WorldWideScience

Sample records for public databases specific

  1. Database Publication Practices

    DEFF Research Database (Denmark)

    Bernstein, P.A.; DeWitt, D.; Heuer, A.

    2005-01-01

    There has been a growing interest in improving the publication processes for database research papers. This panel reports on recent changes in those processes and presents an initial cut at historical data for the VLDB Journal and ACM Transactions on Database Systems.......There has been a growing interest in improving the publication processes for database research papers. This panel reports on recent changes in those processes and presents an initial cut at historical data for the VLDB Journal and ACM Transactions on Database Systems....

  2. Database Publication Practices

    DEFF Research Database (Denmark)

    Bernstein, P.A.; DeWitt, D.; Heuer, A.

    2005-01-01

    There has been a growing interest in improving the publication processes for database research papers. This panel reports on recent changes in those processes and presents an initial cut at historical data for the VLDB Journal and ACM Transactions on Database Systems....

  3. ADANS database specification

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-01-16

    The purpose of the Air Mobility Command (AMC) Deployment Analysis System (ADANS) Database Specification (DS) is to describe the database organization and storage allocation and to provide the detailed data model of the physical design and information necessary for the construction of the parts of the database (e.g., tables, indexes, rules, defaults). The DS includes entity relationship diagrams, table and field definitions, reports on other database objects, and a description of the ADANS data dictionary. ADANS is the automated system used by Headquarters AMC and the Tanker Airlift Control Center (TACC) for airlift planning and scheduling of peacetime and contingency operations as well as for deliberate planning. ADANS also supports planning and scheduling of Air Refueling Events by the TACC and the unit-level tanker schedulers. ADANS receives input in the form of movement requirements and air refueling requests. It provides a suite of tools for planners to manipulate these requirements/requests against mobility assets and to develop, analyze, and distribute schedules. Analysis tools are provided for assessing the products of the scheduling subsystems, and editing capabilities support the refinement of schedules. A reporting capability provides formatted screen, print, and/or file outputs of various standard reports. An interface subsystem handles message traffic to and from external systems. The database is an integral part of the functionality summarized above.

  4. Public chemical compound databases.

    Science.gov (United States)

    Williams, Anthony J

    2008-05-01

    The internet has rapidly become the first port of call for all information searches. The increasing array of chemistry-related resources that are now available provides chemists with a direct path to the information that was previously accessed via library services and was limited by commercial and costly resources. The diversity of the information that can be accessed online is expanding at a dramatic rate, and the support for publicly available resources offers significant opportunities in terms of the benefits to science and society. While the data online do not generally meet the quality standards of manually curated sources, there are efforts underway to gather scientists together and 'crowdsource' an improvement in the quality of the available data. This review discusses the types of public compound databases that are available online and provides a series of examples. Focus is also given to the benefits and disruptions associated with the increased availability of such data and the integration of technologies to data mine this information.

  5. Behaviour specification in database interoperation

    NARCIS (Netherlands)

    Vermeer, W.W.M.; Apers, Peter M.G.

    We discuss the impact of locally implemented behaviour in a federation of object-oriented databases. In particular, given a specification of an integrated view of a number of component databases, we discuss the process of determining the global methods that are implicitly implemented by a given set

  6. Database Support for Research in Public Administration

    Science.gov (United States)

    Tucker, James Cory

    2005-01-01

    This study examines the extent to which databases support student and faculty research in the area of public administration. A list of journals in public administration, public policy, political science, public budgeting and finance, and other related areas was compared to the journal content list of six business databases. These databases…

  7. FEEDBACK ON A PUBLICLY DISTRIBUTED IMAGE DATABASE: THE MESSIDOR DATABASE

    Directory of Open Access Journals (Sweden)

    Etienne Decencière

    2014-08-01

    Full Text Available The Messidor database, which contains hundreds of eye fundus images, has been publicly distributed since 2008. It was created by the Messidor project in order to evaluate automatic lesion segmentation and diabetic retinopathy grading methods. Designing, producing and maintaining such a database entails significant costs. By publicly sharing it, one hopes to bring a valuable resource to the public research community. However, the real interest and benefit of the research community is not easy to quantify. We analyse here the feedback on the Messidor database, after more than 6 years of diffusion. This analysis should apply to other similar research databases.

  8. A Decade of Database Research Publications

    CERN Document Server

    Sakr, Sherif

    2011-01-01

    We analyze the database research publications of four major core database technology conferences (SIGMOD, VLDB, ICDE, EDBT), two main theoretical database conferences (PODS, ICDT) and three database journals (TODS, VLDB Journal, TKDE) over a period of 10 years (2001 - 2010). Our analysis considers only regular papers as we do not include short papers, demo papers, posters, tutorials or panels into our statistics. We rank the research scholars according to their number of publication in each conference/journal separately and in combined. We also report about the growth in the number of research publications and the size of the research community in the last decade.

  9. Gene and protein nomenclature in public databases

    Directory of Open Access Journals (Sweden)

    Zimmer Ralf

    2006-08-01

    Full Text Available Abstract Background Frequently, several alternative names are in use for biological objects such as genes and proteins. Applications like manual literature search, automated text-mining, named entity identification, gene/protein annotation, and linking of knowledge from different information sources require the knowledge of all used names referring to a given gene or protein. Various organism-specific or general public databases aim at organizing knowledge about genes and proteins. These databases can be used for deriving gene and protein name dictionaries. So far, little is known about the differences between databases in terms of size, ambiguities and overlap. Results We compiled five gene and protein name dictionaries for each of the five model organisms (yeast, fly, mouse, rat, and human from different organism-specific and general public databases. We analyzed the degree of ambiguity of gene and protein names within and between dictionaries, to a lexicon of common English words and domain-related non-gene terms, and we compared different data sources in terms of size of extracted dictionaries and overlap of synonyms between those. The study shows that the number of genes/proteins and synonyms covered in individual databases varies significantly for a given organism, and that the degree of ambiguity of synonyms varies significantly between different organisms. Furthermore, it shows that, despite considerable efforts of co-curation, the overlap of synonyms in different data sources is rather moderate and that the degree of ambiguity of gene names with common English words and domain-related non-gene terms varies depending on the considered organism. Conclusion In conclusion, these results indicate that the combination of data contained in different databases allows the generation of gene and protein name dictionaries that contain significantly more used names than dictionaries obtained from individual data sources. Furthermore, curation of

  10. Public Opinion Poll Question Databases: An Evaluation

    Science.gov (United States)

    Woods, Stephen

    2007-01-01

    This paper evaluates five polling resource: iPOLL, Polling the Nations, Gallup Brain, Public Opinion Poll Question Database, and Polls and Surveys. Content was evaluated on disclosure standards from major polling organizations, scope on a model for public opinion polls, and presentation on a flow chart discussing search limitations and usability.

  11. Implementing database system for LHCb publications page

    CERN Document Server

    Abdullayev, Fakhriddin

    2017-01-01

    The LHCb is one of the main detectors of Large Hadron Collider, where physicists and scientists work together on high precision measurements of matter-antimatter asymmetries and searches for rare and forbidden decays, with the aim of discovering new and unexpected forces. The work does not only consist of analyzing data collected from experiments but also in publishing the results of those analyses. The LHCb publications are gathered on LHCb publications page to maximize their availability to both LHCb members and to the high energy community. In this project a new database system was implemented for LHCb publications page. This will help to improve access to research papers for scientists and better integration with current CERN library website and others.

  12. Database specification for the Worldwide Port System (WPS) Regional Integrated Cargo Database (ICDB)

    Energy Technology Data Exchange (ETDEWEB)

    Faby, E.Z.; Fluker, J.; Hancock, B.R.; Grubb, J.W.; Russell, D.L. [Univ. of Tennessee, Knoxville, TN (United States); Loftis, J.P.; Shipe, P.C.; Truett, L.F. [Oak Ridge National Lab., TN (United States)

    1994-03-01

    This Database Specification for the Worldwide Port System (WPS) Regional Integrated Cargo Database (ICDB) describes the database organization and storage allocation, provides the detailed data model of the logical and physical designs, and provides information for the construction of parts of the database such as tables, data elements, and associated dictionaries and diagrams.

  13. Axiomatic Specification of Database Domain Statics

    NARCIS (Netherlands)

    Wieringa, Roel

    1987-01-01

    In the past ten years, much work has been done to add more structure to database models 1 than what is represented by a mere collection of flat relations (Albano & Cardelli [1985], Albano et al. [1986], Borgida eta. [1984], Brodie [1984], Brodie & Ridjanovic [1984], Brodie & Silva (1982], Codd (1979

  14. Axiomatic Specification of Database Domain Statics

    NARCIS (Netherlands)

    Wieringa, Roelf J.

    1987-01-01

    In the past ten years, much work has been done to add more structure to database models 1 than what is represented by a mere collection of flat relations (Albano & Cardelli [1985], Albano et al. [1986], Borgida eta. [1984], Brodie [1984], Brodie & Ridjanovic [1984], Brodie & Silva (1982], Codd

  15. The EpiSLI Database: A Publicly Available Database on Speech and Language

    Science.gov (United States)

    Tomblin, J. Bruce

    2010-01-01

    Purpose: This article describes a database that was created in the process of conducting a large-scale epidemiologic study of specific language impairment (SLI). As such, this database will be referred to as the EpiSLI database. Children with SLI have unexpected and unexplained difficulties learning and using spoken language. Although there is no…

  16. USAID Public-Private Partnerships Database

    Data.gov (United States)

    US Agency for International Development — This dataset brings together information collected since 2001 on PPPs that have been supported by USAID. For the purposes of this dataset a Public-Private...

  17. The Mouse SAGE Site: database of public mouse SAGE libraries.

    Science.gov (United States)

    Divina, Petr; Forejt, Jirí

    2004-01-01

    The Mouse SAGE Site is a web-based database of all available public libraries generated by the Serial Analysis of Gene Expression (SAGE) from various mouse tissues and cell lines. The database contains mouse SAGE libraries organized in a uniform way and provides web-based tools for browsing, comparing and searching SAGE data with reliable tag-to-gene identification. A modified approach based on the SAGEmap database is used for reliable tag identification. The Mouse SAGE Site is maintained on an ongoing basis at the Institute of Molecular Genetics, Academy of Sciences of the Czech Republic and is accessible at the internet address http://mouse.biomed.cas.cz/sage/.

  18. Digital Equipment Corporation's CRDOM Software and Database Publications.

    Science.gov (United States)

    Adams, Michael Q.

    1986-01-01

    Acquaints information professionals with Digital Equipment Corporation's compact optical disk read-only-memory (CDROM) search and retrieval software and growing library of CDROM database publications (COMPENDEX, Chemical Abstracts Services). Highlights include MicroBASIS, boolean operators, range operators, word and phrase searching, proximity…

  19. A publication database for optical long baseline interferometry

    CERN Document Server

    Malbet, Fabien; Lawson, Peter; Taillifet, Esther; Lafrasse, Sylvain

    2010-01-01

    Optical long baseline interferometry is a technique that has generated almost 850 refereed papers to date. The targets span a large variety of objects from planetary systems to extragalactic studies and all branches of stellar physics. We have created a database hosted by the JMMC and connected to the Optical Long Baseline Interferometry Newsletter (OLBIN) web site using MySQL and a collection of XML or PHP scripts in order to store and classify these publications. Each entry is defined by its ADS bibcode, includes basic ADS informations and metadata. The metadata are specified by tags sorted in categories: interferometric facilities, instrumentation, wavelength of operation, spectral resolution, type of measurement, target type, and paper category, for example. The whole OLBIN publication list has been processed and we present how the database is organized and can be accessed. We use this tool to generate statistical plots of interest for the community in optical long baseline interferometry.

  20. NCI at Frederick Scientific Library Reintroduces Scientific Publications Database | Poster

    Science.gov (United States)

    A 20-year-old database of scientific publications by NCI at Frederick, FNLCR, and affiliated employees has gotten a significant facelift. Maintained by the Scientific Library, the redesigned database—which is linked from each of the Scientific Library’s web pages—offers features that were not available in previous versions, such as additional search limits and non-traditional metrics for scholarly and scientific publishing known as altmetrics.

  1. Public Address Systems. Specifications - Installation - Operation.

    Science.gov (United States)

    Palmer, Fred M.

    Provisions for public address in new construction of campus buildings (specifications, installations, and operation of public address systems), are discussed in non-technical terms. Consideration is given to microphones, amplifiers, loudspeakers and the placement and operation of various different combinations. (FS)

  2. Building an organ-specific carcinogenic database for SAR analyses.

    Science.gov (United States)

    Young, John; Tong, Weida; Fang, Hong; Xie, Qian; Pearce, Bruce; Hashemi, Ray; Beger, Richard; Cheeseman, Mitchell; Chen, James; Chang, Yuan-Chin; Kodell, Ralph

    2004-09-10

    FDA reviewers need a means to rapidly predict organ-specific carcinogenicity to aid in evaluating new chemicals submitted for approval. This research addressed the building of a database to use in developing a predictive model for such an application based on structure-activity relationships (SAR). The Internet availability of the Carcinogenic Potency Database (CPDB) provided a solid foundation on which to base such a model. The addition of molecular structures to the CPDB provided the extra ingredient necessary for SAR analyses. However, the CPDB had to be compressed from a multirecord to a single record per chemical database; multiple records representing each gender, species, route of administration, and organ-specific toxicity had to be summarized into a single record for each study. Multiple studies on a single chemical had to be further reduced based on a hierarchical scheme. Structural cleanup involved removal of all chemicals that would impede the accurate generation of SAR type descriptors from commercial software programs; that is, inorganic chemicals, mixtures, and organometallics were removed. Counterions such as Na, K, sulfates, hydrates, and salts were also removed for structural consistency. Structural modification sometimes resulted in duplicate records that also had to be reduced to a single record based on the hierarchical scheme. The modified database containing 999 chemicals was evaluated for liver-specific carcinogenicity using a variety of analysis techniques. These preliminary analyses all yielded approximately the same results with an overall predictability of about 63%, which was comprised of a sensitivity of about 30% and a specificity of about 77%. Copyright Taylor & Francis Inc.

  3. Exploring public databases to characterize urban flood risks in Amsterdam

    Science.gov (United States)

    Gaitan, Santiago; ten Veldhuis, Marie-claire; van de Giesen, Nick

    2015-04-01

    Cities worldwide are challenged by increasing urban flood risks. Precise and realistic measures are required to decide upon investment to reduce their impacts. Obvious flooding factors affecting flood risk include sewer systems performance and urban topography. However, currently implemented sewer and topographic models do not provide realistic predictions of local flooding occurrence during heavy rain events. Assessing other factors such as spatially distributed rainfall and socioeconomic characteristics may help to explain probability and impacts of urban flooding. Several public databases were analyzed: complaints about flooding made by citizens, rainfall depths (15 min and 100 Ha spatio-temporal resolution), grids describing number of inhabitants, income, and housing price (1Ha and 25Ha resolution); and buildings age. Data analysis was done using Python and GIS programming, and included spatial indexing of data, cluster analysis, and multivariate regression on the complaints. Complaints were used as a proxy to characterize flooding impacts. The cluster analysis, run for all the variables except the complaints, grouped part of the grid-cells of central Amsterdam into a highly differentiated group, covering 10% of the analyzed area, and accounting for 25% of registered complaints. The configuration of the analyzed variables in central Amsterdam coincides with a high complaint count. Remaining complaints were evenly dispersed along other groups. An adjusted R2 of 0.38 in the multivariate regression suggests that explaining power can improve if additional variables are considered. While rainfall intensity explained 4% of the incidence of complaints, population density and building age significantly explained around 20% each. Data mining of public databases proved to be a valuable tool to identify factors explaining variability in occurrence of urban pluvial flooding, though additional variables must be considered to fully explain flood risk variability.

  4. Using Bibliographic Knowledge for Ranking in Scientific Publication Databases

    CERN Document Server

    Vesely, Martin; Le Meur, Jean-Yves

    2008-01-01

    Document ranking for scientific publications involves a variety of specialized resources (e.g. author or citation indexes) that are usually difficult to use within standard general purpose search engines that usually operate on large-scale heterogeneous document collections for which the required specialized resources are not always available for all the documents present in the collections. Integrating such resources into specialized information retrieval engines is therefore important to cope with community-specific user expectations that strongly influence the perception of relevance within the considered community. In this perspective, this paper extends the notion of ranking with various methods exploiting different types of bibliographic knowledge that represent a crucial resource for measuring the relevance of scientific publications. In our work, we experimentally evaluated the adequacy of two such ranking methods (one based on freshness, i.e. the publication date, and the other on a novel index, the ...

  5. OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes.

    Science.gov (United States)

    Chetal, Kashish; Janga, Sarath Chandra

    2015-01-01

    Background. In prokaryotic organisms, a substantial fraction of adjacent genes are organized into operons-codirectionally organized genes in prokaryotic genomes with the presence of a common promoter and terminator. Although several available operon databases provide information with varying levels of reliability, very few resources provide experimentally supported results. Therefore, we believe that the biological community could benefit from having a new operon prediction database with operons predicted using next-generation RNA-seq datasets. Description. We present operomeDB, a database which provides an ensemble of all the predicted operons for bacterial genomes using available RNA-sequencing datasets across a wide range of experimental conditions. Although several studies have recently confirmed that prokaryotic operon structure is dynamic with significant alterations across environmental and experimental conditions, there are no comprehensive databases for studying such variations across prokaryotic transcriptomes. Currently our database contains nine bacterial organisms and 168 transcriptomes for which we predicted operons. User interface is simple and easy to use, in terms of visualization, downloading, and querying of data. In addition, because of its ability to load custom datasets, users can also compare their datasets with publicly available transcriptomic data of an organism. Conclusion. OperomeDB as a database should not only aid experimental groups working on transcriptome analysis of specific organisms but also enable studies related to computational and comparative operomics.

  6. Development of a Publicly Available, Comprehensive Database of Fiber and Health Outcomes: Rationale and Methods.

    Directory of Open Access Journals (Sweden)

    Kara A Livingston

    Full Text Available Dietary fiber is a broad category of compounds historically defined as partially or completely indigestible plant-based carbohydrates and lignin with, more recently, the additional criteria that fibers incorporated into foods as additives should demonstrate functional human health outcomes to receive a fiber classification. Thousands of research studies have been published examining fibers and health outcomes.(1 Develop a database listing studies testing fiber and physiological health outcomes identified by experts at the Ninth Vahouny Conference; (2 Use evidence mapping methodology to summarize this body of literature. This paper summarizes the rationale, methodology, and resulting database. The database will help both scientists and policy-makers to evaluate evidence linking specific fibers with physiological health outcomes, and identify missing information.To build this database, we conducted a systematic literature search for human intervention studies published in English from 1946 to May 2015. Our search strategy included a broad definition of fiber search terms, as well as search terms for nine physiological health outcomes identified at the Ninth Vahouny Fiber Symposium. Abstracts were screened using a priori defined eligibility criteria and a low threshold for inclusion to minimize the likelihood of rejecting articles of interest. Publications then were reviewed in full text, applying additional a priori defined exclusion criteria. The database was built and published on the Systematic Review Data Repository (SRDR™, a web-based, publicly available application.A fiber database was created. This resource will reduce the unnecessary replication of effort in conducting systematic reviews by serving as both a central database archiving PICO (population, intervention, comparator, outcome data on published studies and as a searchable tool through which this data can be extracted and updated.

  7. The final COS-B database now publicly available

    Science.gov (United States)

    Mayer-Hasselwander, H. A.; Bennett, K.; Bignami, G. F.; Bloemen, J. B. G. M.; Buccheri, R.; Caraveo, P. A.; Hermsen, W.; Kanbach, G.; Lebrun, F.; Paul, J. A.

    1985-01-01

    The data obtained by the gamma ray satellite COS-B was processed, condensed and integrated together with the relevant mission and experiment parameters into the Final COS-B Database. The database contents and the access programs available with the database are outlined. The final sky coverage and a presentation of the large scale distribution of the observed Milky Way emission are given. The database is announced to be available through the European Space Agency.

  8. Comparison of locus-specific databases for BRCA1 and BRCA2 variants reveals disparity in variant classification within and among databases.

    Science.gov (United States)

    Vail, Paris J; Morris, Brian; van Kan, Aric; Burdett, Brianna C; Moyes, Kelsey; Theisen, Aaron; Kerr, Iain D; Wenstrup, Richard J; Eggington, Julie M

    2015-10-01

    Genetic variants of uncertain clinical significance (VUSs) are a common outcome of clinical genetic testing. Locus-specific variant databases (LSDBs) have been established for numerous disease-associated genes as a research tool for the interpretation of genetic sequence variants to facilitate variant interpretation via aggregated data. If LSDBs are to be used for clinical practice, consistent and transparent criteria regarding the deposition and interpretation of variants are vital, as variant classifications are often used to make important and irreversible clinical decisions. In this study, we performed a retrospective analysis of 2017 consecutive BRCA1 and BRCA2 genetic variants identified from 24,650 consecutive patient samples referred to our laboratory to establish an unbiased dataset representative of the types of variants seen in the US patient population, submitted by clinicians and researchers for BRCA1 and BRCA2 testing. We compared the clinical classifications of these variants among five publicly accessible BRCA1 and BRCA2 variant databases: BIC, ClinVar, HGMD (paid version), LOVD, and the UMD databases. Our results show substantial disparity of variant classifications among publicly accessible databases. Furthermore, it appears that discrepant classifications are not the result of a single outlier but widespread disagreement among databases. This study also shows that databases sometimes favor a clinical classification when current best practice guidelines (ACMG/AMP/CAP) would suggest an uncertain classification. Although LSDBs have been well established for research applications, our results suggest several challenges preclude their wider use in clinical practice.

  9. 75 FR 41180 - Notice of Order: Revisions to Enterprise Public Use Database

    Science.gov (United States)

    2010-07-15

    ... purpose of loan data field in these two databases. 4. Single-family Data Field 27 and Multifamily Data... AGENCY Notice of Order: Revisions to Enterprise Public Use Database AGENCY: Federal Housing Finance... use database (PUDB) for such mortgage data was transferred to FHFA from the U.S. Department of...

  10. Public participation in genetic databases: crossing the boundaries between biobanks and forensic DNA databases through the principle of solidarity.

    Science.gov (United States)

    Machado, Helena; Silva, Susana

    2015-10-01

    The ethical aspects of biobanks and forensic DNA databases are often treated as separate issues. As a reflection of this, public participation, or the involvement of citizens in genetic databases, has been approached differently in the fields of forensics and medicine. This paper aims to cross the boundaries between medicine and forensics by exploring the flows between the ethical issues presented in the two domains and the subsequent conceptualisation of public trust and legitimisation. We propose to introduce the concept of 'solidarity', traditionally applied only to medical and research biobanks, into a consideration of public engagement in medicine and forensics. Inclusion of a solidarity-based framework, in both medical biobanks and forensic DNA databases, raises new questions that should be included in the ethical debate, in relation to both health services/medical research and activities associated with the criminal justice system.

  11. Public participation in genetic databases: crossing the boundaries between biobanks and forensic DNA databases through the principle of solidarity

    Science.gov (United States)

    Machado, Helena; Silva, Susana

    2015-01-01

    The ethical aspects of biobanks and forensic DNA databases are often treated as separate issues. As a reflection of this, public participation, or the involvement of citizens in genetic databases, has been approached differently in the fields of forensics and medicine. This paper aims to cross the boundaries between medicine and forensics by exploring the flows between the ethical issues presented in the two domains and the subsequent conceptualisation of public trust and legitimisation. We propose to introduce the concept of ‘solidarity’, traditionally applied only to medical and research biobanks, into a consideration of public engagement in medicine and forensics. Inclusion of a solidarity-based framework, in both medical biobanks and forensic DNA databases, raises new questions that should be included in the ethical debate, in relation to both health services/medical research and activities associated with the criminal justice system. PMID:26139851

  12. Cancer registries in Japan: National Clinical Database and site-specific cancer registries.

    Science.gov (United States)

    Anazawa, Takayuki; Miyata, Hiroaki; Gotoh, Mitsukazu

    2015-02-01

    The cancer registry is an essential part of any rational program of evidence-based cancer control. The cancer control program is required to strategize in a systematic and impartial manner and efficiently utilize limited resources. In Japan, the National Clinical Database (NCD) was launched in 2010. It is a nationwide prospective registry linked to various types of board certification systems regarding surgery. The NCD is a nationally validated database using web-based data collection software; it is risk adjusted and outcome based to improve the quality of surgical care. The NCD generalizes site-specific cancer registries by taking advantage of their excellent organizing ability. Some site-specific cancer registries, including pancreatic, breast, and liver cancer registries have already been combined with the NCD. Cooperation between the NCD and site-specific cancer registries can establish a valuable platform to develop a cancer care plan in Japan. Furthermore, the prognosis information of cancer patients arranged using population-based and hospital-based cancer registries can help in efficient data accumulation on the NCD. International collaboration between Japan and the USA has recently started and is expected to provide global benchmarking and to allow a valuable comparison of cancer treatment practices between countries using nationwide cancer registries in the future. Clinical research and evidence-based policy recommendation based on accurate data from the nationwide database may positively impact the public.

  13. Data mining of public SNP databases for the selection of intragenic SNPs

    NARCIS (Netherlands)

    Aerts, J.; Wetzels, Y.; Cohen, N.; Aerssens, J.

    2002-01-01

    Different strategies to search public single nucleotide polymorphism (SNP) databases for intragenic SNPs were evaluated. First, we assembled a strategy to annotate SNPs onto candidate genes based on a BLAST search of public SNP databases (Intragenic SNP Annotation by BLAST, ISAB). Only BLAST hits th

  14. Big bad data: law, public health, and biomedical databases.

    Science.gov (United States)

    Hoffman, Sharona; Podgurski, Andy

    2013-03-01

    The accelerating adoption of electronic health record (EHR) systems will have far-reaching implications for public health research and surveillance, which in turn could lead to changes in public policy, statutes, and regulations. The public health benefits of EHR use can be significant. However, researchers and analysts who rely on EHR data must proceed with caution and understand the potential limitations of EHRs. Because of clinicians' workloads, poor user-interface design, and other factors, EHR data can be erroneous, miscoded, fragmented, and incomplete. In addition, public health findings can be tainted by the problems of selection bias, confounding bias, and measurement bias. These flaws may become all the more troubling and important in an era of electronic "big data," in which a massive amount of information is processed automatically, without human checks. Thus, we conclude the paper by outlining several regulatory and other interventions to address data analysis difficulties that could result in invalid conclusions and unsound public health policies. © 2013 American Society of Law, Medicine & Ethics, Inc.

  15. Databases

    Data.gov (United States)

    National Aeronautics and Space Administration — The databases of computational and experimental data from the first Aeroelastic Prediction Workshop are located here. The databases file names tell their contents by...

  16. Public sector risk management: a specific model.

    Science.gov (United States)

    Lawlor, Ted

    2002-07-01

    Risk management programs for state mental health authorities are generally limited in scope and reactive in nature. Recent changes in how mental health care is provided render it necessary to redirect the risk management focus from its present institutional basis to a statewide, network-based paradigm that is integrated across public and private inpatient and community programs alike. These changes include treating an increasing number of individuals in less-secure settings and contracting for an increasing number of public mental health services with private providers. The model proposed here is closely linked to the Quality Management Process.

  17. Databases

    Directory of Open Access Journals (Sweden)

    Nick Ryan

    2004-01-01

    Full Text Available Databases are deeply embedded in archaeology, underpinning and supporting many aspects of the subject. However, as well as providing a means for storing, retrieving and modifying data, databases themselves must be a result of a detailed analysis and design process. This article looks at this process, and shows how the characteristics of data models affect the process of database design and implementation. The impact of the Internet on the development of databases is examined, and the article concludes with a discussion of a range of issues associated with the recording and management of archaeological data.

  18. Literature curation of protein interactions: measuring agreement across major public databases

    Science.gov (United States)

    Turinsky, Andrei L.; Razick, Sabry; Turner, Brian; Wodak, Shoshana J.

