that radioactive waste is a sensitive political issue, making cooperation among countries difficult. It is consistent with the accepted principle that a country that enjoys the benefit of nuclear energy, or the utilization of nuclear technology, should also take full responsibility for managing the generated radioactive waste. However, there are countries whose radioactive waste volumes do not easily justify a national repository, and/or countries that do not have the resources or favourable natural conditions for waste disposal to dedicate to a national repository project or would prefer to collaborate in shared initiatives because of their economic advantages. In such cases it may be appropriate for these countries to engage in a multinational collaborative effort to ensure that they have access to a common repository, in order that they can fulfil their responsibilities for their managing wastes safely. In response to requests from several Member States expressing an interest in multinational disposal options, the IAEA produced in 1998 a TECDOC outlining the important factors to be taken into account in the process of realizing such options. These factors include for example, technical (safety), institutional (legal, safeguards), economic (financial) socio-political (public acceptance) and ethical considerations. The present report reviews the work done in the previous study, taking into account developments since its publication as well as current activities in the field of multinational repositories. The report attempts to define the concepts involved in the creation of multinational repositories, to explore the likely scenarios, to examine the conditions for successful implementation, and to point out the benefits and challenges inherent to

Repository Rodeo Redux

CERN Document Server

Anez, Melissa; Donohue, Tim; Fyson, Will; Simko, Tibor; Wilcox, David

2017-01-01

You’ve got more repository questions and we’ve got more answers! Last year’s Repository Rodeo panel was a huge success, so we’re taking the show on the road to Brisbane for OR2017. Join representatives from the DSpace, Eprints, Fedora, Hydra, and Islandora communities as we (briefly) explain what each of our repositories actually does. We'll also talk about the directions of our respective technical and community developments, and related to the conference theme of Open: Innovation Knowledge Repositories, offer brief observations about the latest, most promising and/or most surprising innovations in our space. This panel will be a great opportunity for newcomers to Open Repositories to get a crash course on the major repository options and meet representatives from each of their communities. After a brief presentation from each representative, we'll open the session up for questions from the audience.

Retrievability as proposed in the US repository concept

International Nuclear Information System (INIS)

Harrington, P.G.

2000-01-01

The Nuclear Waste Policy Act states that any repository shall be designed and constructed to permit retrieval. Reasons for retrieval include public health and safety, environmental concerns, and recovery of economically valuable contents of spent nuclear fuel. The Nuclear Regulatory Commission requires that waste must be retrievable at any time up to 50 years after start of emplacement. The US Department of Energy intends to maintain a retrieval capability throughout the preclosure period. Possible preclosure periods range from a minimum of 50 years to as much as 300 years. Repository closure includes sealing all accessible portions of the repository, including ventilation shafts, access ramps and boreholes. Drip shields will be installed over the waste packages. Access to the repository after closure is not intended. The proposed repository includes horizontal emplacement drifts located in the unsaturated zone. The emplacement drift centerline spacing is 81 meters to provide a subboiling region between drifts for water drainage. A drip shield covers the waste packages. All emplacement drifts remain open until closure of the repository, providing performance benefits such as removing heat and moisture during the preclosure period and lowering postclosure temperatures. This does not impede retrieval, permitting a reversal of the emplacement process to accomplish retrieval under normal conditions. The preclosure period is therefore not to enhance retrievability, but does improve performance, and the resultant extension of the retrievability capability is a secondary effect. Information must be provided from the performance confirmation program to support a regulatory decision to close. Closure would isolate the repository from the accessible environment, preclude preferential flowpaths for water into the mountain, and minimize the possibility of inadvertent intrusion. (author)

Citing a Data Repository: A Case Study of the Protein Data Bank.

Science.gov (United States)

Huang, Yi-Hung; Rose, Peter W; Hsu, Chun-Nan

2015-01-01

The Protein Data Bank (PDB) is the worldwide repository of 3D structures of proteins, nucleic acids and complex assemblies. The PDB's large corpus of data (> 100,000 structures) and related citations provide a well-organized and extensive test set for developing and understanding data citation and access metrics. In this paper, we present a systematic investigation of how authors cite PDB as a data repository. We describe a novel metric based on information cascade constructed by exploring the citation network to measure influence between competing works and apply that to analyze different data citation practices to PDB. Based on this new metric, we found that the original publication of RCSB PDB in the year 2000 continues to attract most citations though many follow-up updates were published. None of these follow-up publications by members of the wwPDB organization can compete with the original publication in terms of citations and influence. Meanwhile, authors increasingly choose to use URLs of PDB in the text instead of citing PDB papers, leading to disruption of the growth of the literature citations. A comparison of data usage statistics and paper citations shows that PDB Web access is highly correlated with URL mentions in the text. The results reveal the trend of how authors cite a biomedical data repository and may provide useful insight of how to measure the impact of a data repository.

PCAS – a precomputed proteome annotation database resource

Directory of Open Access Journals (Sweden)

Luo Jingchu

2003-11-01

Full Text Available Abstract Background Many model proteomes or "complete" sets of proteins of given organisms are now publicly available. Much effort has been invested in computational annotation of those "draft" proteomes. Motif or domain based algorithms play a pivotal role in functional classification of proteins. Employing most available computational algorithms, mainly motif or domain recognition algorithms, we set up to develop an online proteome annotation system with integrated proteome annotation data to complement existing resources. Results We report here the development of PCAS (ProteinCentric Annotation System as an online resource of pre-computed proteome annotation data. We applied most available motif or domain databases and their analysis methods, including hmmpfam search of HMMs in Pfam, SMART and TIGRFAM, RPS-PSIBLAST search of PSSMs in CDD, pfscan of PROSITE patterns and profiles, as well as PSI-BLAST search of SUPERFAMILY PSSMs. In addition, signal peptide and TM are predicted using SignalP and TMHMM respectively. We mapped SUPERFAMILY and COGs to InterPro, so the motif or domain databases are integrated through InterPro. PCAS displays table summaries of pre-computed data and a graphical presentation of motifs or domains relative to the protein. As of now, PCAS contains human IPI, mouse IPI, and rat IPI, A. thaliana, C. elegans, D. melanogaster, S. cerevisiae, and S. pombe proteome. PCAS is available at http://pak.cbi.pku.edu.cn/proteome/gca.php Conclusion PCAS gives better annotation coverage for model proteomes by employing a wider collection of available algorithms. Besides presenting the most confident annotation data, PCAS also allows customized query so users can inspect statistically less significant boundary information as well. Therefore, besides providing general annotation information, PCAS could be used as a discovery platform. We plan to update PCAS twice a year. We will upgrade PCAS when new proteome annotation algorithms

Clinical proteomics

DEFF Research Database (Denmark)

Albrethsen, Jakob; Frederiksen, Hanne; Johannsen, Trine Holm

2018-01-01

Clinical proteomics aims to deliver cost-effective multiplexing of potentially hundreds of diagnostic proteins, including distinct protein isoforms. The analytical strategy known as targeted proteomics is particularly promising because it is compatible with robust mass spectrometry (MS)-platforms...... standards and calibrants. The present challenge is to examine if targeted proteomics of IGF-I can truly measure up to the routine performance that must be expected from a clinical testing platform.......Clinical proteomics aims to deliver cost-effective multiplexing of potentially hundreds of diagnostic proteins, including distinct protein isoforms. The analytical strategy known as targeted proteomics is particularly promising because it is compatible with robust mass spectrometry (MS......)-platforms already implemented in many clinical laboratories for routine quantitation of small molecules (i.e. uHPLC coupled to triple-quadrupole MS). Progress in targeted proteomics of circulating insulin-like growth factor 1 (IGF-I) have provided valuable insights about tryptic peptides, transitions, internal...

Reference Design Description for a Geologic Repository

International Nuclear Information System (INIS)

2000-01-01

One of the current major national environmental problems is the safe disposal of large quantities of spent nuclear fuel and high-level radioactive waste materials, which are rapidly accumulating throughout the country. These radioactive byproducts are generated as the result of national defense activities and from the generation of electricity by commercial nuclear power plants. At present, spent nuclear fuel is accumulating at over 70 power plant sites distributed throughout 33 states. The safe disposal of these high-level radioactive materials at a central disposal facility is a high national priority. This Reference Design Description explains the current design for a potential geologic repository that may be located at Yucca Mountain in Nevada for the disposal of spent nuclear fuel and high-level radioactive waste materials. This document describes a possible design for the three fundamental parts of a repository: a surface facility, subsurface repository, and waste packaging. It also presents the current conceptual design of the key engineering systems for the final four phases of repository processes: operations, monitoring, closure, and postclosure. In accordance with current law, this design does not include an interim storage option. In addition, this Reference Design Description reviews the expected long-term performance of the potential repository. It describes the natural barrier system which, together with the engineered systems, achieves the repository objectives. This design will protect the public and the environment by allowing the safe disposal of radioactive waste received from government-owned custodial spent fuel sites, high-level radioactive waste sites, and commercial power reactor sites. All design elements meet or exceed applicable regulations governing the disposal of high-level radioactive waste. The design will provide safe disposal of waste materials for at least a 10,000 year period. During this time interval, natural radioactive decay

Mass spectrometry data from proteomics-based screening of immunoreactive proteins of fully virulent Brucella strains using sera from naturally infected animals

Directory of Open Access Journals (Sweden)

Gamal Wareth

2015-09-01

Full Text Available Here, we provide the dataset associated with our research article on comprehensive screening of Brucella immunoreactive proteins using sera of naturally infected hosts published in Biochemical and Biophysical Research Communications Wareth et al., 2015 [1]. Whole-cell protein extracts were prepared from Brucella abortus and Brucella melitensis, separated using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE and subsequently western blotting was carried out using sera from bovines (cows and buffaloes and small ruminants (goats and sheep. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org via the PRIDE partner repository [2] with the dataset identifiers PXD001270 and DOI:10.6019/PXD001270.

Current Status of Deep Geological Repository Development

International Nuclear Information System (INIS)

Budnitz, R J

2005-01-01

electricity generated by the power reactors that have produced the waste. Of course, the current international situation is that no nation is currently willing to take any radioactive waste from another nation for deep disposal. This means that every nation will ultimately need to develop its own deep repository. This makes no sense, however--many nations have only a modest amount of waste, or do not have appropriate geological settings for a repository, or both. Ultimately, the need for one or more multi-national or international repositories will emerge, although so far this has not happened. Only one nation, Russia, has announced a policy permitting the import of radioactive wastes from other countries, but Russia's policy is not to import the wastes for deep disposal, but for chemical reprocessing. Various nations have made very different choices as to the schedule for proceeding with a repository. The rationales for each national choice differ significantly. The decision, different from country to country, comes down to balancing various seemingly conflicting values, including (a) whether the technology for deep disposal is judged to be mature enough; (b) whether surface storage during a lengthy delay is judged adequately safe against accidents and adequately secure against terrorists; (c) whether technologies for separating some of the waste constituents for re-use or recycle into reactors, or technologies for transmuting some waste constituents, are sufficiently promising to merit delaying until those technologies are more mature; (d) issues of the cost of disposal and who should bear that cost; (e) issues related to disposal of wastes from nuclear weapons programs, as distinct from wastes from reactor operations; and (f) issues about the linkage between disposal and the future of nuclear power. Finally, the decision to proceed with a repository often is governed by whether the government has the political will or ability to proceed, taking account of public opinion

Region-to-area screening methodology for the crystalline repository project

International Nuclear Information System (INIS)

1984-08-01

The ''Nuclear Waste Policy Act of 1982'' (NWPA), enacted January 7, 1983 as Public Law 97-425, confirmed the responsibility of the US Department of Energy (DOE) for management of high-level radioactive waste. The NWPA directed the DOE to provide safe facilities for isolation of high-level radioactive waste from the environment in federally owned and federally licensed repositories. To achieve the goals of providing licensed repositories for high-level radioactive waste, a technical program has been developed by the DOE to meet all relevant radiological protection criteria and other requirements. By March 1987, the NWPA requires the DOE to recommend to the President a single site, chosen from five nominated sites for construction of the first repository. Rock types being considered as potential hosts for the first repository include salt, basalt, and tuff. The NWPA also requires the DOE to select three candidate sites, chosen from five nominated sites to be recommended to the President by July 1989, as possible locations for the second repository. Potential host rock types for the second federal repository will include crystalline rock. This document outlines the methodology for region-to-area screening of exposed crystalline rock bodies for suitability as sites for further study. 17 refs., 14 figs., 2 tabs

A repository of codes of ethics and technical standards in health informatics.

Science.gov (United States)

Samuel, Hamman W; Zaïane, Osmar R

2014-01-01

We present a searchable repository of codes of ethics and standards in health informatics. It is built using state-of-the-art search algorithms and technologies. The repository will be potentially beneficial for public health practitioners, researchers, and software developers in finding and comparing ethics topics of interest. Public health clinics, clinicians, and researchers can use the repository platform as a one-stop reference for various ethics codes and standards. In addition, the repository interface is built for easy navigation, fast search, and side-by-side comparative reading of documents. Our selection criteria for codes and standards are two-fold; firstly, to maintain intellectual property rights, we index only codes and standards freely available on the internet. Secondly, major international, regional, and national health informatics bodies across the globe are surveyed with the aim of understanding the landscape in this domain. We also look at prevalent technical standards in health informatics from major bodies such as the International Standards Organization (ISO) and the U. S. Food and Drug Administration (FDA). Our repository contains codes of ethics from the International Medical Informatics Association (IMIA), the iHealth Coalition (iHC), the American Health Information Management Association (AHIMA), the Australasian College of Health Informatics (ACHI), the British Computer Society (BCS), and the UK Council for Health Informatics Professions (UKCHIP), with room for adding more in the future. Our major contribution is enhancing the findability of codes and standards related to health informatics ethics by compilation and unified access through the health informatics ethics repository.

Development of a central final repository management for the coordination of the waste for Schacht Konrad from public authorities; Aufbau des zentralen Endlagerungsmanagements fuer die Koordination der Konrad-Abfaelle aus der oeffentlichen Hand

Energy Technology Data Exchange (ETDEWEB)

Graffunder, Iris; Dominke-Bendix, Carola; Waldek, Achim [Energiewerke Nord GmbH (EWN), Eggenstein-Leopoldshafen (Germany). Betriebsstaette Karlsruhe; Wunn, Christoph [admoVa Consulting GmbH, Bad Camberg (Germany)

2012-11-01

The central final repository management is supposed to fulfill the following tasks: active collaboration of Konrad contract draft, signing of internal contracts and agreements, cooperation contract with GNS, cooperation with coordination authorities, inventory taking of wastes (existing inventory and prognosis) and interim storage capacities of public authorities, development of planning and management software, optimization of the final repository documentation, container management, logistics concept, long-term disposal planning and prognosis, planning and coordination of the annual waste amount, management and documentation of disposed waste allocation, coordination of transport schedules, consulting service for waste obligations (final repository requirements, product control, documentation).

DataONE: Gateway to Earth and Environmental Data Repositories

Science.gov (United States)

Koskela, R.; Michener, W. K.; Vieglais, D.; Budden, A. E.

2017-12-01

DataONE (Data Observation Network for Earth) is a National Science Foundation DataNet project that enables universal access to data and also facilitates researchers in fulfilling their need for data management and in providing secure and permanent access to their data. DataONE offers the scientific community a suite of tools and training materials that cover all aspects of the data life cycle from data collection, to management, analysis and publication. Data repositories affiliated with DataONE are referred to as Member Nodes and represent large regional, national and international research networks, agencies, and other institutions. As part of the DataONE Federation, the repositories gain access to a range of value-added services to support their users. These services include usage tracking and reporting, content replication, and the ability to register the services created by the repository. In addition, DataONE and the California Digital Library manage ONEShare, a repository that accepts content submitted through Dash, a platform allowing researchers to easily describe, deposit and share their research data.

International perspective on repositories for low level waste

International Nuclear Information System (INIS)

Bergstroem, Ulla; Pers, Karin; Almen, Ylva

2011-12-01

Nuclear energy production gives rise to different types of radioactive waste. The use of nuclear isotopes within the research, industry and medical sectors also generates radioactive waste. To protect man and the environment from radiation the waste is isolated and contained by deposition in repositories. These repositories may have various designs regarding location, barriers etc depending on the potential danger of the waste. In Sweden, low- and intermediate level waste (LILW) is disposed of in the SFR repository in Forsmark. The repository is located 60 metres down into the bedrock under the bottom of the sea and covered by 6 metres of water. It is planned to extend SFR to accommodate decommissioning waste from the dismantling of the Swedish nuclear power facilities and also for the additional operation waste caused by the planned prolonged operation time. When planning the extension consultations will be carried out with the host municipality, authorities, organisations and general public. In planning the extension, SKB has performed a worldwide compilation of how other countries have, or plan to, handle the final disposal of similar wastes. The aim of this report is to give a brief description of LILW repositories worldwide; including general brief descriptions of many facilities, descriptions of the waste and the barriers as well as safety assessments for a few chosen repositories which represent different designs. The latter is performed, where possible, to compare certain features against the Swedish SFR. To provide a background and context to this study, international organisations and conventions are also presented along with internationally accepted principles regarding the management of radioactive waste. Similar to SFR, suitable locations for the repositories have, in many countries, been found at sites that already have, or used to have nuclear activities, such as reactor sites. Abandoned and disused mines, such as the salt mines in Germany, also

International perspective on repositories for low level waste

Energy Technology Data Exchange (ETDEWEB)

Bergstroem, Ulla; Pers, Karin; Almen, Ylva (SKB International AB (Sweden))

2011-12-15

Nuclear energy production gives rise to different types of radioactive waste. The use of nuclear isotopes within the research, industry and medical sectors also generates radioactive waste. To protect man and the environment from radiation the waste is isolated and contained by deposition in repositories. These repositories may have various designs regarding location, barriers etc depending on the potential danger of the waste. In Sweden, low- and intermediate level waste (LILW) is disposed of in the SFR repository in Forsmark. The repository is located 60 metres down into the bedrock under the bottom of the sea and covered by 6 metres of water. It is planned to extend SFR to accommodate decommissioning waste from the dismantling of the Swedish nuclear power facilities and also for the additional operation waste caused by the planned prolonged operation time. When planning the extension consultations will be carried out with the host municipality, authorities, organisations and general public. In planning the extension, SKB has performed a worldwide compilation of how other countries have, or plan to, handle the final disposal of similar wastes. The aim of this report is to give a brief description of LILW repositories worldwide; including general brief descriptions of many facilities, descriptions of the waste and the barriers as well as safety assessments for a few chosen repositories which represent different designs. The latter is performed, where possible, to compare certain features against the Swedish SFR. To provide a background and context to this study, international organisations and conventions are also presented along with internationally accepted principles regarding the management of radioactive waste. Similar to SFR, suitable locations for the repositories have, in many countries, been found at sites that already have, or used to have nuclear activities, such as reactor sites. Abandoned and disused mines, such as the salt mines in Germany, also

Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories.

Science.gov (United States)

Chockalingam, Sriram; Aluru, Maneesha; Aluru, Srinivas

2016-09-19

Pre-processing of microarray data is a well-studied problem. Furthermore, all popular platforms come with their own recommended best practices for differential analysis of genes. However, for genome-scale network inference using microarray data collected from large public repositories, these methods filter out a considerable number of genes. This is primarily due to the effects of aggregating a diverse array of experiments with different technical and biological scenarios. Here we introduce a pre-processing pipeline suitable for inferring genome-scale gene networks from large microarray datasets. We show that partitioning of the available microarray datasets according to biological relevance into tissue- and process-specific categories significantly extends the limits of downstream network construction. We demonstrate the effectiveness of our pre-processing pipeline by inferring genome-scale networks for the model plant Arabidopsis thaliana using two different construction methods and a collection of 11,760 Affymetrix ATH1 microarray chips. Our pre-processing pipeline and the datasets used in this paper are made available at http://alurulab.cc.gatech.edu/microarray-pp.

Impact of transporting defense high-level waste to a geologic repository

International Nuclear Information System (INIS)

Joy, D.S.; Shappert, L.B.; Boyle, J.W.

1984-12-01

The Nuclear Waste Policy Act of 1982 (Public Law 97-425) provides for the development of repositories for the disposal of high-level radioactive waste and spent nuclear fuel and requires the Secretary of Energy to evaluate five potential repository sites. One factor that is to be examined is transportation of radioactive materials to such a repository and whether transportation might be affected by shipments to a defense-only repository, or to one that accepts both defense and commercial waste. In response to this requirement, The Department of Energy has undertaken an evaluation of the cost and risk associated with the potential shipments. Two waste-flow scenarios are considered which are related to the total quantity of defense high-level waste which will be placed in a repository. The low-flow case is based on a total of 6700 canisters being transported from one site, while the high-flow case assumes that a total of 20,000 canisters will be transported from three sites. For the scenarios considered, the estimated shipping costs range from $105 million to $257 million depending upon the mode of transport and the repository location. The total risks associated with shipping defense high-level waste to a repository are estimated to be significantly smaller than predicted for other transportation activities. In addition, the cost of shipping defense high-level waste to a repository does not depend on whether the site is a defense-only or a commercial repository. Therefore, the transportation considerations are not a basis for the selection of one of the two disposal options

Development of site selection process for an LILW repository in Slovenia

International Nuclear Information System (INIS)

Zeleznik, N.; Kralj, M.; Mele, I.; Veselic, M.

2005-01-01

The activities regarding the LILW repository site selection in Slovenia are planned to meet the requirements of the Act on Ionising Radiation Protection and Nuclear Safety, especially the requirement that the site for a repository should be selected by 2008 and the repository should be in operation by 2013. In November 2004, the official administrative procedure for the siting of the repository started with the first spatial public conference on spatial planning procedure. It was carried out by the Ministry of the Environment and Spatial Planning and ARAO. Immediately after the conference the Program for the preparation of the detailed plan of national importance for the LILW repository was accepted by the Ministry. At the beginning of December 2004, ARAO invited all Slovenian local communities to participate in the site selection process and volunteer a site or area in their local community for further investigation. At the beginning of April 2005 the first phase of the bidding process was concluded. ARAO received applications from eight local communities. A pre-feasibility study to define three of the most promising locations was conducted because only three locations are foreseen by the Program for the preparation of the detailed plan of national importance. Methodologies were prepared for assessment of different parameters of technical, financial, environmental and spatial suitability as well as public acceptability. Comparative, preferential and also exclusion criteria for the respective parameters were defined. The results of the cabinet and fieldwork research were compared and further assessed in order to obtain maximum three local communities with three potential sites in which the probability of siting the LILW repository seems to be the highest. Detailed plans of national importance will be prepared for these sites. (author)

Web Interface Security Vulnerabilities of European Academic Repositories

Directory of Open Access Journals (Sweden)

Matus Formanek

2017-02-01

Full Text Available The given analysis summarizes the status quo of the level of security of web interfaces of selected European academic repositories in the field of library and information science. It focuses on the presence and qualities of the secure HTTPS protocol via SSL/TLS protocols. The security of the transmitted data is particularly important in the network environment of the Internet, especially if log-in user data is transmitted. Disclosure may have a direct impact on saved digital objects and their metadata which together represent the most valuable parts of systems of digital libraries and repositories. Furthermore, the paper points to the most noticeable vulnerabilities of protocols of web interfaces and presents practical recommendations for the expert public. These may contribute to the increase of the level of security of the discussed systems. The authors base their proposals on the currently available scientific publications and scientific articles about the given topic.

Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles)

DEFF Research Database (Denmark)

Kinsinger, Christopher R.; Apffel, James; Baker, Mark

2012-01-01

Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development...... of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed....... This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in the Journal of Proteome Research, Molecular and Cellular Proteomics, Proteomics, and Proteomics Clinical...

Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles)

DEFF Research Database (Denmark)

Kinsinger, Christopher R.; Apffel, James; Baker, Mark

2011-01-01

Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development...... of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed....... This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in the Journal of Proteome Research, Molecular and Cellular Proteomics, Proteomics, and Proteomics Clinical...

MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes.

Science.gov (United States)

Zhang, Yanling; Zhang, Yong; Adachi, Jun; Olsen, Jesper V; Shi, Rong; de Souza, Gustavo; Pasini, Erica; Foster, Leonard J; Macek, Boris; Zougman, Alexandre; Kumar, Chanchal; Wisniewski, Jacek R; Jun, Wang; Mann, Matthias

2007-01-01

Mass spectrometry (MS)-based proteomics has become a powerful technology to map the protein composition of organelles, cell types and tissues. In our department, a large-scale effort to map these proteomes is complemented by the Max-Planck Unified (MAPU) proteome database. MAPU contains several body fluid proteomes; including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth. The liver proteome is represented with 3200 proteins. By employing high resolution MS and stringent validation criteria, false positive identification rates in MAPU are lower than 1:1000. Thus MAPU datasets can serve as reference proteomes in biomarker discovery. MAPU contains the peptides identifying each protein, measured masses, scores and intensities and is freely available at http://www.mapuproteome.com using a clickable interface of cell or body parts. Proteome data can be queried across proteomes by protein name, accession number, sequence similarity, peptide sequence and annotation information. More than 4500 mouse and 2500 human proteins have already been identified in at least one proteome. Basic annotation information and links to other public databases are provided in MAPU and we plan to add further analysis tools.

Towards Interoperable Preservation Repositories: TIPR

Directory of Open Access Journals (Sweden)

Priscilla Caplan

2010-07-01

Full Text Available Towards Interoperable Preservation Repositories (TIPR is a project funded by the Institute of Museum and Library Services to create and test a Repository eXchange Package (RXP. The package will make it possible to transfer complex digital objects between dissimilar preservation repositories.  For reasons of redundancy, succession planning and software migration, repositories must be able to exchange copies of archival information packages with each other. Every different repository application, however, describes and structures its archival packages differently. Therefore each system produces dissemination packages that are rarely understandable or usable as submission packages by other repositories. The RXP is an answer to that mismatch. Other solutions for transferring packages between repositories focus either on transfers between repositories of the same type, such as DSpace-to-DSpace transfers, or on processes that rely on central translation services.  Rather than build translators between many dissimilar repository types, the TIPR project has defined a standards-based package of metadata files that can act as an intermediary information package, the RXP, a lingua franca all repositories can read and write.

Repository simulation model: Final report

International Nuclear Information System (INIS)

1988-03-01

This report documents the application of computer simulation for the design analysis of the nuclear waste repository's waste handling and packaging operations. The Salt Repository Simulation Model was used to evaluate design alternatives during the conceptual design phase of the Salt Repository Project. Code development and verification was performed by the Office of Nuclear Waste Isolation (ONWL). The focus of this report is to relate the experience gained during the development and application of the Salt Repository Simulation Model to future repository design phases. Design of the repository's waste handling and packaging systems will require sophisticated analysis tools to evaluate complex operational and logistical design alternatives. Selection of these design alternatives in the Advanced Conceptual Design (ACD) and License Application Design (LAD) phases must be supported by analysis to demonstrate that the repository design will cost effectively meet DOE's mandated emplacement schedule and that uncertainties in the performance of the repository's systems have been objectively evaluated. Computer simulation of repository operations will provide future repository designers with data and insights that no other analytical form of analysis can provide. 6 refs., 10 figs

Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community

Science.gov (United States)

Cormier, Catherine Y.; Mohr, Stephanie E.; Zuo, Dongmei; Hu, Yanhui; Rolfs, Andreas; Kramer, Jason; Taycher, Elena; Kelley, Fontina; Fiacco, Michael; Turnbull, Greggory; LaBaer, Joshua

2010-01-01

The Protein Structure Initiative Material Repository (PSI-MR; http://psimr.asu.edu) provides centralized storage and distribution for the protein expression plasmids created by PSI researchers. These plasmids are a resource that allows the research community to dissect the biological function of proteins whose structures have been identified by the PSI. The plasmid annotation, which includes the full length sequence, vector information and associated publications, is stored in a freely available, searchable database called DNASU (http://dnasu.asu.edu). Each PSI plasmid is also linked to a variety of additional resources, which facilitates cross-referencing of a particular plasmid to protein annotations and experimental data. Plasmid samples can be requested directly through the website. We have also developed a novel strategy to avoid the most common concern encountered when distributing plasmids namely, the complexity of material transfer agreement (MTA) processing and the resulting delays this causes. The Expedited Process MTA, in which we created a network of institutions that agree to the terms of transfer in advance of a material request, eliminates these delays. Our hope is that by creating a repository of expression-ready plasmids and expediting the process for receiving these plasmids, we will help accelerate the accessibility and pace of scientific discovery. PMID:19906724

Technical progress report: Rhode Island crystalline repository project, calendar year 1985

International Nuclear Information System (INIS)

Vild, B.F.

1985-01-01

A Nuclear Waste Fund established by the Nuclear Waste Policy Act of 1982 provides financial support to affected states to participate in the high-level radioactive waste repository siting program of the US Department of Energy. In Rhode Island, that function is performed by a multidisciplinary Project Review Team consisting of staff from three State agencies. Members of the Review Team attended several meetings in 1985 to voice their concerns directly to DOE. Written comments were also submitted on draft plans and reports. Among the issues raised were inconsistencies in the geologic and environmental data used to screen potential repository sites, the role of Monitored Retrievable Storage (MRS) in the repository program, and regulations regarding the transportation and storage of nuclear waste. The Review Team also began work on a public information booklet describing the repository program in nontechnical terms. That booklet will be distributed widely upon completion

DRIVER: Building a Sustainable Infrastructure of European Scientific Repositories

Directory of Open Access Journals (Sweden)

Norbert Lossau

2008-11-01

Full Text Available DRIVER has a clear vision: All research institutions in Europe and worldwide make all their research publications openly accessible through institutional repositories. The vision follows the Berlin Declaration, which called in October 2003 for ‘free and unrestricted access to sciences and human knowledge representation worldwide’. Initiated by the internationally renowned German research organisation the Max-Planck-Society, and signed by many international research organisations and institutes, the Berlin Declaration has set a political statement. In building a sustainable infrastructure for scientific repositories, DRIVER brings to this statement the reality of scholarly communication in the future.

Guidelines for reporting quantitative mass spectrometry based experiments in proteomics.

Science.gov (United States)

Martínez-Bartolomé, Salvador; Deutsch, Eric W; Binz, Pierre-Alain; Jones, Andrew R; Eisenacher, Martin; Mayer, Gerhard; Campos, Alex; Canals, Francesc; Bech-Serra, Joan-Josep; Carrascal, Montserrat; Gay, Marina; Paradela, Alberto; Navajas, Rosana; Marcilla, Miguel; Hernáez, María Luisa; Gutiérrez-Blázquez, María Dolores; Velarde, Luis Felipe Clemente; Aloria, Kerman; Beaskoetxea, Jabier; Medina-Aunon, J Alberto; Albar, Juan P

2013-12-16

Mass spectrometry is already a well-established protein identification tool and recent methodological and technological developments have also made possible the extraction of quantitative data of protein abundance in large-scale studies. Several strategies for absolute and relative quantitative proteomics and the statistical assessment of quantifications are possible, each having specific measurements and therefore, different data analysis workflows. The guidelines for Mass Spectrometry Quantification allow the description of a wide range of quantitative approaches, including labeled and label-free techniques and also targeted approaches such as Selected Reaction Monitoring (SRM). The HUPO Proteomics Standards Initiative (HUPO-PSI) has invested considerable efforts to improve the standardization of proteomics data handling, representation and sharing through the development of data standards, reporting guidelines, controlled vocabularies and tooling. In this manuscript, we describe a key output from the HUPO-PSI-namely the MIAPE Quant guidelines, which have developed in parallel with the corresponding data exchange format mzQuantML [1]. The MIAPE Quant guidelines describe the HUPO-PSI proposal concerning the minimum information to be reported when a quantitative data set, derived from mass spectrometry (MS), is submitted to a database or as supplementary information to a journal. The guidelines have been developed with input from a broad spectrum of stakeholders in the proteomics field to represent a true consensus view of the most important data types and metadata, required for a quantitative experiment to be analyzed critically or a data analysis pipeline to be reproduced. It is anticipated that they will influence or be directly adopted as part of journal guidelines for publication and by public proteomics databases and thus may have an impact on proteomics laboratories across the world. This article is part of a Special Issue entitled: Standardization and

Building ProteomeTools based on a complete synthetic human proteome

Science.gov (United States)

Zolg, Daniel P.; Wilhelm, Mathias; Schnatbaum, Karsten; Zerweck, Johannes; Knaute, Tobias; Delanghe, Bernard; Bailey, Derek J.; Gessulat, Siegfried; Ehrlich, Hans-Christian; Weininger, Maximilian; Yu, Peng; Schlegl, Judith; Kramer, Karl; Schmidt, Tobias; Kusebauch, Ulrike; Deutsch, Eric W.; Aebersold, Ruedi; Moritz, Robert L.; Wenschuh, Holger; Moehring, Thomas; Aiche, Stephan; Huhmer, Andreas; Reimer, Ulf; Kuster, Bernhard

2018-01-01

The ProteomeTools project builds molecular and digital tools from the human proteome to facilitate biomedical and life science research. Here, we report the generation and multimodal LC-MS/MS analysis of >330,000 synthetic tryptic peptides representing essentially all canonical human gene products and exemplify the utility of this data. The resource will be extended to >1 million peptides and all data will be shared with the community via ProteomicsDB and proteomeXchange. PMID:28135259

Repository performance confirmation

International Nuclear Information System (INIS)

Hansen, Francis D.

2011-01-01

Yucca Mountain license application identified a broad suite of monitoring activities. A revision of the plan was expected to winnow the number of activities down to a manageable size. As a result, an objective process for the next stage of performance confirmation planning was developed as an integral part of an overarching long-term testing and monitoring strategy. The Waste Isolation Pilot Plant compliance monitoring program at once reflects its importance to stakeholders while demonstrating adequate understanding of relevant monitoring parameters. The compliance criteria were stated by regulation and are currently monitored as part of the regulatory rule for disposal. At the outset, the screening practice and parameter selection were not predicated on a direct or indirect correlation to system performance metrics, as was the case for Yucca Mountain. Later on, correlation to performance was established, and the Waste Isolation Pilot Plant continues to monitor ten parameters originally identified in the compliance certification documentation. The monitoring program has proven to be effective for the technical intentions and societal or public assurance. The experience with performance confirmation in the license application process for Yucca Mountain helped identify an objective, quantitative methodology for this purpose. Revision of the existing plan would be based on findings of the total system performance assessment. Identification and prioritization of confirmation activities would then derive from performance metrics associated with performance assessment. Given the understanding of repository performance confirmation, as reviewed in this paper, it is evident that the performance confirmation program for the Yucca Mountain project could be readily re-engaged if licensing activities resumed.

Evaluation of repository safety

Energy Technology Data Exchange (ETDEWEB)

Sagar, B.; Patrick, W.; Dasgupta, B.; Mohanty, S. [Center for Nuclear Waste Regulatory Analyses, San Antonio (United States)

2002-07-01

The United States high-level waste program requires evaluation of radiological safety during two distinct time intervals. The first interval, commonly referred to as the preclosure period, deals with receipt of waste at the site, transfer into disposal containers, if needed, emplacement in the underground openings, monitoring and maintenance activities, backfill and closure of the underground openings, and decontamination and decommissioning of the surface facilities of the geologic repository. The preclosure period may extend from a few tens of years to as long as a few hundred of years, depending on repository design and societal norms regarding a final decision to permanently seal the repository. During the preclosure or operational period, performance confirmation studies are conducted to provide a basis for updating and reevaluating estimates of postclosure performance and, finally, to provide a basis for a closure decision. The postclosure period during which expected repository performance must meet certain standards may range from ten thousands years, as it does in the United States, to millions of years, as it does in some European nations. Waste handling operations in the preclosure period are to be evaluated in relation to their potential effect on workers, members of general public, and the general environment. During this period, releases of radioactivity are to be monitored and appropriate actions taken whenever established limits are approached or exceeded. Preclosure safety is highly dependent on facility design, operational hardware and automated systems, operational sequences, and reliability of humans involved in operations. Preclosure safety analyses conducted before operations begin play a major role in the design process, selection of equipment, and development of operational procedures. Because of the complexity, duration, and spatial scales of the operations, analyses are conducted using mathematical models implemented in computer codes

Evaluation of repository safety

International Nuclear Information System (INIS)

Sagar, B.; Patrick, W.; Dasgupta, B.; Mohanty, S.

2002-01-01

The United States high-level waste program requires evaluation of radiological safety during two distinct time intervals. The first interval, commonly referred to as the preclosure period, deals with receipt of waste at the site, transfer into disposal containers, if needed, emplacement in the underground openings, monitoring and maintenance activities, backfill and closure of the underground openings, and decontamination and decommissioning of the surface facilities of the geologic repository. The preclosure period may extend from a few tens of years to as long as a few hundred of years, depending on repository design and societal norms regarding a final decision to permanently seal the repository. During the preclosure or operational period, performance confirmation studies are conducted to provide a basis for updating and reevaluating estimates of postclosure performance and, finally, to provide a basis for a closure decision. The postclosure period during which expected repository performance must meet certain standards may range from ten thousands years, as it does in the United States, to millions of years, as it does in some European nations. Waste handling operations in the preclosure period are to be evaluated in relation to their potential effect on workers, members of general public, and the general environment. During this period, releases of radioactivity are to be monitored and appropriate actions taken whenever established limits are approached or exceeded. Preclosure safety is highly dependent on facility design, operational hardware and automated systems, operational sequences, and reliability of humans involved in operations. Preclosure safety analyses conducted before operations begin play a major role in the design process, selection of equipment, and development of operational procedures. Because of the complexity, duration, and spatial scales of the operations, analyses are conducted using mathematical models implemented in computer codes

A review of construction techniques available for surface and underground radioactive waste repositories

International Nuclear Information System (INIS)

Godfrey, D.G.; Davies, I.L.; MacKenzie, R.D.

1985-01-01

In terms of engineering requirements the construction of surface or indeed underground radioactive waste repositories is not unduly difficult. The civil engineering techniques likely to be required have generally been carried out previously, albeit not in the context of radioactive waste repositories in this country. The emphasis will have to be very much on the quality of construction. This paper emphasises the need for quality construction and describes the techniques likely to be used in the construction of repositories. Reference is made to the materials likely to be used in the construction of repositories and also to the need for being able to convince the designers, regulating authorities and the general public that the materials used will indeed last for the required time. Brief reference is made at the end of the paper to the civil engineering parameters requiring consideration in the location of repository siting. (author)

Single or multi-repository concept? A personal contribution to the discussion of pros and cons

International Nuclear Information System (INIS)

Closs, K.-D.; Duphorn, K.; Kuehn, K.

2002-01-01

The coalition agreement concluded between the parties in government, i.e. SPD and Alliance 90/The Greens, after the 1998 federal elections provided for an approach to back-end fuel cycle conditions for German nuclear power plants which differed from the practice intended up to that point. Among other things, only one single repository in deep geologic formations is to be available approximately from 2030 on. Exploration of the Gorleben salt dome is to be interrupted because of prevailing doubts while, at the same time, a basic discussion is to be held about potentially suitable host rock varieties and sites. The 'Working Party of Selection Procedures for Repository Sites (AkEnd)' instituted by the federal government is to elaborate scientific siting criteria under these conditions. The authors, who are members of AkEnd, come to the conclusion, based on technical findings and the historical back-end fuel cycle and siting situation in Germany, that a multi-repository concept incorporates substantial advantages. These are the aspects referred to: - Back-end fuel cycle concept: The multi-repository concept offers clearcut advantages in the far advanced Konrad repository project. This is true also against the background of the volume of waste with negligible heat generation to be managed by public authorities. - Long-term safety: Advantages exist, among other things, with respect to technical safety regarding possible compromises in a single-repository concept and the possible restriction of the number of potential sites. - Methods of detection: Spreading the waste over two or more repositories offers benefits in the technical aspects of detection. - Cost: A differentiated assessment of the cost arising in connection with the total amount of waste to be stored in repositories indicates benefits of a multi-repository concept, especially for the public authorities. (orig.) [de

Draft environmental assessment: reference repository location, Hanford Site, Washington. Nuclear Waste Policy Act (Section 112)

International Nuclear Information System (INIS)

1984-12-01

In February 1983, the US Department of Energy (DOE) identified a reference repository location at the Hanford Site in Washington as one of nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the reference repository location at the Hanford Site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for Nuclear Waste Repositories. These evaluations are reported in this draft environmental assessment (EA), which is being issued for public review and comment. The DOE findings and determinations that are based on these evaluations are preliminary and subject to public review and comment. A final EA will be prepared after considering the comments received on the draft EA. The reference repository location at Hanford is located in the Columbia Plateau, one of five distinct geohydrologic settings that are being considered for the first repository. On the basis of the evaluations reported in this draft EA, the DOE has found that the reference repository location at Hanford is not disqualified under the guidelines. The DOE has also found that it is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is proposing to nominate the reference repository location at Hanford as one of five sites suitable for characterization. Furthermore, having performed a comparative evaluation of the five sites proposed for nomination, the DOE has determined that the reference repository location at Hanford is one of three sites preferred for site characterization

Applicability of risk-informed criticality methodology to spent fuel repositories

International Nuclear Information System (INIS)

Mays, C.; Thomas, D.A.; Favet, D.

2000-01-01

An important objective of geologic disposal is keeping the fissionable material in a condition so that a self-sustaining nuclear chain reaction (criticality) is highly unlikely. This objective supports the overall performance objective of any repository, which is to protect the health and safety of the public by limiting radiological exposure. This paper describes a risk-informed, performance-based methodology, which combines deterministic and probabilistic approaches for evaluating the criticality potential of high-level waste and spent nuclear fuel after the repository is sealed and permanently closed (postclosure). (authors)

MitoMiner: a data warehouse for mitochondrial proteomics data.

Science.gov (United States)

Smith, Anthony C; Blackshaw, James A; Robinson, Alan J

2012-01-01

MitoMiner (http://mitominer.mrc-mbu.cam.ac.uk/) is a data warehouse for the storage and analysis of mitochondrial proteomics data gathered from publications of mass spectrometry and green fluorescent protein tagging studies. In MitoMiner, these data are integrated with data from UniProt, Gene Ontology, Online Mendelian Inheritance in Man, HomoloGene, Kyoto Encyclopaedia of Genes and Genomes and PubMed. The latest release of MitoMiner stores proteomics data sets from 46 studies covering 11 different species from eumetazoa, viridiplantae, fungi and protista. MitoMiner is implemented by using the open source InterMine data warehouse system, which provides a user interface allowing users to upload data for analysis, personal accounts to store queries and results and enables queries of any data in the data model. MitoMiner also provides lists of proteins for use in analyses, including the new MitoMiner mitochondrial proteome reference sets that specify proteins with substantial experimental evidence for mitochondrial localization. As further mitochondrial proteomics data sets from normal and diseased tissue are published, MitoMiner can be used to characterize the variability of the mitochondrial proteome between tissues and investigate how changes in the proteome may contribute to mitochondrial dysfunction and mitochondrial-associated diseases such as cancer, neurodegenerative diseases, obesity, diabetes, heart failure and the ageing process.

OPG's deep geologic repository for low and intermediate level waste - public participation and aboriginal engagement

International Nuclear Information System (INIS)

Wilson, M.

2011-01-01

Ontario Power Generation (OPG)'s Public Participation and Aboriginal Engagement Program for the proposed Deep Geologic Repository (DGR) for low and intermediate level waste (L and ILW) began with the signing of a Memorandum of Understanding (MOU) in 2002 between OPG and the Municipality of Kincardine. The MOU set out the terms under which the two parties would jointly study the feasibility of different options for the long-term management of L and ILW at the Bruce nuclear site. A consultant, independent from both the Municipality of Kincardine and OPG, was retained to manage the assessment of options as well as a communication plan to ensure the public and Aboriginal peoples were kept apprised of all activities associated with the MOU. This early commitment to transparency and openness, with its ensuing opportunities for the public and Aboriginal peoples to become informed, ask questions, and engage in meaningful two-way dialogue about the early assessment of options, established the foundation and later became the hallmark of the DGR Project's Public Participation and Aboriginal Engagement program. This paper provides an overview of the development, nature and results of that program as it has evolved through the early investigative stages of options and through the environmental assessment and licencing process for the proposed DGR Project. (author)

Environmental assessment: Reference repository location, Hanford site, Washington

Energy Technology Data Exchange (ETDEWEB)

none,

1986-05-01

In February 1983, the US Department of Energy (DOE) identified a reference repository location at the Hanford Site in Washington as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. The site is in the Columbia Plateau, which is one of five distinct geohydrologic settings considered for the first repository. To determine their suitability, the Hanford Site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EAs. On the basis of the evaluations reported in this EA, the DOE has found that the Hanford site is not disqualified under the guidelines. The DOE has also found that it is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Hanford site as one of five sites suitable for characterization.

Environmental assessment: Reference repository location, Hanford site, Washington

Energy Technology Data Exchange (ETDEWEB)

none,

1986-05-01

In February 1983, the US Department of Energy (DOE) identified a reference repository location at the Hanford Site in Washington as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. The site is in the Columbia Plateau, which is one of five distinct geohydrologic settings considered for the first repository. To determine their suitability, the Hanford site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EAs. On the basis of the evaluations reported in this EA, the DOE has found that the Hanford site is not disqualified under the guidelines. The DOE has also found that is is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Hanford site as one of five sites available for characterization.

Environmental assessment: Reference repository location, Hanford site, Washington

International Nuclear Information System (INIS)

1986-05-01

In February 1983, the US Department of Energy (DOE) identified a reference repository location at the Hanford Site in Washington as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. The site is in the Columbia Plateau, which is one of five distinct geohydrologic settings considered for the first repository. To determine their suitability, the Hanford Site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EAs. On the basis of the evaluations reported in this EA, the DOE has found that the Hanford site is not disqualified under the guidelines. The DOE has also found that it is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Hanford site as one of five sites suitable for characterization

Environmental assessment: Reference repository location, Hanford site, Washington

International Nuclear Information System (INIS)

1986-05-01

In February 1983, the US Department of Energy (DOE) identified a reference repository location at the Hanford Site in Washington as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. The site is in the Columbia Plateau, which is one of five distinct geohydrologic settings considered for the first repository. To determine their suitability, the Hanford site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EAs. On the basis of the evaluations reported in this EA, the DOE has found that the Hanford site is not disqualified under the guidelines. The DOE has also found that is is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Hanford site as one of five sites available for characterization

Preliminary safety assessment study for the conceptual design of a repository in tuff at Yucca Mountain

International Nuclear Information System (INIS)

Jackson, J.L.; Gram, H.F.; Hong, K.J.; Ng, H.S.; Pendergrass, A.M.

1984-12-01

Preliminary estimates of the upper bounds on postulated worst-case radiological releases resulting from possible accidents during the operating period of a prospective repository in tuff at Yucca Mountain are presented. Possible disrupting events are screened to identify the accidents of greatest potential consequence. The radiological dose commitments for the general public and repository personnel are estimated for postulated releases caused by natural phenomena, man-made events, and operational accidents. All postulated worst-case releases result in doses to the public that are lower than the 0.5-rem, whole-body dose-per-accident limit set by the Nuclear Regulatory Commission (NRC) in 10 CFR 60. Doses to repository personnel are within the NRC's 5.0-rem/yr occupational exposure limit set in 10 CFR 20 for normal operations. Doses are within this limit for all accidents except the transportation accident and fire in a drift. A preliminary risk assessment has also been performed. Based on this preliminary safety study, the proposed site boundaries and design criteria routinely used in constructing nuclear facilities appear to be adequate to protect the safety of the general public during the operating phase of the repository

Waste repository planned for Bruce Site

International Nuclear Information System (INIS)

King, F.

2004-01-01

Ontario Power Generation (OPG) and Kincardine, the municipality nearest the Bruce site, have agreed in principal to the construction of a deep geologic repository for low and medium level radioactive waste on the site. The two parties signed the 'Kincardine Hosting Agreement' on October 13, 2004 to proceed with planning, seek regulatory approval and further public consultation of the proposed project. A construction Licence is not expected before 2013. (author)

Enhanced Publications Linking Publications and Research Data in Digital Repositories

CERN Document Server

Vernooy-Gerritsen, Marjan

2009-01-01

The traditional publication will be overhauled by the 'Enhanced Publication'. This is a publication that is enhanced with research data, extra materials, post publication data, and database records. It has an object-based structure with explicit l

Perceived risk, trust in government, and response to repository siting in the United States

International Nuclear Information System (INIS)

Kraft, M.E.

1991-01-01

Conflicts over the siting of high-level radioactive waste repositories have been intense and unrelenting. Public and state opposition to implementation of the US Nuclear Waste Policy Act is tied closely to the perception of unacceptably high repository risks and to lack of trust and confidence in governmental agencies, particularly the DOE. This paper explores the relationship of perceived risk, trust in government, and opposition to repository siting in the US in an attempt to clarify the conditions of successful implementation of nuclear waste policy in the decades ahead

The Open Data Repository's Data Publisher

Science.gov (United States)

Stone, N.; Lafuente, B.; Downs, R. T.; Bristow, T.; Blake, D. F.; Fonda, M.; Pires, A.

2015-12-01

Data management and data publication are becoming increasingly important components of research workflows. The complexity of managing data, publishing data online, and archiving data has not decreased significantly even as computing access and power has greatly increased. The Open Data Repository's Data Publisher software (http://www.opendatarepository.org) strives to make data archiving, management, and publication a standard part of a researcher's workflow using simple, web-based tools and commodity server hardware. The publication engine allows for uploading, searching, and display of data with graphing capabilities and downloadable files. Access is controlled through a robust permissions system that can control publication at the field level and can be granted to the general public or protected so that only registered users at various permission levels receive access. Data Publisher also allows researchers to subscribe to meta-data standards through a plugin system, embargo data publication at their discretion, and collaborate with other researchers through various levels of data sharing. As the software matures, semantic data standards will be implemented to facilitate machine reading of data and each database will provide a REST application programming interface for programmatic access. Additionally, a citation system will allow snapshots of any data set to be archived and cited for publication while the data itself can remain living and continuously evolve beyond the snapshot date. The software runs on a traditional LAMP (Linux, Apache, MySQL, PHP) server and is available on GitHub (http://github.com/opendatarepository) under a GPLv2 open source license. The goal of the Open Data Repository is to lower the cost and training barrier to entry so that any researcher can easily publish their data and ensure it is archived for posterity. We gratefully acknowledge the support for this study by the Science-Enabling Research Activity (SERA), and NASA NNX11AP82A

MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes

DEFF Research Database (Denmark)

Zhang, Yanling; Zhang, Yong; Adachi, Jun

2007-01-01

and stringent validation criteria, false positive identification rates in MAPU are lower than 1:1000. Thus MAPU datasets can serve as reference proteomes in biomarker discovery. MAPU contains the peptides identifying each protein, measured masses, scores and intensities and is freely available at http......://www.mapuproteome.com using a clickable interface of cell or body parts. Proteome data can be queried across proteomes by protein name, accession number, sequence similarity, peptide sequence and annotation information. More than 4500 mouse and 2500 human proteins have already been identified in at least one proteome. Basic...... annotation information and links to other public databases are provided in MAPU and we plan to add further analysis tools....

Conflict, location, and politics: Siting a nuclear waste repository

International Nuclear Information System (INIS)

Jacob, G.R.

1988-01-01

Nuclear power and the management of high-level radioactive waste is examined with the goal of explaining the forces driving the formulation of the 1982 Nuclear Waste Policy Act and a subsequent decision to site a nuclear waste repository at Yucca Mountain, Nevada. The study draws upon geographic, political, economic, and organizational factors to examine the commitment to dispose of spent fuel in a geologic repository located in Nevada or in Utah, Texas, Mississippi, Louisiana, or at Hanford Washington. Special attention is given to the impact of location, science and technology on the definition of the nuclear waste problem and political agendas, public participation, and the power of the nuclear establishment. The study finds that the choice of a Yucca Mountain Nevada as the preferred site for a repository was based more on technological precedent and political-economic expediency than on the demonstrated superiority of that site's geology. Conflict over a repository location is interpreted as a symptom of more fundamental conflicts concerning: the credibility of nuclear science, the legitimacy of federal authority and administration, and the priorities of environmental protection and a nuclear economy

Clinical veterinary proteomics: Techniques and approaches to decipher the animal plasma proteome.

Science.gov (United States)

Ghodasara, P; Sadowski, P; Satake, N; Kopp, S; Mills, P C

2017-12-01

Over the last two decades, technological advancements in the field of proteomics have advanced our understanding of the complex biological systems of living organisms. Techniques based on mass spectrometry (MS) have emerged as powerful tools to contextualise existing genomic information and to create quantitative protein profiles from plasma, tissues or cell lines of various species. Proteomic approaches have been used increasingly in veterinary science to investigate biological processes responsible for growth, reproduction and pathological events. However, the adoption of proteomic approaches by veterinary investigators lags behind that of researchers in the human medical field. Furthermore, in contrast to human proteomics studies, interpretation of veterinary proteomic data is difficult due to the limited protein databases available for many animal species. This review article examines the current use of advanced proteomics techniques for evaluation of animal health and welfare and covers the current status of clinical veterinary proteomics research, including successful protein identification and data interpretation studies. It includes a description of an emerging tool, sequential window acquisition of all theoretical fragment ion mass spectra (SWATH-MS), available on selected mass spectrometry instruments. This newly developed data acquisition technique combines advantages of discovery and targeted proteomics approaches, and thus has the potential to advance the veterinary proteomics field by enhancing identification and reproducibility of proteomics data. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nuclear waste repository in basalt: preconceptual design guidelines

International Nuclear Information System (INIS)

1979-06-01

The development of the basalt waste isolation program parallels the growing need for permanent, environmentally safe, and secure means to store nuclear wastes. The repository will be located within the Columbia Plateau basalt formations where these ends can be met and radiological waste can be stored. These wastes will be stored such that the wastes may be retrieved from storage for a period after placement. After the retrieval period, the storage locations will be prepared for terminal storage. The terminal storage requirements will include decommissioning provisions. The facility boundaries will encompass no more than several square miles of land which will be above a subsurface area where the geologic makeup is primarily deep basaltic rock. The repository will receive, from an encapsulation site(s), nuclear waste in the form of canisters (not more than 18.5 feet x 16 inches in diameter) and containers (55-gallon drums). Canisters will contain spent fuel (after an interim 5-year storage period), solidified high-level wastes (HLW), or intermediate-level wastes (ILW). The containers (drums) will package the low-level transuranic wastes (LL-TRU). The storage capacity of the repository will be expanded in a time-phased program which will require that subsurface development (repository expansion) be conducted concurrently with waste storage operations. The repository will be designed to store the nuclear waste generated within the predictable future and to allow for reasonable expansion. The development and assurance of safe waste isolation is of paramount importance. All activities will be dedicated to the protection of public health and the environment. The repository will be licensed by the US Nuclear Regulatory Commission (NRC). Extensive efforts will be made to assure selection of a suitable site which will provide adequate isolation

Nuclear waste repository in basalt: preconceptual design guidelines

Energy Technology Data Exchange (ETDEWEB)

1979-06-01

The development of the basalt waste isolation program parallels the growing need for permanent, environmentally safe, and secure means to store nuclear wastes. The repository will be located within the Columbia Plateau basalt formations where these ends can be met and radiological waste can be stored. These wastes will be stored such that the wastes may be retrieved from storage for a period after placement. After the retrieval period, the storage locations will be prepared for terminal storage. The terminal storage requirements will include decommissioning provisions. The facility boundaries will encompass no more than several square miles of land which will be above a subsurface area where the geologic makeup is primarily deep basaltic rock. The repository will receive, from an encapsulation site(s), nuclear waste in the form of canisters (not more than 18.5 feet x 16 inches in diameter) and containers (55-gallon drums). Canisters will contain spent fuel (after an interim 5-year storage period), solidified high-level wastes (HLW), or intermediate-level wastes (ILW). The containers (drums) will package the low-level transuranic wastes (LL-TRU). The storage capacity of the repository will be expanded in a time-phased program which will require that subsurface development (repository expansion) be conducted concurrently with waste storage operations. The repository will be designed to store the nuclear waste generated within the predictable future and to allow for reasonable expansion. The development and assurance of safe waste isolation is of paramount importance. All activities will be dedicated to the protection of public health and the environment. The repository will be licensed by the US Nuclear Regulatory Commission (NRC). Extensive efforts will be made to assure selection of a suitable site which will provide adequate isolation.

Pig genome sequence - analysis and publication strategy

DEFF Research Database (Denmark)

Archibald, Alan L.; Bolund, Lars; Churcher, Carol

2010-01-01

preferentially selected for sequencing. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement the data have been released into public sequence repositories (Genbank/EMBL, NCBI/Ensembl trace repositories) in a timely manner and in advance of publication. CONCLUSIONS...

Use of modeling in repository licensing

International Nuclear Information System (INIS)

McGarry, J.M. III; Echols, F.S.

1995-01-01

A review of the regulatory history of the Nuclear Regulatory Commission (NRC) regulations applicable to the licensing of a geologic repository, as well as a review of NRC administrative (licensing) decisions and federal case law, support the NRC's use of simplified models, in appropriate circumstances, which provide well-documented and reasonably conservative bounding assumptions, together with the use of expert judgement, natural analogues, and other aids to supplement available information, in reaching its reasonable assurance determination whether the public health and safety will be adequately protected if the Yucca Mountain, Nevada site should be licensed for development as a geologic repository. Specific examples are provided to assist the reader to better understand how such qualitative concepts as open-quote reasonable assurance close-quote, open-quote reasonably conservative close-quote, and open-quote adequate close-quote protection are used in an administrative context to resolve technical issues

NPP Krsko: LILW Repository or Long Term Storage

International Nuclear Information System (INIS)

Lokner, V.; Subasic, D.; Levanat, I.

2008-01-01

Construction of the facilities for LILW and SF management, as planned in Decommissioning and LILW and SF management program for NPP Krsko, would be a rather expensive and challenging project for such a small nuclear program. In order to accommodate waste arising from a single nuclear power plant, one LILW repository should be constructed before the end of the NPP operation, then one SF dry storage, and finally one geological repository. This requires relatively urgent identification within Slovenian/Croatian territory of three locations that meet the criteria for establishment of such facilities and are acceptable to the local communities. There are very few such potential locations. The siting process for the first of the three facilities is well under way in Slovenia, because the country wants to have its LILW repository in operation by the year 2013. In order to facilitate public acceptance, Slovenian government has introduced financial incentives to local communities for the repository construction and operation. These 'compensations for limited land use' may significantly increase the overall costs of disposal if the repository is in operation for a long period. In the recent years, however, a possibility of long term storage (LTS) is gaining an increased attention in the waste management community, and has already been introduced e.g. in the Netherlands. It is a particularly viable option for limited waste quantities. Disposal remains the final solution, but present technologies have made possible a relatively inexpensive storage up to about hundred years, which can accommodate LILW, HLW and SF from nuclear programs as well as research reactor waste and NORM. Such storage would be a safe and simple temporary solution, encompassing all immediate and near future waste management needs. In addition, it would increase flexibility and reduce financing requirements for the final waste disposal: providing additional time for reduction of radiation emission and heat

Update on the national low level radioactive waste repository study

International Nuclear Information System (INIS)

Veitch, S.M.

1997-01-01

Activity to establish a national repository for low-level and short-lived intermediate-level radioactive waste in Australia began in the early 1980's. From the early 1990's computer-based geographic information systems had developed sufficiently so that all of Australia could be quickly reviewed using digital data relevant to site selection criteria. A three-phased approach to site selection was commenced which included an iterative process of data collection, interpretation, and public involvement through discussion papers. All of Australia was reviewed using national-scale data, and eight broad regions were identified and reviewed using regional-scale data. A third phase report will be released shortly which includes details on the process for identifying the preferred region of the eight. This region will be the focus for public involvement and for detailed study to identify a site for the national repository

The role of libraries in open access institutional repositories.

Directory of Open Access Journals (Sweden)

Tony Hernández Peréz

2008-02-01

Full Text Available Nowadays, there are more and more institutional repositories in Spain, as in a large number of countries all over the world, which contains thousands of digital objects in open access, full-text, no-charge and available to free download, print or copy. Nearly every repository is managed and mantained by the library services of the institution they serve. This article explains the reasons for the crisis in the scholarly communication model, the alternative model based on open access to scholarly publication, and the crucial role that the libraries can play in the development of their own digital collections, a challenge and a chance that they can't miss.

Managing and Evaluating Digital Repositories

Science.gov (United States)

Zuccala, Alesia; Oppenheim, Charles; Dhiensa, Rajveen

2008-01-01

Introduction: We examine the role of the digital repository manager, discuss the future of repository management and evaluation and suggest that library and information science schools develop new repository management curricula. Method: Face-to-face interviews were carried out with managers of five different types of repositories and a Web-based…

Monitoring system specifications: retrieval of surf from a salt repository

International Nuclear Information System (INIS)

1980-01-01

The task of developing specifications for a reference monitoring system determined by repository environmental conditions, retrieval operations, and federal regulatory criteria is discussed. The monitoring system specified in this report is capable of measuring (1) package position and orientation, (2) vault deformation, (3) brine accumulation, (4) spent fuel dissolution, (5) temperature, (6) nuclear radiation, and (7) package condition with sufficient accuracy to provide data input to a general risk assessment model. In order to define a monitoring system which can provide probabilistic data on radiological risk to operating personnel and the general public for a salt mine repository, the following information is required: (1) a complete design of the salt SURF repository including inventory, density and waste package design details; (2) probalistic failure rate data on containment integrity of the SURF waste package; (3) probabilistic failure rate data on the monitoring system components

Repository simulation tests

International Nuclear Information System (INIS)

Wicks, G.G.; Bibler, N.E.; Jantzen, C.M.; Plodinec, M.J.

1984-01-01

The repository simulation experiments described in this paper are designed to assess the performance of SRP waste glass under the most realistic repository conditions that can be obtained in the laboratory. These tests simulate the repository environment as closely as possible and introduce systematically the variability of the geology, groundwater chemistry, and waste package components during the leaching of the waste glass. The tests evaluate waste form performance under site-specific conditions, which differ for each of the geologic repositories under consideration. Data from these experiments will aid in the development of a realistic source term that can describe the release of radionuclides from SRP waste glass as a component of proposed waste packages. Hence, this information can be useful to optimize waste package design for SRP waste glass and to provide data for predicting long-term performance and subsequent conformance to regulations. The repository simulation tests also help to bridge the gap in interpreting results derived from tests performed under the control of the laboratory to the uncertainity and variability of field tests. In these experiments, site-specific repository components and conditions are emphasized and only the site specific materials contact the waste forms. An important feature of these tests is that both actual and simulated waste glasses are tested identically. 7 figures, 2 tables

Retrieval effects on ventilation and cooling requirements for a nuclear waste repository

International Nuclear Information System (INIS)

Hambley, D.F.

1985-01-01

The Nuclear Waste Policy Act of 1982 (Public Law 97-425) and the regulations promulgated in Title 10, Part 60 of the Code of Federal Regulations (10CFR60) by the US Nuclear Regulatory Commission (NRC) for an underground repository for spent fuel and high level nuclear waste (HLW) require that it is possible to retrieve waste, for whatever reason, from such a facility for a period of 50 years from initial storage or until the completion of the performance confirmation period, whichever comes first. This paper considers the effects that the retrievability option mandates on ventilation and cooling systems required for normal repository operations. An example is given for a hypothetical repository in salt. 18 refs., 1 tab

Bioinformatics strategies in life sciences: from data processing and data warehousing to biological knowledge extraction.

Science.gov (United States)

Thiele, Herbert; Glandorf, Jörg; Hufnagel, Peter

2010-05-27

With the large variety of Proteomics workflows, as well as the large variety of instruments and data-analysis software available, researchers today face major challenges validating and comparing their Proteomics data. Here we present a new generation of the ProteinScape bioinformatics platform, now enabling researchers to manage Proteomics data from the generation and data warehousing to a central data repository with a strong focus on the improved accuracy, reproducibility and comparability demanded by many researchers in the field. It addresses scientists; current needs in proteomics identification, quantification and validation. But producing large protein lists is not the end point in Proteomics, where one ultimately aims to answer specific questions about the biological condition or disease model of the analyzed sample. In this context, a new tool has been developed at the Spanish Centro Nacional de Biotecnologia Proteomics Facility termed PIKE (Protein information and Knowledge Extractor) that allows researchers to control, filter and access specific information from genomics and proteomic databases, to understand the role and relationships of the proteins identified in the experiments. Additionally, an EU funded project, ProDac, has coordinated systematic data collection in public standards-compliant repositories like PRIDE. This will cover all aspects from generating MS data in the laboratory, assembling the whole annotation information and storing it together with identifications in a standardised format.

Bioinformatics Strategies in Life Sciences: From Data Processing and Data Warehousing to Biological Knowledge Extraction

Directory of Open Access Journals (Sweden)

Thiele Herbert

2010-03-01

Full Text Available With the large variety of Proteomics workflows, as well as the large variety of instruments and data-analysis software available, researchers today face major challenges validating and comparing their Proteomics data. Here we present a new generation of the ProteinScapeTM bioinformatics platform, now enabling researchers to manage Proteomics data from the generation and data warehousing to a central data repository with a strong focus on the improved accuracy, reproducibility and comparability demanded by many researchers in the field. It addresses scientists` current needs in proteomics identification, quantification and validation. But producing large protein lists is not the end point in Proteomics, where one ultimately aims to answer specific questions about the biological condition or disease model of the analyzed sample. In this context, a new tool has been developed at the Spanish Centro Nacional de Biotecnologia Proteomics Facility termed PIKE (Protein information and Knowledge Extractor that allows researchers to control, filter and access specific information from genomics and proteomic databases, to understand the role and relationships of the proteins identified in the experiments. Additionally, an EU funded project, ProDac, has coordinated systematic data collection in public standards-compliant repositories like PRIDE. This will cover all aspects from generating MS data in the laboratory, assembling the whole annotation information and storing it together with identifications in a standardised format.

The repository ecology an approach to understanding repository and service interactions

CERN Document Server

CERN. Geneva; Hagemann, Melissa

2007-01-01

An increasing number of university institutions and other organisations are deciding to deploy repositories and a growing number of formal and informal distributed services are supporting or capitalising on the information these repositories provide. Despite reasonably well understood technical architectures, early majority adopters may struggle to articulate their place within the actualities of a wider information environment. The idea of a repository ecology provides developers and administrators with a useful way of articulating and analysing their place in the information environment, and the technical and organisational interactions they have, or are developing, with other parts of such an environment. This presentation will provide an overview of the concept of a repository ecology and examine some examples from the domains of scholarly communications and elearning.

Coupling fuel cycles with repositories: how repository institutional choices may impact fuel cycle design

International Nuclear Information System (INIS)

Forsberg, C.; Miller, W.F.