    2010-01-01

    Literature curation of protein interaction data faces a number of challenges. Although curators increasingly adhere to standard data representations, the data that various databases actually record from the same published information may differ significantly. Some of the reasons underlying these differences are well known, but their global impact on the interactions collectively curated by major public databases has not been evaluated. Here we quantify the agreement between curated interactions from 15 471 publications shared across nine major public databases. Results show that on average, two databases fully agree on 42% of the interactions and 62% of the proteins curated from the same publication. Furthermore, a sizable fraction of the measured differences can be attributed to divergent assignments of organism or splice isoforms, different organism focus and alternative representations of multi-protein complexes. Our findings highlight the impact of divergent curation policies across databases, and should be relevant to both curators and data consumers interested in analyzing protein-interaction data generated by the scientific community. Database URL: http://wodaklab.org/iRefWeb PMID:21183497

  19. Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas assembled into a publicly accessible database: the GigasDatabase

    Directory of Open Access Journals (Sweden)

    Klopp Christophe

    2009-07-01

    Full Text Available Abstract Background Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available. Description In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster. Conclusion A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit

  20. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.

    Directory of Open Access Journals (Sweden)

    Alexandra M Schnoes

    2009-12-01

    Full Text Available Due to the rapid release of new data from genome sequencing projects, the majority of protein sequences in public databases have not been experimentally characterized; rather, sequences are annotated using computational analysis. The level of misannotation and the types of misannotation in large public databases are currently unknown and have not been analyzed in depth. We have investigated the misannotation levels for molecular function in four public protein sequence databases (UniProtKB/Swiss-Prot, GenBank NR, UniProtKB/TrEMBL, and KEGG for a model set of 37 enzyme families for which extensive experimental information is available. The manually curated database Swiss-Prot shows the lowest annotation error levels (close to 0% for most families; the two other protein sequence databases (GenBank NR and TrEMBL and the protein sequences in the KEGG pathways database exhibit similar and surprisingly high levels of misannotation that average 5%-63% across the six superfamilies studied. For 10 of the 37 families examined, the level of misannotation in one or more of these databases is >80%. Examination of the NR database over time shows that misannotation has increased from 1993 to 2005. The types of misannotation that were found fall into several categories, most associated with "overprediction" of molecular function. These results suggest that misannotation in enzyme superfamilies containing multiple families that catalyze different reactions is a larger problem than has been recognized. Strategies are suggested for addressing some of the systematic problems contributing to these high levels of misannotation.

  1. Molecular scaffold analysis of natural products databases in the public domain.

    Science.gov (United States)

    Yongye, Austin B; Waddell, Jacob; Medina-Franco, José L

    2012-11-01

    Natural products represent important sources of bioactive compounds in drug discovery efforts. In this work, we compiled five natural products databases available in the public domain and performed a comprehensive chemoinformatic analysis focused on the content and diversity of the scaffolds with an overview of the diversity based on molecular fingerprints. The natural products databases were compared with each other and with a set of molecules obtained from in-house combinatorial libraries, and with a general screening commercial library. It was found that publicly available natural products databases have different scaffold diversity. In contrast to the common concept that larger libraries have the largest scaffold diversity, the largest natural products collection analyzed in this work was not the most diverse. The general screening library showed, overall, the highest scaffold diversity. However, considering the most frequent scaffolds, the general reference library was the least diverse. In general, natural products databases in the public domain showed low molecule overlap. In addition to benzene and acyclic compounds, flavones, coumarins, and flavanones were identified as the most frequent molecular scaffolds across the different natural products collections. The results of this work have direct implications in the computational and experimental screening of natural product databases for drug discovery.

  2. Identification of novel tissue-specific genes by analysis of microarray databases: a human and mouse model.

    Science.gov (United States)

    Song, Yan; Ahn, Jinsoo; Suh, Yeunsu; Davis, Michael E; Lee, Kichoon

    2013-01-01

    Understanding the tissue-specific pattern of gene expression is critical in elucidating the molecular mechanisms of tissue development, gene function, and transcriptional regulations of biological processes. Although tissue-specific gene expression information is available in several databases, follow-up strategies to integrate and use these data are limited. The objective of the current study was to identify and evaluate novel tissue-specific genes in human and mouse tissues by performing comparative microarray database analysis and semi-quantitative PCR analysis. We developed a powerful approach to predict tissue-specific genes by analyzing existing microarray data from the NCBI's Gene Expression Omnibus (GEO) public repository. We investigated and confirmed tissue-specific gene expression in the human and mouse kidney, liver, lung, heart, muscle, and adipose tissue. Applying our novel comparative microarray approach, we confirmed 10 kidney, 11 liver, 11 lung, 11 heart, 8 muscle, and 8 adipose specific genes. The accuracy of this approach was further verified by employing semi-quantitative PCR reaction and by searching for gene function information in existing publications. Three novel tissue-specific genes were discovered by this approach including AMDHD1 (amidohydrolase domain containing 1) in the liver, PRUNE2 (prune homolog 2) in the heart, and ACVR1C (activin A receptor, type IC) in adipose tissue. We further confirmed the tissue-specific expression of these 3 novel genes by real-time PCR. Among them, ACVR1C is adipose tissue-specific and adipocyte-specific in adipose tissue, and can be used as an adipocyte developmental marker. From GEO profiles, we predicted the processes in which AMDHD1 and PRUNE2 may participate. Our approach provides a novel way to identify new sets of tissue-specific genes and to predict functions in which they may be involved.

  3. The 2008 Public Release of the International Multi-tokamak Confinement Profile Database

    NARCIS (Netherlands)

    Roach, C. M.; Walters, M.; Budny, R. V.; Imbeaux, F.; Fredian, T. W.; Greenwald, M.; Stillerman, J. A.; Alexander, D. A.; Carlsson, J.; Cary, J. R.; Ryter, F.; Stober, J.; Gohil, P.; Greenfield, C.; Murakami, M.; Bracco, G.; Esposito, B.; Romanelli, M.; Parail, V.; Stubberfield, P.; Voitsekhovitch, I.; Brickley, C.; Field, A. R.; Sakamoto, Y.; Fujita, T.; Fukuda, T.; Hayashi, N.; Hogeweij, G. M. D.; Chudnovskiy, A.; Kinerva, N. A.; Kessel, C. E.; Aniel, T.; Hoang, G. T.; Ongena, J.; Doyle, E. J.; Houlberg, W. A.; Polevoi, A. R.

    2008-01-01

    This paper documents the public release PR08 of the International Tokamak Physics Activity (ITPA) profile database, which should be of particular interest to the magnetic confinement fusion community. Data from a wide variety of interesting discharges from many of the world's leading tokamak ex

  4. Towards a public analysis database for LHC new physics searches using MadAnalysis 5

    CERN Document Server

    Dumont, B; Kraml, S; Bein, S; Chalons, G; Conte, E; Kulkarni, S; Sengupta, D; Wymant, C

    2015-01-01

    We present the implementation, in the MadAnalysis 5 framework, of several ATLAS and CMS searches for supersymmetry in data recorded during the first run of the LHC. We provide extensive details on the validation of our implementations and propose to create a public analysis database within this framework.

  5. STANDARDIZATION AND STRUCTURAL ANNOTATION OF PUBLIC TOXICITY DATABASES: IMPROVING SAR CAPABILITIES AND LINKAGE TO 'OMICS DATA

    Science.gov (United States)

    Standardization and structural annotation of public toxicity databases: Improving SAR capabilities and linkage to 'omics data Ann M. Richard', ClarLynda Williams', Jamie Burch2'Nat Health & Environ Res Lab, US EPA, RTP, NC 27711; 2EPA/NC Central Univ Student COOP Trainee<...

  6. Does an Otolaryngology-Specific Database Have Added Value? A Comparative Feasibility Analysis.

    Science.gov (United States)

    Bellmunt, Angela M; Roberts, Rhonda; Lee, Walter T; Schulz, Kris; Pynnonen, Melissa A; Crowson, Matthew G; Witsell, David; Parham, Kourosh; Langman, Alan; Vambutas, Andrea; Ryan, Sheila E; Shin, Jennifer J

    2016-07-01

    There are multiple nationally representative databases that support epidemiologic and outcomes research, and it is unknown whether an otolaryngology-specific resource would prove indispensable or superfluous. Therefore, our objective was to determine the feasibility of analyses in the National Ambulatory Medical Care Survey (NAMCS) and National Hospital Ambulatory Medical Care Survey (NHAMCS) databases as compared with the otolaryngology-specific Creating Healthcare Excellence through Education and Research (CHEER) database. Parallel analyses in 2 data sets. Ambulatory visits in the United States. To test a fixed hypothesis that could be directly compared between data sets, we focused on a condition with expected prevalence high enough to substantiate availability in both. This query also encompassed a broad span of diagnoses to sample the breadth of available information. Specifically, we compared an assessment of suspected risk factors for sensorineural hearing loss in subjects 0 to 21 years of age, according to a predetermined protocol. We also assessed the feasibility of 6 additional diagnostic queries among all age groups. In the NAMCS/NHAMCS data set, the number of measured observations was not sufficient to support reliable numeric conclusions (percentage standard error among risk factors: 38.6-92.1). Analysis of the CHEER database demonstrated that age, sex, meningitis, and cytomegalovirus were statistically significant factors associated with pediatric sensorineural hearing loss (P otolaryngology-specific database has added utility when compared with already available national ambulatory databases. © American Academy of Otolaryngology—Head and Neck Surgery Foundation 2016.

  7. An Improved Algorithm for Generating Database Transactions from Relational Algebra Specifications

    Directory of Open Access Journals (Sweden)

    Daniel J. Dougherty

    2010-03-01

    Full Text Available Alloy is a lightweight modeling formalism based on relational algebra. In prior work with Fisler, Giannakopoulos, Krishnamurthi, and Yoo, we have presented a tool, Alchemy, that compiles Alloy specifications into implementations that execute against persistent databases. The foundation of Alchemy is an algorithm for rewriting relational algebra formulas into code for database transactions. In this paper we report on recent progress in improving the robustness and efficiency of this transformation.

  8. LBVS: an online platform for ligand-based virtual screening using publicly accessible databases.

    Science.gov (United States)

    Zheng, Minghao; Liu, Zhihong; Yan, Xin; Ding, Qianzhi; Gu, Qiong; Xu, Jun

    2014-11-01

    Abundant data on compound bioactivity and publicly accessible chemical databases increase opportunities for ligand-based drug discovery. In order to make full use of the data, an online platform for ligand-based virtual screening (LBVS) using publicly accessible databases has been developed. LBVS adopts Bayesian learning approach to create virtual screening models because of its noise tolerance, speed, and efficiency in extracting knowledge from data. LBVS currently includes data derived from BindingDB and ChEMBL. Three validation approaches have been employed to evaluate the virtual screening models created from LBVS. The tenfold cross validation results of twenty different LBVS models demonstrate that LBVS achieves an average AUC value of 0.86. Our internal and external testing results indicate that LBVS is predictive for lead identifications. LBVS can be publicly accessed at http://rcdd.sysu.edu.cn/lbvs.

  9. ScafBank: a public comprehensive Scaffold database to support molecular hopping

    Institute of Scientific and Technical Information of China (English)

    Bibo YAN; Mengzhu XUE; Bing XIONG; Ke LIU; Dingyu HU; Jingkang SHEN

    2009-01-01

    Aim:The search for molecules whose bioactivities are similar to those of given compounds or to optimize the initial lead compounds from high throughput screening has attracted increasing interest in recent years.Our goal is to provide a publi-cally searchable database of scaffolds out from a large collection of existing chemical molecules.Results: Although a number of in silico methods have emerged to facilitate this process,which has become known as "scaffold hopping" or "molecular hopping",there is an urgent need for a database system to provide such valuable data in the drug design field.Here we have systematically analyzed a collection of commercially available small molecule databases and a bioactive compound database to identify unique scaffolds and we have built apublically searchable database.The analysis of approximately 4 800 000 of these compounds identified 241 824 unique scaffolds,which are stored in a relational database (http://202.127.30.184:8080/db.html).Each entry in the database is associated with a molecular occurrence and includes its distribution of molecular properties,such as molecular weight,logP,hydrogen bond acceptor number,hydrogen bond donor number,rotatable bond number and ring number.More importantly,for scaffolds derived from the bioactive compounds database,it also contains the original compounds and their target information.Conclusion: This Web-based database system could help researchers in the fields of medicinal and organic chemistry to design novel molecules with properties similar to the original compounds,but built on novel scaffolds.

  10. Information Technologies in Public Health Management: A Database on Biocides to Improve Quality of Life

    Directory of Open Access Journals (Sweden)

    A Grigoriu

    2012-05-01

    Full Text Available Background: Biocides for prolonging the shelf life of a large variety of materials have been extensively used over the last decades. It has estimated that the worldwide biocide consumption to be about 12.4 billion dollars in 2011, and is expected to increase in 2012. As biocides are substances we get in contact with in our everyday lives, access to this type of information is of paramount importance in order to ensure an appropriate living environment. Consequently, a database where information may be quickly processed, sorted, and easily accessed, according to different search criteria, is the most desirable solution. The main aim of this work was to design and implement a relational database with complete information about biocides used in public health management to improve the quality of life.Methods: Design and implementation of a relational database for biocides, by using the software "phpMyAdmin".Results: A database, which allows for an efficient collection, storage, and management of information including chemical properties and applications of a large quantity of biocides, as well as its adequate dissemination into the public health environment.Conclusion: The information contained in the database herein presented promotes an adequate use of biocides, by means of information technologies, which in consequence may help achieve important improvement in our quality of life.

  11. Resolving the problem of multiple accessions of the same transcript deposited across various public databases.

    Science.gov (United States)

    Weirick, Tyler; John, David; Uchida, Shizuka

    2017-03-01

    Maintaining the consistency of genomic annotations is an increasingly complex task because of the iterative and dynamic nature of assembly and annotation, growing numbers of biological databases and insufficient integration of annotations across databases. As information exchange among databases is poor, a 'novel' sequence from one reference annotation could be annotated in another. Furthermore, relationships to nearby or overlapping annotated transcripts are even more complicated when using different genome assemblies. To better understand these problems, we surveyed current and previous versions of genomic assemblies and annotations across a number of public databases containing long noncoding RNA. We identified numerous discrepancies of transcripts regarding their genomic locations, transcript lengths and identifiers. Further investigation showed that the positional differences between reference annotations of essentially the same transcript could lead to differences in its measured expression at the RNA level. To aid in resolving these problems, we present the algorithm 'Universal Genomic Accession Hash (UGAHash)' and created an open source web tool to encourage the usage of the UGAHash algorithm. The UGAHash web tool (http://ugahash.uni-frankfurt.de) can be accessed freely without registration. The web tool allows researchers to generate Universal Genomic Accessions for genomic features or to explore annotations deposited in the public databases of the past and present versions. We anticipate that the UGAHash web tool will be a valuable tool to check for the existence of transcripts before judging the newly discovered transcripts as novel. © The Author 2016. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  12. Documentation for the U.S. Geological Survey Public-Supply Database (PSDB): a database of permitted public-supply wells, surface-water intakes, and systems in the United States

    Science.gov (United States)

    Price, Curtis V.; Maupin, Molly A.

    2014-01-01

    The U.S. Geological Survey (USGS) has developed a database containing information about wells, surface-water intakes, and distribution systems that are part of public water systems across the United States, its territories, and possessions. Programs of the USGS such as the National Water Census, the National Water Use Information Program, and the National Water-Quality Assessment Program all require a complete and current inventory of public water systems, the sources of water used by those systems, and the size of populations served by the systems across the Nation. Although the U.S. Environmental Protection Agency’s Safe Drinking Water Information System (SDWIS) database already exists as the primary national Federal database for information on public water systems, the Public-Supply Database (PSDB) was developed to add value to SDWIS data with enhanced location and ancillary information, and to provide links to other databases, including the USGS’s National Water Information System (NWIS) database.

  13. Government databases and public health research: facilitating access in the public interest.

    Science.gov (United States)

    Adams, Carolyn; Allen, Judy

    2014-06-01

    Access to datasets of personal health information held by government agencies is essential to support public health research and to promote evidence-based public health policy development. Privacy legislation in Australia allows the use and disclosure of such information for public health research. However, access is not always forthcoming in a timely manner and the decision-making process undertaken by government data custodians is not always transparent. Given the public benefit in research using these health information datasets, this article suggests that it is time to recognise a right of access for approved research and that the decisions, and decision-making processes, of government data custodians should be subject to increased scrutiny. The article concludes that researchers should have an avenue of external review where access to information has been denied or unduly delayed.

  14. Genomics and Public Health Research: Can the State Allow Access to Genomic Databases?

    Directory of Open Access Journals (Sweden)

    M Stanton Jean

    2012-04-01

    Full Text Available Because many diseases are multifactorial disorders,the scientific progress in genomics and genetics should be taken into consideration in public health research. In this context, genomic databases will constitute an important source of information. Consequently, it is important to identify and characterize the State's role and authority on matters related to public health,in order to verify whether it has access to such databases while engaging in public health genomic research. We first consider the evolution of the concept of public health, as well as its core functions, using a comparative approach (e.g. WHO, PAHO, CDC and the Canadian province of Quebec. Following an analysis of relevant Quebec legislation, the precautionary principle is examined as a possible avenue to justify State access to and use of genomic databases for research purposes. Finally, we consider the Influenza pandemic plans developed by WHO, Canada, and Quebec,as examples of key tools framing public health decision-making process.We observed that State powers in public health, are not,in Quebec,well adapted to the expansion of genomics research.We propose that the scope of the concept of research in public health should be clear and include the following characteristics:a commitment to the health and well-being of the population and to their determinants; the inclusion of both applied research and basic research; and, an appropriate model of governance (authorization, follow-up,consent, etc..We also suggest that the strategic approach version of the precautionary principle could guide collective choices in these matters.

  15. Databases of publications and observations - as a part of the Crimean Astronomical Virtual Observatory

    CERN Document Server

    Shlyapnikov, A; Gorbunov, M

    2015-01-01

    The paper presents the basic principles of formation of a database (DB) with information about objects and their physical characteristics from observations carried out at the Crimean Astrophysical Observatory (CrAO) and published in "Izvestiya Krymskoi Astrofizicheskoi Observatorii" and other publications. The emphasis is placed on DBs that are not present in the most complete global library catalogs and data tables - VizieR (supported by the Strasbourg ADC). Separately, we consider the formation of a digital archive of observational data obtained at CrAO - as the interactive DB related to the DB of objects and publications. Examples of all the above DB as elements integrated into the Crimean Astronomical Virtual Observatory are presented in the paper. The operation with CrAO database is illustrated using tools of the International Virtual Observatory - Aladin, VOPlot, VOSpec jointly with VizieR DB and Simbad.

  16. ScafBank: a public comprehensive Scaffold database to support molecular hopping

    OpenAIRE

    2009-01-01

    Aim: The search for molecules whose bioactivities are similar to those of given compounds or to optimize the initial lead compounds from high throughput screening has attracted increasing interest in recent years. Our goal is to provide a publically searchable database of scaffolds out from a large collection of existing chemical molecules. Results: Although a number of in silico methods have emerged to facilitate this process, which has become known as ”scaffold hopping” or “molecular hoppin...

  17. Large-scale annotation of small-molecule libraries using public databases.

    Science.gov (United States)

    Zhou, Yingyao; Zhou, Bin; Chen, Kaisheng; Yan, S Frank; King, Frederick J; Jiang, Shumei; Winzeler, Elizabeth A

    2007-01-01

    While many large publicly accessible databases provide excellent annotation for biological macromolecules, the same is not true for small chemical compounds. Commercial data sources also fail to encompass an annotation interface for large numbers of compounds and tend to be cost prohibitive to be widely available to biomedical researchers. Therefore, using annotation information for the selection of lead compounds from a modern day high-throughput screening (HTS) campaign presently occurs only under a very limited scale. The recent rapid expansion of the NIH PubChem database provides an opportunity to link existing biological databases with compound catalogs and provides relevant information that potentially could improve the information garnered from large-scale screening efforts. Using the 2.5 million compound collection at the Genomics Institute of the Novartis Research Foundation (GNF) as a model, we determined that approximately 4% of the library contained compounds with potential annotation in such databases as PubChem and the World Drug Index (WDI) as well as related databases such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) and ChemIDplus. Furthermore, the exact structure match analysis showed 32% of GNF compounds can be linked to third party databases via PubChem. We also showed annotations such as MeSH (medical subject headings) terms can be applied to in-house HTS databases in identifying signature biological inhibition profiles of interest as well as expediting the assay validation process. The automated annotation of thousands of screening hits in batch is becoming feasible and has the potential to play an essential role in the hit-to-lead decision making process.

  18. Assessment of Residential History Generation Using a Public-Record Database

    Directory of Open Access Journals (Sweden)

    David C. Wheeler

    2015-09-01

    Full Text Available In studies of disease with potential environmental risk factors, residential location is often used as a surrogate for unknown environmental exposures or as a basis for assigning environmental exposures. These studies most typically use the residential location at the time of diagnosis due to ease of collection. However, previous residential locations may be more useful for risk analysis because of population mobility and disease latency. When residential histories have not been collected in a study, it may be possible to generate them through public-record databases. In this study, we evaluated the ability of a public-records database from LexisNexis to provide residential histories for subjects in a geographically diverse cohort study. We calculated 11 performance metrics comparing study-collected addresses and two address retrieval services from LexisNexis. We found 77% and 90% match rates for city and state and 72% and 87% detailed address match rates with the basic and enhanced services, respectively. The enhanced LexisNexis service covered 86% of the time at residential addresses recorded in the study. The mean match rate for detailed address matches varied spatially over states. The results suggest that public record databases can be useful for reconstructing residential histories for subjects in epidemiologic studies.

  19. Monogenic diabetes syndromes: Locus‐specific databases for Alström, Wolfram, and Thiamine‐responsive megaloblastic anemia

    Science.gov (United States)

    Astuti, Dewi; Sabir, Ataf; Fulton, Piers; Zatyka, Malgorzata; Williams, Denise; Hardy, Carol; Milan, Gabriella; Favaretto, Francesca; Yu‐Wai‐Man, Patrick; Rohayem, Julia; López de Heredia, Miguel; Hershey, Tamara; Tranebjaerg, Lisbeth; Chen, Jian‐Hua; Chaussenot, Annabel; Nunes, Virginia; Marshall, Bess; McAfferty, Susan; Tillmann, Vallo; Maffei, Pietro; Paquis‐Flucklinger, Veronique; Geberhiwot, Tarekign; Mlynarski, Wojciech; Parkinson, Kay; Picard, Virginie; Bueno, Gema Esteban; Dias, Renuka; Arnold, Amy; Richens, Caitlin; Paisey, Richard; Urano, Fumihiko; Semple, Robert; Sinnott, Richard

    2017-01-01

    Abstract We developed a variant database for diabetes syndrome genes, using the Leiden Open Variation Database platform, containing observed phenotypes matched to the genetic variations. We populated it with 628 published disease‐associated variants (December 2016) for: WFS1 (n = 309), CISD2 (n = 3), ALMS1 (n = 268), and SLC19A2 (n = 48) for Wolfram type 1, Wolfram type 2, Alström, and Thiamine‐responsive megaloblastic anemia syndromes, respectively; and included 23 previously unpublished novel germline variants in WFS1 and 17 variants in ALMS1. We then investigated genotype–phenotype relations for the WFS1 gene. The presence of biallelic loss‐of‐function variants predicted Wolfram syndrome defined by insulin‐dependent diabetes and optic atrophy, with a sensitivity of 79% (95% CI 75%–83%) and specificity of 92% (83%–97%). The presence of minor loss‐of‐function variants in WFS1 predicted isolated diabetes, isolated deafness, or isolated congenital cataracts without development of the full syndrome (sensitivity 100% [93%–100%]; specificity 78% [73%–82%]). The ability to provide a prognostic prediction based on genotype will lead to improvements in patient care and counseling. The development of the database as a repository for monogenic diabetes gene variants will allow prognostic predictions for other diabetes syndromes as next‐generation sequencing expands the repertoire of genotypes and phenotypes. The database is publicly available online at https://lovd.euro-wabb.org. PMID:28432734

  20. Monogenic diabetes syndromes: Locus-specific databases for Alström, Wolfram, and Thiamine-responsive megaloblastic anemia.

    Science.gov (United States)

    Astuti, Dewi; Sabir, Ataf; Fulton, Piers; Zatyka, Malgorzata; Williams, Denise; Hardy, Carol; Milan, Gabriella; Favaretto, Francesca; Yu-Wai-Man, Patrick; Rohayem, Julia; López de Heredia, Miguel; Hershey, Tamara; Tranebjaerg, Lisbeth; Chen, Jian-Hua; Chaussenot, Annabel; Nunes, Virginia; Marshall, Bess; McAfferty, Susan; Tillmann, Vallo; Maffei, Pietro; Paquis-Flucklinger, Veronique; Geberhiwot, Tarekign; Mlynarski, Wojciech; Parkinson, Kay; Picard, Virginie; Bueno, Gema Esteban; Dias, Renuka; Arnold, Amy; Richens, Caitlin; Paisey, Richard; Urano, Fumihiko; Semple, Robert; Sinnott, Richard; Barrett, Timothy G

    2017-07-01

    We developed a variant database for diabetes syndrome genes, using the Leiden Open Variation Database platform, containing observed phenotypes matched to the genetic variations. We populated it with 628 published disease-associated variants (December 2016) for: WFS1 (n = 309), CISD2 (n = 3), ALMS1 (n = 268), and SLC19A2 (n = 48) for Wolfram type 1, Wolfram type 2, Alström, and Thiamine-responsive megaloblastic anemia syndromes, respectively; and included 23 previously unpublished novel germline variants in WFS1 and 17 variants in ALMS1. We then investigated genotype-phenotype relations for the WFS1 gene. The presence of biallelic loss-of-function variants predicted Wolfram syndrome defined by insulin-dependent diabetes and optic atrophy, with a sensitivity of 79% (95% CI 75%-83%) and specificity of 92% (83%-97%). The presence of minor loss-of-function variants in WFS1 predicted isolated diabetes, isolated deafness, or isolated congenital cataracts without development of the full syndrome (sensitivity 100% [93%-100%]; specificity 78% [73%-82%]). The ability to provide a prognostic prediction based on genotype will lead to improvements in patient care and counseling. The development of the database as a repository for monogenic diabetes gene variants will allow prognostic predictions for other diabetes syndromes as next-generation sequencing expands the repertoire of genotypes and phenotypes. The database is publicly available online at https://lovd.euro-wabb.org. © 2017 The Authors. **Human Mutation published by Wiley Periodicals, Inc.

  1. Using linked administrative and disease-specific databases to study end-of-life care on a population level.

    Science.gov (United States)

    Maetens, Arno; De Schreye, Robrecht; Faes, Kristof; Houttekier, Dirk; Deliens, Luc; Gielen, Birgit; De Gendt, Cindy; Lusyne, Patrick; Annemans, Lieven; Cohen, Joachim

    2016-10-18

    The use of full-population databases is under-explored to study the use, quality and costs of end-of-life care. Using the case of Belgium, we explored: (1) which full-population databases provide valid information about end-of-life care, (2) what procedures are there to use these databases, and (3) what is needed to integrate separate databases. Technical and privacy-related aspects of linking and accessing Belgian administrative databases and disease registries were assessed in cooperation with the database administrators and privacy commission bodies. For all relevant databases, we followed procedures in cooperation with database administrators to link the databases and to access the data. We identified several databases as fitting for end-of-life care research in Belgium: the InterMutualistic Agency's national registry of health care claims data, the Belgian Cancer Registry including data on incidence of cancer, and databases administrated by Statistics Belgium including data from the death certificate database, the socio-economic survey and fiscal data. To obtain access to the data, approval was required from all database administrators, supervisory bodies and two separate national privacy bodies. Two Trusted Third Parties linked the databases via a deterministic matching procedure using multiple encrypted social security numbers. In this article we describe how various routinely collected population-level databases and disease registries can be accessed and linked to study patterns in the use, quality and costs of end-of-life care in the full population and in specific diagnostic groups.

  2. [Public scientific knowledge distribution in health information, communication and information technology indexed in MEDLINE and LILACS databases].

    Science.gov (United States)

    Packer, Abel Laerte; Tardelli, Adalberto Otranto; Castro, Regina Célia Figueiredo

    2007-01-01

    This study explores the distribution of international, regional and national scientific output in health information and communication, indexed in the MEDLINE and LILACS databases, between 1996 and 2005. A selection of articles was based on the hierarchical structure of Information Science in MeSH vocabulary. Four specific domains were determined: health information, medical informatics, scientific communications on healthcare and healthcare communications. The variables analyzed were: most-covered subjects and journals, author affiliation and publication countries and languages, in both databases. The Information Science category is represented in nearly 5% of MEDLINE and LILACS articles. The four domains under analysis showed a relative annual increase in MEDLINE. The Medical Informatics domain showed the highest number of records in MEDLINE, representing about half of all indexed articles. The importance of Information Science as a whole is more visible in publications from developed countries and the findings indicate the predominance of the United States, with significant growth in scientific output from China and South Korea and, to a lesser extent, Brazil.

  3. The Government Finance Database: A Common Resource for Quantitative Research in Public Financial Analysis.

    Science.gov (United States)

    Pierson, Kawika; Hand, Michael L; Thompson, Fred

    2015-01-01

    Quantitative public financial management research focused on local governments is limited by the absence of a common database for empirical analysis. While the U.S. Census Bureau distributes government finance data that some scholars have utilized, the arduous process of collecting, interpreting, and organizing the data has led its adoption to be prohibitive and inconsistent. In this article we offer a single, coherent resource that contains all of the government financial data from 1967-2012, uses easy to understand natural-language variable names, and will be extended when new data is available.

  4. Near real-time operation of public image database for ground vehicle navigation

    Science.gov (United States)

    Ali, E.; Kozaitis, S. P.

    2015-02-01

    An effective color night vision system for ground vehicle navigation should operate in near real-time to be practical. We described a system that uses a public database as a source of color information to colorize night vision imagery. Such an approach presents several problems due to differences between acquired and reference imagery. Our system performed registration, colorizing, and reference updating in near real-time in an effort to help drivers of ground vehicles during night to see a colored view of a scene.

  5. Novel statistical tools for management of public databases facilitate community-wide replicability and control of false discovery.

    Science.gov (United States)

    Rosset, Saharon; Aharoni, Ehud; Neuvirth, Hani

    2014-07-01

    Issues of publication bias, lack of replicability, and false discovery have long plagued the genetics community. Proper utilization of public and shared data resources presents an opportunity to ameliorate these problems. We present an approach to public database management that we term Quality Preserving Database (QPD). It enables perpetual use of the database for testing statistical hypotheses while controlling false discovery and avoiding publication bias on the one hand, and maintaining testing power on the other hand. We demonstrate it on a use case of a replication server for GWAS findings, underlining its practical utility. We argue that a shift to using QPD in managing current and future biological databases will significantly enhance the community's ability to make efficient and statistically sound use of the available data resources. © 2014 WILEY PERIODICALS, INC.

  6. Computer-aided detection of pulmonary nodules: a comparative study using the public LIDC/IDRI database

    NARCIS (Netherlands)

    Jacobs, C.; Rikxoort, E.M. van; Murphy, K.; Prokop, M.; Schaefer-Prokop, C.M.; Ginneken, B. van

    2016-01-01

    To benchmark the performance of state-of-the-art computer-aided detection (CAD) of pulmonary nodules using the largest publicly available annotated CT database (LIDC/IDRI), and to show that CAD finds lesions not identified by the LIDC's four-fold double reading process.The LIDC/IDRI database

  7. Toward a mtDNA Locus-Specific Mutation Database Using the LOVD Platform

    Science.gov (United States)

    Elson, Joanna L.; Sweeney, Mary G.; Procaccio, Vincent; Yarham, John W.; Salas, Antonio; Kong, Qing-Peng; van der Westhuizen, Francois H.; Pitceathly, Robert D.S.; Thorburn, David R.; Lott, Marie T.; Wallace, Douglas C.; Taylor, Robert W.; McFarland, Robert

    2015-01-01

    The Human Variome Project (HVP) is a global effort to collect and curate all human genetic variation affecting health. Mutations of mitochondrial DNA (mtDNA) are an important cause of neurogenetic disease in humans; however, identification of the pathogenic mutations responsible can be problematic. In this article, we provide explanations as to why and suggest how such difficulties might be overcome. We put forward a case in support of a new Locus Specific Mutation Database (LSDB) implemented using the Leiden Open-source Variation Database (LOVD) system that will not only list primary mutations, but also present the evidence supporting their role in disease. Critically, we feel that this new database should have the capacity to store information on the observed phenotypes alongside the genetic variation, thereby facilitating our understanding of the complex and variable presentation of mtDNA disease. LOVD supports fast queries of both seen and hidden data and allows storage of sequence variants from high-throughput sequence analysis. The LOVD platform will allow construction of a secure mtDNA database; one that can fully utilize currently available data, as well as that being generated by high-throughput sequencing, to link genotype with phenotype enhancing our understanding of mitochondrial disease, with a view to providing better prognostic information. PMID:22581690

  8. The role of specification in public procurement of innovation

    DEFF Research Database (Denmark)

    Rolfstam, Max

    A taken for granted assertion in the literature discussing how public procurement can be used as a way of stimulating innovation is that functional specification should be applied. Unlike technical specification, where the exact details of the item to be procured is defined, it is assumed that......, by specifying only the function or envisaged performance of the item to be procured, this would allow the submission of bids involving innovative technology and solutions previously unknown to the procurer. The starting point for the article is the perception that these views are commonly held assertions which...

  9. A public turbulence database cluster and applications to study Lagrangian evolution of velocity increments in turbulence

    CERN Document Server

    Li, Yi; Wan, Minping; Yang, Yunke; Meneveau, Charles; Burns, Randal; Chen, Shiyi; Szalay, Alexander; Eyink, Gregory

    2008-01-01

    A public database system archiving a direct numerical simulation (DNS) data set of isotropic, forced turbulence is described in this paper. The data set consists of the DNS output on $1024^3$ spatial points and 1024 time-samples spanning about one large-scale turn-over timescale. This complete $1024^4$ space-time history of turbulence is accessible to users remotely through an interface that is based on the Web-services model. Users may write and execute analysis programs on their host computers, while the programs make subroutine-like calls that request desired parts of the data over the network. The users are thus able to perform numerical experiments by accessing the 27 Terabytes of DNS data using regular platforms such as laptops. The architecture of the database is explained, as are some of the locally defined functions, such as differentiation and interpolation. Test calculations are performed to illustrate the usage of the system and to verify the accuracy of the methods. The database is then used to a...

  10. Learning from decoys to improve the sensitivity and specificity of proteomics database search results.

    Directory of Open Access Journals (Sweden)

    Amit Kumar Yadav

    Full Text Available The statistical validation of database search results is a complex issue in bottom-up proteomics. The correct and incorrect peptide spectrum match (PSM scores overlap significantly, making an accurate assessment of true peptide matches challenging. Since the complete separation between the true and false hits is practically never achieved, there is need for better methods and rescoring algorithms to improve upon the primary database search results. Here we describe the calibration and False Discovery Rate (FDR estimation of database search scores through a dynamic FDR calculation method, FlexiFDR, which increases both the sensitivity and specificity of search results. Modelling a simple linear regression on the decoy hits for different charge states, the method maximized the number of true positives and reduced the number of false negatives in several standard datasets of varying complexity (18-mix, 49-mix, 200-mix and few complex datasets (E. coli and Yeast obtained from a wide variety of MS platforms. The net positive gain for correct spectral and peptide identifications was up to 14.81% and 6.2% respectively. The approach is applicable to different search methodologies--separate as well as concatenated database search, high mass accuracy, and semi-tryptic and modification searches. FlexiFDR was also applied to Mascot results and showed better performance than before. We have shown that appropriate threshold learnt from decoys, can be very effective in improving the database search results. FlexiFDR adapts itself to different instruments, data types and MS platforms. It learns from the decoy hits and sets a flexible threshold that automatically aligns itself to the underlying variables of data quality and size.

  11. FISH REPRODUCTION: BIBLIOMETRIC ANALYSIS OF WORLDWIDE AND BRAZILIAN PUBLICATIONS IN SCOPUS DATABASE

    Directory of Open Access Journals (Sweden)

    Marcella Costa RADAEL

    2015-12-01

    Full Text Available Reproduction is a fundamental part of life being and studies related to fish reproduction have been much accessed. The aim of this study was to perform a bibliometric analysis in intend to identify trends in this kind of publication. During June 2013, were performed searches on Scopus Database, using the term “fish reproduction”, being compiled and presented information related to the number of publications per year, number of publications by country, publications by author, by journal, by institution and most used keywords. Based on the study, it was possible to obtain the following results: Brazil occupies a highlight position in number of papers, being that the Brazilian participation compared to worldwide publishing production is having an exponential increase; in Brazil, there is a high concentration of articles when concerning the top 10 authors and institutions. The present study allows verifying that the term “fish reproduction” has been focused by many scientific papers, being that in Brazil there is a special research effort related to this subject, especially in the last few years. The main contribution concerns to the use of bibliometric methods to describe the growth and concentration of researches in the area of fishfarm and reproduction.

  12. A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions

    Science.gov (United States)

    Creighton, Chad J.; Nagaraja, Ankur K.; Hanash, Samir M.; Matzuk, Martin M.; Gunaratne, Preethi H.

    2008-01-01

    MicroRNAs are short (∼22 nucleotides) noncoding RNAs that regulate the stability and translation of mRNA targets. A number of computational algorithms have been developed to help predict which microRNAs are likely to regulate which genes. Gene expression profiling of biological systems where microRNAs might be active can yield hundreds of differentially expressed genes. The commonly used public microRNA target prediction databases facilitate gene-by-gene searches. However, integration of microRNA–mRNA target predictions with gene expression data on a large scale using these databases is currently cumbersome and time consuming for many researchers. We have developed a desktop software application which, for a given target prediction database, retrieves all microRNA:mRNA functional pairs represented by an experimentally derived set of genes. Furthermore, for each microRNA, the software computes an enrichment statistic for overrepresentation of predicted targets within the gene set, which could help to implicate roles for specific microRNAs and microRNA-regulated genes in the system under study. Currently, the software supports searching of results from PicTar, TargetScan, and miRanda algorithms. In addition, the software can accept any user-defined set of gene-to-class associations for searching, which can include the results of other target prediction algorithms, as well as gene annotation or gene-to-pathway associations. A search (using our software) of genes transcriptionally regulated in vitro by estrogen in breast cancer uncovered numerous targeting associations for specific microRNAs—above what could be observed in randomly generated gene lists—suggesting a role for microRNAs in mediating the estrogen response. The software and Excel VBA source code are freely available at http://sigterms.sourceforge.net. PMID:18812437

  13. A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions.

    Science.gov (United States)

    Creighton, Chad J; Nagaraja, Ankur K; Hanash, Samir M; Matzuk, Martin M; Gunaratne, Preethi H

    2008-11-01

    MicroRNAs are short (approximately 22 nucleotides) noncoding RNAs that regulate the stability and translation of mRNA targets. A number of computational algorithms have been developed to help predict which microRNAs are likely to regulate which genes. Gene expression profiling of biological systems where microRNAs might be active can yield hundreds of differentially expressed genes. The commonly used public microRNA target prediction databases facilitate gene-by-gene searches. However, integration of microRNA-mRNA target predictions with gene expression data on a large scale using these databases is currently cumbersome and time consuming for many researchers. We have developed a desktop software application which, for a given target prediction database, retrieves all microRNA:mRNA functional pairs represented by an experimentally derived set of genes. Furthermore, for each microRNA, the software computes an enrichment statistic for overrepresentation of predicted targets within the gene set, which could help to implicate roles for specific microRNAs and microRNA-regulated genes in the system under study. Currently, the software supports searching of results from PicTar, TargetScan, and miRanda algorithms. In addition, the software can accept any user-defined set of gene-to-class associations for searching, which can include the results of other target prediction algorithms, as well as gene annotation or gene-to-pathway associations. A search (using our software) of genes transcriptionally regulated in vitro by estrogen in breast cancer uncovered numerous targeting associations for specific microRNAs-above what could be observed in randomly generated gene lists-suggesting a role for microRNAs in mediating the estrogen response. The software and Excel VBA source code are freely available at http://sigterms.sourceforge.net.

  14. Comparison of Ethnic-specific Databases in Heidelberg Retina Tomography-3 to Discriminate Between Early Glaucoma and Normal Chinese Eyes.

    Science.gov (United States)

    Tan, Xiu Ling; Yap, Sae Cheong; Li, Xiang; Yip, Leonard W

    2017-01-01

    To compare the diagnostic accuracy of the 3 race-specific normative databases in Heidelberg Retina Tomography (HRT)-3, in differentiating between early glaucomatous and healthy normal Chinese eyes. 52 healthy volunteers and 25 glaucoma patients were recruited for this prospective cross-sectional study. All underwent standardized interviews, ophthalmic examination, perimetry and HRT optic disc imaging. Area under the curve (AUC) receiver operating characteristics, sensitivity and specificity were derived to assess the discriminating abilities of the 3 normative databases, for both Moorfields Regression Analysis (MRA) and Glaucoma Probability Score (GPS). A significantly higher percentage (65%) of patients were classified as "within normal limits" using the MRA-Indian database, as compared to the MRA-Caucasian and MRA-African-American databases. However, for GPS, this was observed using the African-American database. For MRA, the highest sensitivity was obtained with both Caucasian and African-American databases (68%), while the highest specificity was from the Indian database (94%). The AUC for discrimination between glaucomatous and normal eyes by MRA-Caucasian, MRA-African-American and MRA-Indian databases were 0.77 (95% CI, 0.67-0.88), 0.79 (0.69-0.89) and 0.73 (0.63-0.84) respectively. For GPS, the highest sensitivity was obtained using either Caucasian or Indian databases (68%). The highest specificity was seen with the African-American database (98%). The AUC for GPS-Caucasian, GPS-African-American and GPS-Indian databases were 0.76 (95% CI, 0.66-0.87), 0.77 (0.67-0.87) and 0.76 (0.66-0.87) respectively. Comparison of the 3 ethnic databases did not reveal significant differences to differentiate early glaucomatous from normal Chinese eyes.

  15. Introducing a Public Stereoscopic 3D High Dynamic Range (SHDR) Video Database

    Science.gov (United States)

    Banitalebi-Dehkordi, Amin

    2017-03-01

    High dynamic range (HDR) displays and cameras are paving their ways through the consumer market at a rapid growth rate. Thanks to TV and camera manufacturers, HDR systems are now becoming available commercially to end users. This is taking place only a few years after the blooming of 3D video technologies. MPEG/ITU are also actively working towards the standardization of these technologies. However, preliminary research efforts in these video technologies are hammered by the lack of sufficient experimental data. In this paper, we introduce a Stereoscopic 3D HDR database of videos that is made publicly available to the research community. We explain the procedure taken to capture, calibrate, and post-process the videos. In addition, we provide insights on potential use-cases, challenges, and research opportunities, implied by the combination of higher dynamic range of the HDR aspect, and depth impression of the 3D aspect.

  16. Identifying Useful Terms to Retrieve Survival Data Meta-Analyses Publications for Bibliographic Databases Search Strategies

    Directory of Open Access Journals (Sweden)

    Daniel Corneliu LEUCUŢA

    2009-12-01

    Full Text Available Introduction: Quality research and quality evidence based medicine practice has an important pillar in a solid bibliographic documentation. Quality bibliographic documentation makes use of search strategies to retrieve articles from search engines of bibliographic databases. The AIM of this study was the identification of useful search terms to be used in search strategies that try to find meta-analyses of survival data. Materials and methods: A qualitative study based on text analysis was undertaken to identify useful terms for search strategies in abstracts of scientific papers. Survival analysis meta-analyses publication type studies, published between 1996 and 2005, were searched in Medline bibliographic database through Pubmed web interface. Each abstract was analysed and each important terms were noted down if they were considered to be useful in the creation of search strategies for analysis of survival data, or meta-analyses. Results: Pubmed search yielded 773 results. From these search results 401 (52% fulfilled inclusion criteria. The terms that were identified as useful in search strategies for meta-analyses of survival data are presented in the paper.

  17. Identification and correction of abnormal, incomplete and mispredicted proteins in public databases

    Directory of Open Access Journals (Sweden)

    Bányai László

    2008-08-01

    Full Text Available Abstract Background Despite significant improvements in computational annotation of genomes, sequences of abnormal, incomplete or incorrectly predicted genes and proteins remain abundant in public databases. Since the majority of incomplete, abnormal or mispredicted entries are not annotated as such, these errors seriously affect the reliability of these databases. Here we describe the MisPred approach that may provide an efficient means for the quality control of databases. The current version of the MisPred approach uses five distinct routines for identifying abnormal, incomplete or mispredicted entries based on the principle that a sequence is likely to be incorrect if some of its features conflict with our current knowledge about protein-coding genes and proteins: (i conflict between the predicted subcellular localization of proteins and the absence of the corresponding sequence signals; (ii presence of extracellular and cytoplasmic domains and the absence of transmembrane segments; (iii co-occurrence of extracellular and nuclear domains; (iv violation of domain integrity; (v chimeras encoded by two or more genes located on different chromosomes. Results Analyses of predicted EnsEMBL protein sequences of nine deuterostome (Homo sapiens, Mus musculus, Rattus norvegicus, Monodelphis domestica, Gallus gallus, Xenopus tropicalis, Fugu rubripes, Danio rerio and Ciona intestinalis and two protostome species (Caenorhabditis elegans and Drosophila melanogaster have revealed that the absence of expected signal peptides and violation of domain integrity account for the majority of mispredictions. Analyses of sequences predicted by NCBI's GNOMON annotation pipeline show that the rates of mispredictions are comparable to those of EnsEMBL. Interestingly, even the manually curated UniProtKB/Swiss-Prot dataset is contaminated with mispredicted or abnormal proteins, although to a much lesser extent than UniProtKB/TrEMBL or the EnsEMBL or GNOMON

  18. Personal Publications Lists Serve as a Reliable Calibration Parameter to Compare Coverage in Academic Citation Databases with Scientific Social Media

    Directory of Open Access Journals (Sweden)

    Emma Hughes

    2017-03-01

    Full Text Available A Review of: Hilbert, F., Barth, J., Gremm, J., Gros, D., Haiter, J., Henkel, M., Reinhardt, W., & Stock, W.G. (2015. Coverage of academic citation databases compared with coverage of scientific social media: personal publication lists as calibration parameters. Online Information Review 39(2: 255-264. http://dx.doi.org/10.1108/OIR-07-2014-0159 Objective – The purpose of this study was to explore coverage rates of information science publications in academic citation databases and scientific social media using a new method of personal publication lists as a calibration parameter. The research questions were: How many publications are covered in different databases, which has the best coverage, and what institutions are represented and how does the language of the publication play a role? Design – Bibliometric analysis. Setting – Academic citation databases (Web of Science, Scopus, Google Scholar and scientific social media (Mendeley, CiteULike, Bibsonomy. Subjects – 1,017 library and information science publications produced by 76 information scientists at 5 German-speaking universities in Germany and Austria. Methods – Only documents which were published between 1 January 2003 and 31 December 2012 were included. In that time the 76 information scientists had produced 1,017 documents. The information scientists confirmed that their publication lists were complete and these served as the calibration parameter for the study. The citations from the publication lists were searched in three academic databases: Google Scholar, Web of Science (WoS, and Scopus; as well as three social media citation sites: Mendeley, CiteULike, and BibSonomy and the results were compared. The publications were searched for by author name and words from the title. Main results – None of the databases investigated had 100% coverage. In the academic databases, Google Scholar had the highest amount of coverage with an average of 63%, Scopus an average of 31%, and

  19. A site-specific curated database for the microorganisms of activated sludge and anaerobic digesters

    DEFF Research Database (Denmark)

    McIlroy, Simon Jon; Kirkegaard, Rasmus Hansen; McIlroy, Bianca

    the composition and dynamics of the most abundant organisms. However, to understand the relationship between the population dynamics and operational parameters of the system, a functional role must be attributed to each organism. The Microbial Database for Activated Sludge (MiDAS) and Anaerobic Digesters (AD......) presented here provides a site specific curated taxonomy for abundant and important microorganisms and integrates it into a community knowledge web platform about the microbes in activated sludge (AS) and their associated ADs (www.midasfieldguide.org). The MiDAS taxonomy, a manual curation of the SILVA......, to improve the classification of unknown organisms and link these names to the wealth of present and future functional information about their ecology....

  20. The KTOI Ecosystem Project Relational Database : a Report Prepared by Statistical Consulting Services for KTOI Describing the Key Components and Specifications of the KTOI Relational Database.

    Energy Technology Data Exchange (ETDEWEB)

    Shafii, Bahman [Statistical Consulting Services

    2009-09-24

    Data are the central focus of any research project. Their collection and analysis are crucial to meeting project goals, testing scientific hypotheses, and drawing relevant conclusions. Typical research projects often devote the majority of their resources to the collection, storage and analysis of data. Therefore, issues related to data quality should be of foremost concern. Data quality issues are even more important when conducting multifaceted studies involving several teams of researchers. Without the use of a standardized protocol, for example, independent data collection carried out by separate research efforts can lead to inconsistencies, confusion and errors throughout the larger project. A database management system can be utilized to help avoid all of the aforementioned problems. The centralization of data into a common relational unit, i.e. a relational database, shifts the responsibility for data quality and maintenance from multiple individuals to a single database manager, thus allowing data quality issues to be assessed and corrected in a timely manner. The database system also provides an easy mechanism for standardizing data components, such as variable names and values uniformly across all segments of a project. This is particularly an important issue when data are collected on a number of biological/physical response and explanatory variables from various locations and times. The database system can integrate all segments of a large study into one unit, while providing oversight and accessibility to the data collection process. The quality of all data collected is uniformly maintained and compatibility between research efforts ensured. While the physical database would exist in a central location, access will not be physically limited. Advanced database interfaces are created to operate over the internet utilizing a Web-based relational database, allowing project members to access their data from virtually anywhere. These interfaces provide users

  1. Defining new criteria for selection of cell-based intestinal models using publicly available databases

    Directory of Open Access Journals (Sweden)

    Christensen Jon

    2012-06-01

    Full Text Available Abstract Background The criteria for choosing relevant cell lines among a vast panel of available intestinal-derived lines exhibiting a wide range of functional properties are still ill-defined. The objective of this study was, therefore, to establish objective criteria for choosing relevant cell lines to assess their appropriateness as tumor models as well as for drug absorption studies. Results We made use of publicly available expression signatures and cell based functional assays to delineate differences between various intestinal colon carcinoma cell lines and normal intestinal epithelium. We have compared a panel of intestinal cell lines with patient-derived normal and tumor epithelium and classified them according to traits relating to oncogenic pathway activity, epithelial-mesenchymal transition (EMT and stemness, migratory properties, proliferative activity, transporter expression profiles and chemosensitivity. For example, SW480 represent an EMT-high, migratory phenotype and scored highest in terms of signatures associated to worse overall survival and higher risk of recurrence based on patient derived databases. On the other hand, differentiated HT29 and T84 cells showed gene expression patterns closest to tumor bulk derived cells. Regarding drug absorption, we confirmed that differentiated Caco-2 cells are the model of choice for active uptake studies in the small intestine. Regarding chemosensitivity we were unable to confirm a recently proposed association of chemo-resistance with EMT traits. However, a novel signature was identified through mining of NCI60 GI50 values that allowed to rank the panel of intestinal cell lines according to their drug responsiveness to commonly used chemotherapeutics. Conclusions This study presents a straightforward strategy to exploit publicly available gene expression data to guide the choice of cell-based models. While this approach does not overcome the major limitations of such models

  2. Potential translational targets revealed by linking mouse grooming behavioral phenotypes to gene expression using public databases.

    Science.gov (United States)

    Roth, Andrew; Kyzar, Evan J; Cachat, Jonathan; Stewart, Adam Michael; Green, Jeremy; Gaikwad, Siddharth; O'Leary, Timothy P; Tabakoff, Boris; Brown, Richard E; Kalueff, Allan V

    2013-01-10

    Rodent self-grooming is an important, evolutionarily conserved behavior, highly sensitive to pharmacological and genetic manipulations. Mice with aberrant grooming phenotypes are currently used to model various human disorders. Therefore, it is critical to understand the biology of grooming behavior, and to assess its translational validity to humans. The present in-silico study used publicly available gene expression and behavioral data obtained from several inbred mouse strains in the open-field, light-dark box, elevated plus- and elevated zero-maze tests. As grooming duration differed between strains, our analysis revealed several candidate genes with significant correlations between gene expression in the brain and grooming duration. The Allen Brain Atlas, STRING, GoMiner and Mouse Genome Informatics databases were used to functionally map and analyze these candidate mouse genes against their human orthologs, assessing the strain ranking of their expression and the regional distribution of expression in the mouse brain. This allowed us to identify an interconnected network of candidate genes (which have expression levels that correlate with grooming behavior), display altered patterns of expression in key brain areas related to grooming, and underlie important functions in the brain. Collectively, our results demonstrate the utility of large-scale, high-throughput data-mining and in-silico modeling for linking genomic and behavioral data, as well as their potential to identify novel neural targets for complex neurobehavioral phenotypes, including grooming.

  3. BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology.

    Science.gov (United States)

    Gilson, Michael K; Liu, Tiqing; Baitaluk, Michael; Nicola, George; Hwang, Linda; Chong, Jenny

    2016-01-04

    BindingDB, www.bindingdb.org, is a publicly accessible database of experimental protein-small molecule interaction data. Its collection of over a million data entries derives primarily from scientific articles and, increasingly, US patents. BindingDB provides many ways to browse and search for data of interest, including an advanced search tool, which can cross searches of multiple query types, including text, chemical structure, protein sequence and numerical affinities. The PDB and PubMed provide links to data in BindingDB, and vice versa; and BindingDB provides links to pathway information, the ZINC catalog of available compounds, and other resources. The BindingDB website offers specialized tools that take advantage of its large data collection, including ones to generate hypotheses for the protein targets bound by a bioactive compound, and for the compounds bound by a new protein of known sequence; and virtual compound screening by maximal chemical similarity, binary kernel discrimination, and support vector machine methods. Specialized data sets are also available, such as binding data for hundreds of congeneric series of ligands, drawn from BindingDB and organized for use in validating drug design methods. BindingDB offers several forms of programmatic access, and comes with extensive background material and documentation. Here, we provide the first update of BindingDB since 2007, focusing on new and unique features and highlighting directions of importance to the field as a whole.

  4. CONCEPTUAL MODEL OF MARKETING STRATEGIC PLANNING SPECIFIC TO PUBLIC ORGANIZATIONS

    OpenAIRE

    Ionescu Florin Tudor; Barbu Andreea Mihaela

    2012-01-01

    In public services, the political component of the marketing environment has a major importance, as all decisions adopted within central administration influence both the objectives and measures implemented by units of local government and other public service providers. Any discontinuity in the activity of such entities might result in neglecting the real needs of citizens and slowing the reform process in the public sector. Therefore, all initiatives of public organizations must have a unit...

  5. Complementary Value of Databases for Discovery of Scholarly Literature: A User Survey of Online Searching for Publications in Art History

    Science.gov (United States)

    Nemeth, Erik

    2010-01-01

    Discovery of academic literature through Web search engines challenges the traditional role of specialized research databases. Creation of literature outside academic presses and peer-reviewed publications expands the content for scholarly research within a particular field. The resulting body of literature raises the question of whether scholars…

  6. Coverage and quality: A comparison of Web of Science and Scopus databases for reporting faculty nursing publication metrics.

    Science.gov (United States)

    Powell, Kimberly R; Peterson, Shenita R

    2017-03-11

    Web of Science and Scopus are the leading databases of scholarly impact. Recent studies outside the field of nursing report differences in journal coverage and quality. A comparative analysis of nursing publications reported impact. Journal coverage by each database for the field of nursing was compared. Additionally, publications by 2014 nursing faculty were collected in both databases and compared for overall coverage and reported quality, as modeled by Scimajo Journal Rank, peer review status, and MEDLINE inclusion. Individual author impact, modeled by the h-index, was calculated by each database for comparison. Scopus offered significantly higher journal coverage. For 2014 faculty publications, 100% of journals were found in Scopus, Web of Science offered 82%. No significant difference was found in the quality of reported journals. Author h-index was found to be higher in Scopus. When reporting faculty publications and scholarly impact, academic nursing programs may be better represented by Scopus, without compromising journal quality. Programs with strong interdisciplinary work should examine all areas of strength to ensure appropriate coverage. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Segmentation of anatomical structures in chest radiographs using supervised methods: a comparative study on a public database

    DEFF Research Database (Denmark)

    van Ginneken, Bram; Stegmann, Mikkel Bille; Loog, Marco

    2006-01-01

    classification method that employs a multi-scale filter bank of Gaussian derivatives and a k-nearest-neighbors classifier. The methods have been tested on a publicly available database of 247 chest radiographs, in which all objects have been manually segmented by two human observers. A parameter optimization...