2013-01-01

The historical repository siting strategy in the United States has been a top-down approach driven by federal government decision making but it has been a failure. This policy has led to dispatching fuel cycle facilities in different states. The U.S. government is now considering an alternative repository siting strategy based on voluntary agreements with state governments. If that occurs, state governments become key decision makers. They have different priorities. Those priorities may change the characteristics of the repository and the fuel cycle. State government priorities, when considering hosting a repository, are safety, financial incentives and jobs. It follows that states will demand that a repository be the center of the back end of the fuel cycle as a condition of hosting it. For example, states will push for collocation of transportation services, safeguards training, and navy/private SNF (Spent Nuclear Fuel) inspection at the repository site. Such activities would more than double local employment relative to what was planned for the Yucca Mountain-type repository. States may demand (1) the right to take future title of the SNF so if recycle became economic the reprocessing plant would be built at the repository site and (2) the right of a certain fraction of the repository capacity for foreign SNF. That would open the future option of leasing of fuel to foreign utilities with disposal of the SNF in the repository but with the state-government condition that the front-end fuel-cycle enrichment and fuel fabrication facilities be located in that state

Potential host media for a high-level waste repository

Energy Technology Data Exchange (ETDEWEB)

Hustrulid, W

1982-01-01

Earlier studies of burial of radioactive wastes in geologic repositories had concentrated on salt formations for well-publicized reasons. However, under the Carter administration, significant changes were made in the US nuclear waste management program. Changes which were made were: (1) expansion of the number of rock types under consideration; (2) adoption of the multiple-barrier approach to waste containment; (3) additional requirements for waste retrieval; and (4) new criteria proposed by the Nuclear Regulatory Commission for the isolation of high-level waste in geologic repositories. Results of the studies of different types of rocks as repository sites are summarized herein. It is concluded that each generic rock type has certain advantages and disadvantages when considered from various aspects of the waste disposal problem and that characteristics of rocks are so varied that a most favorable or least favorable rock type cannot be easily identified. This lack of definitive characteristics of rocks makes site selection and good engineering barriers very important for containment of the wastes. (BLM)

Further development of public participation in the site-selection and approval process of a final repository in Germany

Energy Technology Data Exchange (ETDEWEB)

Barth, Regine; Kallenbach-Herbert, Beate [OeEo-Institute e.V., Inst. for Applied Ecology, Darmstadt (Germany); Arens, Georg [Federal Office for Radiation Protection (BfS), Salzgitter (Germany)

2006-09-15

This paper reflects the first findings of a current research project funded by the German Federal Office for Radiation Protection and conducted by an interdisciplinary working group of the OEko-Institute. One focus of this project is the systematic analysis of past and existing participatory processes in different nuclear and non-nuclear projects. On the basis of this analysis and a literature review a specific concept for public participation in the site-selection and approval process of a repository for high radioactive waste (HAW repository) in Germany will be derived. The concept shall foster transparency and acceptance. The working group of the OEko-Institute combines long standing research experience and an intimate knowledge of radioactive waste management including political, technical, management and social problems of final disposal on the one hand. On the other hand members play an active role in stakeholder processes of different non-nuclear projects as well as experience with a wide range of participative measures and their impact. This allows an approach which integrates the specific features of radioactive waste disposal with a wider perspective on the demands and opportunities of stakeholder processes. The procedure of site selection for a HAW repository in Germany still has to be specified. The procedure introduced by the 'Committee on a Site Selection Procedure for Repository Sites' (Arbeitskreis Auswahlverfahren Endlagerstandorte - AkEnd) has not been adopted. The Committee had suggested installing a negotiation group to discuss the AkEnd proposals in the so called 'Phase II'. This suggestion could not be followed because not all relevant stakeholders were willing to participate. An internal draft for a federal law implementing main elements of the AkEnd findings was developed by the Ministry for Environment in 2005, but has never been brought to the cabinet. Due to the change of Government in Germany, the next steps still are

Further development of public participation in the site-selection and approval process of a final repository in Germany

International Nuclear Information System (INIS)

Barth, Regine; Kallenbach-Herbert, Beate; Arens, Georg

2006-01-01

This paper reflects the first findings of a current research project funded by the German Federal Office for Radiation Protection and conducted by an interdisciplinary working group of the OEko-Institute. One focus of this project is the systematic analysis of past and existing participatory processes in different nuclear and non-nuclear projects. On the basis of this analysis and a literature review a specific concept for public participation in the site-selection and approval process of a repository for high radioactive waste (HAW repository) in Germany will be derived. The concept shall foster transparency and acceptance. The working group of the OEko-Institute combines long standing research experience and an intimate knowledge of radioactive waste management including political, technical, management and social problems of final disposal on the one hand. On the other hand members play an active role in stakeholder processes of different non-nuclear projects as well as experience with a wide range of participative measures and their impact. This allows an approach which integrates the specific features of radioactive waste disposal with a wider perspective on the demands and opportunities of stakeholder processes. The procedure of site selection for a HAW repository in Germany still has to be specified. The procedure introduced by the 'Committee on a Site Selection Procedure for Repository Sites' (Arbeitskreis Auswahlverfahren Endlagerstandorte - AkEnd) has not been adopted. The Committee had suggested installing a negotiation group to discuss the AkEnd proposals in the so called 'Phase II'. This suggestion could not be followed because not all relevant stakeholders were willing to participate. An internal draft for a federal law implementing main elements of the AkEnd findings was developed by the Ministry for Environment in 2005, but has never been brought to the cabinet. Due to the change of Government in Germany, the next steps still are under consideration

re3data.org - a global registry of research data repositories

Science.gov (United States)

Pampel, Heinz; Vierkant, Paul; Elger, Kirsten; Bertelmann, Roland; Witt, Michael; Schirmbacher, Peter; Rücknagel, Jessika; Kindling, Maxi; Scholze, Frank; Ulrich, Robert

2016-04-01

re3data.org - the registry of research data repositories lists over 1,400 research data repositories from all over the world making it the largest and most comprehensive online catalog of research data repositories on the web. The registry is a valuable tool for researchers, funding organizations, publishers and libraries. re3data.org provides detailed information about research data repositories, and its distinctive icons help researchers to easily identify relevant repositories for accessing and depositing data sets [1]. Funding agencies, like the European Commission [2] and research institutions like the University of Bielefeld [3] already recommend the use of re3data.org in their guidelines and policies. Several publishers and journals like Copernicus Publications, PeerJ, and Nature's Scientific Data recommend re3data.org in their editorial policies as a tool for the easy identification of appropriate data repositories to store research data. Project partners in re3data.org are the Library and Information Services department (LIS) of the GFZ German Research Centre for Geosciences, the Computer and Media Service at the Humboldt-Universität zu Berlin, the Purdue University Libraries and the KIT Library at the Karlsruhe Institute of Technology (KIT). After its fusion with the U.S. American DataBib in 2014, re3data.org continues as a service of DataCite from 2016 on. DataCite is the international organization for the registration of Digital Object Identifiers (DOI) for research data and aims to improve their citation. The poster describes the current status and the future plans of re3data.org. [1] Pampel H, et al. (2013) Making Research Data Repositories Visible: The re3data.org Registry. PLoS ONE 8(11): e78080. doi:10.1371/journal.pone.0078080. [2] European Commission (2015): Guidelines on Open Access to Scientific Publications and Research Data in Horizon 2020. Available: http://ec.europa.eu/research/participants/data/ref/h2020/grants_manual/hi/oa_pilot/h2020-hi

The repository ecology: an approach to understanding repository and service interactions

CERN Multimedia

CERN. Geneva

2007-01-01

An increasing number of university institutions and other organisations are deciding to deploy repositories and a growing number of formal and informal distributed services are supporting or capitalising on the information these repositories provide. Despite reasonably well understood technical architectures, early majority adopters may struggle to articulate their place within the actualities of a wider information environment. The idea of a repository ecology provides developers and administrators with a useful way of articulating and analysing their place in the information environment, and the technical and organisational interactions they have, or are developing, with other parts of such an environment. This presentation will provide an overview of the concept of a repository ecology and examine some examples from the domains of scholarly communications and elearning. View John Robertson's biography

Institutional Repositories in Universities in Nigeria: Desirability and Progress

Science.gov (United States)

Oye, Peter Olorunlake; Oyeniyi, David Ajibola; Mahan, David Ezekiel

2017-01-01

The desire of academic institutions to link up to the virtual repository is a global phenomenon. Traditional scholarly publication through established journals characterized by peer review is being challenged by less formal net-based communication that links scholars essentially instantaneously. The contention is that universities need to preserve…

Prestudy Oskarshamn. Tourism in Oskarshamn with or without a repository; Foerstudie Oskarshamn. Turismen i Oskarshamn med eller utan djupfoervar

Energy Technology Data Exchange (ETDEWEB)

Nordblom, C.J.; Foghagen, C. [Hoegskolan i Kalmar (Sweden). Inst. foer samhaellsvetenskap med ekonomi

1998-11-01

Consequences for the tourism at Oskarshamn from siting a spent fuel repository in the community are studied. Four questionnaire/interview enquires were performed, and the analysis of the results show that no noticeable effects are expected. Still, an uncertainty about the impact of a repository is felt by the public, and more thorough information about the repository and its components is needed

Proteomics research in India: an update.

Science.gov (United States)

Reddy, Panga Jaipal; Atak, Apurva; Ghantasala, Saicharan; Kumar, Saurabh; Gupta, Shabarni; Prasad, T S Keshava; Zingde, Surekha M; Srivastava, Sanjeeva

2015-09-08

After a successful completion of the Human Genome Project, deciphering the mystery surrounding the human proteome posed a major challenge. Despite not being largely involved in the Human Genome Project, the Indian scientific community contributed towards proteomic research along with the global community. Currently, more than 76 research/academic institutes and nearly 145 research labs are involved in core proteomic research across India. The Indian researchers have been major contributors in drafting the "human proteome map" along with international efforts. In addition to this, virtual proteomics labs, proteomics courses and remote triggered proteomics labs have helped to overcome the limitations of proteomics education posed due to expensive lab infrastructure. The establishment of Proteomics Society, India (PSI) has created a platform for the Indian proteomic researchers to share ideas, research collaborations and conduct annual conferences and workshops. Indian proteomic research is really moving forward with the global proteomics community in a quest to solve the mysteries of proteomics. A draft map of the human proteome enhances the enthusiasm among intellectuals to promote proteomic research in India to the world.This article is part of a Special Issue entitled: Proteomics in India. Copyright © 2015 Elsevier B.V. All rights reserved.

Dose calculation for accident situations at WWR-S type spent nuclear fuel repository

International Nuclear Information System (INIS)

Margeanu, S.; Florescu, G.

2006-01-01

Full text: The Spent Nuclear Fuel Repository at IFIN-HH Bucharest (SNFR IFIN-HH) consists in four pools, repository hall, radiological monitoring system, ventilation system and auxiliary systems. At the moment the remaining activity in the repository is about 3500 Ci. Despite of the small activity, for emergency preparedness purposes, several accident scenarios, with a non zero probability of occurrence during the repository lifetime, have been postulated. Evaluations of radiological consequences to personnel, general public and environment, for each accident scenario have been performed. The radioactive inventory was evaluated with ORIGEN code from SCALE computer code system and radiological consequences were evaluated with COSYMA computer code. Assumptions for the source term determination, meteorological conditions and release, are presented. The calculated values of doses and risk are also presented. The impact of these accident scenarios on population and environment is also discussed. (authors)

Surface-type repository for low and intermediate level radioactive waste in the Republic of Croatia

International Nuclear Information System (INIS)

Kucar-Dragicevic, S.; Zarkovic, V.; Subasic, D.

1995-01-01

The low-level intermediate-level (LL/IL) radioactive waste repository siting and construction project is one of the activities related to establishing the rad waste management system in the Republic of Croatia. The repository project design is one in an array of project activities which also include the site selection procedure and public attitude issues. The prepared design documentation gives technical, safety and financial background relevant for making a final decision on the waste disposal type, and it includes the technological, mechanical, civil and financial documentation on the preliminary/basic design level. During the last few years, the preliminary design has been prepared and safety assessment conducted for the tunnel-type LL/IL rad waste repository. As the surface-type repository is one of alternatives for final disposal the design documentation for that repository type was prepared during 1994. (author)

Conference report: 2012 Repository Symposium. Final storage in Germany. New start - ways and consequences of the site selection procedure

International Nuclear Information System (INIS)

Kettler, John

2012-01-01

The Aachen Institute for Nuclear Training invited participants to the 3-day '2012 Repository Symposium - Final Storage in Germany' held in Bonn. The subtitle of the event, 'New Start - Ways and Consequences of the Site Selection Procedure,' expressed the organizers' summary that the Repository Finding Act currently under discussion did not give rise to any expectation of a repository for high-level radioactive waste before 2080. The symposium was attended by more than 120 persons from Germany and abroad. They discussed the basic elements of the site selection procedure and its consequences on the basis of the draft so far known to the public. While extensive public participation is envisaged for the stage of finding a repository, this does not apply to the draft legislation in the same way. The legal determinations are negotiated in a small circle by the political parties and the state governments. Michael Sailer (Oeko-Institut e.V.) holds that agreement on a repository finding act is urgent. Prof. Dr. Bruno Thomauske (RWTH Aachen) arrives at the conclusion mentioned above, that no repository for high-level radioactive waste can start operation before 2080 on the basis of the Repository Finding Act. Dr. Bettina Keienburg, attorney at law, in her paper drew attention to the points of dispute in the draft legislation with regard to changes in competency of public authorities. The draft law indicated a clear shift of competency for finding a repository from the Federal Office for Radiation Protection to a federal agency yet to be set up. Prof. Dr. Christoph Moench outlined the deficiencies of the draft legislation in matters of refinancing and the polluter-pays principle. Among the tentative solutions discussed it was above all the Swedish model which was acclaimed most widely. (orig.)

Establishment of the Slovenian Universities' Repositories and of the National Open Science Portal

Directory of Open Access Journals (Sweden)

Milan Ojsteršek

2014-12-01

Full Text Available AbstractThe paper presents the legal, organisational and technical perspectives regarding the implementation of the Slovenian national open access infrastructure for electronic theses and dissertations as well as for research publications. The infrastructure consists of four institutional repositories and a national portal that aggregates content from the university repositories and other Slovenian archives in order to provide a common search engine, recommendation of similar publications, and similar text detection. We have developed the software which is integrated with the universities' information and authentication systems and with the COBISS.SI. During the project the necessary legal background was defined and processes for mandatory submission of electronic theses and dissertations as well as of research publications were designed. The processes for data exchange between the institutional repositories and the national portal, and the processes for similar text detection and recommendation system were established. Bilingual web and mobile applications, a recommendation system and the interface suitable for persons with disabilities are provided to the users from around the world. The repositories are an effective promotion tool for universities and their researchers. It is expected that they will improve the recognition of Slovenian universities in the world. The complex national open access infrastructure with similar text detection support and integration with other systems will enable the storage of almost eighty percent of peer-reviewed scientific papers, annually published by Slovenian researchers. The majority of electronic theses and dissertations yearly produced at the Slovenian higher education institutions will also be accessible.

ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses

Science.gov (United States)

Stokes, Todd H; Torrance, JT; Li, Henry; Wang, May D

2008-01-01

Background A survey of microarray databases reveals that most of the repository contents and data models are heterogeneous (i.e., data obtained from different chip manufacturers), and that the repositories provide only basic biological keywords linking to PubMed. As a result, it is difficult to find datasets using research context or analysis parameters information beyond a few keywords. For example, to reduce the "curse-of-dimension" problem in microarray analysis, the number of samples is often increased by merging array data from different datasets. Knowing chip data parameters such as pre-processing steps (e.g., normalization, artefact removal, etc), and knowing any previous biological validation of the dataset is essential due to the heterogeneity of the data. However, most of the microarray repositories do not have meta-data information in the first place, and do not have a a mechanism to add or insert this information. Thus, there is a critical need to create "intelligent" microarray repositories that (1) enable update of meta-data with the raw array data, and (2) provide standardized archiving protocols to minimize bias from the raw data sources. Results To address the problems discussed, we have developed a community maintained system called ArrayWiki that unites disparate meta-data of microarray meta-experiments from multiple primary sources with four key features. First, ArrayWiki provides a user-friendly knowledge management interface in addition to a programmable interface using standards developed by Wikipedia. Second, ArrayWiki includes automated quality control processes (caCORRECT) and novel visualization methods (BioPNG, Gel Plots), which provide extra information about data quality unavailable in other microarray repositories. Third, it provides a user-curation capability through the familiar Wiki interface. Fourth, ArrayWiki provides users with simple text-based searches across all experiment meta-data, and exposes data to search engine crawlers

The core proteome and pan proteome of Salmonella Paratyphi A epidemic strains.

Directory of Open Access Journals (Sweden)

Li Zhang

Full Text Available Comparative proteomics of the multiple strains within the same species can reveal the genetic variation and relationships among strains without the need to assess the genomic data. Similar to comparative genomics, core proteome and pan proteome can also be obtained within multiple strains under the same culture conditions. In this study we present the core proteome and pan proteome of four epidemic Salmonella Paratyphi A strains cultured under laboratory culture conditions. The proteomic information was obtained using a Two-dimensional gel electrophoresis (2-DE technique. The expression profiles of these strains were conservative, similar to the monomorphic genome of S. Paratyphi A. Few strain-specific proteins were found in these strains. Interestingly, non-core proteins were found in similar categories as core proteins. However, significant fluctuations in the abundance of some core proteins were also observed, suggesting that there is elaborate regulation of core proteins in the different strains even when they are cultured in the same environment. Therefore, core proteome and pan proteome analysis of the multiple strains can demonstrate the core pathways of metabolism of the species under specific culture conditions, and further the specific responses and adaptations of the strains to the growth environment.

Integrated Proteomic Pipeline Using Multiple Search Engines for a Proteogenomic Study with a Controlled Protein False Discovery Rate.

Science.gov (United States)

Park, Gun Wook; Hwang, Heeyoun; Kim, Kwang Hoe; Lee, Ju Yeon; Lee, Hyun Kyoung; Park, Ji Yeong; Ji, Eun Sun; Park, Sung-Kyu Robin; Yates, John R; Kwon, Kyung-Hoon; Park, Young Mok; Lee, Hyoung-Joo; Paik, Young-Ki; Kim, Jin Young; Yoo, Jong Shin

2016-11-04

In the Chromosome-Centric Human Proteome Project (C-HPP), false-positive identification by peptide spectrum matches (PSMs) after database searches is a major issue for proteogenomic studies using liquid-chromatography and mass-spectrometry-based large proteomic profiling. Here we developed a simple strategy for protein identification, with a controlled false discovery rate (FDR) at the protein level, using an integrated proteomic pipeline (IPP) that consists of four engrailed steps as follows. First, using three different search engines, SEQUEST, MASCOT, and MS-GF+, individual proteomic searches were performed against the neXtProt database. Second, the search results from the PSMs were combined using statistical evaluation tools including DTASelect and Percolator. Third, the peptide search scores were converted into E-scores normalized using an in-house program. Last, ProteinInferencer was used to filter the proteins containing two or more peptides with a controlled FDR of 1.0% at the protein level. Finally, we compared the performance of the IPP to a conventional proteomic pipeline (CPP) for protein identification using a controlled FDR of <1% at the protein level. Using the IPP, a total of 5756 proteins (vs 4453 using the CPP) including 477 alternative splicing variants (vs 182 using the CPP) were identified from human hippocampal tissue. In addition, a total of 10 missing proteins (vs 7 using the CPP) were identified with two or more unique peptides, and their tryptic peptides were validated using MS/MS spectral pattern from a repository database or their corresponding synthetic peptides. This study shows that the IPP effectively improved the identification of proteins, including alternative splicing variants and missing proteins, in human hippocampal tissues for the C-HPP. All RAW files used in this study were deposited in ProteomeXchange (PXD000395).

Repository operational criteria analysis

International Nuclear Information System (INIS)

Hageman, J.P.; Chowdhury, A.H.

1992-08-01

The objective of the ''Repository Operational Criteria (ROC) Feasibility Studies'' (or ROC task) was to conduct comprehensive and integrated analyses of repository design, construction, and operations criteria in 10 CFR Part 60 regulations, considering the interfaces and impacts of any potential changes to those regulations. The study addresses regulatory criteria related to the preclosure aspects of the geologic repository. The study task developed regulatory concepts or potential repository operational criteria (PROC) based on analysis of a repository's safety functions and other regulations for similar facilities. These regulatory concepts or PROC were used as a basis to assess the sufficiency and adequacy of the current criteria in 10 CFR Part 60. Where the regulatory concepts were same as current operational criteria, these criteria were referenced. The operations criteria referenced or the PROC developed are given in this report. Detailed analyses used to develop the regulatory concepts and any necessary PROC for those regulations that may require a minor change are also presented. The results of the ROC task showed a need for further analysis and possible major rule change related to the design bases of a geologic repository operations area, siting, and radiological emergency planning

Consortial routes to effective repositories

OpenAIRE

Moyle, M.; Proudfoot, R.

2009-01-01

A consortial approach to the establishment of repository services can help a group of Higher Education Institutions (HEIs) to share costs, share technology and share expertise. Consortial repository work can tap into existing structures, or it can involve new groupings of institutions with a common interest in exploring repository development. This Briefing Paper outlines some of the potential benefits of collaborative repository activity, and highlights some of the technical and organisation...

Novel proteins from proteomic analysis of the trunk disease fungus Lasiodiplodia theobromae (Botryosphaeriaceae

Directory of Open Access Journals (Sweden)

Carla C. Uranga

2017-06-01

Full Text Available Many basic science questions remain regarding protein functions in the pathogen: host interaction, especially in the trunk disease fungi family, the Botryosphaeriaceae, which are a global problem for economically important plants, especially fruiting trees. Proteomics is a highly useful technology for studying protein expression and for discovering novel proteins in unsequenced and poorly annotated organisms. Current fungal proteomics approaches involve 2D SDS-PAGE and extensive, complex, protein extraction methodologies. In this work, a modified Folch extraction was applied to protein extraction to perform both de novo peptide sequencing and peptide fragmentation analysis/protein identification of the plant and human fungal pathogen Lasiodiplodia theobromae. Both bioinformatics approaches yielded novel peptide sequences from proteins produced by L. theobromae in the presence of exogenous triglycerides and glucose. These proteins and the functions they may possess could be targeted for further functional characterization and validation efforts, due to their potential uses in biotechnology and as new paradigms for understanding fungal biochemistry, such as the finding of allergenic enolases, as well as various novel proteases, including zinc metalloproteinases homologous to those found in snake venom. This work contributes to genomic annotation efforts, which, hand in hand with genomic sequencing, will help improve fungal bioinformatics databases for future studies of Botryosphaeriaceae. All data, including raw data, are available via the ProteomeXchange data repository with identifier PXD005283. This is the first study of its kind in Botryosphaeriaceae.

Trustworthy Digital Repositories: Building Trust the Old Fashion Way, EARNING IT.

Science.gov (United States)

Kinkade, D.; Chandler, C. L.; Shepherd, A.; Rauch, S.; Groman, R. C.; Wiebe, P. H.; Glover, D. M.; Allison, M. D.; Copley, N. J.; Ake, H.; York, A.

2016-12-01

There are several drivers increasing the importance of high quality data management and curation in today's research process (e.g., OSTP PARR memo, journal publishers, funders, academic and private institutions), and proper management is necessary throughout the data lifecycle to enable reuse and reproducibility of results. Many digital data repositories are capable of satisfying the basic management needs of an investigator looking to share their data (i.e., publish data in the public domain), but repository services vary greatly and not all provide mature services that facilitate discovery, access, and reuse of research data. Domain-specific repositories play a vital role in the data curation process by working closely with investigators to create robust metadata, perform first order QC, and assemble and publish research data. In addition, they may employ technologies and services that enable increased discovery, access, and long-term archive. However, smaller domain facilities operate in varying states of capacity and curation ability. Within this repository environment, individual investigators (driven by publishers, funders, or institutions) need to find trustworthy repositories for their data; and funders need to direct investigators to quality repositories to ensure return on their investment. So, how can one determine the best home for valuable research data? Metrics can be applied to varying aspects of data curation, and many credentialing organizations offer services that assess and certify the trustworthiness of a given data management facility. Unfortunately, many of these certifications can be inaccessible to a small repository in cost, time, or scope. Are there alternatives? This presentation will discuss methods and approaches used by the Biological and Chemical Oceanography Data Management Office (BCO-DMO; a domain-specific, intermediate digital data repository) to demonstrate trustworthiness in the face of a daunting accreditation landscape.

[Proteomics and transfusion medicine].

Science.gov (United States)

Lion, N; Prudent, M; Crettaz, D; Tissot, J-D

2011-04-01

The term "proteomics" covers tools and techniques that are used to analyze and characterize complex mixtures of proteins from various biological samples. In this short review, a typical proteomic approach, related to the study of particular and illustrative situation related to transfusion medicine is reported. This "case report" will allow the reader to be familiar with a practical proteomic approach of a real situation, and will permit to describe the tools that are usually used in proteomic labs, and, in a second part, to present various proteomic applications in transfusion medicine. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Social network architecture of human immune cells unveiled by quantitative proteomics.

Science.gov (United States)

Rieckmann, Jan C; Geiger, Roger; Hornburg, Daniel; Wolf, Tobias; Kveler, Ksenya; Jarrossay, David; Sallusto, Federica; Shen-Orr, Shai S; Lanzavecchia, Antonio; Mann, Matthias; Meissner, Felix

2017-05-01

The immune system is unique in its dynamic interplay between numerous cell types. However, a system-wide view of how immune cells communicate to protect against disease has not yet been established. We applied high-resolution mass-spectrometry-based proteomics to characterize 28 primary human hematopoietic cell populations in steady and activated states at a depth of >10,000 proteins in total. Protein copy numbers revealed a specialization of immune cells for ligand and receptor expression, thereby connecting distinct immune functions. By integrating total and secreted proteomes, we discovered fundamental intercellular communication structures and previously unknown connections between cell types. Our publicly accessible (http://www.immprot.org/) proteomic resource provides a framework for the orchestration of cellular interplay and a reference for altered communication associated with pathology.

Workshops for state review of site suitability criteria for high-level radioactive waste repositories: analysis and recommendations

International Nuclear Information System (INIS)

1978-02-01

The purpose of this report is to present the views and recommendations of invited State officials and legislators participating in a workshop concerned with preliminary site suitability criteria for high level radioactive waste repositories. The workshops were open to the public and were conducted by the U. S. Nuclear Regulatory Commission (NRC) during September 1977 in three regional locations across the United States. This contractor report is the second of two reports and consolidates the discussion by State officials on the role of a State in siting a repository, NRC's waste management program, the transportation of high level wastes, the number and location of repositories and concerns with the socio-economic impacts of siting a repository in a community. The recommendations to the NRC can be categorized into four areas. These were: (1) general recommendations, (2) procedural recommendations, (3) recommendations for improving communications, and (4) specific recommendations on the preliminary siting criteria. The recommendations emphasized the need for early State involvement in the siting process, the need for an impacted State to assess repository operations, the need for early solution of waste transportation concerns, and the requirement that any repository developed insure the protection of the public health and safety as its most important characteristic. Other participant recommendations are included in the body of the report

Search for a final repository. Final repository commission and the public. Questions concerning cooperation and progress of the process at half time of the commission; Endlagersuche. Endlager-Kommission und Oeffentlichkeit(en). Fragen nach Zusammenarbeit und Fortschritten im Prozess zur Halbzeit der Kommission

Energy Technology Data Exchange (ETDEWEB)

Mueller, Monika C.M. (ed.) [Evangelische Akademie Loccum (Germany). Arbeitsbereich Naturwissenschaften, Oekologie und Umweltpolitik

2016-08-01

The volume includes the following contributions: Presumptions and success of public participation. Refusal as legitimate and necessary mean. Experiences form the participation process in Switzerland. Cooperation of the final repository commission and the public. Regional participation: the view of a process attendant in the Swiss procedure. Synergies or friction losses? Who is coordinating the institutions/activities and is bringing them together? Players in the nuclear waste conflict - rights and duties in the frame of the search for waste storage as safe as possible. Transparency and Participation - what is the role of online media in the site search process?.

State University’s Institusional Repository as a Storage for Civitas Academia Intelectul Property

Directory of Open Access Journals (Sweden)

Dyah Puspita Srirahayu

2018-01-01

Full Text Available Many works - works the academic community that has not been published so that the intellectual property of an educational institution is not widely known by the general public. Institutional repository created and used to manage the results of these works that can be accessed by all people. This study aimed to describe the institutional repository of high perguruang country in Java Timursebagai container to the intellectual academic community views of content, the software used unit that houses, and ratings on Webometrik. This study uses a quantitative approach with descriptive methods. The population used in this study are all the institutional repository of public universities in East Java, which already are online. The sampling technique is the total sampling. The results of this study found that 50% of state universities in East Java has an IR that can be accessed via the internet, 100% of existing IR content is scientific output, the software used various existing GDL, DSpace, Eprints and others, and IR state universities in Java East 66.7% was ranked in webometrik

Repository design

Energy Technology Data Exchange (ETDEWEB)

John, C M

1982-01-01

Various technical issues of radioactive waste design are addressed in this paper. Two approaches to repository design considered herein are: (1) design to minimize the disturbance of the hot rock; and (2) designs that intentionally modify the hot rock to insure better containment of the wastes. The latter designs range from construction of a highly impermeable barrier around a spherical cavern to creating a matrix of tunnels and boreholes to form a cage within which the hydraulic pressure is nearly constant. Examples of these design alternatives are described in some detail. It is concluded that proposed designs for repositories illustrate that performance criteria considered acceptable for such facilities can be met by appropriate site selection and repository engineering. With these technically feasible design concepts, it is also felt that socioeconomic and institutional issues can be better resolved. (BLM)

Principles of proteome allocation are revealed using proteomic data and genome-scale models

DEFF Research Database (Denmark)

Yang, Laurence; Yurkovich, James T.; Lloyd, Colton J.

2016-01-01

to metabolism and fitness. Using proteomics data, we formulated allocation constraints for key proteome sectors in the ME model. The resulting calibrated model effectively computed the "generalist" (wild-type) E. coli proteome and phenotype across diverse growth environments. Across 15 growth conditions......Integrating omics data to refine or make context-specific models is an active field of constraint-based modeling. Proteomics now cover over 95% of the Escherichia coli proteome by mass. Genome-scale models of Metabolism and macromolecular Expression (ME) compute proteome allocation linked...... of these sectors for the general stress response sigma factor sigma(S). Finally, the sector constraints represent a general formalism for integrating omics data from any experimental condition into constraint-based ME models. The constraints can be fine-grained (individual proteins) or coarse-grained (functionally...

Quantitative Clinical Chemistry Proteomics (qCCP) using mass spectrometry: general characteristics and application.

Science.gov (United States)

Lehmann, Sylvain; Hoofnagle, Andrew; Hochstrasser, Denis; Brede, Cato; Glueckmann, Matthias; Cocho, José A; Ceglarek, Uta; Lenz, Christof; Vialaret, Jérôme; Scherl, Alexander; Hirtz, Christophe

2013-05-01

Proteomics studies typically aim to exhaustively detect peptides/proteins in a given biological sample. Over the past decade, the number of publications using proteomics methodologies has exploded. This was made possible due to the availability of high-quality genomic data and many technological advances in the fields of microfluidics and mass spectrometry. Proteomics in biomedical research was initially used in 'functional' studies for the identification of proteins involved in pathophysiological processes, complexes and networks. Improved sensitivity of instrumentation facilitated the analysis of even more complex sample types, including human biological fluids. It is at that point the field of clinical proteomics was born, and its fundamental aim was the discovery and (ideally) validation of biomarkers for the diagnosis, prognosis, or therapeutic monitoring of disease. Eventually, it was recognized that the technologies used in clinical proteomics studies [particularly liquid chromatography-tandem mass spectrometry (LC-MS/MS)] could represent an alternative to classical immunochemical assays. Prior to deploying MS in the measurement of peptides/proteins in the clinical laboratory, it seems likely that traditional proteomics workflows and data management systems will need to adapt to the clinical environment and meet in vitro diagnostic (IVD) regulatory constraints. This defines a new field, as reviewed in this article, that we have termed quantitative Clinical Chemistry Proteomics (qCCP).

Integrated genomics and proteomics of the Torpedo californica electric organ: concordance with the mammalian neuromuscular junction

Directory of Open Access Journals (Sweden)

Mate Suzanne E

2011-05-01

Full Text Available Abstract Background During development, the branchial mesoderm of Torpedo californica transdifferentiates into an electric organ capable of generating high voltage discharges to stun fish. The organ contains a high density of cholinergic synapses and has served as a biochemical model for the membrane specialization of myofibers, the neuromuscular junction (NMJ. We studied the genome and proteome of the electric organ to gain insight into its composition, to determine if there is concordance with skeletal muscle and the NMJ, and to identify novel synaptic proteins. Results Of 435 proteins identified, 300 mapped to Torpedo cDNA sequences with ≥2 peptides. We identified 14 uncharacterized proteins in the electric organ that are known to play a role in acetylcholine receptor clustering or signal transduction. In addition, two human open reading frames, C1orf123 and C6orf130, showed high sequence similarity to electric organ proteins. Our profile lists several proteins that are highly expressed in skeletal muscle or are muscle specific. Synaptic proteins such as acetylcholinesterase, acetylcholine receptor subunits, and rapsyn were present in the electric organ proteome but absent in the skeletal muscle proteome. Conclusions Our integrated genomic and proteomic analysis supports research describing a muscle-like profile of the organ. We show that it is a repository of NMJ proteins but we present limitations on its use as a comprehensive model of the NMJ. Finally, we identified several proteins that may become candidates for signaling proteins not previously characterized as components of the NMJ.

Building trust with the public in site selection of radioactive waste repository in Croatia

International Nuclear Information System (INIS)

Cerskov Klika, Mirjana; Schaller, Antun

1995-01-01

It should be emphasised that the Republic of Croatia ought to find a solution to dispose not only radioactive waste generated on its own territory, i.e. waste derived from diverse medical, industrial and scientific nuclear applications which does not exceed some 70 cubic metres: in total. It is also obliged to find acceptable solutions for disposal of a half of total radioactive waste accumulating in the Krsko NPP which is situated in Slovenia, but is a joint venture facility of both countries, Slovenia and Croatia. Therefore, one of essential duties of the APO - Hazardous Waste Management Agency is just performance of these activities in Croatia. The site selection process of low- and intermediate radioactive waste disposal in Croatia started in 1988. The site selection process itself is organized in two stages: (1) site survey stage; and 2) site evaluation stage. The first stage, being currently in progress, is related to all activities directed to inclusion of preferred sites into the Regional Plan of Croatia, whilst the second stage includes a necessary on-field investigations at few preferred sites and identification of the most suitable one, i.e. the final repository site. Eight potential areas containing even 42 potential sites have been determined so far. Promotion of several preferred sites is expected to be done until July 1995. Official announcement of preferred sites will be followed by public debate on their acceptance at a level of political-territorial organization, including local communities. The people working in APO - Hazardous Waste Management Agency have been aware of considerable public resistance to most of activities the Agency is dealing with since the very beginning of its operation. Consequently, permanent education and honest information to the public have been taken as the Agency's high priority tasks. Namely, if the public is treated as a competent participant in decision making process then it gets obvious that publicity of work is

Building on existing institutions to perpetuate knowledge of waste repositories

International Nuclear Information System (INIS)

Weitzberg, A.

1982-08-01

Purpose of this report is to examine the function of several existing institutions and to show how they could be effectively used to transmit information about waste repositories for long times into the future. Scope of this report is limited to a discussion of four institutional approaches to the dissemination and retention of information: Widely distributed maps, the marker system of the National Geodetic Survey, the archiving of documents, and one-call systems designed to protect underground utility installations from inadvertent damage by the public. Each of these approaches is discussed in an independent section that describes the background of the institutional approach, discusses methods for applying it to waste repositories, and assesses its potential value. The sole intent of this report is to present supporting data for future decisions about the kinds of communication measures that should be implemented to advise future generations about the locations and hazards of waste repositories

HepSim: A repository with predictions for high-energy physics experiments

International Nuclear Information System (INIS)

Chekanov, S. V.

2015-01-01

A file repository for calculations of cross sections and kinematic distributions using Monte Carlo generators for high-energy collisions is discussed. The repository is used to facilitate effective preservation and archiving of data from theoretical calculations and for comparisons with experimental data. The HepSim data library is publicly accessible and includes a number of Monte Carlo event samples with Standard Model predictions for current and future experiments. The HepSim project includes a software package to automate the process of downloading and viewing online Monte Carlo event samples. Data streaming over a network for end-user analysis is discussed

Decision-Making Risks Concerning the Construction of the Goiania Waste Repository

International Nuclear Information System (INIS)

Paschoa, A.S.; Rozental, J.J.; Tranjan Filho, A.

2001-01-01

As it is well known, an accident with a teletherapy source made of 137 CsCl with an initial activity of 59 TBq occurred in Goiania, in September of 1987. This paper will discuss the decision-making process, and the struggle that followed the decision to build the final repository for the remnants of the Goiania accident. The Goiania final repository was built as planned. The two subsurface structures under the grassy artificial hills hold the overall volume of the remnants of the Goiania accident. The near hill holds 5x10 3 m3 of stabilized wastes without radioactivity, or with very low radioactivity. The far hill holds the remaining 6.5x10 3 m 3 of stabilized wastes with low and medium radioactivity. The central part of each subsurface hill has been shielded by wastes with less and less radioactivity. The overall fenced area occupies 1.85x10 5 m 2 . The external radiation levels are similar to the surrounding background, and much lower than those found in the Brazilian areas of high natural radioactivity. The site is permanently monitored by independent institutions, including Brazilian universities, and national and international organizations. As it was mentioned earlier, the final repository was build to last for at least 400 years. Although the initial decision to adopt a too conservative decontamination criterion in the case of the Goiania accident was bound to produce excessive amount of waste; such decision proved, retrospectively, not to be bad because the excess low radioactive waste produced was used as extra shielding material in final repository. The technical decision-maker should not abandon risk estimates, but should be aware that credibility is the main basis to achieve acceptability of a decision by the general public. Risk perception should be regarded as only a first step towards what may be called knowledge, or comprehension of risk estimates, but risk perception by the general public is still an open issue. The problem of a fixed, or near

Providing a Scientific and Technical Basis for Repository Decisions

International Nuclear Information System (INIS)

2001-01-01

The Nuclear Waste Policy Act (NWPA) of 1982 directed the U. S. Department of Energy (DOE) to research sites and design a deep geologic repository for the disposal of our nation's spent nuclear fuel and high-level radioactive waste. In 1987, Congress amended the NWPA and directed the DOE to focus only on Yucca Mountain, Nevada, to determine whether it is a suitable site for a repository. For more than 15 years, the DOE has been studying Yucca Mountain and has accumulated an enormous amount of scientific and technical information about the mountain and the area surrounding it. The secretary of energy will decide whether to recommend Yucca Mountain to the president as a suitable site for a repository. This decision will be based on the scientific and technical information resulting from the Department of Energy's studies of Yucca Mountain and on the views and comments submitted by other governmental groups and the public. One required basis for the secretary's decision will be a scientific analysis called a total system performance assessment

Addressing concerns about the agricultural impacts of siting a nuclear waste repository in Texas

International Nuclear Information System (INIS)

Boryczka, M.; Darrough, B.

1986-01-01

Public concerns related to the siting of a nuclear repository have included the potential impacts to specific economic sectors. In Texas, local residents have expressed concern about how a repository will affect agriculture. Several major questions have arisen with respect to this issue including: 1) how will a repository's requirements for land and water affect agriculture, 2) how will a repository affect agricultural land values, and 3) how will actual or perceived contamination of locally grown products affect their marketability? This paper describes the concerns raised by local residents and discusses the approach to analyzing the concerns identified. An evaluation of agricultural impacts has been prepared for the Department of Energy's Enviromental Assessment (EA) documents. In addition, activities needed to further evaluate these impacts are planned for site characterization. Both the current analysis and planned activities are described

In silico proteome analysis to facilitate proteomics experiments using mass spectrometry

Directory of Open Access Journals (Sweden)

Lindo Micheal

2003-08-01

Full Text Available Abstract Proteomics experiments typically involve protein or peptide separation steps coupled to the identification of many hundreds to thousands of peptides by mass spectrometry. Development of methodology and instrumentation in this field is proceeding rapidly, and effective software is needed to link the different stages of proteomic analysis. We have developed an application, proteogest, written in Perl that generates descriptive and statistical analyses of the biophysical properties of multiple (e.g. thousands protein sequences submitted by the user, for instance protein sequences inferred from the complete genome sequence of a model organism. The application also carries out in silico proteolytic digestion of the submitted proteomes, or subsets thereof, and the distribution of biophysical properties of the resulting peptides is presented. proteogest is customizable, the user being able to select many options, for instance the cleavage pattern of the digestion treatment or the presence of modifications to specific amino acid residues. We show how proteogest can be used to compare the proteomes and digested proteome products of model organisms, to examine the added complexity generated by modification of residues, and to facilitate the design of proteomics experiments for optimal representation of component proteins.

Centralized mouse repositories.

Science.gov (United States)

Donahue, Leah Rae; Hrabe de Angelis, Martin; Hagn, Michael; Franklin, Craig; Lloyd, K C Kent; Magnuson, Terry; McKerlie, Colin; Nakagata, Naomi; Obata, Yuichi; Read, Stuart; Wurst, Wolfgang; Hörlein, Andreas; Davisson, Muriel T

2012-10-01

Because the mouse is used so widely for biomedical research and the number of mouse models being generated is increasing rapidly, centralized repositories are essential if the valuable mouse strains and models that have been developed are to be securely preserved and fully exploited. Ensuring the ongoing availability of these mouse strains preserves the investment made in creating and characterizing them and creates a global resource of enormous value. The establishment of centralized mouse repositories around the world for distributing and archiving these resources has provided critical access to and preservation of these strains. This article describes the common and specialized activities provided by major mouse repositories around the world.

Demystifying the institutional repository for success

CERN Document Server

Buehler, Marianne

2013-01-01

Institutional repositories remain key to data storage on campus, fulfilling the academic needs of various stakeholders. Demystifying the Institutional Repository for Success is a practical guide to creating and sustaining an institutional repository through marketing, partnering, and understanding the academic needs of all stakeholders on campus. This title is divided into seven chapters, covering: traditional scholarly communication and open access publishing; the academic shift towards open access; what the successful institutional repository looks like; institutional repository collaboratio

Long-term Safety of a Geologic Repository: What does the public want to know?

International Nuclear Information System (INIS)

Kotra, Janet

2008-01-01

Janet Kotra of the U.S. NRC recounted the questions most frequently asked of the Commission's staff, concerning the long-term safety of the planned Yucca Mountain repository. The first question was related to who would decide whether the facility is safe enough. The next question linked to it is if regulatory staff is sufficiently qualified, and if they have access to independent sources of information or depend merely on the information provided by the implementer. The subsequent questions were about what criteria the regulator used and whether they were comprehensive enough. A separate group of questions addressed the safety of the technology, including the geologic features of the site, the engineered structures and the packaging of waste. Issues of documentation, operational control, long-term monitoring, oversight, and enforcement were also raised, along with the transparency of such processes and the accessibility of documents to the public. In addition, several questions were related to the fairness of decision making, public involvement, and the flexibility of the implementation process with regard to future knowledge and RD and D. Ms Kotra propounded that a single question was behind those cited above, namely whether one could rely on the regulator or not. Since it is not realistic to expect an overall consensus on the decision of the regulator agency, the goal should rather be to build confidence in the decision-making process. Key factors of confidence include openness on the part of the regulator and other decision-making institutions, and access to trustworthy representatives of these organisations

The European Repository Landscape 2008 Inventory of Digital Repositories for Research Output

CERN Document Server

Van der Graaf, Maurits

2009-01-01

It is widely acknowledged that a common knowledge base for European research is necessary. Research repositories are an important innovation to the scientific information infrastructure. In 2006, digital repositories in the 27 countries of the European we

Personalized medicine beyond genomics: alternative futures in big data-proteomics, environtome and the social proteome.

Science.gov (United States)

Özdemir, Vural; Dove, Edward S; Gürsoy, Ulvi K; Şardaş, Semra; Yıldırım, Arif; Yılmaz, Şenay Görücü; Ömer Barlas, I; Güngör, Kıvanç; Mete, Alper; Srivastava, Sanjeeva

2017-01-01

No field in science and medicine today remains untouched by Big Data, and psychiatry is no exception. Proteomics is a Big Data technology and a next generation biomarker, supporting novel system diagnostics and therapeutics in psychiatry. Proteomics technology is, in fact, much older than genomics and dates to the 1970s, well before the launch of the international Human Genome Project. While the genome has long been framed as the master or "elite" executive molecule in cell biology, the proteome by contrast is humble. Yet the proteome is critical for life-it ensures the daily functioning of cells and whole organisms. In short, proteins are the blue-collar workers of biology, the down-to-earth molecules that we cannot live without. Since 2010, proteomics has found renewed meaning and international attention with the launch of the Human Proteome Project and the growing interest in Big Data technologies such as proteomics. This article presents an interdisciplinary technology foresight analysis and conceptualizes the terms "environtome" and "social proteome". We define "environtome" as the entire complement of elements external to the human host, from microbiome, ambient temperature and weather conditions to government innovation policies, stock market dynamics, human values, political power and social norms that collectively shape the human host spatially and temporally. The "social proteome" is the subset of the environtome that influences the transition of proteomics technology to innovative applications in society. The social proteome encompasses, for example, new reimbursement schemes and business innovation models for proteomics diagnostics that depart from the "once-a-life-time" genotypic tests and the anticipated hype attendant to context and time sensitive proteomics tests. Building on the "nesting principle" for governance of complex systems as discussed by Elinor Ostrom, we propose here a 3-tiered organizational architecture for Big Data science such as

Office of Geologic Repositories quality assurance plan for high-level radioactive waste repositories

International Nuclear Information System (INIS)

1986-08-01

This document sets forth geologic repository program-wide quality assurance program requirements and defines management's quality assurance responsibilities for the Office of Geologic Repositories and its projects. (LM)

Virtual patient repositories--a comparative analysis.

Science.gov (United States)

Küfner, Julia; Kononowicz, Andrzej A; Hege, Inga

2014-01-01

Virtual Patients (VPs) are an important component of medical education. One way to reduce the costs for creating VPs is sharing through repositories. We conducted a literature review to identify existing repositories and analyzed the 17 included repositories in regards to the search functions and metadata they provide. Most repositories provided some metadata such as title or description, whereas other data, such as educational objectives, were less frequent. Future research could, in cooperation with the repository provider, investigate user expectations and usage patterns.

Technology overview of mined repositories

International Nuclear Information System (INIS)

Gimera, R.; Thirumalai, K.

1982-01-01

Mined repositories present an environmentally viable option for permanent disposal of nuclear waste. This paper reviews the state-of-the-art mining technologies and identifies technological issues and developments necessary to mine a repository in basalt. The thermal loading, isolation, and retrieval requirements of a repository present unique technological challenges unknown to conventional mining practice. The technology issues and developments required in the areas of excavation, roof and ground support, equipment development, instrumentation development, and sealing are presented. Performance assessment methods must be developed to evaluate the adequacies of technologies developed to design, construct, operate, and decommission a repository. A stepwise test-and-development approach is used in the Basalt Waste Isolation Project to develop cost-effective technologies for a repository

Framework and Challenges for Initiating Multinational Cooperation for the Development of a Radioactive Waste Repository

International Nuclear Information System (INIS)

2016-01-01

This publication is concerned with radioactive waste that requires geological disposal. It discusses the partnership arrangements necessary for the development of a multinational repository for disposal of this waste, but it also emphasizes that countries should not rely solely on a multinational solution and should in addition have coherent national plans for disposal (a dual track strategy). The publication focuses on multinational approaches based on the IAEA scenario for cooperation among countries in joint projects for the establishment of a shared geological repository. It describes the phased approach that would be needed, indicating the decision processes to be undertaken by partners in the multinational project, both within a national context and in the scope of the joint endeavour. It highlights a wide range of legal and institutional aspects, including the contractual obligations among partners, the economic and financial arrangements, liabilities, nuclear security, regulatory and legislative aspects, waste transportation arrangements, and social issues. It also addresses the uncertainties and risks involved in the implementation of a multinational repository

Breast Cancer Tissue Repository

National Research Council Canada - National Science Library

Iglehart, J

1997-01-01

The Breast Tissue Repository at Duke enters its fourth year of finding. The purpose of the Repository at Duke is to provide substantial quantities of frozen tissue for explorative molecular studies...

Proteomics in medical microbiology.

Science.gov (United States)

Cash, P

2000-04-01

The techniques of proteomics (high resolution two-dimensional electrophoresis and protein characterisation) are widely used for microbiological research to analyse global protein synthesis as an indicator of gene expression. The rapid progress in microbial proteomics has been achieved through the wide availability of whole genome sequences for a number of bacterial groups. Beyond providing a basic understanding of microbial gene expression, proteomics has also played a role in medical areas of microbiology. Progress has been made in the use of the techniques for investigating the epidemiology and taxonomy of human microbial pathogens, the identification of novel pathogenic mechanisms and the analysis of drug resistance. In each of these areas, proteomics has provided new insights that complement genomic-based investigations. This review describes the current progress in these research fields and highlights some of the technical challenges existing for the application of proteomics in medical microbiology. The latter concern the analysis of genetically heterogeneous bacterial populations and the integration of the proteomic and genomic data for these bacteria. The characterisation of the proteomes of bacterial pathogens growing in their natural hosts remains a future challenge.

Siting the nation's first high-level nuclear waste repository: Social impacts for Utah

International Nuclear Information System (INIS)

Olshansky, S.J.

1986-01-01

The siting of a high-level nuclear waste repository in the United States has been an issue of great controversy, particulary for the states under consideration. In addition to concerns expressed about the geological stability of the proposed sites, numerous social issues have been raised by the general public--most of which have been addressed by the draft environmental impact statements. Among the social impacts raised by the Department of Engery and the general public, those receiving the greatest attention were the potential influence of the repository on local economics, tourism, and the health status of the local residents. The major issues of interest in the present study include 1) the effects of respondent knowledge of nuclear waste disposal issues on opinions of health effects and tourism, particularly as they are affected by visitation patterns, and 2) the effects of occupation and education (in particular) on knowledge of nuclear waste disposal issues and opinions on technical and non-technical aspects of siting the repository. Preliminary results indicate that only about 40 percent of the respondents have visited the national parks in southeastern Utah, but over 70 percent feel they are informed about the issues associated with siting the repository. Over 60 percent of the respondents were very concerned about the possible negative effect the repository could have on jobs, tourism, health effects, and environmental quality. Cross-tabulations indicate that the respondents self rating on knowledge of nuclear disposal issues has a statistically significant influence on responses to socioeconomic issues, yet the same self rating scale is significantly influenced by the frequency with which respondents have visited the national parks in southeastern Utah

Social and economical aspects in the selection of the site for the final Goiania waste repository

International Nuclear Information System (INIS)

Paschoa, A.S.; Tranjan Filho, A.; Rosenthal, J.J.

2000-01-01

Site selection criteria for low and intermediate level waste repositories are usually well established as far as the technological and scientific bases are concerned. However, social, cultural and economical aspects need to be examined on a case by case basis because there are many situations to be faced before succeeding to convince the public and authorities that a waste repository is to be built at any chosen site. In the specific case of Goiania there is an ongoing process that started several years ago, to make the repository accepted by local, state and national authorities, and to answer legitimate questions raised by significant segments of the population. This paper will summarise those more relevant aspects concerning the site selection process for the Goiania repository. (author)

Salt Repository Project Waste Package Program Plan: Draft

International Nuclear Information System (INIS)

Carr, J.A.; Cunnane, J.C.

1986-01-01

Under the direction of the Office of Civilian Radioactive Waste Management (OCRWM) created within the DOE by direction of the Nuclear Waste Policy Act of 1982 (NWPA), the mission of the Salt Repository Project (SRP) is to provide for the development of a candidate salt repository for disposal of high-level radioactive waste (HLW) and spent reactor fuel in a manner that fully protects the health and safety of the public and the quality of the environment. In consideration of the program needs and requirements discussed above, the SRP has decided to develop and issue this SRP Waste Package Program Plan. This document is intended to outline how the SRP plans to develop the waste package design and to show, with reasonable assurance, that the developed design will satisfy applicable requirements/performance objectives. 44 refs., 16 figs., 16 tabs

A radioactive waste repository for Australia: methods for choosing the right site

International Nuclear Information System (INIS)

1992-01-01

This study has developed and used an open and objective approach to site selection. A geographic information system was used to assemble continental-scale information. The information was classified according to suitability criteria and processed to show how the most suitable areas for locating Australia's radioactive waste repository can be identified. The test results show that different regions are identified when different selection criteria are used. The results in this discussion paper are indicative only and are intended to provide a focus for more detailed studies at regional and local levels following public comment on the criteria and methodology. The methodology for identifying a suitable site for a national repository for radioactive wastes will be re-applied with more detailed information to areas identified in this study and on the basis of public comments. 6 figs

Data from proteomic characterization and comparison of mammalian milk fat globule proteomes by iTRAQ analysis

Directory of Open Access Journals (Sweden)

Yongxin Yang

2015-06-01

Full Text Available Milk fat globules memebrane (MFGM-enriched proteomes from Holstein, Jersey, yak, buffalo, goat, camel, horse, and human were extracted and identified by an iTRAQ quantification proteomic approach. Proteomes data were analyzed by bioinformatic and multivariate statistical analysis and used to present the characteristic traits of the MFGM proteins among the studied mammals. The data of this study are also related to the research article “Proteomic characterization and comparison of mammalian milk fat globule proteomes by iTRAQ analysis” in the Journal of Proteomics [1].

Bacterial membrane proteomics.

Science.gov (United States)

Poetsch, Ansgar; Wolters, Dirk

2008-10-01

About one quarter to one third of all bacterial genes encode proteins of the inner or outer bacterial membrane. These proteins perform essential physiological functions, such as the import or export of metabolites, the homeostasis of metal ions, the extrusion of toxic substances or antibiotics, and the generation or conversion of energy. The last years have witnessed completion of a plethora of whole-genome sequences of bacteria important for biotechnology or medicine, which is the foundation for proteome and other functional genome analyses. In this review, we discuss the challenges in membrane proteome analysis, starting from sample preparation and leading to MS-data analysis and quantification. The current state of available proteomics technologies as well as their advantages and disadvantages will be described with a focus on shotgun proteomics. Then, we will briefly introduce the most abundant proteins and protein families present in bacterial membranes before bacterial membrane proteomics studies of the last years will be presented. It will be shown how these works enlarged our knowledge about the physiological adaptations that take place in bacteria during fine chemical production, bioremediation, protein overexpression, and during infections. Furthermore, several examples from literature demonstrate the suitability of membrane proteomics for the identification of antigens and different pathogenic strains, as well as the elucidation of membrane protein structure and function.

Pyteomics--a Python framework for exploratory data analysis and rapid software prototyping in proteomics.

Science.gov (United States)

Goloborodko, Anton A; Levitsky, Lev I; Ivanov, Mark V; Gorshkov, Mikhail V

2013-02-01

Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index http://pypi.python.org/pyteomics, the source code repository at http://hg.theorchromo.ru/pyteomics, documentation at http://packages.python.org/pyteomics. Pyteomics.biolccc documentation is available at http://packages.python.org/pyteomics.biolccc/. Questions on installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com.

Addressing issues raised by stakeholders in the development of a deep geological repository in the Czech Republic

International Nuclear Information System (INIS)

Sumberova, Vera

2004-01-01

The mission of the Radioactive Waste Repository Authority (RAWRA) is to ensure the safe disposal of all existing and future radioactive waste. In order to fulfil this task RAWRA, in addition to the operation of radioactive waste repositories in the Czech Republic, coordinates all those activities relating to the construction of a deep geological repository. This long-term goal implies first creating and then building upon the public's confidence in the decision making process and the project as a whole as well as in RAWRA as a competent and efficient implementer since clearly public acceptance is an essential condition for a successful final outcome. Since its establishment in 1997 RAWRA has been looking for ways in which to inform the public about its activities and how to involve the various stakeholders in the development process. The communication tools employed to achieve this goal have, to date, depended on the specific stage of the process but RAWRA has aimed at a continuous improvement in its activities; consequently a large number of changes have been made to RAWRA's policy and approach in recent years. This paper, which aims to describe RAWRA's dialogue with stakeholders (mainly local communities), provides examples of the way in which issues raised by stakeholders concerning a repository are reflected in RAWRA's approach. (author)

INSTITUTIONAL REPOSITORY: EMPLOYMENT IN EDUCATION

Directory of Open Access Journals (Sweden)

Vasyl P. Oleksyuk

2012-11-01

Full Text Available The article investigated the concept of «institutional repository» and determined the aspects of institutional repositories in higher education. Institutional Repositories are information systems that allow preserving, storing and disseminating scientific knowledge produced in higher education and scientific research institutions. This study presented the main aspects using institutional repositories in educational process (such as storage of scientific and educational information, means of organization activity of students, object of studying. This article produced the structure of communities and collections of the institutional. It is described the experience of implementing of DSpace in the learning process.

Thermal Management and Analysis for a Potential Yucca Mountain Repository

International Nuclear Information System (INIS)

Dr. A. Van Luik

2004-01-01

includes a summary of the technical basis that supports these evaluations. The majority of the material presented here is summarized from the Yucca Mountain Science and Engineering Report [l]. A companion paper in this publication entitled ''Characterizing the Evolution of the In-Drift Environment in a Proposed Yucca Mountain Repository'' schematically illustrates the processes being controlled through the management of thermal loading in its Figure 3

Trust in Digital Repositories

Directory of Open Access Journals (Sweden)

Elizabeth Yakel

2013-06-01

Full Text Available ISO 16363:2012, Space Data and Information Transfer Systems - Audit and Certification of Trustworthy Digital Repositories (ISO TRAC, outlines actions a repository can take to be considered trustworthy, but research examining whether the repository’s designated community of users associates such actions with trustworthiness has been limited. Drawing from this ISO document and the management and information systems literatures, this paper discusses findings from interviews with 66 archaeologists and quantitative social scientists. We found similarities and differences across the disciplines and among the social scientists. Both disciplinary communities associated trust with a repository’s transparency. However, archaeologists mentioned guarantees of preservation and sustainability more frequently than the social scientists, who talked about institutional reputation. Repository processes were also linked to trust, with archaeologists more frequently citing metadata issues and social scientists discussing data selection and cleaning processes. Among the social scientists, novices mentioned the influence of colleagues on their trust in repositories almost twice as much as the experts. We discuss the implications our findings have for identifying trustworthy repositories and how they extend the models presented in the management and information systems literatures.

Proteomics reveals the effects of sustained weight loss on the human plasma proteome

DEFF Research Database (Denmark)

Geyer, Philipp E; Wewer Albrechtsen, Nicolai J; Tyanova, Stefka

2016-01-01

Sustained weight loss is a preferred intervention in a wide range of metabolic conditions, but the effects on an individual's health state remain ill-defined. Here, we investigate the plasma proteomes of a cohort of 43 obese individuals that had undergone 8 weeks of 12% body weight loss followed...... by a year of weight maintenance. Using mass spectrometry-based plasma proteome profiling, we measured 1,294 plasma proteomes. Longitudinal monitoring of the cohort revealed individual-specific protein levels with wide-ranging effects of losing weight on the plasma proteome reflected in 93 significantly...

Translational plant proteomics: a perspective.

Science.gov (United States)

Agrawal, Ganesh Kumar; Pedreschi, Romina; Barkla, Bronwyn J; Bindschedler, Laurence Veronique; Cramer, Rainer; Sarkar, Abhijit; Renaut, Jenny; Job, Dominique; Rakwal, Randeep

2012-08-03

Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic values of plants, food security and safety, and energy sustainability. In this review, we highlight the substantial progress reached in plant proteomics during the past decade which has paved the way for translational plant proteomics. Increasing proteomics knowledge in plants is not limited to model and non-model plants, proteogenomics, crop improvement, and food analysis, safety, and nutrition but to many more potential applications. Given the wealth of information generated and to some extent applied, there is the need for more efficient and broader channels to freely disseminate the information to the scientific community. This article is part of a Special Issue entitled: Translational Proteomics. Copyright © 2012 Elsevier B.V. All rights reserved.

The network to review natural analogue studies and their applications to repository safety assessment and public communication (NAnet)

Energy Technology Data Exchange (ETDEWEB)

Miller, W.M.; Hooker, P.J. [ENVIROS Consulting ltd, 61, the Shore Leith, UK-0 EH6 6RA Edinburgh (United Kingdom)

2004-07-01

Analogue information can increase our conceptual understanding of long-term repository behaviour in support of post-closure performance assessment (PA), provide quantitative data for PA models and provide ways of communicating safety information to non-specialist audiences. These functions of analogue studies have, however, received too little attention in PA reports and safety cases. Many analogue studies have been undertaken in the last two decades costing tens of millions of euros, and these have covered a wide range of phenomena such as uranium ore deposition, natural fission reactors, natural nuclide migration, contaminant containment by clays and sediments, preservation of ancient fossil trees and buried artefacts etc. The different uses of analogues would be easier to manage if a single database of quality approved analogue information were to be created. NAnet, a Thematic Network within the 5. EURATOM FP is aiming to promote more considered applications of analogues in performance and safety assessments and in audience dialogue. NAnet intends critically to review a number of analogue studies in terms of their relevance and limitations to different repository concepts and environments and with regard to their applications in performance assessments, safety cases and communication. On the basis of these reviews, a simple digital database is being developed for the PA community which will allow PA modelers to make quicker and wider use of natural analogue information in performance and safety assessments. It is expected that some of these tools will help radioactive waste institutions to make better use of natural analogue information for communication with different audiences, including the public. (authors)

Application of Proteomics to Cancer Molecular Diagnostics

Institute of Scientific and Technical Information of China (English)

Sam HANASH

2009-01-01

@@ Strategies to achieve personalized medicine and improve public health encompass assessment of an individual's risk for disease, early detection and molecular classification of disease resulting in an informed choice of the most appropriate treatment instituted at an early stage of disease develop- ment. A major contribution of proteomics in this field is the development of blood based tests to achieve the goals of personalized medicine.

Process mining software repositories

NARCIS (Netherlands)

Poncin, W.; Serebrenik, A.; Brand, van den M.G.J.

2011-01-01

Software developers' activities are in general recorded in software repositories such as version control systems, bug trackers and mail archives. While abundant information is usually present in such repositories, successful information extraction is often challenged by the necessity to

The Ec prototype repository project: implications of assessments for refining repository design

International Nuclear Information System (INIS)

Svemar, C.

2004-01-01

The most important issue in the evaluation of the repository performance is the long term safety of the repository. Analyses for this issue focuses on the 'steady state' conditions which start at the time when the repository has been saturated and the groundwater table returned to its normal level. The bentonite buffer around the canisters is saturated and homogeneous, and the canister is located exactly in the centre of the buffer. The backfill in the tunnel has been saturated as well and fills the earlier open spaces in the tunnel completely. The task of the activities taking places prior to the start of the 'steady state' conditions, like excavation, deposition, backfilling and sealing, with due consideration to the processes a consequences they may cause in the long run, is to provide for these 'ideal' conditions, as close as possible. While studying these activities in detail it has become obvious that development of methods and techniques needs to be carefully addressed before the decision is made on how to apply them in the repository. One general finding is that the situation in engineering of details is not that much different from the situation in geological characterisation of a site in detail; one more detail of engineering and the consequences it brings often complicates the situation rather than supports the solution prioritized so far. Many of the practical issues have been studied in the Prototype Repository project in the AEspoe Hard Rock Laboratory (Pusch et al., 2000). The Prototype Repository consists of two sections with four respectively two deposition holes with bentonite buffer and canister, the latter holding electrical heaters. The sections are separated by a concrete plug, and the whole test is to be separated from the rest of the laboratory by an outer plug. The project has two objectives: 1. To demonstrate the integrated function of tile deep repository components under realistic conditions and to compare results with models and

Croatian repository construction project - present status and main obstacles

International Nuclear Information System (INIS)

Kucar Dragicevic, S.; Subasic, D.; Schaller, A.; Lokner, V.; Cerskov Klika, M.

1999-01-01

Croatia has been preparing backgrounds for the construction of the repository for low and intermediate radioactive waste on its territory, almost for a decade, now. In the name of Hrvtaska elektroprivreda, the co-owner of the NE Krsko, APO has been co-ordinating and organising numerous activities and projects during that time period. Siting process, safety assessment, disposal technology and repository design and public acceptance issues are the main fields of activities. The overall status of the project at the moment, including the overview of the present status of the main four aspects of activities, will be presented. Relatively, big and important progress made on the project work out during the last two years, as well as the main obstacles we were faced with during that time period, will be discussed.(author)

Integrated management system for radioactive waste repositories (SGI3R)

International Nuclear Information System (INIS)

Silva, Fabio; Tello, Cledola Cassia Oliveira de

2009-01-01

The implantation of a repository for radioactive wastes is a multidisciplinary project that needs specialists of different areas of knowledge, interaction with public and private institutions, data and information related to radioactive wastes, geology, technology etc. All the activities must be in accordance with norms, requirements and procedures, including national and international legislation. The maintenance of the waste inventory records is an important regulatory requirement and must be available even after the closure of the repository. CDTN - Center of Nuclear Technology Development - is coordinating the Project for the construction of the national repository to dispose the low -and intermediate-level wastes. In order to consolidate all information that will come from this Project, it is being developed and implanted in CDTN a manager system of database, called Integrated Management System for Radioactive Waste Repositories (SGI3R), which will also manage all data from previous work carried out in Brazil and around the world about this subject. The proposal is to build a structure of modules, having as base eight modules: inventory, site selection, types of repository, technology, partners, legislation, communication and documents. The SGI3R running comprises the data processing (inclusion, update and exclusion), integration, standardization, and consistency among the processes. The SGI3R will give support to the stages of this Project, which will allow the preservation of all the available information, preventing duplication of efforts and additional costs, improving, in this way, the Project planning and execution. Additionally the SGI3R will make possible the information access to all stakeholders. (author)

48 CFR 227.7108 - Contractor data repositories.

Science.gov (United States)

2010-10-01

... repositories. 227.7108 Section 227.7108 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS... Technical Data 227.7108 Contractor data repositories. (a) Contractor data repositories may be established when permitted by agency procedures. The contractual instrument establishing the data repository must...

Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow

Directory of Open Access Journals (Sweden)

Toda Tosifusa

2006-10-01

Full Text Available Abstract Background In the post-genome era, most research scientists working in the field of proteomics are confronted with difficulties in management of large volumes of data, which they are required to keep in formats suitable for subsequent data mining. Therefore, a well-developed open source laboratory information management system (LIMS should be available for their proteomics research studies. Results We developed an open source LIMS appropriately customized for 2-D gel electrophoresis-based proteomics workflow. The main features of its design are compactness, flexibility and connectivity to public databases. It supports the handling of data imported from mass spectrometry software and 2-D gel image analysis software. The LIMS is equipped with the same input interface for 2-D gel information as a clickable map on public 2DPAGE databases. The LIMS allows researchers to follow their own experimental procedures by reviewing the illustrations of 2-D gel maps and well layouts on the digestion plates and MS sample plates. Conclusion Our new open source LIMS is now available as a basic model for proteome informatics, and is accessible for further improvement. We hope that many research scientists working in the field of proteomics will evaluate our LIMS and suggest ways in which it can be improved.

Decision-Making Risks Concerning the Construction of the Goiania Waste Repository

Energy Technology Data Exchange (ETDEWEB)

Paschoa, A.S. [Pontificia Univ. Catolica, Rio de Janeiro (Brazil); Rozental, J.J. [Ministry of Environment (Israel); Tranjan Filho, A. [Comissao Nacional de Energia Nuclear (CNEN) (Brazil)

2001-07-01

As it is well known, an accident with a teletherapy source made of {sup 137}CsCl with an initial activity of 59 TBq occurred in Goiania, in September of 1987. This paper will discuss the decision-making process, and the struggle that followed the decision to build the final repository for the remnants of the Goiania accident. The Goiania final repository was built as planned. The two subsurface structures under the grassy artificial hills hold the overall volume of the remnants of the Goiania accident. The near hill holds 5x10{sup 3} m3 of stabilized wastes without radioactivity, or with very low radioactivity. The far hill holds the remaining 6.5x10{sup 3} m{sup 3} of stabilized wastes with low and medium radioactivity. The central part of each subsurface hill has been shielded by wastes with less and less radioactivity. The overall fenced area occupies 1.85x10{sup 5} m{sup 2}. The external radiation levels are similar to the surrounding background, and much lower than those found in the Brazilian areas of high natural radioactivity. The site is permanently monitored by independent institutions, including Brazilian universities, and national and international organizations. As it was mentioned earlier, the final repository was build to last for at least 400 years. Although the initial decision to adopt a too conservative decontamination criterion in the case of the Goiania accident was bound to produce excessive amount of waste; such decision proved, retrospectively, not to be bad because the excess low radioactive waste produced was used as extra shielding material in final repository. The technical decision-maker should not abandon risk estimates, but should be aware that credibility is the main basis to achieve acceptability of a decision by the general public. Risk perception should be regarded as only a first step towards what may be called knowledge, or comprehension of risk estimates, but risk perception by the general public is still an open issue. The

[Self-archiving of biomedical papers in open access repositories].

Science.gov (United States)

Abad-García, M Francisca; Melero, Remedios; Abadal, Ernest; González-Teruel, Aurora

2010-04-01

Open-access literature is digital, online, free of charge, and free of most copyright and licensing restrictions. Self-archiving or deposit of scholarly outputs in institutional repositories (open-access green route) is increasingly present in the activities of the scientific community. Besides the benefits of open access for visibility and dissemination of science, it is increasingly more often required by funding agencies to deposit papers and any other type of documents in repositories. In the biomedical environment this is even more relevant by the impact scientific literature can have on public health. However, to make self-archiving feasible, authors should be aware of its meaning and the terms in which they are allowed to archive their works. In that sense, there are some tools like Sherpa/RoMEO or DULCINEA (both directories of copyright licences of scientific journals at different levels) to find out what rights are retained by authors when they publish a paper and if they allow to implement self-archiving. PubMed Central and its British and Canadian counterparts are the main thematic repositories for biomedical fields. In our country there is none of similar nature, but most of the universities and CSIC, have already created their own institutional repositories. The increase in visibility of research results and their impact on a greater and earlier citation is one of the most frequently advance of open access, but removal of economic barriers to access to information is also a benefit to break borders between groups.

Evaluation of the Overall Costs for the Croatian Repository: Varying Site, Design and Financial Parameters

International Nuclear Information System (INIS)

Kucar-Dragicevic, S.; Subasic, D.; Lebegner, J.

2000-01-01

Preliminary preparations for the construction of a LILW repository in Croatia included a number of activities and projects related to the siting process, safety assessment, disposal technology and repository design, and public acceptance issues. Costs evaluations have always been a part of the developing project documentation. However, only the estimates of the facility construction and equipment acquisition costs had been included, while other costs associated with the project development and management have not been considered up to now. For the first time the infrastructure status at the potential sites has been evaluated, and the costs of the repository operations as well as the post-closure management has been estimated. Cost parameters have been considered from both technical and fiscal points of view, comparing their relative influence on the overall repository costs. Assessment of the total project costs in eight cases for the four preferential sites and two repository designs gave a clearer picture of the development and management costs differences for the considered options. Without considerations of the operational and post-operational repository management expenses, the total project costs appear to have been heavily underestimated. Also, while the construction costs for the tunnel and the surface type repositories are significantly different, this influence of the repository type on the total project costs becomes far less important when the later phases management expenses are added. Finally, the role of fiscal parameters may further diminish the site and technology impacts on the overall costs. (author)

Collaborative Data Publication Utilizing the Open Data Repository's (ODR) Data Publisher

Science.gov (United States)

Stone, N.; Lafuente, B.; Bristow, T.; Keller, R. M.; Downs, R. T.; Blake, D.; Fonda, M.; Dateo, C.; Pires, A.

2017-01-01

Introduction: For small communities in diverse fields such as astrobiology, publishing and sharing data can be a difficult challenge. While large, homogenous fields often have repositories and existing data standards, small groups of independent researchers have few options for publishing standards and data that can be utilized within their community. In conjunction with teams at NASA Ames and the University of Arizona, the Open Data Repository's (ODR) Data Publisher has been conducting ongoing pilots to assess the needs of diverse research groups and to develop software to allow them to publish and share their data collaboratively. Objectives: The ODR's Data Publisher aims to provide an easy-to-use and implement software tool that will allow researchers to create and publish database templates and related data. The end product will facilitate both human-readable interfaces (web-based with embedded images, files, and charts) and machine-readable interfaces utilizing semantic standards. Characteristics: The Data Publisher software runs on the standard LAMP (Linux, Apache, MySQL, PHP) stack to provide the widest server base available. The software is based on Symfony (www.symfony.com) which provides a robust framework for creating extensible, object-oriented software in PHP. The software interface consists of a template designer where individual or master database templates can be created. A master database template can be shared by many researchers to provide a common metadata standard that will set a compatibility standard for all derivative databases. Individual researchers can then extend their instance of the template with custom fields, file storage, or visualizations that may be unique to their studies. This allows groups to create compatible databases for data discovery and sharing purposes while still providing the flexibility needed to meet the needs of scientists in rapidly evolving areas of research. Research: As part of this effort, a number of ongoing

National Radwaste Repository Mochovce

International Nuclear Information System (INIS)

2000-01-01

In this leaflet the National Radioactive Waste Repository in Mochovce (Repository) is described. The Mochovce National Radioactive Waste Repository is a surface multi-barrier type storage facility for solid and treated solidified radioactive wastes generated from the Slovak Republic nuclear power plants operation and decommissioning, research institutes, laboratories and hospitals. The Repository comprises a system of single- and double-row storage boxes. The first double-row is enclosed by a steel-structure building. The 18 x 6 x 5.5 m storage boxes are made of reinforced concrete. The wall thickness is 600 mm. Two-double-rows, i.e. 80 storage boxes were built as part of Stage I (1 row = 20 storage boxes). Each storage box has a storage capacity of 90 fibre concrete containers of 3.1 m 3 volume. The total storage capacity is 7200 containers with the overall storage volume of 22320 m 3

Analysis of Turkey’s Institutional Open Repositories: An Example of Dokuz Eylül University Institutional Open Repository

Directory of Open Access Journals (Sweden)

Korhan Levent Ertürk

2012-03-01

Full Text Available After the declaration of the Budapest Open Access Initiative in 2001, institutional open repositories are known as the most important tool of the self archiving, which is also known as green road. There are 26 institutional repositories, which are all compatible to international standards. All the institutional open repositories of Turkey mentioned before are listed in international open archive directories. In this study institutional open repository of Dokuz Eylül University is examined and institutional open repositories of Turkey are discussed.