  8. 76 FR 60031 - Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single...

    Science.gov (United States)

    2011-09-28

    ... AGENCY Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single-Family... contains Enterprise single-family and multifamily mortgage loan-level data reported to FHFA by the... data characteristics of single-family high-cost loans purchased and securitized by the Enterprises...

  9. 76 FR 77533 - Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single...

    Science.gov (United States)

    2011-12-13

    ... AGENCY Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single-Family... matrices to include certain data fields for high-cost single-family loans purchased and securitized by the... rate spread field has been corrected in the Single Family Census Tract Data Set. Both files...

  10. Dengue virus antibody database: Systematically linking serotype-specificity with epitope mapping in dengue virus

    Science.gov (United States)

    Chaudhury, Sidhartha; Gromowski, Gregory D.; Ripoll, Daniel R.; Khavrutskii, Ilja V.; Desai, Valmik; Wallqvist, Anders

    2017-01-01

    Background A majority infections caused by dengue virus (DENV) are asymptomatic, but a higher incidence of severe illness, such as dengue hemorrhagic fever, is associated with secondary infections, suggesting that pre-existing immunity plays a central role in dengue pathogenesis. Primary infections are typically associated with a largely serotype-specific antibody response, while secondary infections show a shift to a broadly cross-reactive antibody response. Methods/Principal findings We hypothesized that the basis for the shift in serotype-specificity between primary and secondary infections can be found in a change in the antibody fine-specificity. To investigate the link between epitope- and serotype-specificity, we assembled the Dengue Virus Antibody Database, an online repository containing over 400 DENV-specific mAbs, each annotated with information on 1) its origin, including the immunogen, host immune history, and selection methods, 2) binding/neutralization data against all four DENV serotypes, and 3) epitope mapping at the domain or residue level to the DENV E protein. We combined epitope mapping and activity information to determine a residue-level index of epitope propensity and cross-reactivity and generated detailed composite epitope maps of primary and secondary antibody responses. We found differing patterns of epitope-specificity between primary and secondary infections, where secondary responses target a distinct subset of epitopes found in the primary response. We found that secondary infections were marked with an enhanced response to cross-reactive epitopes, such as the fusion-loop and E-dimer region, as well as increased cross-reactivity in what are typically more serotype-specific epitope regions, such as the domain I-II interface and domain III. Conclusions/Significance Our results support the theory that pre-existing cross-reactive memory B cells form the basis for the secondary antibody response, resulting in a broadening of the response

  11. Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database.

    Science.gov (United States)

    Thai, Quan Ke; Chung, Dung Anh; Tran, Hoang-Dung

    2017-06-26

    Canine and wolf mitochondrial DNA haplotypes, which can be used for forensic or phylogenetic analyses, have been defined in various schemes depending on the region analyzed. In recent studies, the 582 bp fragment of the HV1 region is most commonly used. 317 different canine HV1 haplotypes have been reported in the rapidly growing public database GenBank. These reported haplotypes contain several inconsistencies in their haplotype information. To overcome this issue, we have developed a Canis mtDNA HV1 database. This database collects data on the HV1 582 bp region in dog mitochondrial DNA from the GenBank to screen and correct the inconsistencies. It also supports users in detection of new novel mutation profiles and assignment of new haplotypes. The Canis mtDNA HV1 database (CHD) contains 5567 nucleotide entries originating from 15 subspecies in the species Canis lupus. Of these entries, 3646 were haplotypes and grouped into 804 distinct sequences. 319 sequences were recognized as previously assigned haplotypes, while the remaining 485 sequences had new mutation profiles and were marked as new haplotype candidates awaiting further analysis for haplotype assignment. Of the 3646 nucleotide entries, only 414 were annotated with correct haplotype information, while 3232 had insufficient or lacked haplotype information and were corrected or modified before storing in the CHD. The CHD can be accessed at http://chd.vnbiology.com . It provides sequences, haplotype information, and a web-based tool for mtDNA HV1 haplotyping. The CHD is updated monthly and supplies all data for download. The Canis mtDNA HV1 database contains information about canine mitochondrial DNA HV1 sequences with reconciled annotation. It serves as a tool for detection of inconsistencies in GenBank and helps identifying new HV1 haplotypes. Thus, it supports the scientific community in naming new HV1 haplotypes and to reconcile existing annotation of HV1 582 bp sequences.

  12. Identification of functional enolase genes of the silkworm Bombyx mori from public databases with a combination of dry and wet bench processes.

    Science.gov (United States)

    Kikuchi, Akira; Nakazato, Takeru; Ito, Katsuhiko; Nojima, Yosui; Yokoyama, Takeshi; Iwabuchi, Kikuo; Bono, Hidemasa; Toyoda, Atsushi; Fujiyama, Asao; Sato, Ryoichi; Tabunoki, Hiroko

    2017-01-13

    Various insect species have been added to genomic databases over the years. Thus, researchers can easily obtain online genomic information on invertebrates and insects. However, many incorrectly annotated genes are included in these databases, which can prevent the correct interpretation of subsequent functional analyses. To address this problem, we used a combination of dry and wet bench processes to select functional genes from public databases. Enolase is an important glycolytic enzyme in all organisms. We used a combination of dry and wet bench processes to identify functional enolases in the silkworm Bombyx mori (BmEno). First, we detected five annotated enolases from public databases using a Hidden Markov Model (HMM) search, and then through cDNA cloning, Northern blotting, and RNA-seq analysis, we revealed three functional enolases in B. mori: BmEno1, BmEno2, and BmEnoC. BmEno1 contained a conserved key amino acid residue for metal binding and substrate binding in other species. However, BmEno2 and BmEnoC showed a change in this key amino acid. Phylogenetic analysis showed that BmEno2 and BmEnoC were distinct from BmEno1 and other enolases, and were distributed only in lepidopteran clusters. BmEno1 was expressed in all of the tissues used in our study. In contrast, BmEno2 was mainly expressed in the testis with some expression in the ovary and suboesophageal ganglion. BmEnoC was weakly expressed in the testis. Quantitative RT-PCR showed that the mRNA expression of BmEno2 and BmEnoC correlated with testis development; thus, BmEno2 and BmEnoC may be related to lepidopteran-specific spermiogenesis. We identified and characterized three functional enolases from public databases with a combination of dry and wet bench processes in the silkworm B. mori. In addition, we determined that BmEno2 and BmEnoC had species-specific functions. Our strategy could be helpful for the detection of minor genes and functional genes in non-model organisms from public databases.

  13. Specific effects of large asteroids on the orbits of terrestrial planets and the ASETEP database

    Science.gov (United States)

    Aljbaae, S.; Souchay, J.

    2012-04-01

    our 43 selected asteroids. We compared our results for Mars with the analytical ones on the semi-major axis and the longitude. The tow studies agree very well. All our results, consisting of 1032 different curves (43 asteroids × 4 planets × 6 orbital elements) and the related tables that provide the fitted Fourier and Poisson components are gathered the ASETEP database (asteroid effect on the terrestrial planets). Moreover, we include in this database the influence of our sample of 43 asteroids on three fundamental parameters: the distance and the bi-dimensional orientation vector (α, δ) from the EMB to each of the other terrestrial planets. This database, which will be regularly updated by taking into account more asteroids with improved mass determinations, constitutes a precious tool for understanding specifically the influence of the large asteroids on the orbital motion of the terrestrial planets, and also for better understanding how modern ephemeris can be improved. Appendices A-C are available in electronic form at http://www.aanda.org

  14. ETDEWEB versus the World-Wide-Web: a specific database/web comparison

    Energy Technology Data Exchange (ETDEWEB)

    Cutler, D.

    2010-06-28

    A study was performed comparing user search results from the specialized scientific database on energy-related information, ETDEWEB, with search results from the internet search engines Google and Google Scholar. The primary objective of the study was to determine if ETDEWEB (the Energy Technology Data Exchange – World Energy Base) continues to bring the user search results that are not being found by Google and Google Scholar. As a multilateral information exchange initiative, ETDE’s member countries and partners contribute cost- and task-sharing resources to build the largest database of energy-related information in the world. As of early 2010, the ETDEWEB database has 4.3 million citations to world-wide energy literature. One of ETDEWEB’s strengths is its focused scientific content and direct access to full text for its grey literature (over 300,000 documents in PDF available for viewing from the ETDE site and over a million additional links to where the documents can be found at research organizations and major publishers globally). Google and Google Scholar are well-known for the wide breadth of the information they search, with Google bringing in news, factual and opinion-related information, and Google Scholar also emphasizing scientific content across many disciplines. The analysis compared the results of 15 energy-related queries performed on all three systems using identical words/phrases. A variety of subjects was chosen, although the topics were mostly in renewable energy areas due to broad international interest. Over 40,000 search result records from the three sources were evaluated. The study concluded that ETDEWEB is a significant resource to energy experts for discovering relevant energy information. For the 15 topics in this study, ETDEWEB was shown to bring the user unique results not shown by Google or Google Scholar 86.7% of the time. Much was learned from the study beyond just metric comparisons. Observations about the strengths of each

  15. A method for building and evaluating formal specifications of object-oriented conceptual models of database systems

    NARCIS (Netherlands)

    Wieringa, R.J.

    1993-01-01

    This report describes a method called MCM (Method for Conceptual Modeling) for building and evaluating formal specifications of object-oriented models of database system behavior. An important aim of MCM is to bridge the gap between formal specification and informal understanding. Building a MCM mod

  16. A method for building and evaluating formal specifications of object-oriented conceptual models of database systems

    NARCIS (Netherlands)

    Wieringa, Roelf J.

    1993-01-01

    This report describes a method called MCM (Method for Conceptual Modeling) for building and evaluating formal specifications of object-oriented models of database system behavior. An important aim of MCM is to bridge the gap between formal specification and informal understanding. Building a MCM mod

  17. 40 CFR 166.32 - Reporting and recordkeeping requirements for specific, quarantine, and public health exemptions.

    Science.gov (United States)

    2010-07-01

    ... requirements for specific, quarantine, and public health exemptions. 166.32 Section 166.32 Protection of... AGENCIES FOR USE OF PESTICIDES UNDER EMERGENCY CONDITIONS Specific, Quarantine, and Public Health Exemptions § 166.32 Reporting and recordkeeping requirements for specific, quarantine, and public health...

  18. New methodology of solar radiation evaluation using free access databases in specific locations

    Energy Technology Data Exchange (ETDEWEB)

    Pagola, Inigo; Gaston, Martin [CENER (National Renewable Energy Centre), Ciudad de la Innovacion 7, Sarriguren 31621 (Navarre) (Spain); Fernandez-Peruchena, Carlos [CENER (National Renewable Energy Centre), Pabellon de Italia, Isaac Newton 4 5 SO, 41092 Sevilla (Spain); Moreno, Sara [AICIA Pabellon de Italia, Isaac Newton 4 5 SO, Sevilla 41092 Sevilla (Spain); Ramirez, Lourdes [CENER (National Renewable Energy Centre), Urbanizacion La Florida, Somera 7-9 1D, 28023 Madrid (Spain)

    2010-12-15

    In this paper, solar radiation obtained from different frequently used databases is compared in some different locations. In the analyzed databases, the data come from ground measurement networks, or from different models and with different resolutions. The proposed methodology assumes the hypothesis that the uncertainty of the databases is approximately the same as the meteorological uncertainty of the location. Therefore the heterogeneity of the observations is due to different observations. A weighted average is proposed taking into account different time and spatial characteristics of each database, and the estimation of standard deviation of weighted observations that derives the meteorological variability expected. (author)

  19. Characterization and compilation of polymorphic simple sequence repeat (SSR markers of peanut from public database

    Directory of Open Access Journals (Sweden)

    Zhao Yongli

    2012-07-01

    Full Text Available Abstract Background There are several reports describing thousands of SSR markers in the peanut (Arachis hypogaea L. genome. There is a need to integrate various research reports of peanut DNA polymorphism into a single platform. Further, because of lack of uniformity in the labeling of these markers across the publications, there is some confusion on the identities of many markers. We describe below an effort to develop a central comprehensive database of polymorphic SSR markers in peanut. Findings We compiled 1,343 SSR markers as detecting polymorphism (14.5% within a total of 9,274 markers. Amongst all polymorphic SSRs examined, we found that AG motif (36.5% was the most abundant followed by AAG (12.1%, AAT (10.9%, and AT (10.3%.The mean length of SSR repeats in dinucleotide SSRs was significantly longer than that in trinucleotide SSRs. Dinucleotide SSRs showed higher polymorphism frequency for genomic SSRs when compared to trinucleotide SSRs, while for EST-SSRs, the frequency of polymorphic SSRs was higher in trinucleotide SSRs than in dinucleotide SSRs. The correlation of the length of SSR and the frequency of polymorphism revealed that the frequency of polymorphism was decreased as motif repeat number increased. Conclusions The assembled polymorphic SSRs would enhance the density of the existing genetic maps of peanut, which could also be a useful source of DNA markers suitable for high-throughput QTL mapping and marker-assisted selection in peanut improvement and thus would be of value to breeders.

  20. [Open access to academic scholarship as a public policy resource: a study of the Capes database on Brazilian theses and dissertations].

    Science.gov (United States)

    da Silva Rosa, Teresa; Carneiro, Maria José

    2010-12-01

    Access to scientific knowledge is a valuable resource than can inform and validate positions taken in formulating public policy. But access to this knowledge can be challenging, given the diversity and breadth of available scholarship. Communication between the fields of science and of politics requires the dissemination of scholarship and access to it. We conducted a study using an open-access search tool in order to map existent knowledge on a specific topic: agricultural contributions to the preservation of biodiversity. The present article offers a critical view of access to the information available through the Capes database on Brazilian theses and dissertations.

  1. Towards BioDBcore: a community-defined information specification for biological databases

    Science.gov (United States)

    Gaudet, Pascale; Bairoch, Amos; Field, Dawn; Sansone, Susanna-Assunta; Taylor, Chris; Attwood, Teresa K.; Bateman, Alex; Blake, Judith A.; Bult, Carol J.; Cherry, J. Michael; Chisholm, Rex L.; Cochrane, Guy; Cook, Charles E.; Eppig, Janan T.; Galperin, Michael Y.; Gentleman, Robert; Goble, Carole A.; Gojobori, Takashi; Hancock, John M.; Howe, Douglas G.; Imanishi, Tadashi; Kelso, Janet; Landsman, David; Lewis, Suzanna E.; Karsch Mizrachi, Ilene; Orchard, Sandra; Ouellette, B.F. Francis; Ranganathan, Shoba; Richardson, Lorna; Rocca-Serra, Philippe; Schofield, Paul N.; Smedley, Damian; Southan, Christopher; Tan, Tin W.; Tatusova, Tatiana; Whetzel, Patricia L.; White, Owen; Yamasaki, Chisato

    2011-01-01

    The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources; and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases. PMID:21205783

  2. Provider Specific Data for Public Use in SAS Format

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Fiscal Intermediary maintains the Provider Specific File (PSF). The file contains information about the facts specific to the provider that affects computations...

  3. DMPD: DUSP meet immunology: dual specificity MAPK phosphatases in control of theinflammatory response. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 17114416 DUSP meet immunology: dual specificity MAPK phosphatases in control of theinfl...ml) (.csml) Show DUSP meet immunology: dual specificity MAPK phosphatases in control of theinflammatory resp...onse. PubmedID 17114416 Title DUSP meet immunology: dual specificity MAPK phospha...tases in control of theinflammatory response. Authors Lang R, Hammer M, Mages J. Publication J Immunol. 2006

  4. Locus-Specific Databases and Recommendations to Strengthen Their Contribution to the Classification of Variants in Cancer Susceptibility Genes

    NARCIS (Netherlands)

    Greenblatt, Marc S.; Brody, Lawrence C.; Foulkes, William D.; Genuardi, Maurizio; Hofstra, Robert M. W.; Olivier, Magali; Plon, Sharon E.; Sijmons, Rolf H.; Sinilnikova, Olga; Spurdle, Amanda B.

    2008-01-01

    Locus-specific databases (LSDBs) are curated collections of sequence variants in genes associated with disease. LSDBs of cancer-related genes often serve as a critical resource to researchers, diagnostic laboratories, clinicians, and others in the cancer genetics community. LSDBs are poised to play

  5. CONCEPTUAL MODEL OF MARKETING STRATEGIC PLANNING SPECIFIC TO PUBLIC ORGANIZATIONS

    Directory of Open Access Journals (Sweden)

    Ionescu Florin Tudor

    2012-12-01

    Full Text Available In public services, the political component of the marketing environment has a major importance, as all decisions adopted within central administration influence both the objectives and measures implemented by units of local government and other public service providers. Any discontinuity in the activity of such entities might result in neglecting the real needs of citizens and slowing the reform process in the public sector. Therefore, all initiatives of public organizations must have a unitary goal and integrate harmoniously within a single process. A tool from the management-marketing literature that both contributes to this purpose and leads to an increased customer satisfaction and organizational performance is strategic marketing planning. This paper presents, firstly, requirements and particularities of this process in the public sector, focusing on the need for bottom-up planning, meaning from the functional levels of public service organizations, to the corporate level, where strategic decisions are taken. To achieve this goal, there should be included in the planning process the clients and other audiences, which can provide useful information about the services they want, the quality or the accessibility thereof, and news about the services they need in the future. There are also mentioned the factors that can influence the quality of strategic marketing planning in public services domain: the importance of marketing within the organization, marketing knowledge of employees in marketing departments and/or of management personnel, the efficiency of activities within the organization, and the manager’s marketing vision. In the final part of the paper there are presented the stages of the conceptual model of strategic marketing planning in public services field: (1 accepting the idea of bottom-up planning, (2 avoid or eliminate discrepancies between measures taken at high levels and executions carried out at operational

  6. Court Decisions Specific to Public School Responses to Student Concussions

    Science.gov (United States)

    Zirkel, Perry A.

    2016-01-01

    This article provides an up-to-date and comprehensive canvassing of the judicial case law concerning the responses to students with concussions in the public school context. The two categories of court decisions are (a) those concerning continued participation in interscholastic athletics, referred to under the rubric of "return to play"…

  7. Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data

    Science.gov (United States)

    2011-01-01

    Background Gene expression microarray data have been organized and made available as public databases, but the utilization of such highly heterogeneous reference datasets in the interpretation of data from individual test samples is not as developed as e.g. in the field of nucleotide sequence comparisons. We have created a rapid and powerful approach for the alignment of microarray gene expression profiles (AGEP) from test samples with those contained in a large annotated public reference database and demonstrate here how this can facilitate interpretation of microarray data from individual samples. Methods AGEP is based on the calculation of kernel density distributions for the levels of expression of each gene in each reference tissue type and provides a quantitation of the similarity between the test sample and the reference tissue types as well as the identity of the typical and atypical genes in each comparison. As a reference database, we used 1654 samples from 44 normal tissues (extracted from the Genesapiens database). Results Using leave-one-out validation, AGEP correctly defined the tissue of origin for 1521 (93.6%) of all the 1654 samples in the original database. Independent validation of 195 external normal tissue samples resulted in 87% accuracy for the exact tissue type and 97% accuracy with related tissue types. AGEP analysis of 10 Duchenne muscular dystrophy (DMD) samples provided quantitative description of the key pathogenetic events, such as the extent of inflammation, in individual samples and pinpointed tissue-specific genes whose expression changed (SAMD4A) in DMD. AGEP analysis of microarray data from adipocytic differentiation of mesenchymal stem cells and from normal myeloid cell types and leukemias provided quantitative characterization of the transcriptomic changes during normal and abnormal cell differentiation. Conclusions The AGEP method is a widely applicable method for the rapid comprehensive interpretation of microarray data, as

  8. Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB

    Directory of Open Access Journals (Sweden)

    Wang Nai-Jyuan

    2012-01-01

    Full Text Available Abstract Background Plant non-specific lipid transfer proteins (nsLTPs are small and basic proteins. Recently, nsLTPs have been reported involved in many physiological functions such as mediating phospholipid transfer, participating in plant defence activity against bacterial and fungal pathogens, and enhancing cell wall extension in tobacco. However, the lipid transfer mechanism of nsLTPs is still unclear, and comprehensive information of nsLTPs is difficult to obtain. Methods In this study, we identified 595 nsLTPs from 121 different species and constructed an nsLTPs database -- nsLTPDB -- which comprises the sequence information, structures, relevant literatures, and biological data of all plant nsLTPs http://nsltpdb.life.nthu.edu.tw/. Results Meanwhile, bioinformatics and statistics methods were implemented to develop a classification method for nsLTPs based on the patterns of the eight highly-conserved cysteine residues, and to suggest strict Prosite-styled patterns for Type I and Type II nsLTPs. The pattern of Type I is C X2 V X5-7 C [V, L, I] × Y [L, A, V] X8-13 CC × G X12 D × [Q, K, R] X2 CXC X16-21 P X2 C X13-15C, and that of Type II is C X4 L X2 C X9-11 P [S, T] X2 CC X5 Q X2-4 C[L, F]C X2 [A, L, I] × [D, N] P X10-12 [K, R] X4-5 C X3-4 P X0-2 C. Moreover, we referred the Prosite-styled patterns to the experimental mutagenesis data that previously established by our group, and found that the residues with higher conservation played an important role in the structural stability or lipid binding ability of nsLTPs. Conclusions Taken together, this research has suggested potential residues that might be essential to modulate the structural and functional properties of plant nsLTPs. Finally, we proposed some biologically important sites of the nsLTPs, which are described by using a new Prosite-styled pattern that we defined.

  9. IMS Content Packaging v1.2 public draft specification

    NARCIS (Netherlands)

    Burgos, Daniel; Tattersall, Colin; Vogten, Hubert

    2006-01-01

    The IMS Content Packaging Specification provides the functionality to describe and package learning materials, such as an individual course or a collection of courses, into interoperable, distributable packages. Content Packaging addresses the description, structure, and location of online learning

  10. CMP Promoters Database: A systematic study on site-specific transcription factors in CMP genes

    Directory of Open Access Journals (Sweden)

    Meera A

    2009-04-01

    motifs as NKX and AP2 making up the structural feature of the non coding genes are absent from few genes. Keywords: Non-coding sequence, Phylogeny, TCA, Glycolysis, TRANSFAC, Promoter, Database, Central Metabolic Pathway. Received: 17 March 2008 / Received in revised form: 5 February 2009, Accepted: 31 April 2009 Published online: 14 May 2009

  11. BIBLIOMETRIC ANALYSIS OF PUBLICATIONS ON WINE TOURISM IN THE DATABASES Scopus and WoS

    Directory of Open Access Journals (Sweden)

    Durán Sánchez, Amador

    2017-01-01

    on the results of the comparative study, we conclude that WoS and Scopus databases differ in scope, data volume and coverage policies with a high degree of unique sources and articles, resulting both of them complementary and not mutually exclusive. Scopus covers the area of wine tourism better, by including a greater number of journals, papers and signatures."

  12. DOE's Public Database for Green Building Case Studies: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Torcellini, P. A.; Crawley, D. B.

    2003-11-01

    To help capture valuable information on''green building'' case studies, the U.S. Department of Energy has created an online database for collecting, standardizing, and disseminating information about high-performance, green projects. Type of information collected includes green features, design processes, energy performance, and comparison to other high-performance, green buildings.

  13. Attitudes regarding the national forensic DNA database: Survey data from the general public, prison inmates and prosecutors' offices in the Republic of Serbia.

    Science.gov (United States)

    Teodorović, Smilja; Mijović, Dragan; Radovanović Nenadić, Una; Savić, Marina

    2017-01-21

    Worldwide, the establishment of national forensic DNA databases has transformed personal identification in the criminal justice system over the past two decades. It has also stimulated much debate centering on ethical issues, human rights, individual privacy, lack of safeguards and other standards. Therefore, a balance between effectiveness and intrusiveness of a national DNA repository is an imperative and needs to be achieved through a suitable legal framework. On its path to the European Union (EU), the Republic of Serbia is required to harmonize its national policies and legislation with the EU. Specifically, Chapter 24 of the EU acquis communautaire (Justice, Freedom and Security) stipulates the compulsory creation of a forensic DNA registry and adoption of corresponding legislation. This process is expected to occur in 2016. Thus, in light of launching the national DNA database, the goal of this work is to instigate a consultation with the Serbian public regarding their views on various aspects of the forensic DNA databank. Importantly, this study specifically assessed the opinions of distinct categories of citizens, including the general public, the prosecutors' offices staff, prisoners, prison guards, and students majoring in criminalistics. Our findings set a baseline for Serbian attitudes towards DNA databank custody, DNA sample and profile inclusion and retention criteria, ethical issues and concerns. Furthermore, results clearly demonstrate a permissive outlook of the respondents who are professional "beneficiaries" of genetic profiling and a restrictive position taken by the respondents whose genetic material has been acquired by the government. We believe that this opinion poll will be essential in discussions regarding a national DNA database, as well as in motivating further research on the reasons behind the observed views and subsequent development of educational strategies. All of these are, in turn, expected to aid the creation of suitable

  14. NPL-PAD (National Priorities List Publication Assistance Database) for Region 7

    Data.gov (United States)

    U.S. Environmental Protection Agency — THIS DATA ASSET NO LONGER ACTIVE: This is metadata documentation for the National Priorities List (NPL) Publication Assistance Databsae (PAD), a Lotus Notes...

  15. De-identifying a public use microdata file from the Canadian national discharge abstract database.

    Science.gov (United States)

    El Emam, Khaled; Paton, David; Dankar, Fida; Koru, Gunes

    2011-08-23

    The Canadian Institute for Health Information (CIHI) collects hospital discharge abstract data (DAD) from Canadian provinces and territories. There are many demands for the disclosure of this data for research and analysis to inform policy making. To expedite the disclosure of data for some of these purposes, the construction of a DAD public use microdata file (PUMF) was considered. Such purposes include: confirming some published results, providing broader feedback to CIHI to improve data quality, training students and fellows, providing an easily accessible data set for researchers to prepare for analyses on the full DAD data set, and serve as a large health data set for computer scientists and statisticians to evaluate analysis and data mining techniques. The objective of this study was to measure the probability of re-identification for records in a PUMF, and to de-identify a national DAD PUMF consisting of 10% of records. Plausible attacks on a PUMF were evaluated. Based on these attacks, the 2008-2009 national DAD was de-identified. A new algorithm was developed to minimize the amount of suppression while maximizing the precision of the data. The acceptable threshold for the probability of correct re-identification of a record was set at between 0.04 and 0.05. Information loss was measured in terms of the extent of suppression and entropy. Two different PUMF files were produced, one with geographic information, and one with no geographic information but more clinical information. At a threshold of 0.05, the maximum proportion of records with the diagnosis code suppressed was 20%, but these suppressions represented only 8-9% of all values in the DAD. Our suppression algorithm has less information loss than a more traditional approach to suppression. Smaller regions, patients with longer stays, and age groups that are infrequently admitted to hospitals tend to be the ones with the highest rates of suppression. The strategies we used to maximize data utility and

  16. De-identifying a public use microdata file from the Canadian national discharge abstract database

    Directory of Open Access Journals (Sweden)

    Paton David

    2011-08-01

    Full Text Available Abstract Background The Canadian Institute for Health Information (CIHI collects hospital discharge abstract data (DAD from Canadian provinces and territories. There are many demands for the disclosure of this data for research and analysis to inform policy making. To expedite the disclosure of data for some of these purposes, the construction of a DAD public use microdata file (PUMF was considered. Such purposes include: confirming some published results, providing broader feedback to CIHI to improve data quality, training students and fellows, providing an easily accessible data set for researchers to prepare for analyses on the full DAD data set, and serve as a large health data set for computer scientists and statisticians to evaluate analysis and data mining techniques. The objective of this study was to measure the probability of re-identification for records in a PUMF, and to de-identify a national DAD PUMF consisting of 10% of records. Methods Plausible attacks on a PUMF were evaluated. Based on these attacks, the 2008-2009 national DAD was de-identified. A new algorithm was developed to minimize the amount of suppression while maximizing the precision of the data. The acceptable threshold for the probability of correct re-identification of a record was set at between 0.04 and 0.05. Information loss was measured in terms of the extent of suppression and entropy. Results Two different PUMF files were produced, one with geographic information, and one with no geographic information but more clinical information. At a threshold of 0.05, the maximum proportion of records with the diagnosis code suppressed was 20%, but these suppressions represented only 8-9% of all values in the DAD. Our suppression algorithm has less information loss than a more traditional approach to suppression. Smaller regions, patients with longer stays, and age groups that are infrequently admitted to hospitals tend to be the ones with the highest rates of suppression

  17. DMPD: Sweet preferences of MGL: carbohydrate specificity and function. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 18249034 Sweet preferences of MGL: carbohydrate specificity and function. van Vliet....csml) Show Sweet preferences of MGL: carbohydrate specificity and function. PubmedID 18249034 Title Sweet preferences of MGL: carb

  18. Application of Optical Disc Databases and Related Technology to Public Access Settings

    Science.gov (United States)

    1992-03-01

    Librarian 5, no 6: 23. Nelson, Nancy Melin. 1991. CD-ROM growth: unleashing the potential. Library Journal 116, no. 2: 51-53. Nicholls, Paul Travis...1991. The impact of CD-ROM on online. Library Journal 116, no. 2: 61-62. Tenopir, Carol, and Ralph Neufang. 1991. CD-ROM, online and databases on...primer. PC Magazine, 17 December, 44. Zink, Steven D. 1990. Planning for the perils of CD-ROM. Library Journal 115, no. 2: 51-55. 211 INITIAL

  19. Seabird databases and the new paradigm for scientific publication and attribution

    Science.gov (United States)

    Hatch, Scott A.