Progress and challenges for abiotic stress proteomics of crop plants.

Science.gov (United States)

Barkla, Bronwyn J; Vera-Estrella, Rosario; Pantoja, Omar

2013-06-01

Plants are continually challenged to recognize and respond to adverse changes in their environment to avoid detrimental effects on growth and development. Understanding the mechanisms that crop plants employ to resist and tolerate abiotic stress is of considerable interest for designing agriculture breeding strategies to ensure sustainable productivity. The application of proteomics technologies to advance our knowledge in crop plant abiotic stress tolerance has increased dramatically in the past few years as evidenced by the large amount of publications in this area. This is attributed to advances in various technology platforms associated with MS-based techniques as well as the accessibility of proteomics units to a wider plant research community. This review summarizes the work which has been reported for major crop plants and evaluates the findings in context of the approaches that are widely employed with the aim to encourage broadening the strategies used to increase coverage of the proteome. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Radioactive waste repository of high ecological safety

International Nuclear Information System (INIS)

Sobolev, I.; Barinov, A.; Prozorov, L.

2000-01-01

With the purpose to construct a radioactive waste repository of high ecological safety and reliable containment, MosNPO 'Radon' specialists have developed an advanced type repository - large diameter well (LBD) one. A project is started for the development of a technology for LDW repository construction and pilot operation of the new repository for 25-30 years. The 2 LDW repositories constructed at the 'Radon' site and the developed monitoring system are described

Consistency analysis of network traffic repositories

NARCIS (Netherlands)

Lastdrager, Elmer; Lastdrager, E.E.H.; Pras, Aiko

Traffic repositories with TCP/IP header information are very important for network analysis. Researchers often assume that such repositories reliably represent all traffic that has been flowing over the network; little thoughts are made regarding the consistency of these repositories. Still, for

Sellafield repository design concept

International Nuclear Information System (INIS)

1998-01-01

Between 1989 and 1997, UK Nirex Ltd carried out a programme of investigations to evaluate the potential of a site adjacent to the BNFL Sellafield works to host a deep repository for the United Kingdom's intermediate-level and certain low-level radioactive waste. The programme of investigations was wound down following the decision in March 1997 to uphold the rejection of the Company's planning application for the Rock Characterisation Facility (RCF), an underground laboratory which would have allowed further investigations to confirm whether or not the site would be suitable. Since that time, the Company's efforts in relation to the Sellafield site have been directed towards documenting and publishing the work carried out. The design concept for a repository at Sellafield was developed in parallel with the site investigations through an iterative process as knowledge of the site and understanding of the repository system performance increased. This report documents the Sellafield repository design concept as it had been developed, from initial design considerations in 1991 up to the point when the RCF planning application was rejected. It shows, from the context of a project at that particular site, how much information and experience has been gained that will be applicable to the development of a deep waste repository at other potential sites

Design, construction, operation, shutdown and surveillance of repositories for solid radioactive wastes in shallow ground

International Nuclear Information System (INIS)

1984-01-01

This report is a part of the IAEA publications under its Programme on Underground Disposal of Radioactive Wastes and is addressed to administrative and technical authorities and specialists who consider the shallow-ground disposal of low- and intermediate-level solid radioactive wastes of short half-lives. The report emphasizes the technological aspects, however it briefly discusses the safety philosophy and regulatory considerations too. The design, construction, operation, shutdown and surveillance of the repositories in shallow ground are considered in some detail, paying special attention to their interrelated aspects. In particular, a review is given of the following aspects: main design and construction considerations in relation to the natural features of the site; design and construction aspects during the repository development process; activities related to operational and post-operational stages of the repository; major steps in repository operation and essential activities in shutdown and operational and post-operational surveillance

Construction of First Phase of Spent Fuel Repository in Finland: Lessons Learned and Success Factors

International Nuclear Information System (INIS)

Varjoranta, T.; Paltemaa, R.

2015-01-01

The Finnish nuclear legislation defines spent fuel as nuclear waste and requires that it has to be disposed of in the Finnish bedrock. Over 30 years of systematic R&D has been carried out to develop the repository concept, site selection, technologies, safety assessment and the regulatory approach. Activities are based on the Finnish Government’s long term strategies since 1983 and the public acceptance at local, Governmental and Parliament levels, approved and documented in the legal “Decision in Principle” (DiP) in 2000 to locate the repository at Olkiluoto. The DiP provided authorization to construct the first phase of the repository to the depth of the planned disposal. The construction of the 1 st phase of the repository started 2004 and has now reached the depth of 407 m. This paper identifies and discusses lessons learned and key success factors of the progress made. (author)

Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles)

DEFF Research Database (Denmark)

Kinsinger, Christopher R.; Apffel, James; Baker, Mark

2011-01-01

and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the United States National Cancer Institute convened the "International Workshop on Proteomic Data Quality Metrics" in Sydney, Australia, to identify and address issues facing the development and use......Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development...... of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed...

Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles)

DEFF Research Database (Denmark)

Kinsinger, Christopher R.; Apffel, James; Baker, Mark

2012-01-01

and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the United States National Cancer Institute convened the "International Workshop on Proteomic Data Quality Metrics" in Sydney, Australia, to identify and address issues facing the development and use......Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development...... of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed...

Transcriptome and proteomic analysis of mango (Mangifera indica Linn) fruits.

Science.gov (United States)

Wu, Hong-xia; Jia, Hui-min; Ma, Xiao-wei; Wang, Song-biao; Yao, Quan-sheng; Xu, Wen-tian; Zhou, Yi-gang; Gao, Zhong-shan; Zhan, Ru-lin

2014-06-13

Here we used Illumina RNA-seq technology for transcriptome sequencing of a mixed fruit sample from 'Zill' mango (Mangifera indica Linn) fruit pericarp and pulp during the development and ripening stages. RNA-seq generated 68,419,722 sequence reads that were assembled into 54,207 transcripts with a mean length of 858bp, including 26,413 clusters and 27,794 singletons. A total of 42,515(78.43%) transcripts were annotated using public protein databases, with a cut-off E-value above 10(-5), of which 35,198 and 14,619 transcripts were assigned to gene ontology terms and clusters of orthologous groups respectively. Functional annotation against the Kyoto Encyclopedia of Genes and Genomes database identified 23,741(43.79%) transcripts which were mapped to 128 pathways. These pathways revealed many previously unknown transcripts. We also applied mass spectrometry-based transcriptome data to characterize the proteome of ripe fruit. LC-MS/MS analysis of the mango fruit proteome was using tandem mass spectrometry (MS/MS) in an LTQ Orbitrap Velos (Thermo) coupled online to the HPLC. This approach enabled the identification of 7536 peptides that matched 2754 proteins. Our study provides a comprehensive sequence for a systemic view of transcriptome during mango fruit development and the most comprehensive fruit proteome to date, which are useful for further genomics research and proteomic studies. Our study provides a comprehensive sequence for a systemic view of both the transcriptome and proteome of mango fruit, and a valuable reference for further research on gene expression and protein identification. This article is part of a Special Issue entitled: Proteomics of non-model organisms. Copyright © 2014 Elsevier B.V. All rights reserved.

[Methods of quantitative proteomics].

Science.gov (United States)

Kopylov, A T; Zgoda, V G

2007-01-01

In modern science proteomic analysis is inseparable from other fields of systemic biology. Possessing huge resources quantitative proteomics operates colossal information on molecular mechanisms of life. Advances in proteomics help researchers to solve complex problems of cell signaling, posttranslational modification, structure and functional homology of proteins, molecular diagnostics etc. More than 40 various methods have been developed in proteomics for quantitative analysis of proteins. Although each method is unique and has certain advantages and disadvantages all these use various isotope labels (tags). In this review we will consider the most popular and effective methods employing both chemical modifications of proteins and also metabolic and enzymatic methods of isotope labeling.

Proteomic analysis of post translational modifications in cyanobacteria.

Science.gov (United States)

Xiong, Qian; Chen, Zhuo; Ge, Feng

2016-02-16

Cyanobacteria are a diverse group of Gram-negative bacteria and the only prokaryotes capable of oxygenic photosynthesis. Recently, cyanobacteria have attracted great interest due to their crucial roles in global carbon and nitrogen cycles and their ability to produce clean and renewable biofuels. To survive in various environmental conditions, cyanobacteria have developed a complex signal transduction network to sense environmental signals and implement adaptive changes. The post-translational modifications (PTMs) systems play important regulatory roles in the signaling networks of cyanobacteria. The systematic investigation of PTMs could contribute to the comprehensive description of protein species and to elucidate potential biological roles of each protein species in cyanobacteria. Although the proteomic studies of PTMs carried out in cyanobacteria were limited, these data have provided clues to elucidate their sophisticated sensing mechanisms that contribute to their evolutionary and ecological success. This review aims to summarize the current status of PTM studies and recent publications regarding PTM proteomics in cyanobacteria, and discuss the novel developments and applications for the analysis of PTMs in cyanobacteria. Challenges, opportunities and future perspectives in the proteomics studies of PTMs in cyanobacteria are also discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

Translational plant proteomics: A perspective

NARCIS (Netherlands)

Agrawal, G.K.; Pedreschi, R.; Barkla, B.J.; Bindschedler, L.V.; Cramer, R.; Sarkar, A.; Renaut, J.; Job, D.; Rakwal, R.

2012-01-01

Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic

Evolution of Clinical Proteomics and its Role in Medicine | Office of Cancer Clinical Proteomics Research

Science.gov (United States)

NCI's Office of Cancer Clinical Proteomics Research authored a review of the current state of clinical proteomics in the peer-reviewed Journal of Proteome Research. The review highlights outcomes from the CPTC program and also provides a thorough overview of the different technologies that have pushed the field forward. Additionally, the review provides a vision for moving the field forward through linking advances in genomic and proteomic analysis to develop new, molecularly targeted interventions.

Harvesting Statistical Metadata from an Online Repository for Data Analysis and Visualization : Concept Application on Theseus

OpenAIRE

Gebresilassie, Sem

2014-01-01

Theses and publications from Finnish universities of applied sciences are accessible from an open online repository called Theseus. This repository has an application programming interface (API) that provides tools for harvesting its contents. By properly utilizing this API, it is possible to gather and reuse metadata of thesis documents for any other objective. This thesis mainly intends to explain how to gather the author name, title, submission year, keywords, subjects, department, u...

Microbial proteomics: a mass spectrometry primer for biologists

Directory of Open Access Journals (Sweden)

Graham Ciaren

2007-08-01

Full Text Available Abstract It is now more than 10 years since the publication of the first microbial genome sequence and science is now moving towards a post genomic era with transcriptomics and proteomics offering insights into cellular processes and function. The ability to assess the entire protein network of a cell at a given spatial or temporal point will have a profound effect upon microbial science as the function of proteins is inextricably linked to phenotype. Whilst such a situation is still beyond current technologies rapid advances in mass spectrometry, bioinformatics and protein separation technologies have produced a step change in our current proteomic capabilities. Subsequently a small, but steadily growing, number of groups are taking advantage of this cutting edge technology to discover more about the physiology and metabolism of microorganisms. From this research it will be possible to move towards a systems biology understanding of a microorganism. Where upon researchers can build a comprehensive cellular map for each microorganism that links an accurately annotated genome sequence to gene expression data, at a transcriptomic and proteomic level. In order for microbiologists to embrace the potential that proteomics offers, an understanding of a variety of analytical tools is required. The aim of this review is to provide a basic overview of mass spectrometry (MS and its application to protein identification. In addition we will describe how the protein complexity of microbial samples can be reduced by gel-based and gel-free methodologies prior to analysis by MS. Finally in order to illustrate the power of microbial proteomics a case study of its current application within the Bacilliaceae is given together with a description of the emerging discipline of metaproteomics.

Nuclear waste repository design and construction

International Nuclear Information System (INIS)

Bohlke, B.M.; Monsees, J.E.

1987-01-01

Extensive underground excavation will be required for construction of a mined geologic repository for nuclear waste. Hundreds of thousands of feet of drift will be required based on the conceptual layout design for each candidate nuclear waste repository. Comparison of boring and blasting excavation methods are discussed, as are special design and construction requirements (e.g., quality assurance procedures and performance assessment) for the nuclear waste repository. Comparisons are made between boring and blasting construction methods for the repository designs proposed for salt, volcanic tuff, and basalt

Proteomics of Maize Root Development.

Science.gov (United States)

Hochholdinger, Frank; Marcon, Caroline; Baldauf, Jutta A; Yu, Peng; Frey, Felix P

2018-01-01

Maize forms a complex root system with structurally and functionally diverse root types that are formed at different developmental stages to extract water and mineral nutrients from soil. In recent years proteomics has been intensively applied to identify proteins involved in shaping the three-dimensional architecture and regulating the function of the maize root system. With the help of developmental mutants, proteomic changes during the initiation and emergence of shoot-borne, lateral and seminal roots have been examined. Furthermore, root hairs were surveyed to understand the proteomic changes during the elongation of these single cell type structures. In addition, primary roots have been used to study developmental changes of the proteome but also to investigate the proteomes of distinct tissues such as the meristematic zone, the elongation zone as well as stele and cortex of the differentiation zone. Moreover, subcellular fractions of the primary root including cell walls, plasma membranes and secreted mucilage have been analyzed. Finally, the superior vigor of hybrid seedling roots compared to their parental inbred lines was studied on the proteome level. In summary, these studies provide novel insights into the complex proteomic interactions of the elaborate maize root system during development.

Proteomics of Maize Root Development

Directory of Open Access Journals (Sweden)

Frank Hochholdinger

2018-03-01

Full Text Available Maize forms a complex root system with structurally and functionally diverse root types that are formed at different developmental stages to extract water and mineral nutrients from soil. In recent years proteomics has been intensively applied to identify proteins involved in shaping the three-dimensional architecture and regulating the function of the maize root system. With the help of developmental mutants, proteomic changes during the initiation and emergence of shoot-borne, lateral and seminal roots have been examined. Furthermore, root hairs were surveyed to understand the proteomic changes during the elongation of these single cell type structures. In addition, primary roots have been used to study developmental changes of the proteome but also to investigate the proteomes of distinct tissues such as the meristematic zone, the elongation zone as well as stele and cortex of the differentiation zone. Moreover, subcellular fractions of the primary root including cell walls, plasma membranes and secreted mucilage have been analyzed. Finally, the superior vigor of hybrid seedling roots compared to their parental inbred lines was studied on the proteome level. In summary, these studies provide novel insights into the complex proteomic interactions of the elaborate maize root system during development.

Technical, institutional and economic factors important for developing a multinational radioactive waste repository

International Nuclear Information System (INIS)

1998-06-01

Countries planning and implementing nuclear energy programmes should assume responsibility for the safe management and final disposal of radioactive waste from their programmes. However, there are countries whose radioactive waste volumes do not easily justify a national repository, and/or countries which do not have the resources or favorable natural conditions for waste disposal to dedicate to a national repository project. These countries would benefit from multinational co-operation for the disposal. Interest in the concept of a multinational repository for radioactive waste has been expressed by several Member States and the waste management community in the light of the potential benefit to the partner countries from the safety, technical and economic standpoints. However, such an approach involves many political and public acceptance issues and therefore a consensus among countries or regions concerned is a prerequisite. In this context, it was deemed appropriate that the IAEA access the technical, institutional, ethical and economic factors to be taken into account in the process of such consensus building. This report is intended to provide an assessment which can serve as a general basis for establishing a waste management policy and/or further assessing specific issues such as ownership and liability, institutional aspects and problems related to long term commitments. This report is divided into five sections where the first section gives background, objectives, scope and structure of the report. Section 2 discusses multinational repository concept in terms of needs and the role of a multinational repository, interaction between host and partner countries and formulation of a multinational repository. Section 3 identifies basic issues to be considered for establishing a multinational repository, and some specific issues relating to specific waste categories. Section 4 analyses potential benefits and challenges to be addresses in establishing a

National radioactive wasterRepository Mochovce

International Nuclear Information System (INIS)

2000-01-01

In this leaflet the scheme of the Mochovce National radioactive waste repository for the Slovak Republic is presented. The National radioactive waste repository in Mochovce is a surface type storage facility. It is intended for final disposal of solid and solidified low and intermediate radioactive waste produced during the operation of nuclear power plants and institutions located within the territory of the Slovak Republic. The Repository site is situated about 2 km northwest to the Mochovce NPP

Integrating cell biology and proteomic approaches in plants.

Science.gov (United States)

Takáč, Tomáš; Šamajová, Olga; Šamaj, Jozef

2017-10-03

Significant improvements of protein extraction, separation, mass spectrometry and bioinformatics nurtured advancements of proteomics during the past years. The usefulness of proteomics in the investigation of biological problems can be enhanced by integration with other experimental methods from cell biology, genetics, biochemistry, pharmacology, molecular biology and other omics approaches including transcriptomics and metabolomics. This review aims to summarize current trends integrating cell biology and proteomics in plant science. Cell biology approaches are most frequently used in proteomic studies investigating subcellular and developmental proteomes, however, they were also employed in proteomic studies exploring abiotic and biotic stress responses, vesicular transport, cytoskeleton and protein posttranslational modifications. They are used either for detailed cellular or ultrastructural characterization of the object subjected to proteomic study, validation of proteomic results or to expand proteomic data. In this respect, a broad spectrum of methods is employed to support proteomic studies including ultrastructural electron microscopy studies, histochemical staining, immunochemical localization, in vivo imaging of fluorescently tagged proteins and visualization of protein-protein interactions. Thus, cell biological observations on fixed or living cell compartments, cells, tissues and organs are feasible, and in some cases fundamental for the validation and complementation of proteomic data. Validation of proteomic data by independent experimental methods requires development of new complementary approaches. Benefits of cell biology methods and techniques are not sufficiently highlighted in current proteomic studies. This encouraged us to review most popular cell biology methods used in proteomic studies and to evaluate their relevance and potential for proteomic data validation and enrichment of purely proteomic analyses. We also provide examples of

Biological Web Service Repositories Review.

Science.gov (United States)

Urdidiales-Nieto, David; Navas-Delgado, Ismael; Aldana-Montes, José F

2017-05-01

Web services play a key role in bioinformatics enabling the integration of database access and analysis of algorithms. However, Web service repositories do not usually publish information on the changes made to their registered Web services. Dynamism is directly related to the changes in the repositories (services registered or unregistered) and at service level (annotation changes). Thus, users, software clients or workflow based approaches lack enough relevant information to decide when they should review or re-execute a Web service or workflow to get updated or improved results. The dynamism of the repository could be a measure for workflow developers to re-check service availability and annotation changes in the services of interest to them. This paper presents a review on the most well-known Web service repositories in the life sciences including an analysis of their dynamism. Freshness is introduced in this paper, and has been used as the measure for the dynamism of these repositories. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Rhode Island crystalline repository siting project: Technical progress report, Calendar year 1986

International Nuclear Information System (INIS)

Vild, B.

1987-01-01

A Nuclear Waste Fund established by the Nuclear Waste Policy Act of 1982 provides financial support to affected states to participate in the high-level radioactive waste repository siting program of the US Department of Energy. In Rhode Island, that function was performed by a multidisciplinary Project Review Team consisting of staff from three State agencies. Members of the Review Team attended several meetings in 1986 to discuss mutual concerns with Federal, State and Tribal officials. Comments were developed on DOE's Draft Area Recommendation Report. Members of the Review Team also testified at a public hearing in Providence on the Draft ARR, and developed and distributed a public information booklet. In May, Secretary of Energy John Herrington announced the suspension of the crystalline repository siting program. The remainder of the year was spent monitoring litigation challenging that decision and pending legislation. Administrative phase-down of the program was essentially complete by the close of the calendar year

KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems.

Science.gov (United States)

Costa, Rafael S; Veríssimo, André; Vinga, Susana

2014-08-13

The kinetic modeling of biological systems is mainly composed of three steps that proceed iteratively: model building, simulation and analysis. In the first step, it is usually required to set initial metabolite concentrations, and to assign kinetic rate laws, along with estimating parameter values using kinetic data through optimization when these are not known. Although the rapid development of high-throughput methods has generated much omics data, experimentalists present only a summary of obtained results for publication, the experimental data files are not usually submitted to any public repository, or simply not available at all. In order to automatize as much as possible the steps of building kinetic models, there is a growing requirement in the systems biology community for easily exchanging data in combination with models, which represents the main motivation of KiMoSys development. KiMoSys is a user-friendly platform that includes a public data repository of published experimental data, containing concentration data of metabolites and enzymes and flux data. It was designed to ensure data management, storage and sharing for a wider systems biology community. This community repository offers a web-based interface and upload facility to turn available data into publicly accessible, centralized and structured-format data files. Moreover, it compiles and integrates available kinetic models associated with the data.KiMoSys also integrates some tools to facilitate the kinetic model construction process of large-scale metabolic networks, especially when the systems biologists perform computational research. KiMoSys is a web-based system that integrates a public data and associated model(s) repository with computational tools, providing the systems biology community with a novel application facilitating data storage and sharing, thus supporting construction of ODE-based kinetic models and collaborative research projects.The web application implemented using Ruby

Nuclear waste repository transparency technology test bed demonstrations at WIPP

International Nuclear Information System (INIS)

Betsill J, David; Elkins, Ned Z.; Wu, Chuan-Fu; Mewhinney, James D.; Aamodt, Paul

2000-01-01

repository, the Waste Isolation Pilot Plant (WIPP) offers a unique opportunity to serve as an international cooperative test bed for developing and demonstrating technologies and processes in a fully operational repository system setting. To address the substantial national security implications for the US resulting from the lack of integrated, transparent management and disposition of nuclear materials at the back-end of the nuclear fuel and weapons cycles, it is proposed that WIPP be used as a test bed to develop and demonstrate technologies that will enable the transparent and proliferation-resistant geologic isolation of nuclear materials. The objectives of this initiative are to: (1) enhance public confidence in safe, secure geologic isolation of nuclear materials; (2) develop, test, and demonstrate transparency measures and technologies for the back-end of nuclear fuel cycle; and (3) foster international collaborations leading to workable, effective, globally-accepted standards for the transparent monitoring of geological repositories for nuclear materials. Test-bed activities include: development and testing of monitoring measures and technologies; international demonstration experiments; transparency workshops; visiting scientist exchanges; and educational outreach. These activities are proposed to be managed by the Department of Energy/Carlsbad Area Office (DOE/CAO) as part of The Center for Applied Repository and Underground Studies (CARUS)

Thermal management and analysis for a potential yucca mountain repository

International Nuclear Information System (INIS)

Van Luik, A.

2005-01-01

presented here is summarised from the Yucca Mountain Science and Engineering Report. A companion paper in this publication entitled 'Characterizing the Evolution of the In-Drift Environment in a Proposed Yucca Mountain Repository' schematically illustrates the processes being controlled through the management of thermal loading. (author)

Past, Current, and Future Challenges in Linking Data to Publications

Science.gov (United States)

Hanson, B.

2015-12-01

Data are the currency of science and assure the integrity of published research. As the ability to collect, analyze, and visualize data has grown beyond what could be included in a publication, and as the value of the data become more clear (or the lack of availability of data was criticized), publishers and the scientific community developed several solutions to enhance access to underlying data. Most leading journals now require authors to agree as a condition of submission that underlying data will be included or made available; indeed, publication is the key leverage point in exposing much scholarly data. Most journals allow PDF or other supplements and links to data sets hosted by authors or labs, or better, data repositories such as Dryad, and some have banned "data not shown" or any reference to unpublished work. Many of these solutions have proven problematic and recent studies have found that large fraction of data are undiscoverable even a few years after publication. The best solution has been dedicated domain repositories collectively supported by publishers, funders, and the scientific community and where deposition is required before or at the time of publication. These provide quality control and curation and facilitate reuse. However, expanding these beyond a few key repositories and developing standardized workflows and functionality among repositories and between them and publishers has been problematic. Addressing these and other data challenges requires collaborative efforts among funders, publishers, repositories, societies, and researchers. One example is the Coalition on Publishing Data in the the Earth and space sciences, where most major publishers and repositories have signed a joint statement of commitment (COPDESS.org), and are starting work to direct and link published data to domain repositories. Much work remains to be done. Major challenges include establishing data curation practices into the workflow of science from data collection

IAEA safeguards for geological repositories

International Nuclear Information System (INIS)

Moran, B.W.

2005-01-01

In September. 1988, the IAEA held its first formal meeting on the safeguards requirements for the final disposal of spent fuel and nuclear material-bearing waste. The consensus recommendation of the 43 participants from 18 countries at this Advisory Group Meeting was that safeguards should not terminate of spent fuel even after emplacement in, and closure of, a geologic repository.' As a result of this recommendation, the IAEA initiated a series of consultants' meetings and the SAGOR Programme (Programme for the Development of Safeguards for the Final Disposal of Spent Fuel in Geologic Repositories) to develop an approach that would permit IAEA safeguards to verify the non-diversion of spent fuel from a geologic repository. At the end of this process, in December 1997, a second Advisory Group Meeting, endorsed the generic safeguards approach developed by the SAGOR Programme. Using the SAGOR Programme results and consultants' meeting recommendations, the IAEA Department of Safeguards issued a safeguards policy paper stating the requirements for IAEA safeguards at geologic repositories. Following approval of the safeguards policy and the generic safeguards approach, the Geologic Repository Safeguards Experts Group was established to make recommendations on implementing the safeguards approach. This experts' group is currently making recommendations to the IAEA regarding the safeguards activities to be conducted with respect to Finland's repository programme. (author)

Proteomic analysis of the Theileria annulata schizont

Science.gov (United States)

Witschi, M.; Xia, D.; Sanderson, S.; Baumgartner, M.; Wastling, J.M.; Dobbelaere, D.A.E.

2013-01-01

The apicomplexan parasite, Theileria annulata, is the causative agent of tropical theileriosis, a devastating lymphoproliferative disease of cattle. The schizont stage transforms bovine leukocytes and provides an intriguing model to study host/pathogen interactions. The genome of T. annulata has been sequenced and transcriptomic data are rapidly accumulating. In contrast, little is known about the proteome of the schizont, the pathogenic, transforming life cycle stage of the parasite. Using one-dimensional (1-D) gel LC-MS/MS, a proteomic analysis of purified T. annulata schizonts was carried out. In whole parasite lysates, 645 proteins were identified. Proteins with transmembrane domains (TMDs) were under-represented and no proteins with more than four TMDs could be detected. To tackle this problem, Triton X-114 treatment was applied, which facilitates the extraction of membrane proteins, followed by 1-D gel LC-MS/MS. This resulted in the identification of an additional 153 proteins. Half of those had one or more TMD and 30 proteins with more than four TMDs were identified. This demonstrates that Triton X-114 treatment can provide a valuable additional tool for the identification of new membrane proteins in proteomic studies. With two exceptions, all proteins involved in glycolysis and the citric acid cycle were identified. For at least 29% of identified proteins, the corresponding transcripts were not present in the existing expressed sequence tag databases. The proteomics data were integrated into the publicly accessible database resource at EuPathDB (www.eupathdb.org) so that mass spectrometry-based protein expression evidence for T. annulata can be queried alongside transcriptional and other genomics data available for these parasites. PMID:23178997

Proteomic explorations of autism spectrum disorder.

Science.gov (United States)

Szoko, Nicholas; McShane, Adam J; Natowicz, Marvin R

2017-09-01

Proteomics, the large-scale study of protein expression in cells and tissues, is a powerful tool to study the biology of clinical conditions and has provided significant insights in many experimental systems. Herein, we review the basics of proteomic methodology and discuss challenges in using proteomic approaches to study autism. Unlike other experimental approaches, such as genomic approaches, there have been few large-scale studies of proteins in tissues from persons with autism. Most of the proteomic studies on autism used blood or other peripheral tissues; few studies used brain tissue. Some studies found dysregulation of aspects of the immune system or of aspects of lipid metabolism, but no consistent findings were noted. Based on the challenges in using proteomics to study autism, we discuss considerations for future studies. Apart from the complex technical considerations implicit in any proteomic analysis, key nontechnical matters include attention to subject and specimen inclusion/exclusion criteria, having adequate sample size to ensure appropriate powering of the study, attention to the state of specimens prior to proteomic analysis, and the use of a replicate set of specimens, when possible. We conclude by discussing some potentially productive uses of proteomics, potentially coupled with other approaches, for future autism research including: (1) proteomic analysis of banked human brain specimens; (2) proteomic analysis of tissues from animal models of autism; and (3) proteomic analysis of induced pluripotent stem cells that are differentiated into various types of brain cells and neural organoids. Autism Res 2017, 10: 1460-1469. © 2017 International Society for Autism Research, Wiley Periodicals, Inc. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.

Environmental impact assessments and geological repositories for radioactive waste

International Nuclear Information System (INIS)

O'Sullivan, P.; McKirdy, B.; Askarieh, M.; Bond, A.; Russell, S.

1999-01-01

Since 1985 it has been obligatory that facilities in the European Union designed for the permanent storage or disposal of radioactive waste be assessed to determine their effects on the environment. This assessment must be undertaken in advance of any decision by national authorities to give consent for development work to proceed. Member States are given wide discretion on how the above requirements are implemented in practice, e.g. the relevant European Council Directives call for the results of the environmental assessment to be made available to the public before development consent is granted but the detailed arrangements for dissemination of such information and procedures for public consultation are determined by individual Member States. Although the Directives require an assessment of the direct and indirect effects of a project on human beings and on various elements of the natural environment, they are non-specific as to what particular impacts should be addressed, particularly as regards the effects of a project on human beings. Therefore, for example, each Member State may decide whether or not social, health and economic impacts should be included in the assessment. This paper discusses the above issues. It proposes a model approach to environmental impact assessment in the context of geological repositories, including the role of the assessment on the overall decision processes for repository development, the scope and content of the assessment report, and approaches to public involvement

Repository site characterization

International Nuclear Information System (INIS)

Voss, J.W.; Pentz, D.L.

1987-01-01

The characterization of candidate repository sites has a number of programmatic objectives. Principal among these is the acquisition of data: a) to determine the suitability of a site relative to the DOE repository siting guidelines, b) to support model development and calculations to determine the suitability of a site relative to the post closure criteria of the NRC and EPA, c) to support the design of a disposal system, including the waste package and the engineered barrier system, as well as the shafts and underground openings of the repository. In meeting the gaols of site characterization, the authors have an obligation to conduct their investigations within an appropriate budget and schedule. This mandates that a well-constructed and systematic plan for field investigations be developed. Such a plan must fully account for the mechanisms which will control the radiologic performance in the repository. The plan must also flexibly and dynamically respond to the results of each step of field investigation, responding to the spatial variability of earth as well as to enhanced understandings of the performance of the disposal system. Such a plan must ensure that sufficient data are available to support the necessary probabilistic calculations of performance. This paper explores the planning for field data acquisition with specific reference to requirements for demonstrations of the acceptable performance for disposal systems

Gas generation in repositories

International Nuclear Information System (INIS)

Biddle, P.; Rees, J.H.; McGahan, D.; Rushbrook, P.E.

1987-09-01

The nature and quantities of gases likely to be produced by various processes in repositories for low level and intermediate level radioactive wastes are examined in this preliminary study. Many simplifying assumptions are made where published or experimental data is unavailable. The corrosion of the canisters and metallic components in wastes is likely to be the major gas production process in both types of repository. A significant contribution from microbiological activity is expected to occur in low level repositories, predominantly where no cement grouting of the cans has been carried out. A number of areas for further research, required before a more comprehensive study could be carried out, have been identified. (author)

SUBSURFACE REPOSITORY INTEGRATED CONTROL SYSTEM DESIGN

International Nuclear Information System (INIS)

Randle, D.C.

2000-01-01

The primary purpose of this document is to develop a preliminary high-level functional and physical control system architecture for the potential repository at Yucca Mountain. This document outlines an overall control system concept that encompasses and integrates the many diverse process and communication systems being developed for the subsurface repository design. This document presents integrated design concepts for monitoring and controlling the diverse set of subsurface operations. The Subsurface Repository Integrated Control System design will be composed of a series of diverse process systems and communication networks. The subsurface repository design contains many systems related to instrumentation and control (I andC) for both repository development and waste emplacement operations. These systems include waste emplacement, waste retrieval, ventilation, radiological and air monitoring, rail transportation, construction development, utility systems (electrical, lighting, water, compressed air, etc.), fire protection, backfill emplacement, and performance confirmation. Each of these systems involves some level of I andC and will typically be integrated over a data communications network throughout the subsurface facility. The subsurface I andC systems will also interface with multiple surface-based systems such as site operations, rail transportation, security and safeguards, and electrical/piped utilities. In addition to the I andC systems, the subsurface repository design also contains systems related to voice and video communications. The components for each of these systems will be distributed and linked over voice and video communication networks throughout the subsurface facility. The scope and primary objectives of this design analysis are to: (1) Identify preliminary system-level functions and interfaces (Section 6.2). (2) Examine the overall system complexity and determine how and on what levels the engineered process systems will be monitored

TOXsIgN: a cross-species repository for toxicogenomic signatures.

Science.gov (United States)

Darde, Thomas A; Gaudriault, Pierre; Beranger, Rémi; Lancien, Clément; Caillarec-Joly, Annaëlle; Sallou, Olivier; Bonvallot, Nathalie; Chevrier, Cécile; Mazaud-Guittot, Séverine; Jégou, Bernard; Collin, Olivier; Becker, Emmanuelle; Rolland, Antoine D; Chalmel, Frédéric

2018-01-27

At the same time that toxicologists express increasing concern about reproducibility in this field, the development of dedicated databases has already smoothed the path toward improving the storage and exchange of raw toxicogenomic data. Nevertheless, none provides access to analyzed and interpreted data as originally reported in scientific publications. Given the increasing demand for access to this information, we developed TOXsIgN, a repository for TOXicogenomic sIgNatures. The TOXsIgN repository provides a flexible environment that facilitates online submission, storage, and retrieval of toxicogenomic signatures by the scientific community. It currently hosts 754 projects that describe more than 450 distinct chemicals and their 8491 associated signatures. It also provides users with a working environment containing a powerful search engine as well as bioinformatics/biostatistics modules that enable signature comparisons or enrichment analyses. The TOXsIgN repository is freely accessible at http://toxsign.genouest.org. Website implemented in Python, JavaScript, and MongoDB, with all major browsers supported. frederic.chalmel@inserm.fr. Supplementary data are available at Bioinformatics online. © The Author (2018). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Preliminary design of the repository. Stage 2

International Nuclear Information System (INIS)

Saanio, T.; Kirkkomaeki, T.; Keto, P.; Kukkola, T.; Raiko, H.