    2010-01-01

    For more than 300 years, the peer-reviewed journal article has been the principal medium for packaging and delivering scientific data. With new tools for managing digital data, a new paradigm is emerging—one that demands open and direct access to data and that enables and rewards a broad-based approach to scientific questions. Ground-breaking papers in the future will increasingly be those that creatively mine and synthesize vast stores of data available on the Internet. This is especially true for conservation science, in which essential data can be readily captured in standard record formats. For seabird professionals, a number of globally shared databases are in the offing, or should be. These databases will capture the salient results of inventories and monitoring, pelagic surveys, diet studies, and telemetry. A number of real or perceived barriers to data sharing exist, but none is insurmountable. Our discipline should take an important stride now by adopting a specially designed markup language for annotating and sharing seabird data.

  20. A Database of Transition-Metal-Coordinated Peptide Cross-Sections: Selective Interaction with Specific Amino Acid Residues

    Science.gov (United States)

    Dilger, Jonathan M.; Glover, Matthew S.; Clemmer, David E.

    2017-07-01

    Ion mobility mass spectrometry (IMS-MS) techniques were used to generate a database of 2288 collision cross sections of transition-metal-coordinated tryptic peptide ions. This database consists of cross sections for 1253 [Pep + X]2+ and 1035 [Pep + X + H]3+, where X2+ corresponds to Mn2+, Co2+, Ni2+, Cu2+, or Zn2+. This number of measurements enables the extraction of structural trends for transition-metal-coordinated peptide ions. The range of structures and changes in collision cross sections for X2+-coordinated species (compared with protonated species of the same charge state) is similar to Mg2+-coordinated species. This suggests that the structures are largely determined by similarities in cation size with differences among the cross section distributions presumably caused by X2+ interactions with specific functional groups offered by the residue R-groups or the peptide backbone. Cross section contributions for individual residues upon X2+ solvation are assessed with the derivation of intrinsic size parameters (ISPs). The comparison of the [Pep + X]2+ ISPs with those previously reported for [Pep + Mg]2+ ions displays a lower contribution to the cross section for His, carboxyamidomethylated Cys, and Met, and is consistent with specific metal-residue interactions identified within protein X-ray crystallography databases.

  1. Development of a panel of unigene-derived polymorphic EST-SSR markers in lentil using public database information

    Institute of Scientific and Technical Information of China (English)

    Debjyoti Sen Gupta; Peng Cheng; Gaurav Sablok; Dil Thavarajah; Pushparajah Thavarajah; Clarice J Coyne; Shiv Kumar; Michael Baum; Rebecca J McGee

    2016-01-01

    Lentil (Lens culinaris Medik.), a diploid (2n=14) with a genome size greater than 4000 Mbp, is an important cool season food legume grown worldwide. The availability of genomic resources is limited in this crop species. The objective of this study was to develop polymorphic markers in lentil using publicly available curated expressed sequence tag information (ESTs). In this study, 9513 ESTs were downloaded from the National Center for Biotechnology Information (NCBI) database to develop unigene-based simple sequence repeat (SSR) markers. The ESTs were assembled into 4053 unigenes and then analyzed to identify 374 SSRs using the MISA microsatellite identification tool. Among the 374 SSRs, 26 compound SSRs were observed. Primer pairs for these SSRs were designed using Primer3 version 1.14. To classify the functional annotation of ESTs and EST–SSRs, BLASTx searches (using E-value 1 × 10−5) against the public UniProt (http://www.uniprot.org/) and NCBI (http://www.ncbi.nlh.nih.gov/) data-bases were performed. Further functional annotation was performed using PLAZA (version 3.0) comparative genomics and GO annotation was summarized using the Plant GO slim category. Among the synthesized 312 primers, 219 successfully amplified Lens DNA. A diverse panel of 24 Lens genotypes was used to identify polymorphic markers. A polymorphic set of 57 markers successfully discriminated the test genotypes. This set of polymorphic markers with functional annotation data could be used as molecular tools in lentil breeding.

  2. Automatic detection of lung nodules in computed tomography images: training and validation of algorithms using public research databases

    Science.gov (United States)

    Camarlinghi, Niccolò

    2013-09-01

    Lung cancer is one of the main public health issues in developed countries. Lung cancer typically manifests itself as non-calcified pulmonary nodules that can be detected reading lung Computed Tomography (CT) images. To assist radiologists in reading images, researchers started, a decade ago, the development of Computer Aided Detection (CAD) methods capable of detecting lung nodules. In this work, a CAD composed of two CAD subprocedures is presented: , devoted to the identification of parenchymal nodules, and , devoted to the identification of the nodules attached to the pleura surface. Both CADs are an upgrade of two methods previously presented as Voxel Based Neural Approach CAD . The novelty of this paper consists in the massive training using the public research Lung International Database Consortium (LIDC) database and on the implementation of new features for classification with respect to the original VBNA method. Finally, the proposed CAD is blindly validated on the ANODE09 dataset. The result of the validation is a score of 0.393, which corresponds to the average sensitivity of the CAD computed at seven predefined false positive rates: 1/8, 1/4, 1/2, 1, 2, 4, and 8 FP/CT.

  3. Estimating species diversity and distribution in the era of Big Data: to what extent can we trust public databases?

    Science.gov (United States)

    Maldonado, Carla; Molina, Carlos I.; Zizka, Alexander; Persson, Claes; Taylor, Charlotte M.; Albán, Joaquina; Chilquillo, Eder; Antonelli, Alexandre

    2015-01-01

    Abstract Aim Massive digitalization of natural history collections is now leading to a steep accumulation of publicly available species distribution data. However, taxonomic errors and geographical uncertainty of species occurrence records are now acknowledged by the scientific community – putting into question to what extent such data can be used to unveil correct patterns of biodiversity and distribution. We explore this question through quantitative and qualitative analyses of uncleaned versus manually verified datasets of species distribution records across different spatial scales. Location The American tropics. Methods As test case we used the plant tribe Cinchoneae (Rubiaceae). We compiled four datasets of species occurrences: one created manually and verified through classical taxonomic work, and the rest derived from GBIF under different cleaning and filling schemes. We used new bioinformatic tools to code species into grids, ecoregions, and biomes following WWF's classification. We analysed species richness and altitudinal ranges of the species. Results Altitudinal ranges for species and genera were correctly inferred even without manual data cleaning and filling. However, erroneous records affected spatial patterns of species richness. They led to an overestimation of species richness in certain areas outside the centres of diversity in the clade. The location of many of these areas comprised the geographical midpoint of countries and political subdivisions, assigned long after the specimens had been collected. Main conclusion Open databases and integrative bioinformatic tools allow a rapid approximation of large‐scale patterns of biodiversity across space and altitudinal ranges. We found that geographic inaccuracy affects diversity patterns more than taxonomic uncertainties, often leading to false positives, i.e. overestimating species richness in relatively species poor regions. Public databases for species distribution are valuable and should be

  4. Using Surface Treatment Specification Databases to Anticipate and Accelerate Response to Regulatory Changes

    Science.gov (United States)

    2012-08-28

    Substance declarations, MSDS data, specifications 3. Tools REPORT Substances in article, Article 33 ... INTEGRATE, ACCESS from: PLM , CAD, ERP...specifications, materials & processes for regulatory impact & obsolescence risk Use existing infrastructure (e.g. CAD, PLM ) to deploy strategy into engineers

  5. Intelligence in young adulthood and cause-specific mortality in the Danish Conscription Database

    DEFF Research Database (Denmark)

    Christensen, G.T.; Mortensen, E. L.; Christensen, K.

    2016-01-01

    An inverse association has been reported between early life intelligence and all-cause mortality. The aim of this study was to investigate whether this well-established association differed according to the underlying cause of death and across different birth cohorts. The associations between young...... adult intelligence and mortality from natural and external causes were investigated in the Danish Conscription Database (DCD), which is a cohort of more than 700,000 men born 1939–1959 and followed in Danish registers from young adulthood until late mid-life. Young adult intelligence was inversely...... related to all-cause mortality with a 28% higher risk of dying during the study period per 1 standard deviation (SD) decrease in intelligence test score (HR = 1.28 95% CI = 1.27–1.29). The strength of the observed inverse associations did not vary much across main groups of natural and external causes...

  6. Towards development of a high quality public domain global roads database

    Directory of Open Access Journals (Sweden)

    Andrew Nelson

    2006-12-01

    Full Text Available There is clear demand for a global spatial public domain roads data set with improved geographic and temporal coverage, consistent coding of road types, and clear documentation of sources. The currently best available global public domain product covers only one-quarter to one-third of the existing road networks, and this varies considerably by region. Applications for such a data set span multiple sectors and would be particularly valuable for the international economic development, disaster relief, and biodiversity conservation communities, not to mention national and regional agencies and organizations around the world. The building blocks for such a global product are available for many countries and regions, yet thus far there has been neither strategy nor leadership for developing it. This paper evaluates the best available public domain and commercial data sets, assesses the gaps in global coverage, and proposes a number of strategies for filling them. It also identifies stakeholder organizations with an interest in such a data set that might either provide leadership or funding for its development. It closes with a proposed set of actions to begin the process.

  7. Approaching the taxonomic affiliation of unidentified sequences in public databases – an example from the mycorrhizal fungi

    Directory of Open Access Journals (Sweden)

    Ryberg Martin

    2005-07-01

    Full Text Available Abstract Background During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. Although the number of sequences available for comparison in public databases such as GenBank increases exponentially, only a minuscule fraction of all organisms have been sequenced, leaving taxon sampling a momentous problem for sequence-based taxonomic identification. When querying GenBank with a set of unidentified sequences, a considerable proportion typically lack fully identified matches, forming an ever-mounting pile of sequences that the researcher will have to monitor manually in the hope that new, clarifying sequences have been submitted by other researchers. To alleviate these concerns, a project to automatically monitor select unidentified sequences in GenBank for taxonomic progress through repeated local BLAST searches was initiated. Mycorrhizal fungi – a field where species identification often is prohibitively complex – and the much used ITS locus were chosen as test bed. Results A Perl script package called emerencia is presented. On a regular basis, it downloads select sequences from GenBank, separates the identified sequences from those insufficiently identified, and performs BLAST searches between these two datasets, storing all results in an SQL database. On the accompanying web-service http://emerencia.math.chalmers.se, users can monitor the taxonomic progress of insufficiently identified sequences over time, either through active searches or by signing up for e-mail notification upon disclosure of better matches. Other search categories, such as listing all insufficiently identified sequences (and their present best fully identified matches publication-wise, are also available. Discussion The ever-increasing use of DNA sequences for identification purposes

  8. Sustainability Initiatives and Organizational Performance: An Analysis of Publications in the WEB of SCIENCE DATABASE

    Directory of Open Access Journals (Sweden)

    Eduardo Luís Hepper

    2016-07-01

    Full Text Available Brazil is going through a time of reflection about the preservation of natural resources, an issue that is increasingly considered in its agenda. The search for balance between environmental, social and economic aspects has been a challenge for business survival over the years and has led companies to adopt initiatives focused on sustainability. The objective of this article is to analyse how the international scientific production addresses sustainable practices and initiatives and their relationship with organizational performance. Considering this scope, a bibliometric study of the publications located on Web of Science - Social Sciences Citation Index (WoS-SSCI was developed. There were 33 articles identified and selected on the subject. Journals that stand out in quantity of articles and number of citations are the Journal of Cleaner Production and Strategic Management Journal, respectively. Analysing the results, a growing concern about this issue and the increase in publications was noticed after the 2000s. The results found, in general, associate sustainable practices to positive organizational performance, such as increased profit on the product sold, quality improvement, improved reputation, and waste reduction, among others gains identified.

  9. On the level of coverage and citation of publications by mechanicians of the national academy of sciences of Ukraine in the Scopus database

    Science.gov (United States)

    Guz, A. N.; Rushchitsky, J. J.

    2009-11-01

    The paper analyzes the level of coverage and citation of publications by mechanicians of the National Academy of Sciences of Ukraine (NASU) in the Scopus database. Two groups of mechanicians are considered. One group includes 66 doctors of sciences of the S. P. Timoshenko Institute of Mechanics as representatives of the oldest institute of the NASU. The other group includes 34 members (academicians and corresponding members) of the Division of Mechanics of the NASU as representatives of the authoritative community of mechanicians in Ukraine. The results are presented for each scientist in the form of two indices—the total number of publications accessible in the database as the level of coverage of the scientist's publications in this database and the h-index as the citation level of these publications. This paper may be considered to continue the papers [6-12] published in Prikladnaya Mekhanika (International Applied Mechanics) in 2005-2009

  10. Creating a data exchange strategy for radiotherapy research: towards federated databases and anonymised public datasets.

    Science.gov (United States)

    Skripcak, Tomas; Belka, Claus; Bosch, Walter; Brink, Carsten; Brunner, Thomas; Budach, Volker; Büttner, Daniel; Debus, Jürgen; Dekker, Andre; Grau, Cai; Gulliford, Sarah; Hurkmans, Coen; Just, Uwe; Krause, Mechthild; Lambin, Philippe; Langendijk, Johannes A; Lewensohn, Rolf; Lühr, Armin; Maingon, Philippe; Masucci, Michele; Niyazi, Maximilian; Poortmans, Philip; Simon, Monique; Schmidberger, Heinz; Spezi, Emiliano; Stuschke, Martin; Valentini, Vincenzo; Verheij, Marcel; Whitfield, Gillian; Zackrisson, Björn; Zips, Daniel; Baumann, Michael

    2014-12-01

    Disconnected cancer research data management and lack of information exchange about planned and ongoing research are complicating the utilisation of internationally collected medical information for improving cancer patient care. Rapidly collecting/pooling data can accelerate translational research in radiation therapy and oncology. The exchange of study data is one of the fundamental principles behind data aggregation and data mining. The possibilities of reproducing the original study results, performing further analyses on existing research data to generate new hypotheses or developing computational models to support medical decisions (e.g. risk/benefit analysis of treatment options) represent just a fraction of the potential benefits of medical data-pooling. Distributed machine learning and knowledge exchange from federated databases can be considered as one beyond other attractive approaches for knowledge generation within "Big Data". Data interoperability between research institutions should be the major concern behind a wider collaboration. Information captured in electronic patient records (EPRs) and study case report forms (eCRFs), linked together with medical imaging and treatment planning data, are deemed to be fundamental elements for large multi-centre studies in the field of radiation therapy and oncology. To fully utilise the captured medical information, the study data have to be more than just an electronic version of a traditional (un-modifiable) paper CRF. Challenges that have to be addressed are data interoperability, utilisation of standards, data quality and privacy concerns, data ownership, rights to publish, data pooling architecture and storage. This paper discusses a framework for conceptual packages of ideas focused on a strategic development for international research data exchange in the field of radiation therapy and oncology.

  11. A curated public database for multilocus sequence typing (MLST) and analysis of Haemophilus parasuis based on an optimized typing scheme.

    Science.gov (United States)

    Mullins, Michael A; Register, Karen B; Brunelle, Brian W; Aragon, Virginia; Galofré-Mila, Nuria; Bayles, Darrell O; Jolley, Keith A

    2013-03-23

    Haemophilus parasuis causes Glässer's disease and pneumonia in swine. Serotyping is often used to classify isolates but requires reagents that are costly to produce and not standardized or widely available. Sequence-based methods, such as multilocus sequence typing (MLST), offer many advantages over serotyping. An MLST scheme was previously proposed for H. parasuis but genome sequence data only recently available reveals the primers recommended, based on sequences of related bacteria, are not optimal. Here we report modifications to enhance the original method, including primer redesign to eliminate mismatches with H. parasuis sequences and to avoid regions of high sequence heterogeneity, standardization of primer T(m)s and identification of universal PCR conditions that result in robust and reproducible amplification of all targets. The modified typing method was applied to a collection of 127 isolates from North and South America, Europe and Asia. An alignment of the concatenated sequences obtained from seven target housekeeping genes identified 278 variable nucleotide sites that define 116 unique sequence types. A comparison of the original and modified methods using a subset of 86 isolates indicates little difference in overall locus diversity, discriminatory power or in the clustering of strains within Neighbor-Joining trees. Data from the optimized MLST were used to populate a newly created and publicly available H. parasuis database. An accompanying database designed to capture provenance and epidemiological information for each isolate was also created. The modified MLST scheme is highly discriminatory but more robust, reproducible and user-friendly than the original. The MLST database provides a novel resource for investigation of H. parasuis outbreaks and for tracking strain evolution.

  12. A Tool for Sheep Product Quality: Custom Microarrays from Public Databases

    OpenAIRE

    Lorraine Pariset; Alessio Valentini; Susana Bueno; Gianluca Prosperini; Silvia Bongiorni; Giovanni Chillemi

    2009-01-01

    Milk and dairy products are an essential food and an economic resource in many countries. Milk component synthesis and secretion by the mammary gland involve expression of a large number of genes whose nutritional regulation remains poorly defined. The purpose of this study was to gain an understanding of the genomic influence on milk quality and synthesis by comparing two sheep breeds with different milking attitude (Sarda and Gentile di Puglia) using sheep-specific microarray technology. Fr...

  13. Matching the Diversity of Sulfated Biomolecules: Creation of a Classification Database for Sulfatases Reflecting Their Substrate Specificity

    Science.gov (United States)

    Barbeyron, Tristan; Brillet-Guéguen, Loraine; Carré, Wilfrid; Carrière, Cathelène; Caron, Christophe; Czjzek, Mirjam; Hoebeke, Mark; Michel, Gurvan

    2016-01-01

    Sulfatases cleave sulfate groups from various molecules and constitute a biologically and industrially important group of enzymes. However, the number of sulfatases whose substrate has been characterized is limited in comparison to the huge diversity of sulfated compounds, yielding functional annotations of sulfatases particularly prone to flaws and misinterpretations. In the context of the explosion of genomic data, a classification system allowing a better prediction of substrate specificity and for setting the limit of functional annotations is urgently needed for sulfatases. Here, after an overview on the diversity of sulfated compounds and on the known sulfatases, we propose a classification database, SulfAtlas (http://abims.sb-roscoff.fr/sulfatlas/), based on sequence homology and composed of four families of sulfatases. The formylglycine-dependent sulfatases, which constitute the largest family, are also divided by phylogenetic approach into 73 subfamilies, each subfamily corresponding to either a known specificity or to an uncharacterized substrate. SulfAtlas summarizes information about the different families of sulfatases. Within a family a web page displays the list of its subfamilies (when they exist) and the list of EC numbers. The family or subfamily page shows some descriptors and a table with all the UniProt accession numbers linked to the databases UniProt, ExplorEnz, and PDB. PMID:27749924

  14. Exploration of Preterm Birth Rates Using the Public Health Exposome Database and Computational Analysis Methods

    Directory of Open Access Journals (Sweden)

    Anne D. Kershenbaum

    2014-11-01

    Full Text Available Recent advances in informatics technology has made it possible to integrate, manipulate, and analyze variables from a wide range of scientific disciplines allowing for the examination of complex social problems such as health disparities. This study used 589 county-level variables to identify and compare geographical variation of high and low preterm birth rates. Data were collected from a number of publically available sources, bringing together natality outcomes with attributes of the natural, built, social, and policy environments. Singleton early premature county birth rate, in counties with population size over 100,000 persons provided the dependent variable. Graph theoretical techniques were used to identify a wide range of predictor variables from various domains, including black proportion, obesity and diabetes, sexually transmitted infection rates, mother’s age, income, marriage rates, pollution and temperature among others. Dense subgraphs (paracliques representing groups of highly correlated variables were resolved into latent factors, which were then used to build a regression model explaining prematurity (R-squared = 76.7%. Two lists of counties with large positive and large negative residuals, indicating unusual prematurity rates given their circumstances, may serve as a starting point for ways to intervene and reduce health disparities for preterm births.

  15. A Tool for Sheep Product Quality: Custom Microarrays from Public Databases

    Directory of Open Access Journals (Sweden)

    Lorraine Pariset

    2009-12-01

    Full Text Available Milk and dairy products are an essential food and an economic resource in many countries. Milk component synthesis and secretion by the mammary gland involve expression of a large number of genes whose nutritional regulation remains poorly defined. The purpose of this study was to gain an understanding of the genomic influence on milk quality and synthesis by comparing two sheep breeds with different milking attitude (Sarda and Gentile di Puglia using sheep-specific microarray technology. From sheep ESTs deposited at NCBI, we have generated the first annotated microarray developed for sheep with a coverage of most of the genome.

  16. A tool for sheep product quality: custom microarrays from public databases.

    Science.gov (United States)

    Bongiorni, Silvia; Chillemi, Giovanni; Prosperini, Gianluca; Bueno, Susana; Valentini, Alessio; Pariset, Lorraine

    2009-02-01

    Milk and dairy products are an essential food and an economic resource in many countries. Milk component synthesis and secretion by the mammary gland involve expression of a large number of genes whose nutritional regulation remains poorly defined. The purpose of this study was to gain an understanding of the genomic influence on milk quality and synthesis by comparing two sheep breeds with different milking attitude (Sarda and Gentile di Puglia) using sheep-specific microarray technology. From sheep ESTs deposited at NCBI, we have generated the first annotated microarray developed for sheep with a coverage of most of the genome.

  17. VISTA Enhancer Browser--A Database of Tissue-Specific HumanEnhancers

    Energy Technology Data Exchange (ETDEWEB)

    Visel, Axel; Minovitsky, Simon; Dubchak, Inna; Pennacchio, Len A.

    2006-08-01

    Despite the known existence of distant-acting cis-regulatoryelements in the human genome, only a small fraction of these elements hasbeen identified and experimentally characterized in vivo. This paucity ofenhancer collections with defined activities has thus hinderedcomputational approaches for the genome-wide prediction of enhancers andtheir functions. To fill this void, we utilize comparative genomeanalysis to identify candidate enhancer elements in the human genomecoupled with the experimental determination of their in vivo enhanceractivity in transgenic mice (1). These data are available through theVISTA Enhancer Browser (http://enhancer.lbl.gov). This growing databasecurrently contains over 250 experimentally tested DNA fragments, of whichmore than 100 have been validated as tissue-specific enhancers. For eachpositive enhancer, we provide digital images of whole-mount embryostaining at embryonic day 11.5 and an anatomical description of thereporter gene expression pattern. Users can retrieve elements near singlegenes of interest, search for enhancers that target reporter geneexpression to a particular tissue, or download entire collections ofenhancers with a defined tissue specificity or conservation depth. Theseexperimentally validated training sets are expected to provide a basisfor a wide range of downstream computational and functional studies ofenhancer function.

  18. Predicting 30-day Hospital Readmission with Publicly Available Administrative Database. A Conditional Logistic Regression Modeling Approach.

    Science.gov (United States)

    Zhu, K; Lou, Z; Zhou, J; Ballester, N; Kong, N; Parikh, P

    2015-01-01

    more than 10% over the standard classification models, which can be translated to correct labeling of additional 400 - 500 readmissions for heart failure patients in the state of California over a year. Lastly, several key predictor identified from the HCUP data include the disposition location from discharge, the number of chronic conditions, and the number of acute procedures. It would be beneficial to apply simple decision rules obtained from the decision tree in an ad-hoc manner to guide the cohort stratification. It could be potentially beneficial to explore the effect of pairwise interactions between influential predictors when building the logistic regression models for different data strata. Judicious use of the ad-hoc CLR models developed offers insights into future development of prediction models for hospital readmissions, which can lead to better intuition in identifying high-risk patients and developing effective post-discharge care strategies. Lastly, this paper is expected to raise the awareness of collecting data on additional markers and developing necessary database infrastructure for larger-scale exploratory studies on readmission risk prediction.

  19. Databases and their application

    NARCIS (Netherlands)

    E.C. Grimm; R.H.W Bradshaw; S. Brewer; S. Flantua; T. Giesecke; A.M. Lézine; H. Takahara; J.W.,Jr Williams

    2013-01-01

    During the past 20 years, several pollen database cooperatives have been established. These databases are now constituent databases of the Neotoma Paleoecology Database, a public domain, multiproxy, relational database designed for Quaternary-Pliocene fossil data and modern surface samples. The poll

  20. Public health-specific National Incident Management System trainings: building a system for preparedness.

    Science.gov (United States)

    Kohn, Sivan; Barnett, Daniel J; Galastri, Costanza; Semon, Natalie L; Links, Jonathan M

    2010-01-01

    Local health departments (LHDs) are at the hub of the public health emergency preparedness system. Since the 2003 issuance of Homeland Security Presidential Directive-5, LHDs have faced challenges to comply with a new set of all-hazards, 24/7 organizational response expectations, as well as the National Incident Management System (NIMS). To help local public health practitioners address these challenges, the Centers for Disease Control and Prevention-funded Johns Hopkins Center for Public Health Preparedness (JH-CPHP) created and implemented a face-to-face, public health-specific NIMS training series for LHDs. This article presents the development, evolution, and delivery of the JH-CPHP NIMS training program. In this context, the article also describes a case example of practice-academic collaboration between the National Association of County and City Health Officials and JH-CPHP to develop public health-oriented NIMS course content.

  1. Comparable Measures of Accessibility to Public Transport Using the General Transit Feed Specification

    Directory of Open Access Journals (Sweden)

    Jinjoo Bok

    2016-03-01

    Full Text Available Public transport plays a critical role in the sustainability of urban settings. The mass mobility and quality of urban lives can be improved by establishing public transport networks that are accessible to pedestrians within a reasonable walking distance. Accessibility to public transport is characterized by the ease with which inhabitants can reach means of transportation such as buses or metros. By measuring the degree of accessibility to public transport networks using a common data format, a comparative study can be conducted between different cities or metropolitan areas with different public transit systems. The General Transit Feed Specification (GTFS by Google Developers allows this by offering a common format based on text files and sharing the data set voluntarily produced and contributed by the public transit agencies of many participating cities around the world. This paper suggests a method to assess and compare public transit accessibility in different urban areas using the GTFS feed and demographic data. To demonstrate the value of the new method, six examples of metropolitan areas and their public transit accessibility are presented and compared.

  2. Investigation of realistic PET simulations incorporating tumor patient's specificity using anthropomorphic models: creation of an oncology database.

    Science.gov (United States)

    Papadimitroulas, Panagiotis; Loudos, George; Le Maitre, Amandine; Hatt, Mathieu; Tixier, Florent; Efthimiou, Nikos; Nikiforidis, George C; Visvikis, Dimitris; Kagadis, George C

    2013-11-01

    The GATE Monte Carlo simulation toolkit is used for the implementation of realistic PET simulations incorporating tumor heterogeneous activity distributions. The reconstructed patient images include noise from the acquisition process, imaging system's performance restrictions and have limited spatial resolution. For those reasons, the measured intensity cannot be simply introduced in GATE simulations, to reproduce clinical data. Investigation of the heterogeneity distribution within tumors applying partial volume correction (PVC) algorithms was assessed. The purpose of the present study was to create a simulated oncology database based on clinical data with realistic intratumor uptake heterogeneity properties. PET/CT data of seven oncology patients were used in order to create a realistic tumor database investigating the heterogeneity activity distribution of the simulated tumors. The anthropomorphic models (NURBS based cardiac torso and Zubal phantoms) were adapted to the CT data of each patient, and the activity distribution was extracted from the respective PET data. The patient-specific models were simulated with the Monte Carlo Geant4 application for tomography emission (GATE) in three different levels for each case: (a) using homogeneous activity within the tumor, (b) using heterogeneous activity distribution in every voxel within the tumor as it was extracted from the PET image, and (c) using heterogeneous activity distribution corresponding to the clinical image following PVC. The three different types of simulated data in each case were reconstructed with two iterations and filtered with a 3D Gaussian postfilter, in order to simulate the intratumor heterogeneous uptake. Heterogeneity in all generated images was quantified using textural feature derived parameters in 3D according to the ground truth of the simulation, and compared to clinical measurements. Finally, profiles were plotted in central slices of the tumors, across lines with heterogeneous

  3. International scientific seminar «Chronicle of Nature – a common database for scientific analysis and joint planning of scientific publications»

    Directory of Open Access Journals (Sweden)

    Juri P. Kurhinen

    2016-05-01

    Full Text Available Provides information about the results of the international scienti fic seminar «Сhronicle of Nature – a common database for scientific analysis and joint planning of scientific publications», held at Findland-Russian project «Linking environmental change to biodiversity change: large scale analysis оf Eurasia ecosystem».

  4. A locus-specific database for mutations in GDAP1 allows analysis of genotype-phenotype correlations in Charcot-Marie-Tooth diseases type 4A and 2K

    Directory of Open Access Journals (Sweden)

    Cassereau Julien

    2011-12-01

    Full Text Available Abstract Background The ganglioside-induced differentiation-associated protein 1 gene (GDAP1, which is involved in the Charcot-Marie-Tooth disease (CMT, the most commonly inherited peripheral neuropathy, encodes a protein anchored to the mitochondrial outer membrane. The phenotypic presentations of patients carrying GDAP1 mutations are heterogeneous, making it difficult to determine genotype-phenotype correlations, since the majority of the mutations have been found in only a few unrelated patients. Locus-specific databases (LSDB established in the framework of the Human Variome Project provide powerful tools for the investigation of such rare diseases. Methods and Results We report the development of a publicly accessible LSDB for the GDAP1 gene. The GDAP1 LSDB has adopted the Leiden Open-source Variation Database (LOVD software platform. This database, which now contains 57 unique variants reported in 179 cases of CMT, offers a detailed description of the molecular, clinical and electrophysiological data of the patients. The usefulness of the GDAP1 database is illustrated by the finding that GDAP1 mutations lead to primary axonal damage in CMT, with secondary demyelination in the more severe cases of the disease. Conclusion Findings of this nature should lead to a better understanding of the pathophysiology of CMT. Finally, the GDAP1 LSDB, which is part of the mitodyn.org portal of databases of genes incriminated in disorders involving mitochondrial dynamics and bioenergetics, should yield new insights into mitochondrial diseases.

  5. Putative Vitis vinifera Rop- and Rab-GAP-, GEF-, and GDI-interacting proteins uncovered with novel methods for public genomic and EST database analysis.

    Science.gov (United States)

    Abbal, Philippe; Tesniere, Catherine

    2010-01-01

    To understand how grapevine Rop and Rab proteins achieve their functional versatility in signalling, identification of the putative VvRop- and VvRab-interacting proteins was performed using newly designed tools. In this study, sequences encoding eight full-length proteins for VvRop GTPase-activating proteins (GAPs), five for VvRabGAPs, six for VvRop guanine nucleotide exchange factors (GEFs), one for VvRabGEF, five for VvRop GDP dissociation inhibitors (GDIs), and three for VvRabGDIs were identified. These proteins had a CRIB motif or PH domain, a TBC domain, a PRONE domain, a DENN domain, or GDI signatures, respectively. By bootstrap analysis, an unrooted consensus phylogenetic tree was constructed which indicated that VvRopGDIs and VvRopGEFs--but not VvRopGAP--belonged to the same clade, and that VvRabGEF1 protein was more closely related to VvRopGAPs than to the other putative VvRab-interacting proteins. Twenty-two genes out of 28 encoding putative VvRop- and VvRab-interacting proteins could be located on identified grapevine chromosomes. Generally one gene was anchored on one chromosome, but in some cases up to four genes were located on the same chromosome. Expression patterns of the genes encoding putative VvRop- and VvRab-interacting proteins were also examined using a newly developed tool based on public expressed sequence tag (EST) database analysis. Expression patterns were sometimes found to be specific to an organ or a developmental stage. Although some limitations exist, the use of EST database analysis is stressed, in particular in the case of species where expression data are obtained at high costs in terms of time and effort.

  6. One-Session Exposure Treatment for Social Anxiety with Specific Fear of Public Speaking

    Science.gov (United States)

    Hindo, Cindy S.; Gonzalez-Prendes, A. Antonio

    2011-01-01

    Objectives: This pilot study evaluated the effectiveness of one-session, exposure-based therapy, to treat social anxiety disorder (SAD) with specific fear of public speaking. Methods: A quasi-experimental pre-posttest design with repeated measures-within-subject Analysis of Variance and paired sample t-tests was used to compare pretest, posttest…

  7. One-Session Exposure Treatment for Social Anxiety with Specific Fear of Public Speaking

    Science.gov (United States)

    Hindo, Cindy S.; Gonzalez-Prendes, A. Antonio

    2011-01-01

    Objectives: This pilot study evaluated the effectiveness of one-session, exposure-based therapy, to treat social anxiety disorder (SAD) with specific fear of public speaking. Methods: A quasi-experimental pre-posttest design with repeated measures-within-subject Analysis of Variance and paired sample t-tests was used to compare pretest, posttest…

  8. Database systems for knowledge-based discovery.

    Science.gov (United States)

    Jagarlapudi, Sarma A R P; Kishan, K V Radha

    2009-01-01

    Several database systems have been developed to provide valuable information from the bench chemist to biologist, medical practitioner to pharmaceutical scientist in a structured format. The advent of information technology and computational power enhanced the ability to access large volumes of data in the form of a database where one could do compilation, searching, archiving, analysis, and finally knowledge derivation. Although, data are of variable types the tools used for database creation, searching and retrieval are similar. GVK BIO has been developing databases from publicly available scientific literature in specific areas like medicinal chemistry, clinical research, and mechanism-based toxicity so that the structured databases containing vast data could be used in several areas of research. These databases were classified as reference centric or compound centric depending on the way the database systems were designed. Integration of these databases with knowledge derivation tools would enhance the value of these systems toward better drug design and discovery.

  9. E-SovTox: An online database of the main publicly-available sources of toxicity data concerning REACH-relevant chemicals published in the Russian language.

    Science.gov (United States)

    Sihtmäe, Mariliis; Blinova, Irina; Aruoja, Villem; Dubourguier, Henri-Charles; Legrand, Nicolas; Kahru, Anne

    2010-08-01

    A new open-access online database, E-SovTox, is presented. E-SovTox provides toxicological data for substances relevant to the EU Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) system, from publicly-available Russian language data sources. The database contains information selected mainly from scientific journals published during the Soviet Union era. The main information source for this database - the journal, Gigiena Truda i Professional'nye Zabolevania [Industrial Hygiene and Occupational Diseases], published between 1957 and 1992 - features acute, but also chronic, toxicity data for numerous industrial chemicals, e.g. for rats, mice, guinea-pigs and rabbits. The main goal of the abovementioned toxicity studies was to derive the maximum allowable concentration limits for industrial chemicals in the occupational health settings of the former Soviet Union. Thus, articles featured in the database include mostly data on LD50 values, skin and eye irritation, skin sensitisation and cumulative properties. Currently, the E-SovTox database contains toxicity data selected from more than 500 papers covering more than 600 chemicals. The user is provided with the main toxicity information, as well as abstracts of these papers in Russian and in English (given as provided in the original publication). The search engine allows cross-searching of the database by the name or CAS number of the compound, and the author of the paper. The E-SovTox database can be used as a decision-support tool by researchers and regulators for the hazard assessment of chemical substances.

  10. Quantitative Study and Structure Visualization of Scientific Publications in the Field of Information Management in Web of Science Database during 1988-2009

    Directory of Open Access Journals (Sweden)

    Afshin Hamdipour

    2012-12-01

    Full Text Available The present study endeavored to analysis the scientific publications that were indexed in the Web of Science database as the information management records and the visualization of science structure in this field during 1988-2009. The research method was scientometrics. During the study period, 1120 records in the field of information management have been published. These records were extracted in the form of plain text files and stored in a PC. Then they were analyzed by ISI.exe and HistCite softwares. Author's coefficient collaboration (CC was grown from zero in 1988 to 0.33 in 2009. Average coefficient collaboration between the authors was 0.22 which confirmed low authors collaboration in this area. The records have been published in 63 languages. Among these records the English language with 93.8 % possessed the highest proportion. City University London and the University of Sheffield in England had the most common publications in information management field. Based on the number of published records, T.D. Wilson with 13 records and 13 citations ranked as the first. The average number of global citations to 112 documents has been equal to 8.78. Despite the participation of different countries in the production of documents, more than 28.9% of records have been produced in the United States. According to results, 10 countries have published more than 72.4 percent of the records. City University London and the University of Sheffield have had highest frequency in this area. 15 journals have published 564 records (50.4% of the total productions. Finally, by implementation of scientific software HistCite map drawing clustered and authors, articles and four effective specific subjects were introduced..

  11. Opportunistic prostate-specific antigen screening in Italy: 6 years of monitoring from the Italian general practice database.

    Science.gov (United States)

    D'Ambrosio, Gaetano Giorgio; Campo, Salvatore; Cancian, Maurizio; Pecchioli, Serena; Mazzaglia, Giampiero

    2010-11-01

    The practice of prostate-specific antigen (PSA) screening has been increasing in Italy despite uncertain scientific evidence and contrary recommendations from most scientific societies. In 2002, a survey of PSA screening diffusion among general practices was performed, looking for screening frequency and age pattern of screened individuals. The objective of this study was to assess whether the features of PSA screening did change after 6 years in the same considered setting. Using the data obtained from 500 Italian general practitioners providing information to the Health Search/CSD Patient database, we selected, for the study purpose 351,091 male individuals. We assumed PSA prescriptions performed during 2005-2008 in individuals without prostate cancer, or benign prostate disease, or urological symptoms history to have a screening purpose. Screening frequency was analyzed in the overall series, by year and by patient's age. Exposure to PSA screening (at least on PSA test in the considered period) of males aged over 50 years raised from 31.4% (confidence interval 95% 31.08-31.70%) during 2002 to 46.4% (confidence interval 95% 46.19-46.68%) during 2008. The highest yearly exposure to PSA screening (55%) and the highest frequency of repeat testing was observed in the 70-79 age range. PSA screening practice has continued to increase in Italy and is often performed in elderly people without any scientific rationale.

  12. Intended Use of a Building in Terms of Updating the Cadastral Database and Harmonizing the Data with other Public Records

    Directory of Open Access Journals (Sweden)

    Buśko Małgorzata

    2017-06-01

    Full Text Available According to the original wording of the Regulation on the register of land and buildings of 2001, in the real estate cadastre there was one attribute associated with the use of a building structure - its intended use, which was applicable until the amendment to the Regulation was introduced in 2013. Then, additional attributes were added, i.e. the type of the building according to the Classification of Fixed Assets (KST, the class of the building according to the Polish Classification of Types of Constructions (PKOB and, at the same time, the main functional use and other functions of the building remained in the Regulation as well. The record data on buildings are captured for the real estate cadastre from other data sets, for example those maintained by architectural and construction authorities. At the same time, the data contained in the cadastre, after they have been entered or changed in the database, are transferred to other registers, such as tax records, or land and mortgage court registers. This study is the result of the analysis of the laws applicable to the specific units and registers. A list of discrepancies in the attributes occurring in the different registers was prepared. The practical part of the study paid particular attention to the legal bases and procedures for entering the function of a building in the real estate cadastre, which is extremely significant, as it is the attribute determining the property tax basis.

  13. The Politics of Information: Building a Relational Database To Support Decision-Making at a Public University.

    Science.gov (United States)

    Friedman, Debra; Hoffman, Phillip

    2001-01-01

    Describes creation of a relational database at the University of Washington supporting ongoing academic planning at several levels and affecting the culture of decision making. Addresses getting started; sharing the database; questions, worries, and issues; improving access to high-demand courses; the advising function; management of instructional…

  14. Genome databases

    Energy Technology Data Exchange (ETDEWEB)

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  15. Public policies and health systems in Sahelian Africa: theoretical context and empirical specificity.

    Science.gov (United States)

    Olivier de Sardan, Jean-Pierre; Ridde, Valéry

    2015-01-01

    This research on user fee removal in three African countries is located at the interface of public policy analysis and health systems research. Public policy analysis has gradually become a vast and multifaceted area of research consisting of a number of perspectives. But the context of public policies in Sahelian Africa has some specific characteristics. They are largely shaped by international institutions and development agencies, on the basis of very common 'one-size-fits-all' models; the practical norms that govern the actual behaviour of employees are far removed from official norms; public goods and services are co-delivered by a string of different actors and institutions, with little coordination between them; the State is widely regarded by the majority of citizens as untrustworthy. In such a context, setting up and implementing health user fee exemptions in Burkina Faso, Mali and Niger was beset by major problems, lack of coherence and bottlenecks that affect public policy-making and implementation in these countries.

  16. Native Health Research Database

    Science.gov (United States)

    ... APP WITH JAVASCRIPT TURNED OFF. THE NATIVE HEALTH DATABASE REQUIRES JAVASCRIPT IN ORDER TO FUNCTION. PLEASE ENTER ... To learn more about searching the Native Health Database, click here. Keywords Title Author Source of Publication ...

  17. 基于PDA的知识库与数据库集成和通用推理算法%PDA-oriented Integration of Knowledge Base and Database and Public Inference

    Institute of Scientific and Technical Information of China (English)

    欧阳建权; 钱跃良; 李锦涛; 刘任任

    2002-01-01

    This paper studies the correspondence relation between the knowledge and the database to combine the synthetic knowledge representation[1] and the relation database;defines the fields in the database as the feature in the knowledge base such as rule,weight and result for integrating the knowledge base and database.At alst,the paper introduces a public PDA-oriented inference algorism.

  18. Obesity, prostate-specific antigen nadir, and biochemical recurrence after radical prostatectomy: biology or technique? Results from the SEARCH database.

    Science.gov (United States)

    Ho, Tammy; Gerber, Leah; Aronson, William J; Terris, Martha K; Presti, Joseph C; Kane, Christopher J; Amling, Christopher L; Freedland, Stephen J

    2012-11-01

    Obesity is associated with an increased risk of biochemical recurrence (BCR) after radical prostatectomy (RP). It is unclear whether this is due to technical challenges related to operating on obese men or other biologic factors. To examine whether obesity predicts higher prostate-specific antigen (PSA) nadir (as a measure of residual PSA-producing tissue) after RP and if this accounts for the greater BCR risk in obese men. A retrospective analysis of 1038 RP patients from 2001 to 2010 in the multicenter US Veterans Administration-based Shared Equal Access Regional Cancer Hospital database with median follow-up of 41 mo. All patients underwent RP. We evaluated the relationship between body mass index (BMI) and ultrasensitive PSA nadir within 6 mo after RP. Adjusted proportional hazards models were used to examine the association between BMI and BCR with and without PSA nadir. Mean BMI was 28.5 kg/m2. Higher BMI was associated with higher PSA nadir on both univariable (p=0.001) and multivariable analyses (pobesity only significantly predicted BCR in men with an undetectable nadir (p=0.006). Unfortunately, other clinically relevant end points such as metastasis or mortality were not available. Obese men are more likely to have a higher PSA nadir, suggesting that either more advanced disease or technical issues confound an ideal operation. However, even after adjusting for the increased PSA nadir, obesity remained predictive of BCR, suggesting that tumors in obese men are growing faster. This provides further support for the idea that obesity is biologically associated with prostate cancer progression. Published by Elsevier B.V.

  19. Reflections on a decade of research by ASEAN dental faculties: analysis of publications from ISI-WOS databases from 2000 to 2009.

    Science.gov (United States)

    Sirisinha, Stitaya; Koontongkaew, Sittichai; Phantumvanit, Prathip; Wittayawuttikul, Ruchareka

    2011-05-01

    This communication analyzed research publications in dentistry in the Institute of Scientific Information Web of Science databases of 10 dental faculties in the Association of South-East Asian Nations (ASEAN) from 2000 to 2009. The term used for the "all-document types" search was "Faculty of Dentistry/College of Dentistry." Abstracts presented at regional meetings were also included in the analysis. The Times Higher Education System QS World University Rankings showed that universities in the region fare poorly in world university rankings. Only the National University of Singapore and Nanyang Technological University appeared in the top 100 in 2009; 19 universities in the region, including Indonesia, Malaysia, the Philippines, Singapore, and Thailand, appeared in the top 500. Data from the databases showed that research publications by dental institutes in the region fall short of their Asian counterparts. Singapore and Thailand are the most active in dental research of the ASEAN countries.

  20. 通过CORBA规范访问数据库的方法和途径%The Methods of Accessing Database by CORBA Specification

    Institute of Scientific and Technical Information of China (English)

    鲍剑洋; 吴文清

    2001-01-01

    文章提出了通过CORBA规范访问数据库的途径,探讨了通过CORBA开发应用程序的基本步骤。%In this paper,the way of accessing database by CORBA specification is proposed,the prodedure of developing CORBA program is investigated.

  1. EOSCUBE: A Constraint Database System for High-Level Specification and Efficient Generation of EOSDIS Products. Phase 1; Proof-of-Concept

    Science.gov (United States)

    Brodsky, Alexander; Segal, Victor E.

    1999-01-01

    The EOSCUBE constraint database system is designed to be a software productivity tool for high-level specification and efficient generation of EOSDIS and other scientific products. These products are typically derived from large volumes of multidimensional data which are collected via a range of scientific instruments.

  2. Female Media Use Behavior and Agreement with Publicly Promoted Agenda-Specific Health Messages

    Directory of Open Access Journals (Sweden)

    Shu-Yu Lyu

    2014-12-01

    Full Text Available This study set out to explore the relationship between female media use behavior and agreement with agenda-specific publicly promoted health messages. A random digit dial telephone cross-sectional survey was conducted using a nationally representative sample of female residents aged 25 and over. Respondents’ agreement with health messages was measured by a six-item Health Information Scale (HIS. Data were analyzed using chi-square tests and multiple logistic regression. This survey achieved a response rate of 86% (n = 1074. In this study the longest duration of daily television news watching (OR = 2.32, high self-efficacy (OR = 1.56, and greater attention to medical and health news (OR = 5.41 were all correlates of greater agreement with the selected health messages. Surprisingly, Internet use was not significant in the final model. Many women that public health interventions need to be targeting are not receptive to health information that can be accessed through Internet searches. However, they may be more readily targeted by television campaigns. Agenda-specific public health campaigns aiming to empower women to serve as nodes of information transmission and achieve efficient trickle down through the family unit might do better to invest more heavily in television promotion.

  3. Further Research is Required to Determine Which Database Products Best Support Research in Public Administration. A review of: Tucker, James, Corey. “Database Support for Research in Public Administration.” Behavioral & Social Sciences Librarian 24.1 (2005: 47-60.

    Directory of Open Access Journals (Sweden)

    David Hook

    2006-06-01

    Full Text Available Objective – To examine the extent to which six commercial database products support student and faculty research in the area of public administration. Design – Bibliometric study. Setting – Academic library in the United States. Subjects – Six commercial business‐related database products were examined: Proquest’s ABI/INFORM Global edition (ABI, EBSCO’s Business Source Premier (BSP, Gale’s General BusinessFile ASAP (GBF, EBSCO’s Academic Search Premier (ASP, EBSCO’s Expanded Academic Index (EAI and Proquest’s International Academic Research Library (ARL. Three of the databases (ABI, BSP, GBF were chosen because they address the management, human resource, and financing elements of public administration. The other three (ASP, EAI, ARL were included because of their multidisciplinary coverage. Methods – A list of journal titles covering public administration was assembled from the Institute of Scientific Information’s Social Sciences Citation Index and previously published lists of recommended journals in the field. The author then compared the compiled list of journal titles against the journal titles indexed by the six database products. He further analyzed the results by level of journal coverage (abstract only, full‐text, and full‐text with embargo and subject area based on categories described in Ulrich’s Periodicals Directory. Main Results – The study found that three of the six database products ‐‐EAI, BSP, and ARL ‐‐ provide indexing for the greatest number of public administration journals contained in the compiled list. EIA and ARL cover the greatest number of those that are full‐text journals, while BSP and ASP cover the greatest number of those full‐text journals limited by publisher embargoes. Conclusion – The author concludes that of the six databases examined, EAI, BSP, and ARL are the best for public administration research, based on their strength in the subject areas of public

  4. Scaling up health knowledge at European level requires sharing integrated data: an approach for collection of database specification.

    Science.gov (United States)

    Menditto, Enrica; Bolufer De Gea, Angela; Cahir, Caitriona; Marengoni, Alessandra; Riegler, Salvatore; Fico, Giuseppe; Costa, Elisio; Monaco, Alessandro; Pecorelli, Sergio; Pani, Luca; Prados-Torres, Alexandra

    2016-01-01

    Computerized health care databases have been widely described as an excellent opportunity for research. The availability of "big data" has brought about a wave of innovation in projects when conducting health services research. Most of the available secondary data sources are restricted to the geographical scope of a given country and present heterogeneous structure and content. Under the umbrella of the European Innovation Partnership on Active and Healthy Ageing, collaborative work conducted by the partners of the group on "adherence to prescription and medical plans" identified the use of observational and large-population databases to monitor medication-taking behavior in the elderly. This article describes the methodology used to gather the information from available databases among the Adherence Action Group partners with the aim of improving data sharing on a European level. A total of six databases belonging to three different European countries (Spain, Republic of Ireland, and Italy) were included in the analysis. Preliminary results suggest that there are some similarities. However, these results should be applied in different contexts and European countries, supporting the idea that large European studies should be designed in order to get the most of already available databases.

  5. [Need of specific criteria for psychotherapy referral in the public health system: A proposal].

    Science.gov (United States)

    García-Haro, J; Fernández-Briz, N

    2015-01-01

    This study discusses the need of specific criteria for psychotherapy referral in the public services. the use of psychotherapy as a supplement to traditional medication, and its comparison with informal methods of support, has been questioned. This study proposes the establishment of basic criteria for the integration of psychotherapy, based on an analysis of the conditions that allow it to function. It thus aims to contribute to improving the reputation and the practice conditions of psychotherapy in the public health system. Copyright © 2013 Sociedad Española de Médicos de Atención Primaria (SEMERGEN). Publicado por Elsevier España, S.L.U. All rights reserved.

  6. Public policies and health systems in Sahelian Africa: theoretical context and empirical specificity

    Science.gov (United States)

    2015-01-01

    This research on user fee removal in three African countries is located at the interface of public policy analysis and health systems research. Public policy analysis has gradually become a vast and multifaceted area of research consisting of a number of perspectives. But the context of public policies in Sahelian Africa has some specific characteristics. They are largely shaped by international institutions and development agencies, on the basis of very common 'one-size-fits-all' models; the practical norms that govern the actual behaviour of employees are far removed from official norms; public goods and services are co-delivered by a string of different actors and institutions, with little coordination between them; the State is widely regarded by the majority of citizens as untrustworthy. In such a context, setting up and implementing health user fee exemptions in Burkina Faso, Mali and Niger was beset by major problems, lack of coherence and bottlenecks that affect public policy-making and implementation in these countries. Health systems research for its part started to gain momentum less than twenty years ago and is becoming a discipline in its own right. But French-speaking African countries scarcely feature in it, and social sciences are not yet fully integrated. This special issue wants to fill the gap. In the Sahel, the bad health indicators reflect a combination of converging factors: lack of health centres, skilled staff, and resources; bad quality of care delivery, corruption, mismanagement; absence of any social security or meaningful commitment to the worst-off; growing competition from drug peddlers on one side, from private clinics on the other. Most reforms of the health system have various 'blind spots'. They do not take in account the daily reality of its functioning, its actual governance, the implicit rationales of the actors involved, and the quality of healthcare provision. In order to document the numerous neglected problems of the health

  7. Hawaiʻi Coral Disease database (HICORDIS: species-specific coral health data from across the Hawaiian archipelago

    Directory of Open Access Journals (Sweden)

    Jamie M. Caldwell

    2016-09-01

    Full Text Available The Hawaiʻi Coral Disease database (HICORDIS houses data on colony-level coral health condition observed across the Hawaiian archipelago, providing information to conduct future analyses on coral reef health in an era of changing environmental conditions. Colonies were identified to the lowest taxonomic classification possible (species or genera, measured and assessed for visual signs of health condition. Data were recorded for 286,071 coral colonies surveyed on 1819 transects at 660 sites between 2005 and 2015. The database contains observations for 60 species from 22 genera with 21 different health conditions. The goals of the HICORDIS database are to: i provide open access, quality controlled and validated coral health data assembled from disparate surveys conducted across Hawaiʻi; ii facilitate appropriate crediting of data; and iii encourage future analyses of coral reef health. In this article, we describe and provide data from the HICORDIS database. The data presented in this paper were used in the research article “Satellite SST-based Coral Disease Outbreak Predictions for the Hawaiian Archipelago” (Caldwell et al., 2016 [1].

  8. MetIDB: A Publicly Accessible Database of Predicted and Experimental 1H NMR Spectra of Flavonoids

    NARCIS (Netherlands)

    Mihaleva, V.V.; Beek, te T.A.; Zimmeren, van F.; Moco, S.I.A.; Laatikainen, R.; Niemitz, M.; Korhonen, S.P.; Driel, van M.A.; Vervoort, J.

    2013-01-01

    Identification of natural compounds, especially secondary metabolites, has been hampered by the lack of easy to use and accessible reference databases. Nuclear magnetic resonance (NMR) spectroscopy is the most selective technique for identification of unknown metabolites. High quality 1H NMR (proton

  9. Reducing the probability of false positive research findings by pre-publication validation – Experience with a large multiple sclerosis database

    Directory of Open Access Journals (Sweden)

    Heinz Moritz

    2008-04-01

    Full Text Available Abstract Background Published false positive research findings are a major problem in the process of scientific discovery. There is a high rate of lack of replication of results in clinical research in general, multiple sclerosis research being no exception. Our aim was to develop and implement a policy that reduces the probability of publishing false positive research findings. We have assessed the utility to work with a pre-publication validation policy after several years of research in the context of a large multiple sclerosis database. Methods The large database of the Sylvia Lawry Centre for Multiple Sclerosis Research was split in two parts: one for hypothesis generation and a validation part for confirmation of selected results. We present case studies from 5 finalized projects that have used the validation policy and results from a simulation study. Results In one project, the "relapse and disability" project as described in section II (example 3, findings could not be confirmed in the validation part of the database. The simulation study showed that the percentage of false positive findings can exceed 20% depending on variable selection. Conclusion We conclude that the validation policy has prevented the publication of at least one research finding that could not be validated in an independent data set (and probably would have been a "true" false-positive finding over the past three years, and has led to improved data analysis, statistical programming, and selection of hypotheses. The advantages outweigh the lost statistical power inherent in the process.

  10. On the use of age-specific effective dose coefficients in radiation protection of the public

    Energy Technology Data Exchange (ETDEWEB)

    Kocher, D.C.; Eckerman, K.F.