2007-04-01

Spent nuclear fuel from Finnish nuclear power plants will be disposed of in deep bedrock in Olkiluoto, Eurajoki. The repository is planned to be excavated at a depth of 400 - 500 metres. Access routes to the repository include a 1:10 inclined access tunnel, and vertical shafts. The fuel is encapsulated in the encapsulation plant above ground and transferred to the repository in the canister lift. Deposition tunnels, central tunnels and technical rooms are excavated at the disposal level. The canisters are deposited in deposition holes that are covered with bentonite blocks. The deposition holes are bored in the floors of the deposition tunnels. The central tunnel system consists of two parallel central tunnels that are inter-connected at certain distances. Two parallel central tunnels improve the fire safety of the rooms and also allow flexible backfilling and closing of the deposition tunnels in stages at the operational phase of the repository. An underground rock characterization facility, ONKALO, is excavated at the disposal level to support and confirm investigations carried out from above ground. ONKALO is designed so that it can later serve as part of the repository. ONKALO excavations were started in 2004. The repository will be excavated in the 2010s and operation will start in 2020. The fifth nuclear power unit makes the operational phase of the repository very long. Parts of the repository will be excavated and closed over the long operational period. The repository can be constructed at one or several levels. The one-storey alternative is the so-called reference alternative in this preliminary design report. The two-storey alternative is also taken into account in the ONKALO designs. The preliminary designs of the repository are presented as located in Olkiluoto. The location of the repository will be revised when more information on the bedrock has been gained. More detailed data of the circumstances will be obtained from above ground investigations

Preliminary design of the repository, stage 2

International Nuclear Information System (INIS)

Saanio, T.; Kirkkomaeki, T.; Keto, P.; Kukkola, T.; Raiko, H.

2007-01-01

Spent nuclear fuel from Finnish nuclear power plants will be disposed of in deep bedrock in Olkiluoto, Eurajoki. The repository is planned to be excavated at a depth of 400 - 500 metres. Access routes to the repository include a 1:10 inclined access tunnel, and vertical shafts. The fuel is encapsulated in the encapsulation plant above ground and transferred to the repository in the canister lift. Deposition tunnels, central tunnels and technical rooms are excavated at the disposal level. The canisters are deposited in deposition holes that are covered with bentonite blocks. The deposition holes are bored in the floors of the deposition tunnels. The central tunnel system consists of two parallel central tunnels that are inter-connected at certain distances. Two parallel central tunnels improve the fire safety of the rooms and also allow flexible backfilling and closing of the deposition tunnels in stages at the operational phase of the repository. An underground rock characterization facility, ONKALO, is excavated at the disposal level to support and confirm investigations carried out from above ground. ONKALO is designed so that it can later serve as part of the repository. ONKALO excavations were started in 2004. The repository will be excavated in the 2010s and operation will start in 2020. The fifth nuclear power unit makes the operational phase of the repository very long. Parts of the repository will be excavated and closed over the long operational period. The repository can be constructed at one or several levels. The one-storey alternative is the so-called reference alternative in this preliminary design report. The two-storey alternative is also taken into account in the ONKALO designs. The preliminary designs of the repository are presented as located in Olkiluoto. The location of the repository will be revised when more information on the bedrock has been gained. More detailed data of the circumstances will be obtained from above ground investigations

Is Croatia Going to Build a Radioactive Waste Repository?

International Nuclear Information System (INIS)

Knapp, Alemka; Levanat, Ivica; Saponja-Milutinovc, Diana

2014-01-01

Site selection process for low and intermediate level radioactive waste repository in Croatia was ended in 1999, nominating Trgovska gora as the potential macrolocation for the facility. Feasibility of the Trgovska gora disposal project was analyzed in a number of studies prepared by APO Ltd. from the mid-nineties up to 2003. An affirmative, though preliminary and largely generic safety assessment was completed. Specific microlocations were selected and analyzed based on literature data (garnished with low-resolution digital satellite pictures), and the best microlocation was tentatively narrowed down to Pavlovo brdo. After 2003, no further activities related to the repository project were undertaken for nearly ten years, until in its public procurement plan for 2013 the Croatian Fund for financing the NPP Krsko decommissioning and waste disposal dedicated over half a million euro to continuation of the project. In general, safe radioactive waste disposal pre-requires establishment of a complex national framework with appropriate functionality and competence; with such a framework established, decisive first steps towards building a repository are to identify potentially suitable locations and to ensure local community consent and cooperation. The rest should mainly be routine. But in Croatia, both lack of proper framework and the project history of indecisiveness may adversely affect further developments. Trgovska gora was designated as the potential location in the national land use plan only after three other potential locations had been dismissed by political decisions based on the largely assumed adverse attitudes of local communities. Repository project now appears to depend on cooperation of a single local community hosting the only potential site. The site has never been visited by any repository project participants, nor has the local community ever been officially contacted in an open and straightforward way, despite the 20-year old history of the project

Nuclear waste repository siting

International Nuclear Information System (INIS)

Soloman, B.D.; Cameron, D.M.

1987-01-01

This paper discusses the geopolitics of nuclear waste disposal in the USA. Constitutional choice and social equity perspectives are used to argue for a more open and just repository siting program. The authors assert that every potential repository site inevitably contains geologic, environmental or other imperfections and that the political process is the correct one for determining sites selected

Granite-repository - geochemical environment

International Nuclear Information System (INIS)

1979-04-01

Some geochemical data of importance for a radioactive waste repository in hard rock are reviewed. The ground water composition at depth is assessed. The ground water chemistry in the vicinity of uranium ores is discussed. The redox system in Swedish bedrock is described. Influences of extreme climatic changes and of repository mining and construction are also evaluated

Workshop: Creating Your Institutional Research Repository

KAUST Repository

Grenz, Daryl M.

2016-11-08

In 2002, the Scholarly Publishing and Academic Resources Coalition (SPARC) proposed the concept of an institutional repository to simultaneously disrupt and enhance the state of scholarly communications in the academic world. Thirteen years later, thousands of universities and other institutions have answered this call, but many more have not due to gaps in budgets, awareness and, most of all, practical guidance on creating an institutional repository. This workshop provides you with an essential primer on what it takes to establish a fully-functioning institutional repository. Every aspect of the process will be covered, including policies, procedures, staffing guidelines, workflows and repository technologies.

A scoping review of online repositories of quality improvement projects, interventions and initiatives in healthcare.

Science.gov (United States)

Bytautas, Jessica P; Gheihman, Galina; Dobrow, Mark J

2017-04-01

Quality improvement (QI) is becoming an important focal point for health systems. There is increasing interest among health system stakeholders to learn from and share experiences on the use of QI methods and approaches in their work. Yet there are few easily accessible, online repositories dedicated to documenting QI activity. We conducted a scoping review of publicly available, web-based QI repositories to (i) identify current approaches to sharing information on QI practices; (ii) categorise these approaches based on hosting, scope and size, content acquisition and eligibility, content format and search, and evaluation and engagement characteristics; and (iii) review evaluations of the design, usefulness and impact of their online QI practice repositories. The search strategy consisted of traditional database and grey literature searches, as well as expert consultation, with the ultimate aim of identifying and describing QI repositories of practices undertaken in a healthcare context. We identified 13 QI repositories and found substantial variation across the five categories. The QI repositories used different terminology (eg, practices vs case studies) and approaches to content acquisition, and varied in terms of primary areas of focus. All provided some means for organising content according to categories or themes and most provided at least rudimentary keyword search functionality. Notably, none of the QI repositories included evaluations of their impact. With growing interest in sharing and spreading best practices and increasing reliance on QI as a key contributor to health system performance, the role of QI repositories is likely to expand. Designing future QI repositories based on knowledge of the range and type of features available is an important starting point for improving their usefulness and impact. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Safeguards for geological repositories

International Nuclear Information System (INIS)

Fattah, A.

2000-01-01

Direct disposal of spent nuclear fuel in geological repositories is a recognised option for closing nuclear fuel cycles. Geological repositories are at present in stages of development in a number of countries and are expected to be built and operated early next century. A State usually has an obligation to safely store any nuclear material, which is considered unsuitable to re-enter the nuclear fuel cycle, isolated from the biosphere. In conjunction with this, physical protection has to be accounted for to prevent inadvertent access to such material. In addition to these two criteria - which are fully under the State's jurisdiction - a third criterion reflecting international non-proliferation commitments needs to be addressed. Under comprehensive safeguards agreements a State concedes verification of nuclear material for safeguards purposes to the IAEA. The Agency can thus provide assurance to the international community that such nuclear material has been used for peaceful purposes only as declared by the State. It must be emphasised that all three criteria mentioned constitute a 'unit'. None can be sacrificed for the sake of the other, but compromises may have to be sought in order to make their combination as effective as possible. Based on comprehensive safeguards agreements signed and ratified by the State, safeguards can be terminated only when the material has been consumed or diluted in such a way that it can no longer be utilised for any nuclear activities or has become practicably irrecoverable. As such safeguards for nuclear material in geological repositories have to be continued even after the repository has been back-filled and sealed. The effective application of safeguards must assure continuity-of-knowledge that the nuclear material in the repository has not been diverted for an unknown purpose. The nuclear material disposed in a geological repository may eventually have a higher and long term proliferation risk because the inventory is

A structural model analysis of public opposition to a high-level radioactive waste facility

International Nuclear Information System (INIS)

Flynn, J.; Mertz, C.K.; Slovic, P.; Burns, W.

1991-09-01

Studies show that most Nevada residents and almost all state officials oppose the proposed high-level radioactive waste repository project at Yucca Mountain. Surveys of the public show that individual citizens view the Yucca Mountain repository as having high risk; nuclear experts, in contrast, believe the risks are very low. Policy analysts have suggested that public risk perceptions may be reduced by better program management, increased trust in the federal government, and increased economic benefits for accepting a repository. The model developed in this study is designed to examine the relationship between public perceptions of risk, trust in risk management, and potential economic impacts of the current repository program using a confirmatory multivariate method known as covariance structure analysis. The results indicate that perceptions of potential economic gains have little relationship to opposition to the repository. On the other hand, risk perceptions and the level of trust in repository management are closely related to each other and to opposition. The impacts of risk perception and trust in management on opposition to the repository result from a combination of their direct influences as well as their indirect influences operating through perceptions that the repository would have serious negative impacts on the state's economy due to stigmatization and reduced tourism

Modelling saline intrusion for repository performance assessment

International Nuclear Information System (INIS)

Jackson, C.P.

1989-04-01

UK Nirex Ltd are currently considering the possibility of disposal of radioactive waste by burial in deep underground repositories. The natural pathway for radionuclides from such a repository to return to Man's immediate environment (the biosphere) is via groundwater. Thus analyses of the groundwater flow in the neighbourhood of a possible repository, and consequent radionuclide transport form an important part of a performance assessment for a repository. Some of the areas in the UK that might be considered as possible locations for a repository are near the coast. If a repository is located in a coastal region seawater may intrude into the groundwater flow system. As seawater is denser than fresh water buoyancy forces acting on the intruding saline water may have significant effects on the groundwater flow system, and consequently on the time for radionuclides to return to the biosphere. Further, the chemistry of the repository near-field may be strongly influenced by the salinity of the groundwater. It is therefore important for Nirex to have a capability for reliably modelling saline intrusion to an appropriate degree of accuracy in order to make performance assessments for a repository in a coastal region. This report describes work undertaken in the Nirex Research programme to provide such a capability. (author)

Analisis Konten dan Kebijakan Akses Institutional Repository

Directory of Open Access Journals (Sweden)

Amirul Ulum

2016-07-01

Abstract; Institutional repository has become a major concern of higher education in Indonesia. The number of institutional respository was increased, one of the reason is the ranking web of repositories has been conducted by the Cybermetrics Lab in 2008. At that time, many institutions started to build institutional repository in order to manage the scientific work and also trying to reach the better ranks. Meanwhile, it is an achievement of institution performance which can be promote and increase visibility for the institution. University of Surabaya has also developed the institutional repository and managed by the library. The aims of this study is to analyze the content availability and access policies defined by the University of Surabaya repository  providing services to the academic community and external users. The method used in this study by using observations of the institutional repository University of Surabaya with a literature review to clarify the analysis of the content and access policies. The results of this study indicate that the library's role is has the authority to manage the scientific work of academic community can be done through the institutional repository. However there is still need for library to be proactive to communicate regulations on mandatory deposit of scientific work and create intensive promotion of the institutional repository.

1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions.

Science.gov (United States)

Joshi, Hiren J; Christiansen, Katy M; Fitz, Joffrey; Cao, Jun; Lipzen, Anna; Martin, Joel; Smith-Moritz, A Michelle; Pennacchio, Len A; Schackwitz, Wendy S; Weigel, Detlef; Heazlewood, Joshua L

2012-05-15

The sequencing of over a thousand natural strains of the model plant Arabidopsis thaliana is producing unparalleled information at the genetic level for plant researchers. To enable the rapid exploitation of these data for functional proteomics studies, we have created a resource for the visualization of protein information and proteomic datasets for sequenced natural strains of A. thaliana. The 1001 Proteomes portal can be used to visualize amino acid substitutions or non-synonymous single-nucleotide polymorphisms in individual proteins of A. thaliana based on the reference genome Col-0. We have used the available processed sequence information to analyze the conservation of known residues subject to protein phosphorylation among these natural strains. The substitution of amino acids in A. thaliana natural strains is heavily constrained and is likely a result of the conservation of functional attributes within proteins. At a practical level, we demonstrate that this information can be used to clarify ambiguously defined phosphorylation sites from phosphoproteomic studies. Protein sets of available natural variants are available for download to enable proteomic studies on these accessions. Together this information can be used to uncover the possible roles of specific amino acids in determining the structure and function of proteins in the model plant A. thaliana. An online portal to enable the community to exploit these data can be accessed at http://1001proteomes.masc-proteomics.org/

Xylem sap proteomics.

Science.gov (United States)

de Bernonville, Thomas Dugé; Albenne, Cécile; Arlat, Matthieu; Hoffmann, Laurent; Lauber, Emmanuelle; Jamet, Elisabeth

2014-01-01

Proteomic analysis of xylem sap has recently become a major field of interest to understand several biological questions related to plant development and responses to environmental clues. The xylem sap appears as a dynamic fluid undergoing changes in its proteome upon abiotic and biotic stresses. Unlike cell compartments which are amenable to purification in sufficient amount prior to proteomic analysis, the xylem sap has to be collected in particular conditions to avoid contamination by intracellular proteins and to obtain enough material. A model plant like Arabidopsis thaliana is not suitable for such an analysis because efficient harvesting of xylem sap is difficult. The analysis of the xylem sap proteome also requires specific procedures to concentrate proteins and to focus on proteins predicted to be secreted. Indeed, xylem sap proteins appear to be synthesized and secreted in the root stele or to originate from dying differentiated xylem cells. This chapter describes protocols to collect xylem sap from Brassica species and to prepare total and N-glycoprotein extracts for identification of proteins by mass spectrometry analyses and bioinformatics.

Process model repositories and PNML

NARCIS (Netherlands)

Hee, van K.M.; Post, R.D.J.; Somers, L.J.A.M.; Werf, van der J.M.E.M.; Kindler, E.

2004-01-01

Bringing system and process models together in repositories facilitates the interchange of model information between modelling tools, and allows the combination and interlinking of complementary models. Petriweb is a web application for managing such repositories. It supports hierarchical process

Radioactive waste repository study

International Nuclear Information System (INIS)

1978-11-01

This is the second part of a report of a preliminary study for AECL. It considers the requirements for an underground waste repository for the disposal of wastes produced by the Canadian Nuclear Fuel Program. The following topics are discussed with reference to the repository: 1) geotechnical assessment, 2) hydrogeology and waste containment, 3) thermal loading and 4) rock mechanics. (author)

Farm animal proteomics - A review

DEFF Research Database (Denmark)

Bendixen, Emøke; Danielsen, Marianne; Hollung, Kristin

2011-01-01

In agricultural sciences as in all other areas of life science, the implementation of proteomics and other post-genomic tools is an important step towards more detailed understanding of the complex biological systems that control physiology and pathology of living beings. Farm animals are raised...... and cattle are relevant not only for farm animal sciences, but also for adding to our understanding of complex biological mechanisms of health and disease in humans. The aim of this review is to present an overview of the specific topics of interest within farm animal proteomics, and to highlight some...... of the areas where synergy between classic model organism proteomics and farm animal proteomics is rapidly emerging. Focus will be on introducing the special biological traits that play an important role in food production, and on how proteomics may help optimize farm animal production...

Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment.

Science.gov (United States)

Welker, F

2018-02-20

The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identifications at increased evolutionary distances due to a larger number of protein sequence differences between the database sequence and the analyzed organism. Error-tolerant proteomic search algorithms should theoretically overcome this problem at both the peptide and protein level; however, this has not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against sequence databases at increasing evolutionary distances: the human (0 Ma), chimpanzee (6-8 Ma) and orangutan (16-17 Ma) reference proteomes, respectively. Incorrectly suggested amino acid substitutions are absent when employing adequate filtering criteria for mutable Peptide Spectrum Matches (PSMs), but roughly half of the mutable PSMs were not recovered. As a result, peptide and protein identification rates are higher in error-tolerant mode compared to non-error-tolerant searches but did not recover protein identifications completely. Data indicates that peptide length and the number of mutations between the target and database sequences are the main factors influencing mutable PSM identification. The error-tolerant results suggest that the cross-species proteomics problem is not overcome at increasing evolutionary distances, even at the protein level. Peptide and protein loss has the potential to significantly impact divergence dating and proteome comparisons when using ancient samples as there is a bias towards the identification of conserved sequences and proteins. Effects are minimized

Area recommendation report for the crystalline repository project: An evaluation

International Nuclear Information System (INIS)

Beck, J.E.; Lowe, H.; Yurkovich, S.P.

1986-01-01

An evaluation is given of DOE's recommendation of the Elk River complex in North Carolina for siting the second repository. Twelve recommendations are made including a strong suggestion that the Cherokee Tribe appeal both through political and legal avenues for inclusion as an affected area primarily due to projected impacts upon economy and public health as a consequence of the potential for reduced tourism

Open DOAR the Directory of Open Access Repositories

CERN Multimedia

CERN. Geneva

2005-01-01

The last year has seen wide-spread growth in the idea of using open access repositories as a part of a research institution's accepted infrastructure. Policy development from institutions and funding bodies has also supported the growth of the repository network. The next stage of expansion will be in the provision of services and cross-repository facilities and resources. Of course, it is hoped that these will then establish a feed-back loop to encourage repository population and further repository establishment, as the potential of open access to research materials is realised. The growth of repositories has been organic, with a variety of different repositories based in departments, institutions, funding agencies or subject communities, with a range of content, both in type and subject. Existing repositories are expanding their holdings, from eprints to associated research data-sets, or with learning objects and multimedia material. This presentation will look at the development of the Directory of Open Ac...

Evaluasi Website Repositori Institusi Universitas Surabaya

Directory of Open Access Journals (Sweden)

Amirul Ulum

2015-11-01

Full Text Available The  development  of  institutional  repositories  (IRs  in Indonesia within the broader framework of open access has significant impact on preserving intellectual capital and scholarly communication. Institutional  repositories  play  a  fundamental  role  in  centralizing, preserving,  and  making  accessible  institution’s  intellectual  capital. Evaluation of the system is to determine the functionality the system to meet the users need. Using a descriptive analysis this study wants to evaluate institutional repositories of University of Surabaya. The result is usefull for institution to develop the repository systems.

Proteomic analysis of human tooth pulp: proteomics of human tooth.

Science.gov (United States)

Eckhardt, Adam; Jágr, Michal; Pataridis, Statis; Mikšík, Ivan

2014-12-01

The unique pulp-dentin complex demonstrates strong regenerative potential, which enables it to respond to disease and traumatic injury. Identifying the proteins of the pulp-dentin complex is crucial to understanding the mechanisms of regeneration, tissue calcification, defense processes, and the reparation of dentin by dental pulp. The lack of knowledge of these proteins limits the development of more efficient therapies. The proteomic profile of human tooth pulp was investigated and compared with the proteome of human dentin and blood. The samples of tooth pulp were obtained from 5 sound permanent human third molars of 5 adults (n = 5). The extracted proteins were separated by 2-dimensional gel electrophoresis, analyzed by nano-liquid chromatography tandem mass spectrometry, and identified by correlating mass spectra to the proteomic databases. A total of 342 proteins were identified with high confidence, and 2 proteins were detected for the first time in an actual human sample. The identified tooth pulp proteins have a variety of functions: structural, catalytic, transporter, protease activity, immune response, and many others. In a comparison with dentin and blood plasma, 140 (pulp/dentin) shared proteins were identified, 37 of which were not observed in plasma. It can be suggested that they might participate in the unique pulp-dentin complex. This proteomic investigation of human tooth pulp, together with the previously published study of human dentin, is one of the most comprehensive proteome lists of human teeth to date. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Changes over lactation in breast milk serum proteins involved in the maturation of immune and digestive system of the infant

Directory of Open Access Journals (Sweden)

Lina Zhang

2016-06-01

Full Text Available Here we provide data from shot-gun proteomics, using filtered-aided sample preparation (FASP, dimethyl labeling and LC–MS/MS, to quantify the changes in the repertoire of human milk proteins over lactation. Milk serum proteins were analyzed at week 1, 2, 3 4, 8, 16, and 24 in milk from four individual mothers. A total of 247 proteins were identified, of which 200 proteins were quantified. The data supplied in this article supports the accompanying publication (Zhang et al., 2006 [1]. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Vizcaíno et al., 2016 [2] via the PRIDE partner repository with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD003465.

The SocioEconomic analysis of repository siting (SEARS): Guide to data base preparation: Final draft

International Nuclear Information System (INIS)

Hamm, R.R.; Murdock, S.H.; Leistritz, F.L.; Kiel, B.; Parpia, B.

1984-11-01

This guide describes the data bases in the SocioEconomic Analysis of Repository Siting (SEARS) modeling system. This model is a user-interactive, computerized model for projecting the economic, demographic, public service, and fiscal impacts of repository siting. This guide provides a description of the data bases, sources of data, data formats, and preprocessing programs for adapting and implementing the SEARS system and is seen as an essential reference for technical users of the model. It should be used in conjunction with reports describing the model's features and characteristics. 95 refs., 3 tabs

Mining the granule proteome

DEFF Research Database (Denmark)

Albrethsen, Jakob; Goetze, Jens P; Johnsen, Anders H

2015-01-01

Proteomics of secretory granules is an emerging strategy for identifying secreted proteins, including potentially novel candidate biomarkers and peptide hormones. In addition, proteomics can provide information about the abundance, localization and structure (post-translational modification) of g...

Advances of Proteomic Sciences in Dentistry.

Science.gov (United States)

Khurshid, Zohaib; Zohaib, Sana; Najeeb, Shariq; Zafar, Muhammad Sohail; Rehman, Rabia; Rehman, Ihtesham Ur

2016-05-13

Applications of proteomics tools revolutionized various biomedical disciplines such as genetics, molecular biology, medicine, and dentistry. The aim of this review is to highlight the major milestones in proteomics in dentistry during the last fifteen years. Human oral cavity contains hard and soft tissues and various biofluids including saliva and crevicular fluid. Proteomics has brought revolution in dentistry by helping in the early diagnosis of various diseases identified by the detection of numerous biomarkers present in the oral fluids. This paper covers the role of proteomics tools for the analysis of oral tissues. In addition, dental materials proteomics and their future directions are discussed.

Safety Report within the licence application for the siting of a radioactive waste repository/disposal facility

International Nuclear Information System (INIS)

Horyna, J.; Sinaglova, R.

2004-01-01

The initial safety specification report, which is submitted to the licensing authority as one of the application documents, is the basic document assessing the planned repository/disposal facility with respect to the suitability of the chosen site for this purpose. The following topics are covered: General information; Description and evidence of suitability of the site chosen; Description and tentative assessment of the repository/disposal facility design; Tentative assessment of impacts of running the facility on the employees, general public and environment (radionuclide inventory, transport routes, radionuclide release in normal, abnormal and emergency situations); Proposed concept of repository/disposal facility shutdown; and Assessment of quality assurance in the site selection, in preparatory work for the construction of the facility and in the subsequent stages. (P.A.)

Proteomics - new analytical approaches

International Nuclear Information System (INIS)

Hancock, W.S.

2001-01-01

Full text: Recent developments in the sequencing of the human genome have indicated that the number of coding gene sequences may be as few as 30,000. It is clear, however, that the complexity of the human species is dependent on the much greater diversity of the corresponding protein complement. Estimates of the diversity (discrete protein species) of the human proteome range from 200,000 to 300,000 at the lower end to 2,000,000 to 3,000,000 at the high end. In addition, proteomics (the study of the protein complement to the genome) has been subdivided into two main approaches. Global proteomics refers to a high throughput examination of the full protein set present in a cell under a given environmental condition. Focused proteomics refers to a more detailed study of a restricted set of proteins that are related to a specified biochemical pathway or subcellular structure. While many of the advances in proteomics will be based on the sequencing of the human genome, de novo characterization of protein microheterogeneity (glycosylation, phosphorylation and sulfation as well as the incorporation of lipid components) will be required in disease studies. To characterize these modifications it is necessary to digest the protein mixture with an enzyme to produce the corresponding mixture of peptides. In a process analogous to sequencing of the genome, shot-gun sequencing of the proteome is based on the characterization of the key fragments produced by such a digest. Thus, a glycopeptide and hence a specific glycosylation motif will be identified by a unique mass and then a diagnostic MS/MS spectrum. Mass spectrometry will be the preferred detector in these applications because of the unparalleled information content provided by one or more dimensions of mass measurement. In addition, highly efficient separation processes are an absolute requirement for advanced proteomic studies. For example, a combination of the orthogonal approaches, HPLC and HPCE, can be very powerful

The waste isolation pilot plant transuranic waste repository: A case study in radioactive waste disposal safety and risk

Energy Technology Data Exchange (ETDEWEB)

Eriksson, Leif G. [GRAM, Inc., Albuquerque, NM (United States)

1999-12-01

The Waste Isolation Pilot Plant (WIPP) deep geological defense-generated transuranic radioactive waste (TRUW) repository in the United States was certified on the 13 of May 1998 and opened on the 26 of March 1999. Two sets of safety/performance assessment calculations supporting the certification of the WIPP TRUW repository show that the maximum annual individual committed effective dose will be 32 times lower than the regulatory limit and that the cumulative amount of radionuclide releases will be at least 10 times, more likely at least 20 times, lower than the regulatory limits. Yet, perceptions remain among the public that the WIPP TRUW repository imposes an unacceptable risk.

The waste isolation pilot plant transuranic waste repository: A case study in radioactive waste disposal safety and risk

International Nuclear Information System (INIS)

Eriksson, Leif G.

1999-01-01

The Waste Isolation Pilot Plant (WIPP) deep geological defense-generated transuranic radioactive waste (TRUW) repository in the United States was certified on the 13 of May 1998 and opened on the 26 of March 1999. Two sets of safety/performance assessment calculations supporting the certification of the WIPP TRUW repository show that the maximum annual individual committed effective dose will be 32 times lower than the regulatory limit and that the cumulative amount of radionuclide releases will be at least 10 times, more likely at least 20 times, lower than the regulatory limits. Yet, perceptions remain among the public that the WIPP TRUW repository imposes an unacceptable risk

Alternative measure for performance of HLW geologic repository

International Nuclear Information System (INIS)

Joonhang, Ahn; Chambre, P.L.

2001-01-01

A repository performance model that can show effects of canister multiplicity and repository configuration has been developed. Masses of a radionuclide in the repository and in the far field are proposed as performance measures. Canister multiplicity has significant effects on the release of long-lived radionuclides from the repository. As more canisters are included in the same water stream, the radionuclide concentration in the stream increases, but becomes independent of the number of canisters for sufficiently many canisters. Effects of reduction of radionuclide mass in the repository on the repository performance are clearly observed if the canister multiplicity is taken into account and the mass-based measures are applied. (author)

Natural Analogues - One Way to Help Build Public Confidence in the Predicted Performance of a Mined Geologic Repository for Nuclear Waste

Energy Technology Data Exchange (ETDEWEB)

Stuckless, J. S.

2002-02-26

The general public needs to have a way to judge the predicted long-term performance of the potential high-level nuclear waste repository at Yucca Mountain. The applicability and reliability of mathematical models used to make this prediction are neither easily understood nor accepted by the public. Natural analogues can provide the average person with a tool to assess the predicted performance and other scientific conclusions. For example, hydrologists with the Yucca Mountain Project have predicted that most of the water moving through the unsaturated zone at Yucca Mountain, Nevada will move through the host rock and around tunnels. Thus, seepage into tunnels is predicted to be a small percentage of available infiltration. This hypothesis can be tested experimentally and with some quantitative analogues. It can also be tested qualitatively using a variety of analogues such as (1) well-preserved Paleolithic to Neolithic paintings in caves and rock shelters, (2) biological remains preserved in caves and rock shelters, and (3) artifacts and paintings preserved in man-made underground openings. These examples can be found in materials that are generally available to the non-scientific public and can demonstrate the surprising degree of preservation of fragile and easily destroyed materials for very long periods of time within the unsaturated zone.

Accelerator Physics Code Web Repository

CERN Document Server

Zimmermann, Frank; Bellodi, G; Benedetto, E; Dorda, U; Giovannozzi, Massimo; Papaphilippou, Y; Pieloni, T; Ruggiero, F; Rumolo, G; Schmidt, F; Todesco, E; Zotter, Bruno W; Payet, J; Bartolini, R; Farvacque, L; Sen, T; Chin, Y H; Ohmi, K; Oide, K; Furman, M; Qiang, J; Sabbi, G L; Seidl, P A; Vay, J L; Friedman, A; Grote, D P; Cousineau, S M; Danilov, V; Holmes, J A; Shishlo, A; Kim, E S; Cai, Y; Pivi, M; Kaltchev, D I; Abell, D T; Katsouleas, Thomas C; Boine-Frankenheim, O; Franchetti, G; Hofmann, I; Machida, S; Wei, J

2006-01-01

In the framework of the CARE HHH European Network, we have developed a web-based dynamic acceleratorphysics code repository. We describe the design, structure and contents of this repository, illustrate its usage, and discuss our future plans, with emphasis on code benchmarking.

ACCELERATION PHYSICS CODE WEB REPOSITORY.

Energy Technology Data Exchange (ETDEWEB)

WEI, J.

2006-06-26

In the framework of the CARE HHH European Network, we have developed a web-based dynamic accelerator-physics code repository. We describe the design, structure and contents of this repository, illustrate its usage, and discuss our future plans, with emphasis on code benchmarking.

Boosting the globalization of plant proteomics through INPPO: current developments and future prospects.

Science.gov (United States)

Agrawal, Ganesh Kumar; Sarkar, Abhijit; Agrawal, Raj; Ndimba, Bongani Kaiser; Tanou, Georgia; Dunn, Michael J; Kieselbach, Thomas; Cramer, Rainer; Wienkoop, Stefanie; Chen, Sixue; Rafudeen, Mohammed Suhail; Deswal, Renu; Barkla, Bronwyn J; Weckwerth, Wolfram; Heazlewood, Joshua L; Renaut, Jenny; Job, Dominique; Chakraborty, Niranjan; Rakwal, Randeep

2012-02-01

The International Plant Proteomics Organization (INPPO) is a non-profit-organization consisting of people who are involved or interested in plant proteomics. INPPO is constantly growing in volume and activity, which is mostly due to the realization among plant proteomics researchers worldwide for the need of such a global platform. Their active participation resulted in the rapid growth within the first year of INPPO's official launch in 2011 via its website (www.inppo.com) and publication of the 'Viewpoint paper' in a special issue of PROTEOMICS (May 2011). Here, we will be highlighting the progress achieved in the year 2011 and the future targets for the year 2012 and onwards. INPPO has achieved a successful administrative structure, the Core Committee (CC; composed of President, Vice-President, and General Secretaries), Executive Council (EC), and General Body (GB) to achieve INPPO objectives. Various committees and subcommittees are in the process of being functionalized via discussion amongst scientists around the globe. INPPO's primary aim to popularize the plant proteomics research in biological sciences has also been recognized by PROTEOMICS where a section dedicated to plant proteomics has been introduced starting January 2012, following the very first issue of this journal devoted to plant proteomics in May 2011. To disseminate organizational activities to the scientific community, INPPO has launched a biannual (in January and July) newsletter entitled 'INPPO Express: News & Views' with the first issue published in January 2012. INPPO is also planning to have several activities in 2012, including programs within the Education Outreach committee in different countries, and the development of research ideas and proposals with priority on crop and horticultural plants, while keeping tight interactions with proteomics programs on model plants such as Arabidopsis thaliana, rice, and Medicago truncatula. Altogether, the INPPO progress and upcoming activities

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database

KAUST Repository

Komatsu, Setsuko

2017-05-10

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max ‘Enrei’). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. Biological significanceThe Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database.

Science.gov (United States)

Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

2017-06-23

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max 'Enrei'). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. The Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all predicted proteins from

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database

KAUST Repository

Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

2017-01-01

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max ‘Enrei’). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. Biological significanceThe Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all

Attached and planktonic Listeria monocytogenes global proteomic responses and associated influence of strain genetics and temperature.

Science.gov (United States)

Mata, Marcia M; da Silva, Wladimir P; Wilson, Richard; Lowe, Edwin; Bowman, John P

2015-02-06

Contamination of industrial and domestic food usage environments by the attachement of bacterial food-borne pathogen Listeria monocytogenes has public health and economic implications. Comprehensive proteomics experiments using label-free liquid chromatography/tandem mass spectrometry were used to compare the proteomes of two different L. monocytogenes strains (Siliken_1/2c and F2365_4b), which show very different capacities to attach to surfaces. Growth temperature and strain type were highly influential on the proteomes in both attached and planktonic cells. On the basis of the proteomic data, it is highly unlikely that specific surface proteins play a direct role in adherence to inanimate surfaces. Instead, strain-dependent responses related to cell envelope polymer biosynthesis and stress response regulation likely contribute to a different ability to attach and also to survive external stressors. Collectively, the divergent proteome-level responses observed define strain- and growth-temperature-dependent differences relevant to attachment efficacy, highlight relevant proteins involved in stress protection in attached cells, and suggest that strain differences and growth conditions are important in relation to environmental persistence.