    1998-11-01

    Current radiation protection standards for the public include a limit on effective dose in any year for individuals in critical groups. This paper considers the question of how the annual dose limit should be applied in controlling routine exposures of populations consisting of individuals of all ages. The authors assume that the fundamental objective of radiation protection is limitation of lifetime risk and, therefore, that standards for controlling routine exposures of the public should provide a reasonable correspondence with lifetime risk, taking into account the age dependence of intakes and doses and the variety of radionuclides and exposure pathways of concern. Using new calculations of the per capita (population-averaged) risk of cancer mortality per unit activity inhaled or ingested in the US Environmental Protection Agency`s Federal Guidance Report No. 13, the authors show that applying a limit on annual effective dose only to adults, which was the usual practice in radiation protection of the public before the development of age-specific effective dose coefficients, provides a considerably better correspondence with lifetime risk than applying the annual dose limit to the critical group of any age.

  11. Scaling up health knowledge at European level requires sharing integrated data: an approach for collection of database specification

    Directory of Open Access Journals (Sweden)

    Menditto E

    2016-06-01

    Full Text Available Enrica Menditto,1 Angela Bolufer De Gea,2 Caitriona Cahir,3,4 Alessandra Marengoni,5 Salvatore Riegler,1 Giuseppe Fico,6 Elisio Costa,7 Alessandro Monaco,8 Sergio Pecorelli,5 Luca Pani,8 Alexandra Prados-Torres9 1School of Pharmacy, CIRFF/Center of Pharmacoeconomics, University of Naples Federico II, Naples, Italy; 2Directorate-General for Health and Food Safety, European Commission, Brussels, Belgium; 3Division of Population Health Sciences, Royal College of Surgeons in Ireland, 4Department of Pharmacology and Therapeutics, St James’s Hospital, Dublin, Ireland; 5Department of Clinical and Experimental Science, University of Brescia, Brescia; 6Life Supporting Technologies, Photonics Technology and Bioengineering Department, School of Telecomunications Engineering, Polytechnic University of Madrid, Madrid, Spain; 7Faculty of Pharmacy, University of Porto, Porto, Portugal; 8Italian Medicines Agency – AIFA, Rome, Italy; 9EpiChron Research Group on Chronic Diseases, Aragón Health Sciences Institute (IACS, IIS Aragón REDISSEC ISCIII, Miguel Servet University Hospital, University of Zaragoza, Zaragoza, Spain Abstract: Computerized health care databases have been widely described as an excellent opportunity for research. The availability of “big data” has brought about a wave of innovation in projects when conducting health services research. Most of the available secondary data sources are restricted to the geographical scope of a given country and present heterogeneous structure and content. Under the umbrella of the European Innovation Partnership on Active and Healthy Ageing, collaborative work conducted by the partners of the group on “adherence to prescription and medical plans” identified the use of observational and large-population databases to monitor medication-taking behavior in the elderly. This article describes the methodology used to gather the information from available databases among the Adherence Action Group partners

  12. ARTI Refrigerant Database

    Energy Technology Data Exchange (ETDEWEB)

    Calm, J.M.

    1992-11-09

    The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air- conditioning and refrigeration equipment. The database identifies sources of specific information on R-32, R-123, R-124, R-125, R-134, R-134a, R-141b, R-142b, R-143a, R-152a, R-245ca, R-290 (propane), R- 717 (ammonia), ethers, and others as well as azeotropic and zeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, ester, and other synthetics as well as mineral oils. It also references documents on compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. A computerized version is available that includes retrieval software.

  13. A Chronostratigraphic Relational Database Ontology

    Science.gov (United States)

    Platon, E.; Gary, A.; Sikora, P.

    2005-12-01

    A chronostratigraphic research database was donated by British Petroleum to the Stratigraphy Group at the Energy and Geoscience Institute (EGI), University of Utah. These data consists of over 2,000 measured sections representing over three decades of research into the application of the graphic correlation method. The data are global and includes both microfossil (foraminifera, calcareous nannoplankton, spores, pollen, dinoflagellate cysts, etc) and macrofossil data. The objective of the donation was to make the research data available to the public in order to encourage additional chronostratigraphy studies, specifically regarding graphic correlation. As part of the National Science Foundation's Cyberinfrastructure for the Geosciences (GEON) initiative these data have been made available to the public at http://css.egi.utah.edu. To encourage further research using the graphic correlation method, EGI has developed a software package, StrataPlot that will soon be publicly available from the GEON website as a standalone software download. The EGI chronostratigraphy research database, although relatively large, has many data holes relative to some paleontological disciplines and geographical areas, so the challenge becomes how do we expand the data available for chronostratigrahic studies using graphic correlation. There are several public or soon-to-be public databases available to chronostratigraphic research, but they have their own data structures and modes of presentation. The heterogeneous nature of these database schemas hinders their integration and makes it difficult for the user to retrieve and consolidate potentially valuable chronostratigraphic data. The integration of these data sources would facilitate rapid and comprehensive data searches, thus helping advance studies in chronostratigraphy. The GEON project will host a number of databases within the geology domain, some of which contain biostratigraphic data. Ontologies are being developed to provide

  14. Urbanism, public safety and living. Specific reference to the city of Barcelona

    Directory of Open Access Journals (Sweden)

    Juli Ponce

    2013-07-01

    Full Text Available The relation between urban concentration and public safety is acknowledged at international level, such as the contribution of planning and urban design to the mitigation and/or resolution of some conflicts within the urban space. In Spain some recent residential models, tending toward physical-social segregation, sprawl and fragmentation, have enlarged insecurity perception among citizens and increased the recourse to forms of privatization of safety supply. Spanish state legislation and autonomous regional legislation have recently tried to integrate crime prevention within planning and building practices through the promulgation of specific laws and rules. The paper reviews the main instruments used and discusses about possible future sceneries of the European city.

  15. Public management and network specificity: Effects of colleges’ ties with professional organizations on graduates’ labour market success and satisfaction

    NARCIS (Netherlands)

    Akkerman, Agnes; Torenvlied, René

    2013-01-01

    Research on managerial networking in the public sector reports positive effects of network activity on performance. However, little is known about which network relations influence different aspects of performance. We argue that for specific organizational goals, organizations should direct their

  16. An isomer-specific high-energy collision-induced dissociation MS/MS database for forensic applications: a proof-of-concept on chemical warfare agent markers.

    Science.gov (United States)

    Subramaniam, Raja; Östin, Anders; Nygren, Yvonne; Juhlin, Lars; Nilsson, Calle; Åstot, Crister

    2011-09-01

    Spectra database search has become the most popular technique for the identification of unknown chemicals, minimizing the need for authentic reference chemicals. In the present study, an isomer-specific high-energy collision-induced dissociation (CID) MS/MS spectra database of 12 isomeric O-hexyl methylphosphonic acids (degradation markers of nerve agents) was created. Phosphonate anions were produced by the electrospray ionization of phosphonic acids or negative-ion chemical ionization of their fluorinated derivatives and were analysed in a hybrid magnetic-sector-time-of-flight tandem mass spectrometer. A centre-of-mass energy (E(com)) of 65 eV led to an optimal sequential carbon-carbon bond breakage, which was interpreted in terms of charge remote fragmentation. The proposed mechanism is discussed in comparison with the routinely used low-energy CID MS/MS. Even-mass (odd-electron) charge remote fragmentation ion series were diagnostic of the O-alkyl chain structure and can be used to interpret unknown spectra. Together with the odd-mass ion series, they formed highly reproducible, isomer-specific spectra that gave significantly higher database matches and probability factors (by 1.5 times) than did the EI MS spectra of the trimethylsilyl derivatives of the same isomers. In addition, ionization by negative-ion chemical ionization and electrospray ionization resulted in similar spectra, which further highlights the general potential of the high-energy CID MS/MS technique.

  17. Family medicine publications in Taiwan: An analysis of the Web of Science database from 1993 to 2012

    Directory of Open Access Journals (Sweden)

    Ming-Hwai Lin

    2014-11-01

    Conclusion: Publications from departments/institutes of family medicine in Taiwan increased rapidly from 1993 to 2012. However, the trends of decreased citation number of articles and journal impact factor, as well as the small amount of articles published in the Primary Health Care Category, deserve further attention and effort.

  18. Psychiatric inpatient expenditures and public health insurance programmes: analysis of a national database covering the entire South Korean population

    Directory of Open Access Journals (Sweden)

    Chung Woojin

    2010-09-01

    Full Text Available Abstract Background Medical spending on psychiatric hospitalization has been reported to impose a tremendous socio-economic burden on many developed countries with public health insurance programmes. However, there has been no in-depth study of the factors affecting psychiatric inpatient medical expenditures and differentiated these factors across different types of public health insurance programmes. In view of this, this study attempted to explore factors affecting medical expenditures for psychiatric inpatients between two public health insurance programmes covering the entire South Korean population: National Health Insurance (NHI and National Medical Care Aid (AID. Methods This retrospective, cross-sectional study used a nationwide, population-based reimbursement claims dataset consisting of 1,131,346 claims of all 160,465 citizens institutionalized due to psychiatric diagnosis between January 2005 and June 2006 in South Korea. To adjust for possible correlation of patients characteristics within the same medical institution and a non-linearity structure, a Box-Cox transformed, multilevel regression analysis was performed. Results Compared with inpatients 19 years old or younger, the medical expenditures of inpatients between 50 and 64 years old were 10% higher among NHI beneficiaries but 40% higher among AID beneficiaries. Males showed higher medical expenditures than did females. Expenditures on inpatients with schizophrenia as compared to expenditures on those with neurotic disorders were 120% higher among NHI beneficiaries but 83% higher among AID beneficiaries. Expenditures on inpatients of psychiatric hospitals were greater on average than expenditures on inpatients of general hospitals. Among AID beneficiaries, institutions owned by private groups treated inpatients with 32% higher costs than did government institutions. Among NHI beneficiaries, inpatients medical expenditures were positively associated with the proportion of

  19. Constructing the 'gender-specific body': A critical discourse analysis of publications in the field of gender-specific medicine.

    Science.gov (United States)

    Annandale, Ellen; Hammarström, Anne

    2011-11-01

    Gender-specific medicine, a new and increasingly influential ethos within medical research and practice, has received little critical attention to date. The objective of this article is to critically examine the attributes of gender-specific medicine as imparted by its advocates. Through a critical discourse analysis of its two leading academic journals, we identify five interrelated discourses: of male/female difference; of hegemonic biology; of men's disadvantages; of biological and social reductionism; and of the fragmented body. Together these comprise a master discourse of the 'gender-specific body'. The discourse of the 'gender-specific body' is discussed in relation to the current neoliberal political agenda which frames healthcare as a market good and locates health and illness in individual bodies rather than in the wider social arrangements of society. We argue that the 'gender-specific body' threatens not only to turn back the clock to a vision of the biological body as fixed and determinate, but to extend this ever deeper into the social imagination. Lost in the process is any meaningful sense of the human body as a relatively open system which develops in interaction with its social world. We propose that, as it gains momentum, the 'gender-specific body' is likely progressively to circumscribe our thinking about the health of women and men in potentially problematic ways.

  20. Generic versus specific competencies of entry-level public health graduates: employers' perceptions in Poland, the UK, and the Netherlands.

    Science.gov (United States)

    Biesma, Regien G; Pavlova, Milena; Vaatstra, Rina; van Merode, Godefridus G; Czabanowska, Katarzyna; Smith, Tony; Groot, Wim

    2008-08-01

    Constant changes in society and the public health domain force public health professionals into new roles and the development of new competencies. Public health professionals will need to be trained to respond to this challenge. The aim of this comparative study among Poland, the UK and the Netherlands is to identify competence needs for Master of Public Health graduates entering the labour market from a European perspective. A self-administered questionnaire was sent to employers in the three countries, rating the importance of competency in public health on a master's level. In all three countries, interpersonal competencies, like team working and communication skills, are rated as highly important. However, employers in the UK and Poland generally rate public health specific competencies as much more important than their Dutch colleagues. It is concluded that while public health specific knowledge is providing a useful starting point for entry-level public health professionals, employers increasingly recognise the value of generic competencies such as communication and team working skills. The results suggest a stronger emphasis on teaching methods that encourage active learning and the integration of skills, which is crucial for enhancing graduates' employability, and foster an open attitude to multidisciplinary working, which is essential in modern health care.

  1. Validation of White-Matter Lesion Change Detection Methods on a Novel Publicly Available MRI Image Database.

    Science.gov (United States)

    Lesjak, Žiga; Pernuš, Franjo; Likar, Boštjan; Špiclin, Žiga

    2016-10-01

    Changes of white-matter lesions (WMLs) are good predictors of the progression of neurodegenerative diseases like multiple sclerosis (MS). Based on longitudinal magnetic resonance (MR) imaging the changes can be monitored, while the need for their accurate and reliable quantification led to the development of several automated MR image analysis methods. However, an objective comparison of the methods is difficult, because publicly unavailable validation datasets with ground truth and different sets of performance metrics were used. In this study, we acquired longitudinal MR datasets of 20 MS patients, in which brain regions were extracted, spatially aligned and intensity normalized. Two expert raters then delineated and jointly revised the WML changes on subtracted baseline and follow-up MR images to obtain ground truth WML segmentations. The main contribution of this paper is an objective, quantitative and systematic evaluation of two unsupervised and one supervised intensity based change detection method on the publicly available datasets with ground truth segmentations, using common pre- and post-processing steps and common evaluation metrics. Besides, different combinations of the two main steps of the studied change detection methods, i.e. dissimilarity map construction and its segmentation, were tested to identify the best performing combination.

  2. DMTB: the magnetotactic bacteria database

    Science.gov (United States)

    Pan, Y.; Lin, W.

    2012-12-01

    Magnetotactic bacteria (MTB) are of interest in biogeomagnetism, rock magnetism, microbiology, biomineralization, and advanced magnetic materials because of their ability to synthesize highly ordered intracellular nano-sized magnetic minerals, magnetite or greigite. Great strides for MTB studies have been made in the past few decades. More than 600 articles concerning MTB have been published. These rapidly growing data are stimulating cross disciplinary studies in such field as biogeomagnetism. We have compiled the first online database for MTB, i.e., Database of Magnestotactic Bacteria (DMTB, http://database.biomnsl.com). It contains useful information of 16S rRNA gene sequences, oligonucleotides, and magnetic properties of MTB, and corresponding ecological metadata of sampling sites. The 16S rRNA gene sequences are collected from the GenBank database, while all other data are collected from the scientific literature. Rock magnetic properties for both uncultivated and cultivated MTB species are also included. In the DMTB database, data are accessible through four main interfaces: Site Sort, Phylo Sort, Oligonucleotides, and Magnetic Properties. References in each entry serve as links to specific pages within public databases. The online comprehensive DMTB will provide a very useful data resource for researchers from various disciplines, e.g., microbiology, rock magnetism and paleomagnetism, biogeomagnetism, magnetic material sciences and others.

  3. Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries

    Directory of Open Access Journals (Sweden)

    Rodrigues NB

    2002-01-01

    Full Text Available In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3% sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds. Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8% contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds. The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds. From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci.

  4. Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries.

    Science.gov (United States)

    Rodrigues, N B; Loverde, P T; Romanha, A J; Oliveira, G

    2002-01-01

    In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3%) sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds). Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8%) contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds). The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds). From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci.

  5. ARTI refrigerant database

    Energy Technology Data Exchange (ETDEWEB)

    Calm, J.M.

    1997-02-01

    The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers and those using alterative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on various refrigerants. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyolester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates.

  6. ARTI Refrigerant Database

    Energy Technology Data Exchange (ETDEWEB)

    Cain, J.M. (Calm (James M.), Great Falls, VA (United States))

    1993-04-30

    The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included. The database identifies sources of specific information on R-32, R-123, R-124, R-125, R-134, R-134a, R-141b, R-142b, R-143a, R-152a, R-245ca, R-290 (propane), R-717 (ammonia), ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, ester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents to accelerate availability of the information and will be completed or replaced in future updates.

  7. ARTI Refrigerant Database

    Energy Technology Data Exchange (ETDEWEB)

    Cain, J.M. [Calm (James M.), Great Falls, VA (United States)

    1993-04-30

    The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included. The database identifies sources of specific information on R-32, R-123, R-124, R-125, R-134, R-134a, R-141b, R-142b, R-143a, R-152a, R-245ca, R-290 (propane), R-717 (ammonia), ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, ester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents to accelerate availability of the information and will be completed or replaced in future updates.

  8. ARTI refrigerant database

    Energy Technology Data Exchange (ETDEWEB)

    Calm, J.M. [Calm (James M.), Great Falls, VA (United States)

    1998-08-01

    The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufactures and those using alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on many refrigerants including propane, ammonia, water, carbon dioxide, propylene, ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyolester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates.

  9. Scientific publications and research groups on alcohol consumption and related problems worldwide: authorship analysis of papers indexed in PubMed and Scopus databases (2005 to 2009).

    Science.gov (United States)

    González-Alcaide, Gregorio; Castelló-Cogollos, Lourdes; Castellano-Gómez, Miguel; Agullo-Calatayud, Víctor; Aleixandre-Benavent, Rafael; Alvarez, Francisco Javier; Valderrama-Zurián, Juan Carlos

    2013-01-01

    The research of alcohol consumption-related problems is a multidisciplinary field. The aim of this study is to analyze the worldwide scientific production in the area of alcohol-drinking and alcohol-related problems from 2005 to 2009. A MEDLINE and Scopus search on alcohol (alcohol-drinking and alcohol-related problems) published from 2005 to 2009 was carried out. Using bibliometric indicators, the distribution of the publications was determined within the journals that publish said articles, specialty of the journal (broad subject terms), article type, language of the publication, and country where the journal is published. Also, authorship characteristics were assessed (collaboration index and number of authors who have published more than 9 documents). The existing research groups were also determined. About 24,100 documents on alcohol, published in 3,862 journals, and authored by 69,640 authors were retrieved from MEDLINE and Scopus between the years 2005 and 2009. The collaboration index of the articles was 4.83 ± 3.7. The number of consolidated research groups in the field was identified as 383, with 1,933 authors. Documents on alcohol were published mainly in journals covering the field of "Substance-Related Disorders," 23.18%, followed by "Medicine," 8.7%, "Psychiatry," 6.17%, and "Gastroenterology," 5.25%. Research on alcohol is a consolidated field, with an average of 4,820 documents published each year between 2005 and 2009 in MEDLINE and Scopus. Alcohol-related publications have a marked multidisciplinary nature. Collaboration was common among alcohol researchers. There is an underrepresentation of alcohol-related publications in languages other than English and from developing countries, in MEDLINE and Scopus databases. Copyright © 2012 by the Research Society on Alcoholism.

  10. A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).

    Science.gov (United States)

    Wu, Tsung-Jung; Shamsaddini, Amirhossein; Pan, Yang; Smith, Krista; Crichton, Daniel J; Simonyan, Vahan; Mazumder, Raja

    2014-01-01

    Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. Database URL: BioMuta: http

  11. Systematic review of systemic sclerosis-specific instruments for the EULAR Outcome Measures Library: An evolutional database model of validated patient-reported outcomes.

    Science.gov (United States)

    Ingegnoli, Francesca; Carmona, Loreto; Castrejon, Isabel

    2017-04-01

    The EULAR Outcome Measures Library (OML) is a freely available database of validated patient-reported outcomes (PROs). The aim of this study was to provide a comprehensive review of validated PROs specifically developed for systemic sclerosis (SSc) to feed the EULAR OML. A sensitive search was developed in Medline and Embase to identify all validation studies, cohort studies, reviews, or meta-analyses in which the objective were the development or validation of specific PROs evaluating organ involvement, disease activity or damage in SSc. A reviewer screened title and abstracts, selected the studies, and collected data concerning validation using ad hoc forms based on the COSMIN checklist. From 13,140 articles captured, 74 met the predefined criteria. After excluding two instruments as they were unavailable in English the selected 23 studies provided information on seven SSc-specific PROs on different SSc domains: burden of illness (symptom burden index), functional status (Scleroderma Assessment Questionnaire), functional ability (scleroderma Functional Score), Raynaud's phenomenon (Raynaud's condition score), mouth involvement (Mouth Handicap in SSc), gastro-intestinal involvement (University of California Los Angeles-Scleroderma Clinical Trial Consortium Gastro-Intestinal tract 2.0), and skin involvement (skin self-assessment). Each of them is partially validated and has different psychometric requirements. Seven SSc-specific PROs have a minimum validation and were included in the EULAR OML. Further development in the area of disease-specific PROs in SSc is warranted. Copyright © 2017 Elsevier Inc. All rights reserved.

  12. Using consensus methods to develop a country-specific Master of Public Health curriculum for the Republic of Maldives

    Directory of Open Access Journals (Sweden)

    Robotin MC

    2016-02-01

    Full Text Available Monica C Robotin,1,2 Muthau Shaheem,3 Aishath S Ismail3 1Faculty of Medicine, School of Public Health, University of Sydney, 2Cancer Programs Division, Cancer Council New South Wales, Sydney, Australia; 3Faculty of Health Sciences, Maldives National University, Male, Maldives Background: Over the last four decades, the health status of Maldivian people improved considerably, as reflected in child and maternal mortality indicators and the eradication or control of many communicable diseases. However, changing disease patterns are now undermining these successes, so the local public health practitioners need new skills to perform effectively in this changing environment. To address these needs, in 2013 the Faculty of Health Sciences of the Maldives National University developed the country's first Master of Public Health (MPH program.Methods: The process commenced with a wide scoping exercise and an analysis of the curricular structure of MPH programs of high-ranking universities. Thereafter, a stakeholder consultation using consensus methods reached agreement on overall course structure and the competencies required for local MPH graduates. Subsequently, a working group developed course descriptors and identified local public health research priorities, which could be addressed by MPH students.Results: Ten semistructured interviews explored specific training needs of prospective MPH students, key public health competencies required by local employers and preferred MPH training models. The recommendations informed a nominal group meeting, where participants agreed on MPH core competencies, overall curricular structure and core subjects. The 17 public health electives put forward by the group were prioritized using an online Delphi process. Participants ranked them by their propensity to address local public health needs and the locally available teaching expertise. The first student cohort commenced their MPH studies in January 2014.Conclusion

  13. Disaster Debris Recovery Database

    Data.gov (United States)

    U.S. Environmental Protection Agency — The US EPA Region 5 Disaster Debris Recovery Database includes public datasets of over 3,500 composting facilities, demolition contractors, haulers, transfer...

  14. Global Volcano Locations Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NGDC maintains a database of over 1,500 volcano locations obtained from the Smithsonian Institution Global Volcanism Program, Volcanoes of the World publication. The...

  15. Geographic specificity and positionality of public input in transportation: a rural transportation planning case from Central Texas

    Directory of Open Access Journals (Sweden)

    Greg P. Griffin

    2014-01-01

    Full Text Available Current transportation planning processes often incorporate public input, but the types of engagement techniques can affect the ability of practitioners to meaningfully include local ideas. This study incorporates literature integrating communicative rationality with participatory mapping, supported by a case study focusing on two public engagement techniques. A transportation planning process in Central Texas is evaluated in terms of the geographic specificity and positionality of comments received from open-ended responses on a questionnaire and a facilitated mapping session, and reviews this input for relevance to developing a transportation plan. Although all input received from the public can be valuable in the process, location-based comments may be more actionable by transportation planners. Participants’ perceived roles likely affect their level of engagement, which planners can facilitate to maximize the quality of involvement. Planners are advised to understand the positionality of project stakeholders and professionals, designing involvement methods considering geographic specificity appropriate for each project.

  16. Public management and network specificity: Effects of colleges’ ties with professional organizations on graduates’ labour market success and satisfaction

    NARCIS (Netherlands)

    Akkerman, Agnes; Torenvlied, Rene

    2013-01-01

    Research on managerial networking in the public sector reports positive effects of network activity on performance. However, little is known about which network relations influence different aspects of performance. We argue that for specific organizational goals, organizations should direct their ne

  17. Public Management and Network Specificity. Effects of colleges’ ties with professional organizations on graduates’ labour market success and satisfaction

    NARCIS (Netherlands)

    Akkerman, A.; Torenvlied, R.

    2013-01-01

    Research on managerial networking in the public sector reports positive effects of network activity on performance. However, little is known about which network relations influence different aspects of performance. We argue that for specific organizational goals, organizations should direct their ne

  18. Daas: A Web-based System for User-specific Dietary Analysis and Advice for the Public Healthcare Domain

    Institute of Scientific and Technical Information of China (English)

    Deirdre Nugent; Kudakwashe Dube; Wu Bing

    2003-01-01

    This paper presents a Dietary Analysis and Advice System (DAAS), a web-based system for providing, within the public healthcare domain, user-specific diet advice based on a preliminary analysis of current diet or eating habits and lifestyle, using knowledge from domain expertise and experts' interpretation of national dietary guidelines.

  19. Bibliometric assessment of publication output of child and adolescent psychiatric/psychological affiliations between 2005 and 2010 based on the databases PubMed and Scopus.

    Science.gov (United States)

    Albayrak, Ozgür; Föcker, Manuel; Wibker, Katrin; Hebebrand, Johannes

    2012-06-01

    We aimed to determine the quantitative scientific publication output of child and adolescent psychiatric/psychological affiliations during 2005-2010 by country based on both, "PubMed" and "Scopus" and performed a bibliometric qualitative evaluation for 2009 using "PubMed". We performed our search by affiliation related to child and adolescent psychiatric/psychological institutions using "PubMed". For the quantitative analysis for 2005-2010, we counted the number of abstracts. For the qualitative analysis for 2009 we derived the impact factor of each abstract's journal from "Journal Citation Reports". We related total impact factor scores to the gross domestic product (GDP) and population size of each country. Additionally, we used "Scopus" to determine the number of abstracts for each country that was identified via "PubMed" for 2009 and compared the ranking of countries between the two databases. 61 % of the publications between 2005 and 2010 originated from European countries and 26 % from the USA. After adjustment for GDP and population size, the ranking positions changed in favor of smaller European countries with a population size of less than 20 million inhabitants. The ranking of countries for the count of articles in 2009 as derived from "Scopus" was similar to that identified via the "PubMed" search. The performed search revealed only minor differences between "Scopus" and "PubMed" related to the ranking of countries. Our data indicate a sharp difference between countries with a high versus low GDP with regard to scientific publication output in child and adolescent psychiatry/psychology.

  20. Open Geoscience Database

    Science.gov (United States)

    Bashev, A.

    2012-04-01

    Currently there is an enormous amount of various geoscience databases. Unfortunately the only users of the majority of the databases are their elaborators. There are several reasons for that: incompaitability, specificity of tasks and objects and so on. However the main obstacles for wide usage of geoscience databases are complexity for elaborators and complication for users. The complexity of architecture leads to high costs that block the public access. The complication prevents users from understanding when and how to use the database. Only databases, associated with GoogleMaps don't have these drawbacks, but they could be hardly named "geoscience" Nevertheless, open and simple geoscience database is necessary at least for educational purposes (see our abstract for ESSI20/EOS12). We developed a database and web interface to work with them and now it is accessible at maps.sch192.ru. In this database a result is a value of a parameter (no matter which) in a station with a certain position, associated with metadata: the date when the result was obtained; the type of a station (lake, soil etc); the contributor that sent the result. Each contributor has its own profile, that allows to estimate the reliability of the data. The results can be represented on GoogleMaps space image as a point in a certain position, coloured according to the value of the parameter. There are default colour scales and each registered user can create the own scale. The results can be also extracted in *.csv file. For both types of representation one could select the data by date, object type, parameter type, area and contributor. The data are uploaded in *.csv format: Name of the station; Lattitude(dd.dddddd); Longitude(ddd.dddddd); Station type; Parameter type; Parameter value; Date(yyyy-mm-dd). The contributor is recognised while entering. This is the minimal set of features that is required to connect a value of a parameter with a position and see the results. All the complicated data

  1. Using a relational database to index infectious disease information.

    Science.gov (United States)

    Brown, Jay A

    2010-05-01

    Mapping medical knowledge into a relational database became possible with the availability of personal computers and user-friendly database software in the early 1990s. To create a database of medical knowledge, the domain expert works like a mapmaker to first outline the domain and then add the details, starting with the most prominent features. The resulting "intelligent database" can support the decisions of healthcare professionals. The intelligent database described in this article contains profiles of 275 infectious diseases. Users can query the database for all diseases matching one or more specific criteria (symptom, endemic region of the world, or epidemiological factor). Epidemiological factors include sources (patients, water, soil, or animals), routes of entry, and insect vectors. Medical and public health professionals could use such a database as a decision-support software tool.