Reference Design Description for a Geologic Repository, Rev. 03, ICN 02

International Nuclear Information System (INIS)

Gerald Shideler

2001-01-01

One of the current major national environmental problems is the safe disposal of large quantities of spent nuclear fuel and high-level radioactive waste materials, which are rapidly accumulating throughout the country. These radioactive byproducts are generated as the result of national defense activities and from the generation of electricity by commercial nuclear power plants. At present, spent nuclear fuel is accumulating at over 70 power plant sites distributed throughout 33 states. The safe disposal of these high-level radioactive materials at a central disposal facility is a high national priority. This Reference Design Description explains the current design for a potential geologic repository that may be located at Yucca Mountain in Nevada for the disposal of spent nuclear fuel and high-level radioactive waste materials. This document describes a possible design for the three fundamental parts of a repository: a surface facility, subsurface repository, and waste packaging. It also presents the current conceptual design of the key engineering systems for the final four phases of repository processes: operations, monitoring, closure, and postclosure. In accordance with current law, this design does not include an interim storage option. In addition, this Reference Design Description reviews the expected long-term performance of the potential repository. It describes the natural barrier system which, together with the engineered systems, achieves the repository objectives. This design will protect the public and the environment by allowing the safe disposal of radioactive waste received from government-owned custodial spent fuel sites, high-level radioactive waste sites, and commercial power reactor sites. All design elements meet or exceed applicable regulations governing the disposal of high-level radioactive waste. The design will provide safe disposal of waste materials for at least a 10,000 year period. During this time interval, natural radioactive decay

Building Public Confidence in Nuclear Activities

International Nuclear Information System (INIS)

Isaacs, T

2002-01-01

Achieving public acceptance has become a central issue in discussions regarding the future of nuclear power and associated nuclear activities. Effective public communication and public participation are often put forward as the key building blocks in garnering public acceptance. A recent international workshop in Finland provided insights into other features that might also be important to building and sustaining public confidence in nuclear activities. The workshop was held in Finland in close cooperation with Finnish stakeholders. This was most appropriate because of the recent successes in achieving positive decisions at the municipal, governmental, and Parliamentary levels, allowing the Finnish high-level radioactive waste repository program to proceed, including the identification and approval of a proposed candidate repository site. Much of the workshop discussion appropriately focused on the roles of public participation and public communications in building public confidence. It was clear that well constructed and implemented programs of public involvement and communication and a sense of fairness were essential in building the extent of public confidence needed to allow the repository program in Finland to proceed. It was also clear that there were a number of other elements beyond public involvement that contributed substantially to the success in Finland to date. And, in fact, it appeared that these other factors were also necessary to achieving the Finnish public acceptance. In other words, successful public participation and communication were necessary but not sufficient. What else was important? Culture, politics, and history vary from country to country, providing differing contexts for establishing and maintaining public confidence. What works in one country will not necessarily be effective in another. Nonetheless, there appear to be certain elements that might be common to programs that are successful in sustaining public confidence and some of

Building Public Confidence in Nuclear Activities

International Nuclear Information System (INIS)

Isaacs, T

2002-01-01

Achieving public acceptance has become a central issue in discussions regarding the future of nuclear power and associated nuclear activities. Effective public communication and public participation are often put forward as the key building blocks in garnering public acceptance. A recent international workshop in Finland provided insights into other features that might also be important to building and sustaining public confidence in nuclear activities. The workshop was held in Finland in close cooperation with Finnish stakeholders. This was most appropriate because of the recent successes in achieving positive decisions at the municipal, governmental, and Parliamentary levels, allowing the Finnish high-level radioactive waste repository program to proceed, including the identification and approval of a proposed candidate repository site Much of the workshop discussion appropriately focused on the roles of public participation and public communications in building public confidence. It was clear that well constructed and implemented programs of public involvement and communication and a sense of fairness were essential in building the extent of public confidence needed to allow the repository program in Finland to proceed. It was also clear that there were a number of other elements beyond public involvement that contributed substantially to the success in Finland to date. And, in fact, it appeared that these other factors were also necessary to achieving the Finnish public acceptance. In other words, successful public participation and communication were necessary but not sufficient. What else was important? Culture, politics, and history vary from country to country, providing differing contexts for establishing and maintaining public confidence. What works in one country will not necessarily be effective in another. Nonetheless, there appear to be certain elements that might be common to programs that are successful in sustaining public confidence, and some of

The proteome of human saliva

Science.gov (United States)

Griffin, Timothy J.

2013-05-01

Human saliva holds tremendous potential for transforming disease and health diagnostics given its richness of molecular information and non-invasive collection. Enumerating its molecular constituents is an important first step towards reaching this potential. Among the molecules in saliva, proteins and peptides arguably have the most value: they can directly indicate biochemical functions linked to a health condition/disease state, and they are attractive targets for biomarker assay development. However, cataloging and defining the human salivary proteome is challenging given the dynamic, chemically heterogeneous and complex nature of the system. In addition, the overall human saliva proteome is composed of several "sub-proteomes" which include: intact full length proteins, proteins carrying post-translational modifications (PTMs), low molecular weight peptides, and the metaproteome, derived from protein products from nonhuman organisms (e.g. microbes) present in the oral cavity. Presented here will be a summary of communal efforts to meet the challenge of characterizing the multifaceted saliva proteome, focusing on the use of mass spectrometry as the proteomic technology of choice. Implications of these efforts to characterize the salivary proteome in the context of disease diagnostics will also be discussed.

Consistency of Network Traffic Repositories: An Overview

NARCIS (Netherlands)

Lastdrager, E.; Lastdrager, E.E.H.; Pras, Aiko

2009-01-01

Traffc repositories with TCP/IP header information are very important for network analysis. Researchers often assume that such repositories reliably represent all traffc that has been flowing over the network; little thoughts are made regarding the consistency of these repositories. Still, for

48 CFR 227.7207 - Contractor data repositories.

Science.gov (United States)

2010-10-01

... repositories. 227.7207 Section 227.7207 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS... Computer Software and Computer Software Documentation 227.7207 Contractor data repositories. Follow 227.7108 when it is in the Government's interests to have a data repository include computer software or to...

Reference repository design concept for bedded salt

Energy Technology Data Exchange (ETDEWEB)

Carpenter, D.W.; Martin, R.W.

1980-10-08

A reference design concept is presented for the subsurface portions of a nuclear waste repository in bedded salt. General geologic, geotechnical, hydrologic and geochemical data as well as descriptions of the physical systems are provided for use on generic analyses of the pre- and post-sealing performance of repositories in this geologic medium. The geology of bedded salt deposits and the regional and repository horizon stratigraphy are discussed. Structural features of salt beds including discontinuities and dissolution features are presented and their effect on repository performance is discussed. Seismic hazards and the potential effects of earthquakes on underground repositories are presented. The effect on structural stability and worker safety during construction from hydrocarbon and inorganic gases is described. Geohydrologic considerations including regional hydrology, repository scale hydrology and several hydrological failure modes are presented in detail as well as the hydrological considerations that effect repository design. Operational phase performance is discussed with respect to operations, ventilation system, shaft conveyances, waste handling and retrieval systems and receival rates of nuclear waste. Performance analysis of the post sealing period of a nuclear repository is discussed, and parameters to be used in such an analysis are presented along with regulatory constraints. Some judgements are made regarding hydrologic failure scenarios. Finally, the design and licensing process, consistent with the current licensing procedure is described in a format that can be easily understood.

Reference repository design concept for bedded salt

International Nuclear Information System (INIS)

Carpenter, D.W.; Martin, R.W.

1980-01-01

A reference design concept is presented for the subsurface portions of a nuclear waste repository in bedded salt. General geologic, geotechnical, hydrologic and geochemical data as well as descriptions of the physical systems are provided for use on generic analyses of the pre- and post-sealing performance of repositories in this geologic medium. The geology of bedded salt deposits and the regional and repository horizon stratigraphy are discussed. Structural features of salt beds including discontinuities and dissolution features are presented and their effect on repository performance is discussed. Seismic hazards and the potential effects of earthquakes on underground repositories are presented. The effect on structural stability and worker safety during construction from hydrocarbon and inorganic gases is described. Geohydrologic considerations including regional hydrology, repository scale hydrology and several hydrological failure modes are presented in detail as well as the hydrological considerations that effect repository design. Operational phase performance is discussed with respect to operations, ventilation system, shaft conveyances, waste handling and retrieval systems and receival rates of nuclear waste. Performance analysis of the post sealing period of a nuclear repository is discussed, and parameters to be used in such an analysis are presented along with regulatory constraints. Some judgements are made regarding hydrologic failure scenarios. Finally, the design and licensing process, consistent with the current licensing procedure is described in a format that can be easily understood

Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment

DEFF Research Database (Denmark)

Welker, F.

2018-01-01

Background: The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identificati......Background: The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein...... not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against......), but roughly half of the mutable PSMs were not recovered. As a result, peptide and protein identification rates are higher in error-tolerant mode compared to non-error-tolerant searches but did not recover protein identifications completely. Data indicates that peptide length and the number of mutations...

POPULATING INSTITUTIONAL REPOSITORY: FACULTY’S CONTRIBUTION AND ROLES OF LIBRARIANS

Directory of Open Access Journals (Sweden)

A. Abrizah

2012-07-01

: (a Understanding the IR software used; (b Publicity and advocacy of IR; (c Establishing an institutional mandate; (d Educating faculty regarding self-archiving issues; (e Submission review for content and metadata; and (f Training of authors. Based on methodical IR development informed by best practices in the Open Access community, the findings from this study have been used for repository design customizations and functionality enhancements that complement the needs, interests and concerns of the faculty. An outcome of the research is an institutional repository (IR to support for a new pattern for scholarly communication, apart from servicing the university’s research output.

Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

KAUST Repository

Marondedze, Claudius; Wong, Aloysius Tze; Groen, Arnoud; Serano, Natalia Lorena Gorron; Jankovic, Boris R.; Lilley, Kathryn; Gehring, Christoph A; Thomas, Ludivine

2014-01-01

The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins.

Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

Directory of Open Access Journals (Sweden)

Claudius Marondedze

2014-12-01

Full Text Available The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins.

Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

KAUST Repository

Marondedze, Claudius

2014-12-31

The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins.

Hydrothermal conditions around a radioactive waste repository

International Nuclear Information System (INIS)

Thunvik, R.; Braester, C.

1981-12-01

Numerical solutions for the hydrothermal conditions around a hard rock repository for nuclear fuel waste are presented. The objective of the present investigation is to illustrate in principle the effect of heat released from a hypothetical radioactive waste repository with regard to anisotropy in the rock permeability. Permeability and porosity are assumed to be constant or to decrease exponentially with depth. The hypothetical repository is situated below a horizontal ground surface or below the crest of a hill, and it is assumed that the water table follows the topography. Major interest in the analysis is directed towards the influence of anisotropy in the permeability on the flow patterns and travel times for water particles, being traced from the repository to the ground surface. The presented results show that anisotropy in the permeability may have a significant influence on the flow conditions around the repository and subsequently also on the travel times from the repository. (Authors)

Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage.

Science.gov (United States)

Van, Phu T; Schmid, Amy K; King, Nichole L; Kaur, Amardeep; Pan, Min; Whitehead, Kenia; Koide, Tie; Facciotti, Marc T; Goo, Young Ah; Deutsch, Eric W; Reiss, David J; Mallick, Parag; Baliga, Nitin S

2008-09-01

The relatively small numbers of proteins and fewer possible post-translational modifications in microbes provide a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a PeptideAtlas (PA) covering 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636 000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has highlighted plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore, we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics.

Repository operational criteria comparative analysis

International Nuclear Information System (INIS)

Hageman, J.P.; Chowdhury, A.H.

1994-06-01

The objective of the ''Repository Operational Criteria (ROC) Feasibility Studies'' (or ROC task) was to conduct comprehensive and integrated analyses of repository design, construction, and operations criteria in 10 CFR Part 60 regulations considering the interfaces among the components of the regulations and impacts of any potential changes to those regulations. The ROC task addresses regulatory criteria and uncertainties related to the preclosure aspects of the geologic repository. Those parts of 10 CFR Part 60 that require routine guidance or minor changes to the rule were addressed in Hageman and Chowdhury, 1992. The ROC task shows a possible need for further regulatory clarity, by major changes to the rule, related to the design bases and siting of a geologic repository operations area and radiological emergency planning in order to assure defense-in-depth. The analyses, presented in this report, resulted in the development and refinement of regulatory concepts and their supporting rationale for recommendations for potential major changes to 10 CFR Pan 0 regulations

Network-based analysis of proteomic profiles

KAUST Repository

Wong, Limsoon

2016-01-26

Mass spectrometry (MS)-based proteomics is a widely used and powerful tool for profiling systems-wide protein expression changes. It can be applied for various purposes, e.g. biomarker discovery in diseases and study of drug responses. Although RNA-based high-throughput methods have been useful in providing glimpses into the underlying molecular processes, the evidences they provide are indirect. Furthermore, RNA and corresponding protein levels have been known to have poor correlation. On the other hand, MS-based proteomics tend to have consistency issues (poor reproducibility and inter-sample agreement) and coverage issues (inability to detect the entire proteome) that need to be urgently addressed. In this talk, I will discuss how these issues can be addressed by proteomic profile analysis techniques that use biological networks (especially protein complexes) as the biological context. In particular, I will describe several techniques that we have been developing for network-based analysis of proteomics profile. And I will present evidence that these techniques are useful in identifying proteomics-profile analysis results that are more consistent, more reproducible, and more biologically coherent, and that these techniques allow expansion of the detected proteome to uncover and/or discover novel proteins.

Arabidopsis peroxisome proteomics

Directory of Open Access Journals (Sweden)

John D. Bussell

2013-04-01

Full Text Available The analytical depth of investigation of the peroxisomal proteome of the model plant Arabidopsis thaliana has not yet reached that of other major cellular organelles such as chloroplasts or mitochondria. This is primarily due to the difficulties associated with isolating and obtaining purified samples of peroxisomes from Arabidopsis. So far only a handful of research groups have been successful in obtaining such fractions. To make things worse, enriched peroxisome fractions frequently suffer from significant organellar contamination, lowering confidence in localization assignment of the identified proteins. As with other cellular compartments, identification of peroxisomal proteins forms the basis for investigations of the dynamics of the peroxisomal proteome. It is therefore not surprising that, in terms of functional analyses by proteomic means, there remains a considerable gap between peroxisomes and chloroplasts or mitochondria. Alternative strategies are needed to overcome the obstacle of hard-to-obtain organellar fractions. This will help to close the knowledge gap between peroxisomes and other organelles and provide a full picture of the physiological pathways shared between organelles. In this review we briefly summarize the status quo and discuss some of the methodological alternatives to classic organelle proteomic approaches.

Citing and Reading Behaviours in High-Energy Physics : How a Community Stopped Worrying about Journals and Learned to Love Repositories

CERN Document Server

Gentil-Beccot, A; Brooks, T

2010-01-01

Contemporary scholarly discourse follows many alternative routes in addition to the three-century old tradition of publication in peer-reviewed journals. The field of High- Energy Physics (HEP) has explored alternative communication strategies for decades, initially via the mass mailing of paper copies of preliminary manuscripts, then via the inception of the first online repositories and digital libraries. This field is uniquely placed to answer recurrent questions raised by the current trends in scholarly communication: is there an advantage for scientists to make their work available through repositories, often in preliminary form? Is there an advantage to publishing in Open Access journals? Do scientists still read journals or do they use digital repositories? The analysis of citation data demonstrates that free and immediate online dissemination of preprints creates an immense citation advantage in HEP, whereas publication in Open Access journals presents no discernible advantage. In addition, the analys...

What do we mean by a cold repository?

International Nuclear Information System (INIS)

Halsey, W.G.

1994-01-01

The topic of thermal loading of a potential repository at Yucca Mountain in Nevada has been the subject of intense discussion within the project technical community. While terms such as ''Hot Repository'' and ''Cold Repository'' are frequently used, they have not been clearly defined. In particular, the definition of a cold repository has remained the opinion of each individual. This has led to confusion and misunderstanding. In this paper, a number of observed definitions for a cold repository are discussed along with the technical implications, assumptions and inconsistencies. Finally, a common language is suggested

Records for radioactive waste management up to repository closure: Managing the primary level information (PLI) set

International Nuclear Information System (INIS)

2004-07-01

The objective of this publication is to highlight the importance of the early establishment of a comprehensive records system to manage primary level information (PLI) as an integrated set of information, not merely as a collection of information, throughout all the phases of radioactive waste management. Early establishment of a comprehensive records system to manage Primary Level Information as an integrated set of information throughout all phases of radioactive waste management is important. In addition to the information described in the waste inventory record keeping system (WIRKS), the PLI of a radioactive waste repository consists of the entire universe of information, data and records related to any aspect of the repository's life cycle. It is essential to establish PLI requirements based on integrated set of needs from Regulators and Waste Managers involved in the waste management chain and to update these requirements as needs change over time. Information flow for radioactive waste management should be back-end driven. Identification of an Authority that will oversee the management of PLI throughout all phases of the radioactive waste management life cycle would guarantee the information flow to future generations. The long term protection of information essential to future generations can only be assured by the timely establishment of a comprehensive and effective RMS capable of capturing, indexing and evaluating all PLI. The loss of intellectual control over the PLI will make it very difficult to subsequently identify the ILI and HLI information sets. At all times prior to the closure of a radioactive waste repository, there should be an identifiable entity with a legally enforceable financial and management responsibility for the continued operation of a PLI Records Management System. The information presented in this publication will assist Member States in ensuring that waste and repository records, relevant for retention after repository closure

Proteomics Insights into Autophagy.

Science.gov (United States)

Cudjoe, Emmanuel K; Saleh, Tareq; Hawkridge, Adam M; Gewirtz, David A

2017-10-01

Autophagy, a conserved cellular process by which cells recycle their contents either to maintain basal homeostasis or in response to external stimuli, has for the past two decades become one of the most studied physiological processes in cell biology. The 2016 Nobel Prize in Medicine and Biology awarded to Dr. Ohsumi Yoshinori, one of the first scientists to characterize this cellular mechanism, attests to its importance. The induction and consequent completion of the process of autophagy results in wide ranging changes to the cellular proteome as well as the secretome. MS-based proteomics affords the ability to measure, in an unbiased manner, the ubiquitous changes that occur when autophagy is initiated and progresses in the cell. The continuous improvements and advances in mass spectrometers, especially relating to ionization sources and detectors, coupled with advances in proteomics experimental design, has made it possible to study autophagy, among other process, in great detail. Innovative labeling strategies and protein separation techniques as well as complementary methods including immuno-capture/blotting/staining have been used in proteomics studies to provide more specific protein identification. In this review, we will discuss recent advances in proteomics studies focused on autophagy. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Semantically Enabled Metadata Repository for Solar Irradiance Data Products

Science.gov (United States)

Wilson, A.; Cox, M.; Lindholm, D. M.; Nadiadi, I.; Traver, T.

2014-12-01

The Laboratory for Atmospheric and Space Physics, LASP, has been conducting research in Atmospheric and Space science for over 60 years, and providing the associated data products to the public. LASP has a long history, in particular, of making space-based measurements of the solar irradiance, which serves as crucial input to several areas of scientific research, including solar-terrestrial interactions, atmospheric, and climate. LISIRD, the LASP Interactive Solar Irradiance Data Center, serves these datasets to the public, including solar spectral irradiance (SSI) and total solar irradiance (TSI) data. The LASP extended metadata repository, LEMR, is a database of information about the datasets served by LASP, such as parameters, uncertainties, temporal and spectral ranges, current version, alerts, etc. It serves as the definitive, single source of truth for that information. The database is populated with information garnered via web forms and automated processes. Dataset owners keep the information current and verified for datasets under their purview. This information can be pulled dynamically for many purposes. Web sites such as LISIRD can include this information in web page content as it is rendered, ensuring users get current, accurate information. It can also be pulled to create metadata records in various metadata formats, such as SPASE (for heliophysics) and ISO 19115. Once these records are be made available to the appropriate registries, our data will be discoverable by users coming in via those organizations. The database is implemented as a RDF triplestore, a collection of instances of subject-object-predicate data entities identifiable with a URI. This capability coupled with SPARQL over HTTP read access enables semantic queries over the repository contents. To create the repository we leveraged VIVO, an open source semantic web application, to manage and create new ontologies and populate repository content. A variety of ontologies were used in

Radioactive waste repository study

International Nuclear Information System (INIS)

1978-11-01

This is the first part of a report of a preliminary study for Atomic Energy of Canada Limited. It considers the requirements for an underground waste repository for the disposal of wastes produced by the Canadian Nuclear Fuel Program. The following topics are discussed with reference to the repository: 1) underground layout, 2) cost estimates, 3) waste handling, 4) retrievability, decommissioning, sealing and monitoring, and 5) research and design engineering requirements. (author)

MAJOR REPOSITORY DESIGN ISSUES

International Nuclear Information System (INIS)

JACK N. BAILEY, DWAYNE CHESTNUT, JAMES COMPTON AND RICHARD D. SNELL

1997-01-01

The Yucca Mountain Project is focused on producing a four-part viability assessment in late FY98. Its four components (design, performance assessment, cost estimate, and licensing development plan) must be consistent. As a tool to compare design and performance assessment options, a series of repository pictures were developed for the sequential time phases of a repository. The boundaries of the time phases correspond to evolution in the engineered barrier system (EBS)

Preclosure seismic design methodology for a geologic repository at Yucca Mountain. Topical report YMP/TR-003-NP

International Nuclear Information System (INIS)

1996-10-01

This topical report describes the methodology and criteria that the U.S. Department of Energy (DOE) proposes to use for preclosure seismic design of structures, systems, and components (SSCs) of the proposed geologic repository operations area that are important to safety. Title 10 of the Code of Federal Regulations, Part 60 (10 CFR 60), Disposal of High-Level Radioactive Wastes in Geologic Repositories, states that for a license to be issued for operation of a high-level waste repository, the U.S. Nuclear Regulatory Commission (NRC) must find that the facility will not constitute an unreasonable risk to the health and safety of the public. Section 60.131 (b)(1) requires that SSCs important to safety be designed so that natural phenomena and environmental conditions anticipated at the geologic repository operations area will not interfere with necessary safety functions. Among the natural phenomena specifically identified in the regulation as requiring safety consideration are the hazards of ground shaking and fault displacement due to earthquakes

An analysis of repository waste-handling operations

International Nuclear Information System (INIS)

Dennis, A.W.

1990-09-01

This report has been prepared to document the operational analysis of waste-handling facilities at a geologic repository for high-level nuclear waste. The site currently under investigation for the geologic repository is located at Yucca Mountain, Nye County, Nevada. The repository waste-handling operations have been identified and analyzed for the year 2011, a steady-state year during which the repository receives spent nuclear fuel containing the equivalent of 3000 metric tons of uranium (MTU) and defense high-level waste containing the equivalent of 400 MTU. As a result of this analysis, it has been determined that the waste-handling facilities are adequate to receive, prepare, store, and emplace the projected quantity of waste on an annual basis. In addition, several areas have been identified where additional work is required. The recommendations for future work have been divided into three categories: items that affect the total waste management system, operations within the repository boundary, and the methodology used to perform operational analyses for repository designs. 7 refs., 48 figs., 11 tabs

Social impact mitigation and nuclear waste repository siting

International Nuclear Information System (INIS)

Peelle, E.

1980-01-01

Some aspects of the socioeconomic impacts of siting, constructing, and operating radioactive waste repositories in rural areas are discussed. These include public perceptions of high risk and uncertainty; limited benefits and no incentives; dissociations of costs and benefits; remoteness and inaccessibility of the decision making process for large energy facilities; no institutions to provide protection and accountability for those who may be affected by the siting; the fact that not all risks or impacts are fully mitigable; and constraints on DOE's present ability or authority to mitigate impacts

[Progress in stable isotope labeled quantitative proteomics methods].

Science.gov (United States)

Zhou, Yuan; Shan, Yichu; Zhang, Lihua; Zhang, Yukui

2013-06-01

Quantitative proteomics is an important research field in post-genomics era. There are two strategies for proteome quantification: label-free methods and stable isotope labeling methods which have become the most important strategy for quantitative proteomics at present. In the past few years, a number of quantitative methods have been developed, which support the fast development in biology research. In this work, we discuss the progress in the stable isotope labeling methods for quantitative proteomics including relative and absolute quantitative proteomics, and then give our opinions on the outlook of proteome quantification methods.

Memory provisions for the Manche Surface Repository

International Nuclear Information System (INIS)

Dumont, Jean-Noel; Espiet-Subert, Florence

2015-01-01

The French La Manche repository site received its last radioactive waste package in 1994. In 2003, the official surveillance phase of the closed repository started under the supervision of Andra (the national industrial operator), the French Nuclear Safety Authority (ASN) and society (e.g. the local municipalities). Florence Espiet explained that information on the existence of the repository, its content, how it was operated and how it works needs to be preserved. It also is planned to review the information periodically for a minimum of 300 years. She described the creation of two documents on memory (a detailed and a summary one), both on permanent paper, and the preservation of the land registration. The latter constitutes 'passive' provisions for preserving memory. In addition, a number of 'active' provisions are and will be put in place: guided visits, exhibitions, partnerships with organisations dealing with memory preservation, and the creation of a think tank. The latter consists of local citizens and politicians, retired employees from Andra and artists that meet several times a year and reflect on memory preservation from the perspective of, for instance, local history, education, arts and rituals. Finally, two types of markers will be used to preserve the repository's memory: i) three herbaria cataloguing the plants growing on the site of the repository, including a very short description of the repository, will be stored at different sites in France; ii) a stele indicating the main characteristics of the repository, potentially linked to an art work, will be erected at the repository

NIH Common Fund - Disruptive Proteomics Technologies - Challenges and Opportunities | Office of Cancer Clinical Proteomics Research

Science.gov (United States)

This Request for Information (RFI) is directed toward determining how best to accelerate research in disruptive proteomics technologies. The Disruptive Proteomics Technologies (DPT) Working Group of the NIH Common Fund wishes to identify gaps and opportunities in current technologies and methodologies related to proteome-wide measurements.  For the purposes of this RFI, “disruptive” is defined as very rapid, very significant gains, similar to the "disruptive" technology development that occurred in DNA sequencing technology.

A decade of proteomics accomplished! Central and Eastern European Proteomic Conference (CEEPC) celebrates its 10th Anniversary in Budapest, Hungary.

Science.gov (United States)

Gadher, Suresh Jivan; Drahos, László; Vékey, Károly; Kovarova, Hana

2017-07-01

The Central and Eastern European Proteomic Conference (CEEPC) proudly celebrated its 10th Anniversary with an exciting scientific program inclusive of proteome, proteomics and systems biology in Budapest, Hungary. Since 2007, CEEPC has represented 'state-of the-art' proteomics in and around Central and Eastern Europe and these series of conferences have become a well-recognized event in the proteomic calendar. Fresher challenges and global healthcare issues such as ageing and chronic diseases are driving clinical and scientific research towards regenerative, reparative and personalized medicine. To this end, proteomics may enable diverse intertwining research fields to reach their end goals. CEEPC will endeavor to facilitate these goals.

Environmental impact assessments and geological repositories: A model process

International Nuclear Information System (INIS)

Webster, S.

2000-01-01

In a recent study carried out for the European Commission, the scope and application of environmental impact assessment (EIA) legislation and current EIA practice in European Union Member States and applicant countries of Central and Eastern Europe was investigated, specifically in relation to the geological disposal of radioactive waste. This paper reports the study's investigations into a model approach to EIA in the context of geological repositories, including the role of the assessment in the overall decision processes and public involvement. (author)

Proteome reference map of Drosophila melanogaster head.

Science.gov (United States)

Lee, Tian-Ren; Huang, Shun-Hong; Lee, Chi-Ching; Lee, Hsiao-Yun; Chan, Hsin-Tzu; Lin, Kuo-Sen; Chan, Hong-Lin; Lyu, Ping-Chiang

2012-06-01

Drosophila melanogaster has been used as a genetic model organism to understand the fundamental molecular mechanisms in human biology including memory formation that has been reported involving protein synthesis and/or post-translational modification. In this study, we employed a proteomic platform based on fluorescent 2DE and MALDI-TOF MS to build a standard D. melanogaster head proteome map for proteome-proteome comparison. In order to facilitate the comparison, an interactive database has been constructed for systematically integrating and analyzing the proteomes from different conditions and further implicated to study human diseases related to D. melanogaster model. In summary, the fundamental head proteomic database and bioinformatic analysis will be useful for further elucidating the biological mechanisms such as memory formation and neurodegenerative diseases. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Safety analysis in subsurface repositories

International Nuclear Information System (INIS)

1985-06-01

The development of mathematical models to represent the repository-geosphere-biosphere system, and the development of a structure for data acquisition, processing, and use to analyse the safety of subsurface repositories, are presented. To study the behavior of radionuclides in geosphere a laboratory to determine the hydrodynamic dispersion coefficient was constructed. (M.C.K.) [pt

How many geologic repositories will be needed

International Nuclear Information System (INIS)

Evans, T.J.; Halstead, R.J.

1987-01-01

DOE's postponement of site-specific work on the second repository program had rekindled debate over the number of geologic repositories needed for disposal of high level radioactive waste. The multiple repository approach grew out of the March, 1979 IRG report, which recommended co-disposal of civilian and defense HLW in a system of regional repositories. The multiple repository approach was adopted by DOE, and incorporated in the Nuclear Waste Policy Act passed by Congress in December, 1982. Since the late 1970's, the slower than anticipated growth of the nuclear power industry has substantially reduced earlier estimates of the amount of civilian spent fuel which will require geologic disposal. Reactors currently in operation (78.5 GWe) and reactors in the construction pipeline (28 GWe) are expected to discharge about 103,200 MTU of spent fuel by the year 2036, assuming no increase in fuel burnup rate. By the year 2020, defense high level radioactive wastes equivalent to as much as 27,000 MTU could require geologic disposal. Small amounts of high level waste from other sources will also require geologic disposal. Total disposal requirements appear to be less than 140,000 MTU. The five sites nominated for the first repository, as well as hypothetical sites in granite, the host rock under primary consideration for the second repository, all appear capable of accommodating up to 140,000 MTU

Refinancing of the search for a repository and of the repository for heat generating radioactive waste. Pt. 1

International Nuclear Information System (INIS)

Moench, Christoph

2013-01-01

The final disposal of radioactive waste is a state task that is assigned to the Federal Government pursuant to section 9a (3) sentence 1 of the Atomic Energy Act (AtG). Since the early 1970's, the Federal Government has been actively searching for and exploring final disposal sites for radioactive waste. In a proceeding accompanied by the intensive participation of technical experts and the public, the Gorleben salt dome (Salzstock) has emerged as a presumably suitable disposal site from a mining standpoint (eignungshoeffig) according to the current status of the exploration. The cost of these exploratory measures - and the subsequent construction - will be financed by the waste producers, in particular the utility companies, by means of advance payments on their contributions. Part I of this article will evaluate the selection and exploration of the Gorleben salt dome to date and examine the provisions on the pre-financing burden from the point of view of constitutional law. Constitutional objections can also be raised against the regulation in section 21b (4) AtG that was introduced in 1998, which excludes a refunding of the pre-financing contributions even if the repository is never erected or operated. Part II of this article, which will appear in the next issue, will take up the question of whether a search for an alternative repository site, as the Federal Ministry for the Environment (BMU) envisions in the working draft of an 'Act on the search for and selection of a site for a repository for heat generating radioactive waste' (Gesetz zur Suche und Auswahl eines Standortes fuer ein Endlager fuer waermeentwickelnde radioaktive Abfaelle), is likewise to be refinanced as a contribution by the parties obliged to make advance payments. (orig.)

Digital Repositories An investigation of best practices for content recruitment to academic digital repositories and the conditions for their livelihood

CERN Document Server

Hagen, Reidun Anette

2009-01-01

A digital repository is a web accessible database, aimed at preserving the research material of an institution or scientific community. A digital repository serves as a tool for dissemination of research material and can increase the impact of the research by making it freely accessible. Digital repositories are often mentioned as a possible aid in relation to the Open Access debate; how research material should be freely accessible to anyone, anywhere at any time. However, for a digital repository to fully unleash its potential as a crucial component of Open Access, it is reliant on the ability to successfully collect and organize content. To a large extent this involves initiating self-archiving of research material by scientists throughout the academic world. This is not a trivial task, and many current repositories are inadequate in this respect, remaining empty, unvisited shelves. This thesis explores best practices for content recruitment to digital repositories, through the review of literature, and an...

Proteomics in pulmonary research: selected methodical aspects

Directory of Open Access Journals (Sweden)

Martin Petrek

2007-10-01

Full Text Available Recent years witness rapid expansion of applications of proteomics to clinical research including non-malignant lung disorders. These developments bring along the need for standardisation of proteomic experiments. This paper briefly reviews basic methodical aspects of appliedproteomic studies using SELDI-TOF mass spectrometry platform as example but also emphasizes general aspects of quality assurance in proteomics. Key-words: lung proteome, quality assurance, SELDI-TOF MS

PolicyNet Publication System

Data.gov (United States)

Social Security Administration — The PolicyNet Publication System project will merge the Oracle-based Policy Repository (POMS) and the SQL-Server CAMP system (MSOM) into a new system with an Oracle...

Genome Variation Map: a data repository of genome variations in BIG Data Center

OpenAIRE

Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

2017-01-01

Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research a...

The potato tuber mitochondrial proteome

DEFF Research Database (Denmark)

Salvato, Fernanda; Havelund, Jesper Foged; Chen, Mingjie

2014-01-01

Mitochondria are called the powerhouses of the cell. To better understand the role of mitochondria in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from dormant potato tubers (Solanum tuberosum 'Folva') and their proteome investigated. Proteins...... manner using normalized spectral counts including as many as 5-fold more "extreme" proteins (low mass, high isoelectric point, hydrophobic) than previous mitochondrial proteome studies. We estimate that this compendium of proteins represents a high coverage of the potato tuber mitochondrial proteome...

Low and Intermediate Level Waste Repository: Radiation and Public

International Nuclear Information System (INIS)

Cerskov Klika, M.

1998-01-01

Some of basic elements related to public participation in radioactive waste management in Croatia are underlined in the paper. Most of them are created or led by the APO-Hazardous Waste Management Agency. Present efforts in improvement of public participation in the field radioactive waste management are important in particular due to negligible role of public in environmentally related issues during former Yugoslav political system. For this reason it is possible to understand the public fearing to be deceived or neglected again. Special attention is paid to the current APO editions related to public information and education in the field of radioactive waste management. It is important because only the well-informed public can present an active and respectful factor in hazardous and radioactive waste management process. (author)

Secreted autoantibody repertoires in Sjögren's syndrome and systemic lupus erythematosus: A proteomic approach.

Science.gov (United States)

Al Kindi, Mahmood A; Colella, Alex D; Chataway, Tim K; Jackson, Michael W; Wang, Jing J; Gordon, Tom P

2016-04-01

The structures of epitopes bound by autoantibodies against RNA-protein complexes have been well-defined over several decades, but little is known of the clonality, immunoglobulin (Ig) variable (V) gene usage and mutational status of the autoantibodies themselves at the level of the secreted (serum) proteome. A novel proteomic workflow is presented based on affinity purification of specific Igs from serum, high-resolution two-dimensional gel electrophoresis, and de novo and database-driven sequencing of V-region proteins by mass spectrometry. Analysis of anti-Ro52/Ro60/La proteomes in primary Sjögren's syndrome (SS) and anti-Sm and anti-ribosomal P proteomes in systemic lupus erythematosus (SLE) has revealed that these antibody responses are dominated by restricted sets of public (shared) clonotypes, consistent with common pathways of production across unrelated individuals. The discovery of shared sets of specific V-region peptides can be exploited for diagnostic biomarkers in targeted mass spectrometry platforms and for tracking and removal of pathogenic clones. Copyright © 2016 Elsevier B.V. All rights reserved.

Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles)*

Science.gov (United States)

Kinsinger, Christopher R.; Apffel, James; Baker, Mark; Bian, Xiaopeng; Borchers, Christoph H.; Bradshaw, Ralph; Brusniak, Mi-Youn; Chan, Daniel W.; Deutsch, Eric W.; Domon, Bruno; Gorman, Jeff; Grimm, Rudolf; Hancock, William; Hermjakob, Henning; Horn, David; Hunter, Christie; Kolar, Patrik; Kraus, Hans-Joachim; Langen, Hanno; Linding, Rune; Moritz, Robert L.; Omenn, Gilbert S.; Orlando, Ron; Pandey, Akhilesh; Ping, Peipei; Rahbar, Amir; Rivers, Robert; Seymour, Sean L.; Simpson, Richard J.; Slotta, Douglas; Smith, Richard D.; Stein, Stephen E.; Tabb, David L.; Tagle, Danilo; Yates, John R.; Rodriguez, Henry

2011-01-01

Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the United States National Cancer Institute convened the “International Workshop on Proteomic Data Quality Metrics” in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed up on two primary needs for the wide use of quality metrics: 1) an evolving list of comprehensive quality metrics and 2) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in the Journal of Proteome Research, Molecular and Cellular Proteomics, Proteomics, and Proteomics Clinical Applications as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals. PMID:22052993

Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles)

Science.gov (United States)

Kinsinger, Christopher R.; Apffel, James; Baker, Mark; Bian, Xiaopeng; Borchers, Christoph H.; Bradshaw, Ralph; Brusniak, Mi-Youn; Chan, Daniel W.; Deutsch, Eric W.; Domon, Bruno; Gorman, Jeff; Grimm, Rudolf; Hancock, William; Hermjakob, Henning; Horn, David; Hunter, Christie; Kolar, Patrik; Kraus, Hans-Joachim; Langen, Hanno; Linding, Rune; Moritz, Robert L.; Omenn, Gilbert S.; Orlando, Ron; Pandey, Akhilesh; Ping, Peipei; Rahbar, Amir; Rivers, Robert; Seymour, Sean L.; Simpson, Richard J.; Slotta, Douglas; Smith, Richard D.; Stein, Stephen E.; Tabb, David L.; Tagle, Danilo; Yates, John R.; Rodriguez, Henry

2011-01-01

Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the U.S. National Cancer Institute (NCI) convened the “International Workshop on Proteomic Data Quality Metrics” in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed up on two primary needs for the wide use of quality metrics: (1) an evolving list of comprehensive quality metrics and (2) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in the Journal of Proteome Research, Molecular and Cellular Proteomics, Proteomics, and Proteomics Clinical Applications as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals. PMID:22053864

Building Scientific Data's list of recommended data repositories

Science.gov (United States)

Hufton, A. L.; Khodiyar, V.; Hrynaszkiewicz, I.

2016-12-01

When Scientific Data launched in 2014 we provided our authors with a list of recommended data repositories to help them identify data hosting options that were likely to meet the journal's requirements. This list has grown in size and scope, and is now a central resource for authors across the Nature-titled journals. It has also been used in the development of data deposition policies and recommended repository lists across Springer Nature and at other publishers. Each new addition to the list is assessed according to a series of criteria that emphasize the stability of the resource, its commitment to principles of open science and its implementation of relevant community standards and reporting guidelines. A preference is expressed for repositories that issue digital object identifiers (DOIs) through the DataCite system and that share data under the Creative Commons CC0 waiver. Scientific Data currently lists fourteen repositories that focus on specific areas within the Earth and environmental sciences, as well as the broad scope repositories, Dryad and figshare. Readers can browse and filter datasets published at the journal by the host repository using ISA-explorer, a demo tool built by the ISA-tools team at Oxford University1. We believe that well-maintained lists like this one help publishers build a network of trust with community data repositories and provide an important complement to more comprehensive data repository indices and more formal certification efforts. In parallel, Scientific Data has also improved its policies to better support submissions from authors using institutional and project-specific repositories, without requiring each to apply for listing individually. Online resources Journal homepage: http://www.nature.com/scientificdata Data repository criteria: http://www.nature.com/sdata/policies/data-policies#repo-criteria Recommended data repositories: http://www.nature.com/sdata/policies/repositories Archived copies of the list: https

References: AePW publications

Data.gov (United States)

National Aeronautics and Space Administration — This page is the repository for the publications resulting from the AePW. This includes the special sessions at conferences: AIAA ASM 2012, Grapevine TX; AIAA SDM...

SUMMIT (Serially Unified Multicenter Multiple Sclerosis Investigation): creating a repository of deeply phenotyped contemporary multiple sclerosis cohorts.

Science.gov (United States)

Bove, Riley; Chitnis, Tanuja; Cree, Bruce Ac; Tintoré, Mar; Naegelin, Yvonne; Uitdehaag, Bernard Mj; Kappos, Ludwig; Khoury, Samia J; Montalban, Xavier; Hauser, Stephen L; Weiner, Howard L

2017-08-01

There is a pressing need for robust longitudinal cohort studies in the modern treatment era of multiple sclerosis. Build a multiple sclerosis (MS) cohort repository to capture the variability of disability accumulation, as well as provide the depth of characterization (clinical, radiologic, genetic, biospecimens) required to adequately model and ultimately predict a patient's course. Serially Unified Multicenter Multiple Sclerosis Investigation (SUMMIT) is an international multi-center, prospectively enrolled cohort with over a decade of comprehensive follow-up on more than 1000 patients from two large North American academic MS Centers (Brigham and Women's Hospital (Comprehensive Longitudinal Investigation of Multiple Sclerosis at the Brigham and Women's Hospital (CLIMB; BWH)) and University of California, San Francisco (Expression/genomics, Proteomics, Imaging, and Clinical (EPIC))). It is bringing online more than 2500 patients from additional international MS Centers (Basel (Universitätsspital Basel (UHB)), VU University Medical Center MS Center Amsterdam (MSCA), Multiple Sclerosis Center of Catalonia-Vall d'Hebron Hospital (Barcelona clinically isolated syndrome (CIS) cohort), and American University of Beirut Medical Center (AUBMC-Multiple Sclerosis Interdisciplinary Research (AMIR)). We provide evidence for harmonization of two of the initial cohorts in terms of the characterization of demographics, disease, and treatment-related variables; demonstrate several proof-of-principle analyses examining genetic and radiologic predictors of disease progression; and discuss the steps involved in expanding SUMMIT into a repository accessible to the broader scientific community.

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.

Science.gov (United States)

Cole, Charles; Krampis, Konstantinos; Karagiannis, Konstantinos; Almeida, Jonas S; Faison, William J; Motwani, Mona; Wan, Quan; Golikov, Anton; Pan, Yang; Simonyan, Vahan; Mazumder, Raja

2014-01-27

from the CSR website (http://hive.biochemistry.gwu.edu/dna.cgi?cmd=csr). Availability of thousands of sequenced samples from patients provides a rich repository of sequence information that can be utilized to identify individual level SNVs and their effect on the human proteome beyond what the dbSNP database provides.

Management of radioactive waste at Novi Han Repository

International Nuclear Information System (INIS)

Stefanova, I.G.; Mateeva, M.D.; Milanov, M.V.

2002-01-01

The Novi Han Repository is the only existing repository in Bulgaria for the disposal of radioactive waste from nuclear applications in industry, medicine and research. The repository was constructed in the early sixties according to the existing requirements. It was operated by the Institute for Nuclear Research and Nuclear Energy for more than thirty years without any accident or release of radioactivity to the environment, but without any investment for upgrading. As a consequence, the Bulgarian Nuclear Safety Authority temporarily stopped the operation of the repository in 1994. The measures for upgrading the Novi Han Repository, supported by the IAEA under TC Project BUL/4/005 'Increasing Safety of Novi Han Repository', are presented in this paper. They comprise: assessment of radionuclide inventory and future waste arisings, characterisation of disposal vaults, characterisation of the site, safety assessment, upgrading of the monitoring system, option study for the selection of treatment and conditioning processes and the development of a conceptual design for low and intermediate level waste processing and storage facility, immediate measures for improvement of the existing disposal vaults and infrastructure, construction of above-ground temporary storage structures, and resuming the operation of the Novi Han Repository. The necessary activities for re-licensing of the Novi Han Repository, construction of a waste processing and storage facility and a disposal facility for spent sealed sources are discussed. (author)

Safeguarding Structural Data Repositories against Bad Apples.

Science.gov (United States)

Minor, Wladek; Dauter, Zbigniew; Helliwell, John R; Jaskolski, Mariusz; Wlodawer, Alexander

2016-02-02

Structural biology research generates large amounts of data, some deposited in public databases or repositories, but a substantial remainder never becomes available to the scientific community. In addition, some of the deposited data contain less or more serious errors that may bias the results of data mining. Thorough analysis and discussion of these problems is needed to ameliorate this situation. This perspective is an attempt to propose some solutions and encourage both further discussion and action on the part of the relevant organizations, in particular the PDB and various bodies of the International Union of Crystallography. Copyright © 2016 Elsevier Ltd. All rights reserved.

Red blood cell (RBC) membrane proteomics--Part I: Proteomics and RBC physiology.

Science.gov (United States)

Pasini, Erica M; Lutz, Hans U; Mann, Matthias; Thomas, Alan W

2010-01-03

Membrane proteomics is concerned with accurately and sensitively identifying molecules involved in cell compartmentalisation, including those controlling the interface between the cell and the outside world. The high lipid content of the environment in which these proteins are found often causes a particular set of problems that must be overcome when isolating the required material before effective HPLC-MS approaches can be performed. The membrane is an unusually dynamic cellular structure since it interacts with an ever changing environment. A full understanding of this critical cell component will ultimately require, in addition to proteomics, lipidomics, glycomics, interactomics and study of post-translational modifications. Devoid of nucleus and organelles in mammalian species other than camelids, and constantly in motion in the blood stream, red blood cells (RBCs) are the sole mammalian oxygen transporter. The fact that mature mammalian RBCs have no internal membrane-bound organelles, somewhat simplifies proteomics analysis of the plasma membrane and the fact that it has no nucleus disqualifies microarray based methods. Proteomics has the potential to provide a better understanding of this critical interface, and thereby assist in identifying new approaches to diseases. (c) 2009 Elsevier B.V. All rights reserved.

CAED Document Repository

Data.gov (United States)

U.S. Environmental Protection Agency — Compliance Assurance and Enforcement Division Document Repository (CAEDDOCRESP) provides internal and external access of Inspection Records, Enforcement Actions, and...

Evaluation on radiation protection aspect and radiological risk at Mukim Belanja repository

Energy Technology Data Exchange (ETDEWEB)

Azmi, Siti Nur Aisyah, E-mail: nuclear.aisyahazmi@gmail.com; Kenoh, Hamiza; Majid, Amran Ab. [Nuclear Technology Research Centre, Universiti Kebangsaan Malaysia, Bangi, Selangor (Malaysia)

2016-01-22

Asian Rare Earth (ARE) is a locally incorporated company that operated a mineral processing operation to extract rare earth element. ARE has received much attention from the public since the beginning of their operation until the work of decommissioning and decontamination of the plant. Due to the existence of Naturally Occurring Radioactive Material (NORM) in the residue, the decommissioning and disposal was done by the company in collaboration with the Perak State Government and the Atomic Energy Licensing Board (AELB). The main objective of this study is to review the level of compliance of the existing Radiation Protection Regulations enforced by AELB particularly in the achievement of allowed exposure dose limit. The next objective was to study the impact of the construction of the Mukim Belanja Repository to workers and public. This study was conducted by analyzing documents that were issued and conducting the area monitoring using a Geiger Muller detector (GM) and Sodium Iodide (NaI(Tl)) survey meters. The measurements were made at 5 cm and 1 m from the ground surface at 27 measurement stations. The external doses measured were within the background levels of the surrounding area. The annual effective dose using the highest reading at 5 cm and 1 m from ground surface by GM detector was calculated to be 1.36 mSv/year and 1.21 mSv/year respectively. Whereas the annual effective dose using the highest reading at 5 cm and 1 m from ground surface by using NaI(Tl) detector was calculated to be 3.31 mSv/year and 2.83 mSv/year respectively. The calculated cancer risks from the study showed that the risk is small compared with the risks derived from natural radiation based on global annual radiation dose to humans. This study therefore indicated that the repository is able to constrain the dose exposure from the disposed NORM waste. The study also revealed that the construction of the repository has complied with all the rules and regulations subjected to

Upgrading of radon's type near surface repository in Latvia

International Nuclear Information System (INIS)

Abramenkovs, A.

2006-01-01

In 1959, the Soviet government decided to construct the near surface radioactive wastes repository 'Radons' near the Baldone city. It was put in operation in 1962. The changes in the development of the repository were induced by the necessarily to upgrade it for disposal of radioactive wastes from the decommissioning of the Salaspils Research Reactor (SRR). The safety assessment of repository was performed during 2000-2001 under the PHARE project for necessary upgrades of repository. The outline design for new vaults and interim storage for long lived radioactive wastes was elaborated during 2003-2004 years. The Environmental Impact Assessment (EIA) for upgrade of Baldone repository was performed during 2004-2005 years. It was found, that additional efforts must be devoted for solution of social aspects o for successful operation and upgrade of repository. It was shown by EIA, that the local population has a negative opinion against the upgrade of repository in Latvia. The main recommendations for upgrades were connected with increasing the safety of repository, increasing of PR activities for education of society and developing of compensation mechanism for local municipality. (author)

Computational Omics Pre-Awardees | Office of Cancer Clinical Proteomics Research

Science.gov (United States)

The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) is pleased to announce the pre-awardees of the Computational Omics solicitation. Working with NVIDIA Foundation's Compute the Cure initiative and Leidos Biomedical Research Inc., the NCI, through this solicitation, seeks to leverage computational efforts to provide tools for the mining and interpretation of large-scale publicly available ‘omics’ datasets.

Proteomic Analysis of Chinese Hamster Ovary Cells

DEFF Research Database (Denmark)

Baycin-Hizal, Deniz; Tabb, David L.; Chaerkady, Raghothama

2012-01-01

To complement the recent genomic sequencing of Chinese hamster ovary (CHO) cells, proteomic analysis was performed on CHO cells including the cellular proteome, secretome, and glycoproteome using tandem mass spectrometry (MS/MS) of multiple fractions obtained from gel electrophoresis, multidimens......To complement the recent genomic sequencing of Chinese hamster ovary (CHO) cells, proteomic analysis was performed on CHO cells including the cellular proteome, secretome, and glycoproteome using tandem mass spectrometry (MS/MS) of multiple fractions obtained from gel electrophoresis...

Selection of Corrosion Resistant Materials for Nuclear Waste Repositories

International Nuclear Information System (INIS)

R.B. Rebak

2006-01-01

Several countries are considering geological repositories to dispose of nuclear waste. The environment of most of the currently considered repositories will be reducing in nature, except for the repository in the US, which is going to be oxidizing. For the reducing repositories, alloys such as carbon steel, stainless steels and titanium are being evaluated. For the repository in the US, some of the most corrosion resistant commercially available alloys are being investigated. This paper presents a summary of the behavior of the different materials under consideration for the repositories and the current understanding of the degradation modes of the proposed alloys in ground water environments from the point of view of general corrosion, localized corrosion and environmentally assisted cracking

Semen proteomics and male infertility.

Science.gov (United States)

Jodar, Meritxell; Soler-Ventura, Ada; Oliva, Rafael

2017-06-06

Semen is a complex body fluid containing an admixture of spermatozoa suspended in secretions from the testes and epididymis which are mixed at the time of ejaculation with secretions from other accessory sex glands such as the prostate and seminal vesicles. High-throughput technologies have revealed that, contrary to the idea that sperm cells are simply a silent delivery vehicle of the male genome to the oocyte, the sperm cells in fact provide both a specific epigenetically marked DNA together with a complex population of proteins and RNAs crucial for embryogenesis. Similarly, -omic technologies have also enlightened that seminal fluid seems to play a much greater role than simply being a medium to carry the spermatozoa through the female reproductive tract. In the present review, we briefly overview the sperm cell biology, consider the key issues in sperm and seminal fluid sample preparation for high-throughput proteomic studies, describe the current state of the sperm and seminal fluid proteomes generated by high-throughput proteomic technologies and provide new insights into the potential communication between sperm and seminal fluid. In addition, comparative proteomic studies open a window to explore the potential pathogenic mechanisms of infertility and the discovery of potential biomarkers with clinical significance. The review updates the numerous proteomics studies performed on semen, including spermatozoa and seminal fluid. In addition, an integrative analysis of the testes, sperm and seminal fluid proteomes is also included providing insights into the molecular mechanisms that regulate the generation, maturation and transit of spermatozoa. Furthermore, the compilation of several differential proteomic studies focused on male infertility reveals potential pathways disturbed in specific subtypes of male infertility and points out towards future research directions in the field. Copyright © 2016 Elsevier B.V. All rights reserved.

Using Invenio for managing and running open data repositories

CERN Multimedia

Simko, Tibor; Nielsen, Lars Holm

2017-01-01

We present how a research data repository manager can build custom open data solutions to ingest, describe, preserve, and disseminate the open research environments, datasets and software using the Invenio digital library framework. We discuss a concrete use case example of the CERN Open Data and Zenodo services, describing technological challenges in preparing large sets of data for general public. We address the questions of efficient linking and sharing of large quantities of data without unnecessary duplication on the backend, the role of the file transfer protocols, as well as the means to visualise data to make it more accessible and interactive for general public. The technological challenges and discussed solutions can be applied to any research discipline outside the domain of particle physics.

Numerical modeling of magma-repository interactions

NARCIS (Netherlands)

Bokhove, Onno

2001-01-01

This report explains the numerical programs behind a comprehensive modeling effort of magma-repository interactions. Magma-repository interactions occur when a magma dike with high-volatile content magma ascends through surrounding rock and encounters a tunnel or drift filled with either a magmatic

Transparency and Public Involvement in Siting a Nuclear Waste Repository in Germany

International Nuclear Information System (INIS)

Lennartz, Hans-Albert; Mussel, Christine; Nies, Alexander

2001-01-01

The 1998 election of the Federal Parliament led to a significant reorientation of German energy policy. In June 2000, the Federal Government (FG) has achieved an agreement with the utility companies in which they respect the decision of the FG to put an orderly end to nuclear power generation by prohibiting the erection of new, and limiting the operational period of existing power plants. The agreement also contains cornerstones of a new radioactive waste management policy: New interim storage facilities will be built at reactor sites in order to minimise transports to the existing central interim storage facilities at Ahaus and Gorleben; The utilities will use all acceptable contractual possibilities with their international partners to end reprocessing as soon as possible. By mid 2005 at the latest, spent fuel management in Germany will be limited to direct disposal; The exploration of the salt dome at Gorleben will be interrupted for at least three, and at most ten years, to clarify conceptual and safety questions. Correspondingly, the FG has initiated an amendment of the atomic energy act and the development of a new plan for radioactive waste management. In the field of radioactive waste disposal, the Federal Government pursues two new objectives: For the disposal of all kinds and amounts of radioactive waste, one single repository in deep geologic formations shall be erected around 2030; The suitability of further sites in different host formations shall be examined. Feasibility and consequences of the first objective have still to be carefully examined in detail. Development of a new disposal concept and final decisions on both the existing disposal projects as well as on new potential sites are therefore an ambitious challenge for the coming years. The second objective brings up a key question which several leading countries presently attempt to successfully address: how to select sites which are both suitable for safe disposal and accepted in the public

Transparency and Public Involvement in Siting a Nuclear Waste Repository in Germany

Energy Technology Data Exchange (ETDEWEB)

Lennartz, Hans-Albert; Mussel, Christine [WIBERA/PWIBERA/PriceWaterhouseCoopers Deutsche Rev., Hannover (Germany); Nies, Alexander [Federal Ministry for the Environment, Bonn (Germany)

2001-07-01

The 1998 election of the Federal Parliament led to a significant reorientation of German energy policy. In June 2000, the Federal Government (FG) has achieved an agreement with the utility companies in which they respect the decision of the FG to put an orderly end to nuclear power generation by prohibiting the erection of new, and limiting the operational period of existing power plants. The agreement also contains cornerstones of a new radioactive waste management policy: New interim storage facilities will be built at reactor sites in order to minimise transports to the existing central interim storage facilities at Ahaus and Gorleben; The utilities will use all acceptable contractual possibilities with their international partners to end reprocessing as soon as possible. By mid 2005 at the latest, spent fuel management in Germany will be limited to direct disposal; The exploration of the salt dome at Gorleben will be interrupted for at least three, and at most ten years, to clarify conceptual and safety questions. Correspondingly, the FG has initiated an amendment of the atomic energy act and the development of a new plan for radioactive waste management. In the field of radioactive waste disposal, the Federal Government pursues two new objectives: For the disposal of all kinds and amounts of radioactive waste, one single repository in deep geologic formations shall be erected around 2030; The suitability of further sites in different host formations shall be examined. Feasibility and consequences of the first objective have still to be carefully examined in detail. Development of a new disposal concept and final decisions on both the existing disposal projects as well as on new potential sites are therefore an ambitious challenge for the coming years. The second objective brings up a key question which several leading countries presently attempt to successfully address: how to select sites which are both suitable for safe disposal and accepted in the public

Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project.

Science.gov (United States)

Omenn, Gilbert S; Lane, Lydie; Lundberg, Emma K; Overall, Christopher M; Deutsch, Eric W

2017-12-01

The Human Proteome Organization (HUPO) Human Proteome Project (HPP) continues to make progress on its two overall goals: (1) completing the protein parts list, with an annual update of the HUPO draft human proteome, and (2) making proteomics an integrated complement to genomics and transcriptomics throughout biomedical and life sciences research. neXtProt version 2017-01-23 has 17 008 confident protein identifications (Protein Existence [PE] level 1) that are compliant with the HPP Guidelines v2.1 ( https://hupo.org/Guidelines ), up from 13 664 in 2012-12 and 16 518 in 2016-04. Remaining to be found by mass spectrometry and other methods are 2579 "missing proteins" (PE2+3+4), down from 2949 in 2016. PeptideAtlas 2017-01 has 15 173 canonical proteins, accounting for nearly all of the 15 290 PE1 proteins based on MS data. These resources have extensive data on PTMs, single amino acid variants, and splice isoforms. The Human Protein Atlas v16 has 10 492 highly curated protein entries with tissue and subcellular spatial localization of proteins and transcript expression. Organ-specific popular protein lists have been generated for broad use in quantitative targeted proteomics using SRM-MS or DIA-SWATH-MS studies of biology and disease.

Multinational/regional repository - an illusion or solution

International Nuclear Information System (INIS)

Mele, I.

2006-01-01

The concept and current status of multinational and regional repositories are presented in the paper. Particular emphasis is given to the results and findings of the recent EU project SAPIERR, investigating the feasibility of regional repository concepts in Europe. Prospects for further development of multinational repositories are also brought forward and the impact and potential benefits of this approach to our national disposal programme are discussed as well. (author)

The Lincoln Repository presentation: ten reasons why you should put a copy of your work in the Repository

OpenAIRE

Stainthorp, Paul

2010-01-01

Slideshow presentation created to promote the Lincoln Repository to staff at the University of Lincoln. Consists of ten reasons why academic authors should consider depositing copies of their work in the Repository.

Data repositories for medical education research: issues and recommendations.

Science.gov (United States)

Schwartz, Alan; Pappas, Cleo; Sandlow, Leslie J

2010-05-01

The authors explore issues surrounding digital repositories with the twofold intention of clarifying their creation, structure, content, and use, and considering the implementation of a global digital repository for medical education research data sets-an online site where medical education researchers would be encouraged to deposit their data in order to facilitate the reuse and reanalysis of the data by other researchers. By motivating data sharing and reuse, investigators, medical schools, and other stakeholders might see substantial benefits to their own endeavors and to the progress of the field of medical education.The authors review digital repositories in medicine, social sciences, and education, describe the contents and scope of repositories, and present extant examples. The authors describe the potential benefits of a medical education data repository and report results of a survey of the Society for Directors of Research in Medicine Education, in which participants responded to questions about data sharing and a potential data repository. Respondents strongly endorsed data sharing, with the caveat that principal investigators should choose whether or not to share data they collect. A large majority believed that a repository would benefit their unit and the field of medical education. Few reported using existing repositories. Finally, the authors consider challenges to the establishment of such a repository, including taxonomic organization, intellectual property concerns, human subjects protection, technological infrastructure, and evaluation standards. The authors conclude with recommendations for how a medical education data repository could be successfully developed.

Technical, normative and social aspects of the site selection process for radioactive waste repositories

International Nuclear Information System (INIS)

Branco, Otavio E.A.; Rodrigues, Paulo C.H.; Carvalho Filho, Carlos A.; Cota, Stela D.S.; Ferreira, Vinicius V.M.; Peres, Sueli S.; Hiromoto, Goro

2009-01-01

In force since 2001, the Federal Law 10.308 states, in article 37, that the Comissao Nacional de Energia Nuclear - CNEN should start studies for the implementation of a final radioactive waste repository, 'in the shortest timeframe technically feasible'. Nevertheless, not only technical aspects have to be taken into account to accomplish with this schedule, but, also factors of political, economic and social nature. In this paper, the importance and impact of public acceptance aspects are discussed, as well as the methodology of site selection for radioactive wastes repositories, and proposals to accommodate the emanated criteria from the existing legislation. Additionally, practical results from the international experience in the implementation of such deposits are presented. (author)

The development of safeguards for geological repositories

International Nuclear Information System (INIS)

Van der Meer, K.

2009-01-01

Traditionally, research and development on geological repositories for High Level Waste (HLW) focuses on the short- and long-term safety aspects of the repository. If the repository will also be used for the disposal of spent fuel, safeguards aspects have to be taken into account. Safety and safeguards requirements may be contradictory; the safety of a geological repository is based on the non-intrusion of the geological containment, while safeguards require regular inspections of position and amount of the spent fuel. Examples to reconcile these contradictory requirements are the use of information required for the safety assessment of the geological repository for safeguards purposes and the adaptation of the safeguards approach to use non-intrusive inspection techniques. The principles of an inspection approach for a geological repository are now generally accepted within the IAEA. The practical applicability of the envisaged inspection techniques is still subject to investigation. It is specifically important for the Belgian situation that an inspection technique can be used in clay, the geological medium in which Belgium intends to dispose its HLW and spent fuel. The work reported in this chapter is the result of an international cooperation in the framework of the IAEA, in which SCK-CEN participates

Investigative study of standards for digital repositories and related services

CERN Document Server

Foulonneau, Muriel; Badolato, Anne-Marie

2008-01-01

This study is meant for institutional repository managers, service providers, repository software developers and generally, all players taking an active part in the creation of the digital repository infrastructure for e-research and e-learning. It reviews the current standards, protocols and applications in the domain of digital repositories. Special attention is being paid to the interoperability of repositories to enhance the exchange of data in repositories. It aims to stimulate discussion about these topics and supports initiatives for the integration of and, where needed, development of

Cryptonite: A Secure and Performant Data Repository on Public Clouds

Energy Technology Data Exchange (ETDEWEB)

Kumbhare, Alok; Simmhan, Yogesh; Prasanna, Viktor

2012-06-29

Cloud storage has become immensely popular for maintaining synchronized copies of files and for sharing documents with collaborators. However, there is heightened concern about the security and privacy of Cloud-hosted data due to the shared infrastructure model and an implicit trust in the service providers. Emerging needs of secure data storage and sharing for domains like Smart Power Grids, which deal with sensitive consumer data, require the persistence and availability of Cloud storage but with client-controlled security and encryption, low key management overhead, and minimal performance costs. Cryptonite is a secure Cloud storage repository that addresses these requirements using a StrongBox model for shared key management.We describe the Cryptonite service and desktop client, discuss performance optimizations, and provide an empirical analysis of the improvements. Our experiments shows that Cryptonite clients achieve a 40% improvement in file upload bandwidth over plaintext storage using the Azure Storage Client API despite the added security benefits, while our file download performance is 5 times faster than the baseline for files greater than 100MB.

Refinancing of the search for a repository and of the repository for heat generating radioactive Waste. Pt. 2

International Nuclear Information System (INIS)

Moench, Christoph

2013-01-01

Part I of this article, which appeared in the preceding issue, described in general terms the background to the search for a disposal site and the result of the exploration to date of the repository, which would appear to be suitable from a mining standpoint according to the present knowledge. According to the rules in effect up to now, the exploration and construction would be financed by advance payments on the contributions of the waste producing companies, in particular the utility companies. The working draft of an 'Act on the search for and selection of a site for a repository for heat generating radioactive waste' (Gesetz zur Suche und Auswahl eines Standortes fuer ein Endlager fuer waermeentwickelnde radioaktive Abfaelle) from autumn 2012 provides for a new version of section 21b Atomic Energy Act, under which the costs for 'carrying out a repository selection procedure pursuant to the Repository Selection Act (Standort-auswahlgesetz)' would be allocated to the future users of the repository who are obliged to make contributions as a 'necessary expense'. Part II evaluates this provision of the working draft on the basis of the financial constitutional law. A comparison of sites is not a measure that could be allocated to the future users of the repository who are obliged to make contributions as a 'necessary expense'. Moreover, there is a lack of responsibility for the financing and of a legally relevant advantage that would be conferred by a cumulative alternative repository search for the later users of the repository who are obliged to provide the pre-financing. The costs can therefore not be allocated to the later users as either a contribution or a special charge, not even by way of an association with mandatory membership (Zwangsverband). They must be borne by the state. Consequently, the allocation stipulated by provision would constitute an impermissible charge under financial constitutional law. (orig.)

Proteomic approaches in brain research and neuropharmacology.

Science.gov (United States)

Vercauteren, Freya G G; Bergeron, John J M; Vandesande, Frans; Arckens, Lut; Quirion, Rémi

2004-10-01

Numerous applications of genomic technologies have enabled the assembly of unprecedented inventories of genes, expressed in cells under specific physiological and pathophysiological conditions. Complementing the valuable information generated through functional genomics with the integrative knowledge of protein expression and function should enable the development of more efficient diagnostic tools and therapeutic agents. Proteomic analyses are particularly suitable to elucidate posttranslational modifications, expression levels and protein-protein interactions of thousands of proteins at a time. In this review, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) investigations of brain tissues in neurodegenerative diseases such as Alzheimer's disease, Down syndrome and schizophrenia, and the construction of 2D-PAGE proteome maps of the brain are discussed. The role of the Human Proteome Organization (HUPO) as an international coordinating organization for proteomic efforts, as well as challenges for proteomic technologies and data analysis are also addressed. It is expected that the use of proteomic strategies will have significant impact in neuropharmacology over the coming decade.

La importancia de la proteómica en la salud pública: The significance of proteomics in public health

Directory of Open Access Journals (Sweden)

Rosa Victoria Pando-Robles

2009-01-01

Full Text Available La salud pública en el nuevo milenio tiene como reto integrar los avances de la genómica al derecho fundamental de la salud de todos los seres humanos. La proteómica, entendida como la disciplina científica que estudia los proteomas, es de vital importancia en la investigación en salud, ya que el conocimiento de las proteínas y moléculas efectoras de la función celular permitirá un mejor entendimiento de la fisiología humana. En este trabajo se describen los antecedentes y los conocimientos básicos del análisis proteómico basado en la espectrometría de masas y se comentan los usos de la proteómica en la búsqueda de biomarcadores para el diagnóstico y pronóstico de diferentes enfermedades, los avances en la comprensión de los trastornos crónicos y algunas enfermedades infecciosas. De manera adicional, se delinean las ventajas de la espectrometría de masas en la genotipificación de patógenos y el estudio de los polimorfismos de una sola base (SNP, por sus siglas en inglés.The proteome is defined as the entirety of proteins expressed by a genome in a given time under specific physiological conditions. In an organism, the cells contain the same genome; however, they express different proteins in response to a specific micro-environment. Proteomics is responsible for the study of proteomes, using a wide range of methodological techniques. Actually, proteomics is a key tool in health research because it has made possible systematic analysis of hundreds of proteins in clinical samples with the promise of discovering new protein biomarkers for different disease conditions. Finally, proteomic strategy is a technology well-suited to provide a better understanding of systems biology and human health.

Institutional Repositories as Infrastructures for Long-Term Preservation

Science.gov (United States)

Francke, Helena; Gamalielsson, Jonas; Lundell, Björn

2017-01-01

Introduction: The study describes the conditions for long-term preservation of the content of the institutional repositories of Swedish higher education institutions based on an investigation of how deposited files are managed with regards to file format and how representatives of the repositories describe the functions of the repositories.…

Proteomic landscape in Central and Eastern Europe: the 9th Central and Eastern European Proteomic Conference, Poznan, Poland

Czech Academy of Sciences Publication Activity Database

Gadher, S. J.; Marczak, L.; Luczak, M.; Stobiecki, M.; Widlak, P.; Kovářová, Hana

2016-01-01

Roč. 13, č. 1 (2016), s. 5-7 ISSN 1478-9450. [Central and Eastern European Proteomic Conference (CEEPC) /9./. Poznaň, 15.06.2015-18.06.2015] Institutional support: RVO:67985904 Keywords : Central and Eastern Proteomic Conference * proteomics * mass spectrometry imaging Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.849, year: 2016

The repository commission. A historic chance to solve an ongoing conflict

International Nuclear Information System (INIS)

Kleemann, Ulrich

2015-01-01

Germany's Commission on the Disposal of High-level Radioactive Waste, which was set up in compliance with the country's Repository Site Selection Act, has been tasked with drawing up criteria for a site selection process and evaluating the act by mid-2016. Lessons can be learned from the failed Asse and Gorleben repository projects, and the selection process should take these into account. Transparency and widespread public participation are crucial to reaching a broad consensus on the issue of permanent disposal. The commission must also produce a plan for avoiding and correcting errors during the selection process. Key elements of a selection process already exist or can be adapted to reflect the current state of the art with relatively little effort. Working from this basis, it should be possible to achieve a result that can end the ongoing conflict surrounding permanent disposal.

Socioeconomic impacts of repositories

International Nuclear Information System (INIS)

Thomas, J.K.; Hamm, R.R.; Murdock, S.H.

1983-01-01

Federal and state decision makers, community leaders, and residents must know how communities will be changed by the impacts of a high-level nuclear waste repository. This chapter identifies the factors affecting an assessment of socioeconomic impacts and the types of impacts (economic, demographic, fiscal, community service, and social) likely to occur as a result of repository development. Each of these types can be divided into standard (those which typically results from any large-scale development) and special impact categories (those which result from the fact that radioactive materials will be handled). 3 tables

Some inspirations drawn from the SKB license-application report for the construction of the final repository for spent nuclear fuel in Sweden

International Nuclear Information System (INIS)

Xu Guoqing

2014-01-01

The following problems are described in this paper: the current state of nuclear energy and spent fuel in Sweden, the brief process of repository site selection and the concise geological settings of candidate site Forsmark, the option of repository design, the data presented in license-application report on repository, construction, the review work presented by OECD/NEA international peer review team (IRT) and some considerations noted by the author: 1) Why the design of underground engineering, also known as 5 shafts + l ramp, is adopted? 2) Why the timescale for the assessment is one million years? 3) Why the computer codes used in performance assessment at Forsmark candidate repository site are different from those used at Yucca Mountain candidate repository site? 4) How to carry out the public involvement, support from local government and volumtary siting in China? 5) What is the most important in the R and D program of HLW disposal? 6) What shall we do for the future license-application report for the construction of the final repository in China? (author)