  2. Reclamation research database

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2007-07-01

    A reclamation research database was compiled to help stakeholders search publications and research related to the reclamation of Alberta's oil sands region. New publications are added to the database by the Cumulative Environmental Management Association (CEMA), a nonprofit association whose mandate is to develop frameworks and guidelines for the management of cumulative environmental effects in the oil sands region. A total of 514 research papers have been compiled in the database to date. Topics include recent research on hydrology, aquatic and terrestrial ecosystems, laboratory studies on biodegradation, and the effects of oil sands processing on micro-organisms. The database includes a wide variety of studies related to reconstructed wetlands as well as the ecological effects of hydrocarbons on phytoplankton and other organisms. The database format included information on research format availability, as well as information related to the author's affiliations. Links to external abstracts were provided where available, as well as details of source information.

  3. The ExploreSurge Trail Guide and Hiking Workshop: discipline-specific education for public health nurses.

    Science.gov (United States)

    Stanley, Sharon A R; Polivka, Barbara J; Gordon, Deanna; Taulbee, Kelly; Kieffer, Gloria; McCorkle, Sheryl M

    2008-01-01

    Generic preparedness education and training for the public health workforce has increased in availability over the past 5 years. Registered Nurses also have more opportunities available for participation in emergency and disaster preparedness curricula. Discipline- and specialty-specific training and education for public health nurses (PHNs) incorporating their population-based practice, however, remains a largely unexplored area that is not accessible except for sporadic local venues. The Public Health Nursing Surge Curriculum provides 50 hr of nursing continuing education and activity-based aggregate focused learning experiences that are completed within a 12-month period, including an in-classroom seminar. The Public Health Nursing Surge Curriculum was developed on a foundation of 25 competencies linking PHNs and their population-based practice to surge capability. The curriculum was built in partnership with statewide public health directors of nursing over a 12-month period and is evaluated by a 3-level process to include self-rated confidence in performance. The curriculum's use of a blended learning methodology enables staff-level PHNs to master individual competencies toward surge capability within the public health response system.

  4. 75 FR 16635 - Refuge Specific Regulations; Public Use; Kodiak National Wildlife Refuge

    Science.gov (United States)

    2010-04-01

    ... viewing program was successful in reducing human impacts to bears and also proved popular with the public... changes to update the authority citation for the regulation, correct an error in the current regulation... (such as hotels, gas stations, bear-viewing guides, etc.) (NAIC [North American Industry Classification...

  5. The Molecular Biology Database Collection: 2008 update.

    Science.gov (United States)

    Galperin, Michael Y

    2008-01-01

    The Nucleic Acids Research online Molecular Biology Database Collection is a public repository that lists more than 1000 databases described in this and previous Nucleic Acids Research annual database issues, as well as a selection of molecular biology databases described in other journals. All databases included in this Collection are freely available to the public. The 2008 update includes 1078 databases, 110 more than the previous one. The links to more than 80 databases have been updated and 25 obsolete databases have been removed from the list. The complete database list and summaries are available online at the Nucleic Acids Research web site, http://nar.oxfordjournals.org/.

  6. Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software.

    Science.gov (United States)

    Peach, Megan L; Zakharov, Alexey V; Liu, Ruifeng; Pugliese, Angelo; Tawa, Gregory; Wallqvist, Anders; Nicklaus, Marc C

    2012-10-01

    Metabolism has been identified as a defining factor in drug development success or failure because of its impact on many aspects of drug pharmacology, including bioavailability, half-life and toxicity. In this article, we provide an outline and descriptions of the resources for metabolism-related property predictions that are currently either freely or commercially available to the public. These resources include databases with data on, and software for prediction of, several end points: metabolite formation, sites of metabolic transformation, binding to metabolizing enzymes and metabolic stability. We attempt to place each tool in historical context and describe, wherever possible, the data it was based on. For predictions of interactions with metabolizing enzymes, we show a typical set of results for a small test set of compounds. Our aim is to give a clear overview of the areas and aspects of metabolism prediction in which the currently available resources are useful and accurate, and the areas in which they are inadequate or missing entirely.

  7. SPECIFIC ACCOUNTING POLICIES ON PUBLIC INSTITUTIONS RELATED TO PROVISIONS, CONTIGENT LIABILITIES AND CONTIGENT ASSETS

    Directory of Open Access Journals (Sweden)

    Ţenovici Cristina Otilia

    2013-04-01

    Full Text Available Nowadays, the activity performed by professional accountants should be transparent and the communication process should be an efficient one so that the data transmitted is relevant and reliable. Such characteristics can become achievable only within a quality accounting referential, based on international accounting standards likely to integrate the public field particularities. The need to obtain comparable and transparent information in the public sector has determined the emergence of IPSAS standards, high quality standards with benefice consequences upon the world economy. The purpose of the disclose study is to analyse the development of accountancy in Romania and the level of accounting harmonization and convergence with IPSAS 19 “Provisions, contingent liabilities and contingent assets”. We are also focusing on performing a comparison between the main characteristics of the disclose national and international regulations, with the mention of resemblances and differences on provisions, contingent liabilities and contingent assets in order to identify the range of convergent and divergent issues.

  8. Native Pig and Chicken Breed Database: NPCDB.

    Science.gov (United States)

    Jeong, Hyeon-Soo; Kim, Dae-Won; Chun, Se-Yoon; Sung, Samsun; Kim, Hyeon-Jeong; Cho, Seoae; Kim, Heebal; Oh, Sung-Jong

    2014-10-01

    Indigenous (native) breeds of livestock have higher disease resistance and adaptation to the environment due to high genetic diversity. Even though their extinction rate is accelerated due to the increase of commercial breeds, natural disaster, and civil war, there is a lack of well-established databases for the native breeds. Thus, we constructed the native pig and chicken breed database (NPCDB) which integrates available information on the breeds from around the world. It is a nonprofit public database aimed to provide information on the genetic resources of indigenous pig and chicken breeds for their conservation. The NPCDB (http://npcdb.snu.ac.kr/) provides the phenotypic information and population size of each breed as well as its specific habitat. In addition, it provides information on the distribution of genetic resources across the country. The database will contribute to understanding of the breed's characteristics such as disease resistance and adaptation to environmental changes as well as the conservation of indigenous genetic resources.

  9. The NCBI Taxonomy database.

    Science.gov (United States)

    Federhen, Scott

    2012-01-01

    The NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy) is the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases. It includes organism names and taxonomic lineages for each of the sequences represented in the INSDC's nucleotide and protein sequence databases. The taxonomy database is manually curated by a small group of scientists at the NCBI who use the current taxonomic literature to maintain a phylogenetic taxonomy for the source organisms represented in the sequence databases. The taxonomy database is a central organizing hub for many of the resources at the NCBI, and provides a means for clustering elements within other domains of NCBI web site, for internal linking between domains of the Entrez system and for linking out to taxon-specific external resources on the web. Our primary purpose is to index the domain of sequences as conveniently as possible for our user community.

  10. Annotation of novel neuropeptide precursors in the migratory locust based on transcript screening of a public EST database and mass spectrometry

    Directory of Open Access Journals (Sweden)

    De Loof Arnold

    2006-08-01

    Full Text Available Abstract Background For holometabolous insects there has been an explosion of proteomic and peptidomic information thanks to large genome sequencing projects. Heterometabolous insects, although comprising many important species, have been far less studied. The migratory locust Locusta migratoria, a heterometabolous insect, is one of the most infamous agricultural pests. They undergo a well-known and profound phase transition from the relatively harmless solitary form to a ferocious gregarious form. The underlying regulatory mechanisms of this phase transition are not fully understood, but it is undoubtedly that neuropeptides are involved. However, neuropeptide research in locusts is hampered by the absence of genomic information. Results Recently, EST (Expressed Sequence Tag databases from Locusta migratoria were constructed. Using bioinformatical tools, we searched these EST databases specifically for neuropeptide precursors. Based on known locust neuropeptide sequences, we confirmed the sequence of several previously identified neuropeptide precursors (i.e. pacifastin-related peptides, which consolidated our method. In addition, we found two novel neuroparsin precursors and annotated the hitherto unknown tachykinin precursor. Besides one of the known tachykinin peptides, this EST contained an additional tachykinin-like sequence. Using neuropeptide precursors from Drosophila melanogaster as a query, we succeeded in annotating the Locusta neuropeptide F, allatostatin-C and ecdysis-triggering hormone precursor, which until now had not been identified in locusts or in any other heterometabolous insect. For the tachykinin precursor, the ecdysis-triggering hormone precursor and the allatostatin-C precursor, translation of the predicted neuropeptides in neural tissues was confirmed with mass spectrometric techniques. Conclusion In this study we describe the annotation of 6 novel neuropeptide precursors and the neuropeptides they encode from the

  11. Relational databases

    CERN Document Server

    Bell, D A

    1986-01-01

    Relational Databases explores the major advances in relational databases and provides a balanced analysis of the state of the art in relational databases. Topics covered include capture and analysis of data placement requirements; distributed relational database systems; data dependency manipulation in database schemata; and relational database support for computer graphics and computer aided design. This book is divided into three sections and begins with an overview of the theory and practice of distributed systems, using the example of INGRES from Relational Technology as illustration. The

  12. Specialist Bibliographic Databases

    OpenAIRE

    Gasparyan, Armen Yuri; Yessirkepov, Marlen; Voronov, Alexander A.; Trukhachev, Vladimir I.; Kostyukova, Elena I.; Gerasimov, Alexey N.; Kitas, George D.

    2016-01-01

    Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and d...

  13. Biofuel Database

    Science.gov (United States)

    Biofuel Database (Web, free access)   This database brings together structural, biological, and thermodynamic data for enzymes that are either in current use or are being considered for use in the production of biofuels.

  14. Onzekere databases

    NARCIS (Netherlands)

    van Keulen, Maurice

    Een recente ontwikkeling in het databaseonderzoek betret zogenaamde 'onzekere databases'. Dit artikel beschrijft wat onzekere databases zijn, hoe ze gebruikt kunnen worden en welke toepassingen met name voordeel zouden kunnen hebben van deze technologie.

  15. Community Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This excel spreadsheet is the result of merging at the port level of several of the in-house fisheries databases in combination with other demographic databases such...

  16. Database Administrator

    Science.gov (United States)

    Moore, Pam

    2010-01-01

    The Internet and electronic commerce (e-commerce) generate lots of data. Data must be stored, organized, and managed. Database administrators, or DBAs, work with database software to find ways to do this. They identify user needs, set up computer databases, and test systems. They ensure that systems perform as they should and add people to the…

  17. Database Administrator

    Science.gov (United States)

    Moore, Pam

    2010-01-01

    The Internet and electronic commerce (e-commerce) generate lots of data. Data must be stored, organized, and managed. Database administrators, or DBAs, work with database software to find ways to do this. They identify user needs, set up computer databases, and test systems. They ensure that systems perform as they should and add people to the…

  18. Use of administrative medical databases in population-based research.

    Science.gov (United States)

    Gavrielov-Yusim, Natalie; Friger, Michael

    2014-03-01

    Administrative medical databases are massive repositories of data collected in healthcare for various purposes. Such databases are maintained in hospitals, health maintenance organisations and health insurance organisations. Administrative databases may contain medical claims for reimbursement, records of health services, medical procedures, prescriptions, and diagnoses information. It is clear that such systems may provide a valuable variety of clinical and demographic information as well as an on-going process of data collection. In general, information gathering in these databases does not initially presume and is not planned for research purposes. Nonetheless, administrative databases may be used as a robust research tool. In this article, we address the subject of public health research that employs administrative data. We discuss the biases and the limitations of such research, as well as other important epidemiological and biostatistical key points specific to administrative database studies.

  19. A review of drug-induced liver injury databases.

    Science.gov (United States)

    Luo, Guangwen; Shen, Yiting; Yang, Lizhu; Lu, Aiping; Xiang, Zheng

    2017-07-17

    Drug-induced liver injuries have been a major focus of current research in drug development, and are also one of the major reasons for the failure and withdrawal of drugs in development. Drug-induced liver injuries have been systematically recorded in many public databases, which have become valuable resources in this field. In this study, we provide an overview of these databases, including the liver injury-specific databases LiverTox, LTKB, Open TG-GATEs, LTMap and Hepatox, and the general databases, T3DB, DrugBank, DITOP, DART, CTD and HSDB. The features and limitations of these databases are summarized and discussed in detail. Apart from their powerful functions, we believe that these databases can be improved in several ways: by providing the data about the molecular targets involved in liver toxicity, by incorporating information regarding liver injuries caused by drug interactions, and by regularly updating the data.

  20. Comparison of sequencing the D2 region of the large subunit ribosomal RNA gene (MicroSEQ®) versus the internal transcribed spacer (ITS) regions using two public databases for identification of common and uncommon clinically relevant fungal species.

    Science.gov (United States)

    Arbefeville, S; Harris, A; Ferrieri, P

    2017-09-01

    Fungal infections cause considerable morbidity and mortality in immunocompromised patients. Rapid and accurate identification of fungi is essential to guide accurately targeted antifungal therapy. With the advent of molecular methods, clinical laboratories can use new technologies to supplement traditional phenotypic identification of fungi. The aims of the study were to evaluate the sole commercially available MicroSEQ® D2 LSU rDNA Fungal Identification Kit compared to the in-house developed internal transcribed spacer (ITS) regions assay in identifying moulds, using two well-known online public databases to analyze sequenced data. 85 common and uncommon clinically relevant fungi isolated from clinical specimens were sequenced for the D2 region of the large subunit (LSU) of ribosomal RNA (rRNA) gene with the MicroSEQ® Kit and the ITS regions with the in house developed assay. The generated sequenced data were analyzed with the online GenBank and MycoBank public databases. The D2 region of the LSU rRNA gene identified 89.4% or 92.9% of the 85 isolates to the genus level and the full ITS region (f-ITS) 96.5% or 100%, using GenBank or MycoBank, respectively, when compared to the consensus ID. When comparing species-level designations to the consensus ID, D2 region of the LSU rRNA gene aligned with 44.7% (38/85) or 52.9% (45/85) of these isolates in GenBank or MycoBank, respectively. By comparison, f-ITS possessed greater specificity, followed by ITS1, then ITS2 regions using GenBank or MycoBank. Using GenBank or MycoBank, D2 region of the LSU rRNA gene outperformed phenotypic based ID at the genus level. Comparing rates of ID between D2 region of the LSU rRNA gene and the ITS regions in GenBank or MycoBank at the species level against the consensus ID, f-ITS and ITS2 exceeded performance of the D2 region of the LSU rRNA gene, but ITS1 had similar performance to the D2 region of the LSU rRNA gene using MycoBank. Our results indicated that the MicroSEQ® D2 LSU r

  1. The Danish Fetal Medicine database

    DEFF Research Database (Denmark)

    Ekelund, Charlotte; Kopp, Tine Iskov; Tabor, Ann

    2016-01-01

    trimester ultrasound scan performed at all public hospitals in Denmark are registered in the database. Main variables/descriptive data: Data on maternal characteristics, ultrasonic, and biochemical variables are continuously sent from the fetal medicine units’Astraia databases to the central database via...... analyses are sent to the database. Conclusion: It has been possible to establish a fetal medicine database, which monitors first-trimester screening for chromosomal abnormalities and second-trimester screening for major fetal malformations with the input from already collected data. The database...

  2. Hawaii bibliographic database

    Science.gov (United States)

    Wright, Thomas L.; Takahashi, Taeko Jane

    The Hawaii bibliographic database has been created to contain all of the literature, from 1779 to the present, pertinent to the volcanological history of the Hawaiian-Emperor volcanic chain. References are entered in a PC- and Macintosh-compatible EndNote Plus bibliographic database with keywords and s or (if no ) with annotations as to content. Keywords emphasize location, discipline, process, identification of new chemical data or age determinations, and type of publication. The database is updated approximately three times a year and is available to upload from an ftp site. The bibliography contained 8460 references at the time this paper was submitted for publication. Use of the database greatly enhances the power and completeness of library searches for anyone interested in Hawaiian volcanism.

  3. Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites

    Directory of Open Access Journals (Sweden)

    Kemp Bruce E

    2008-05-01

    Full Text Available Abstract Background We have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases. The method, named Predikin, identifies key conserved substrate-determining residues in the kinase catalytic domain that contact the substrate in the region of the phosphorylation site and so determine the sequence surrounding the phosphorylation site. Predikin was implemented originally as a web application written in Javascript. Results Here, we describe a new version of Predikin, completely revised and rewritten as a modular framework that provides multiple enhancements compared with the original. Predikin now consists of two components: (i PredikinDB, a database of phosphorylation sites that links substrates to kinase sequences and (ii a Perl module, which provides methods to classify protein kinases, reliably identify substrate-determining residues, generate scoring matrices and score putative phosphorylation sites in query sequences. The performance of Predikin as measured using receiver operator characteristic (ROC graph analysis equals or surpasses that of existing comparable methods. The Predikin website has been redesigned to incorporate the new features. Conclusion New features in Predikin include the use of SQL queries to PredikinDB to generate predictions, scoring of predictions, more reliable identification of substrate-determining residues and putative phosphorylation sites, extended options to handle protein kinase and substrate data and an improved web interface. The new features significantly enhance the ability of Predikin to analyse protein kinases and their substrates. Predikin is available at http://predikin.biosci.uq.edu.au.

  4. Morquio A syndrome-associated mutations: a review of alterations in the GALNS gene and a new locus-specific database.

    Science.gov (United States)

    Morrone, Amelia; Caciotti, Anna; Atwood, Robert; Davidson, Kathryn; Du, Chaoyi; Francis-Lyon, Patricia; Harmatz, Paul; Mealiffe, Matthew; Mooney, Sean; Oron, Tal Ronnen; Ryles, April; Zawadzki, Karl A; Miller, Nicole

    2014-11-01

    Morquio A syndrome (mucopolysaccharidosis IVA) is an autosomal recessive disorder that results from deficient activity of the enzyme N-acetylgalactosamine-6-sulfatase (GALNS) due to alterations in the GALNS gene, which causes major skeletal and connective tissue abnormalities and effects on multiple organ systems. The GALNS alterations associated with Morquio A are numerous and heterogeneous, and new alterations are continuously identified. To aid detection and interpretation of GALNS alterations, from previously published research, we provide a comprehensive and up-to-date listing of 277 unique GALNS alterations associated with Morquio A identified from 1,091 published GALNS alleles. In agreement with previous findings, most reported GALNS alterations are missense changes and even the most frequent alterations are relatively uncommon. We found that 48% of patients are assessed as homozygous for a GALNS alteration, 39% are assessed as heterozygous for two identified GALNS alterations, and in 13% of patients only one GALNS alteration is detected. We report here the creation of a locus-specific database for the GALNS gene (http://galns.mutdb.org/) that catalogs all reported alterations in GALNS to date. We highlight the challenges both in alteration detection and genotype-phenotype interpretation caused in part by the heterogeneity of GALNS alterations and provide recommendations for molecular testing of GALNS.

  5. The Gun Violence Database

    OpenAIRE

    Pavlick, Ellie; Callison-Burch, Chris

    2016-01-01

    We describe the Gun Violence Database (GVDB), a large and growing database of gun violence incidents in the United States. The GVDB is built from the detailed information found in local news reports about gun violence, and is constructed via a large-scale crowdsourced annotation effort through our web site, http://gun-violence.org/. We argue that centralized and publicly available data about gun violence can facilitate scientific, fact-based discussion about a topic that is often dominated by...

  6. National Database of Geriatrics

    DEFF Research Database (Denmark)

    Kannegaard, Pia Nimann; Vinding, Kirsten L; Hare-Bruun, Helle

    2016-01-01

    AIM OF DATABASE: The aim of the National Database of Geriatrics is to monitor the quality of interdisciplinary diagnostics and treatment of patients admitted to a geriatric hospital unit. STUDY POPULATION: The database population consists of patients who were admitted to a geriatric hospital unit....... Geriatric patients cannot be defined by specific diagnoses. A geriatric patient is typically a frail multimorbid elderly patient with decreasing functional ability and social challenges. The database includes 14-15,000 admissions per year, and the database completeness has been stable at 90% during the past......, percentage of discharges with a rehabilitation plan, and the part of cases where an interdisciplinary conference has taken place. Data are recorded by doctors, nurses, and therapists in a database and linked to the Danish National Patient Register. DESCRIPTIVE DATA: Descriptive patient-related data include...

  7. Plant Genome Duplication Database.

    Science.gov (United States)

    Lee, Tae-Ho; Kim, Junah; Robertson, Jon S; Paterson, Andrew H

    2017-01-01

    Genome duplication, widespread in flowering plants, is a driving force in evolution. Genome alignments between/within genomes facilitate identification of homologous regions and individual genes to investigate evolutionary consequences of genome duplication. PGDD (the Plant Genome Duplication Database), a public web service database, provides intra- or interplant genome alignment information. At present, PGDD contains information for 47 plants whose genome sequences have been released. Here, we describe methods for identification and estimation of dates of genome duplication and speciation by functions of PGDD.The database is freely available at http://chibba.agtec.uga.edu/duplication/.

  8. Records Management Database

    Data.gov (United States)

    US Agency for International Development — The Records Management Database is tool created in Microsoft Access specifically for USAID use. It contains metadata in order to access and retrieve the information...

  9. Alternatives to project-specific consent for access to personal information for health research: insights from a public dialogue.

    Science.gov (United States)

    Willison, Donald J; Swinton, Marilyn; Schwartz, Lisa; Abelson, Julia; Charles, Cathy; Northrup, David; Cheng, Ji; Thabane, Lehana

    2008-11-19

    The role of consent for research use of health information is contentious. Most discussion has focused on when project-specific consent may be waived but, recently, a broader range of consent options has been entertained, including broad opt-in for multiple studies with restrictions and notification with opt-out. We sought to elicit public values in this matter and to work toward an agreement about a common approach to consent for use of personal information for health research through deliberative public dialogues. We conducted seven day-long public dialogues, involving 98 participants across Canada. Immediately before and after each dialogue, participants completed a fixed-response questionnaire rating individuals' support for 3 approaches to consent in the abstract and their consent choices for 5 health research scenarios using personal information. They also rated how confident different safeguards made them feel that their information was being used responsibly. Broad opt-in consent for use of personal information garnered the greatest support in the abstract. When presented with specific research scenarios, no one approach to consent predominated. When profit was introduced into the scenarios, consent choices shifted toward greater control over use. Despite lively and constructive dialogues, and considerable shifting in opinion at the individual level, at the end of the day, there was no substantive aggregate movement in opinion. Personal controls were among the most commonly cited approaches to improving people's confidence in the responsible use of their information for research. Because no one approach to consent satisfied even a simple majority of dialogue participants and the importance placed on personal controls, a mechanism should be developed for documenting consent choice for different types of research, including ways for individuals to check who has accessed their medical record for purposes other than clinical care. This could be done, for

  10. Alternatives to project-specific consent for access to personal information for health research: Insights from a public dialogue

    Directory of Open Access Journals (Sweden)

    Abelson Julia

    2008-11-01

    Full Text Available Abstract Background The role of consent for research use of health information is contentious. Most discussion has focused on when project-specific consent may be waived but, recently, a broader range of consent options has been entertained, including broad opt-in for multiple studies with restrictions and notification with opt-out. We sought to elicit public values in this matter and to work toward an agreement about a common approach to consent for use of personal information for health research through deliberative public dialogues. Methods We conducted seven day-long public dialogues, involving 98 participants across Canada. Immediately before and after each dialogue, participants completed a fixed-response questionnaire rating individuals' support for 3 approaches to consent in the abstract and their consent choices for 5 health research scenarios using personal information. They also rated how confident different safeguards made them feel that their information was being used responsibly. Results Broad opt-in consent for use of personal information garnered the greatest support in the abstract. When presented with specific research scenarios, no one approach to consent predominated. When profit was introduced into the scenarios, consent choices shifted toward greater control over use. Despite lively and constructive dialogues, and considerable shifting in opinion at the individual level, at the end of the day, there was no substantive aggregate movement in opinion. Personal controls were among the most commonly cited approaches to improving people's confidence in the responsible use of their information for research. Conclusion Because no one approach to consent satisfied even a simple majority of dialogue participants and the importance placed on personal controls, a mechanism should be developed for documenting consent choice for different types of research, including ways for individuals to check who has accessed their medical record

  11. Genomic Databases for Crop Improvement

    Directory of Open Access Journals (Sweden)

    David Edwards

    2012-03-01

    Full Text Available Genomics is playing an increasing role in plant breeding and this is accelerating with the rapid advances in genome technology. Translating the vast abundance of data being produced by genome technologies requires the development of custom bioinformatics tools and advanced databases. These range from large generic databases which hold specific data types for a broad range of species, to carefully integrated and curated databases which act as a resource for the improvement of specific crops. In this review, we outline some of the features of plant genome databases, identify specific resources for the improvement of individual crops and comment on the potential future direction of crop genome databases.

  12. An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and Specificity analysis.

    Energy Technology Data Exchange (ETDEWEB)

    Kapp, Eugene; Schutz, Frederick; Connolly, Lisa M.; Chakel, John A.; Meza, Jose E.; Miller, Christine A.; Fenyo, David; Eng, Jimmy K.; Adkins, Joshua N.; Omenn, Gilbert; Simpson, Richard

    2005-08-01

    MS/MS and associated database search algorithms are essential proteomic tools for identifying peptides. Due to their widespread use, it is now time to perform a systematic analysis of the various algorithms currently in use. Using blood specimens used in the HUPO Plasma Proteome Project, we have evaluated five search algorithms with respect to their sensitivity and specificity, and have also accurately benchmarked them based on specified false-positive (FP) rates. Spectrum Mill and SEQUEST performed well in terms of sensitivity, but were inferior to MASCOT, X-Tandem, and Sonar in terms of specificity. Overall, MASCOT, a probabilistic search algorithm, correctly identified most peptides based on a specified FP rate. The rescoring algorithm, Peptide Prophet, enhanced the overall performance of the SEQUEST algorithm, as well as provided predictable FP error rates. Ideally, score thresholds should be calculated for each peptide spectrum or minimally, derived from a reversed-sequence search as demonstrated in this study based on a validated data set. The availability of open-source search algorithms, such as X-Tandem, makes it feasible to further improve the validation process (manual or automatic) on the basis of ''consensus scoring'', i.e., the use of multiple (at least two) search algorithms to reduce the number of FPs. complement.

  13. The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database

    Directory of Open Access Journals (Sweden)

    Okba Selama

    2013-01-01

    Full Text Available Databases are an essential tool and resource within the field of bioinformatics. The primary aim of this study was to generate an overview of global bacterial biodiversity and biogeography using available data from the two largest public online databases, NCBI Nucleotide and GBIF. The secondary aim was to highlight the contribution each geographic area has to each database. The basis for data analysis of this study was the metadata provided by both databases, mainly, the taxonomy and the geographical area origin of isolation of the microorganism (record. These were directly obtained from GBIF through the online interface, while E-utilities and Python were used in combination with a programmatic web service access to obtain data from the NCBI Nucleotide Database. Results indicate that the American continent, and more specifically the USA, is the top contributor, while Africa and Antarctica are less well represented. This highlights the imbalance of exploration within these areas rather than any reduction in biodiversity. This study describes a novel approach to generating global scale patterns of bacterial biodiversity and biogeography and indicates that the Proteobacteria are the most abundant and widely distributed phylum within both databases.

  14. The world bacterial biogeography and biodiversity through databases: a case study of NCBI Nucleotide Database and GBIF Database.

    Science.gov (United States)

    Selama, Okba; James, Phillip; Nateche, Farida; Wellington, Elizabeth M H; Hacène, Hocine

    2013-01-01

    Databases are an essential tool and resource within the field of bioinformatics. The primary aim of this study was to generate an overview of global bacterial biodiversity and biogeography using available data from the two largest public online databases, NCBI Nucleotide and GBIF. The secondary aim was to highlight the contribution each geographic area has to each database. The basis for data analysis of this study was the metadata provided by both databases, mainly, the taxonomy and the geographical area origin of isolation of the microorganism (record). These were directly obtained from GBIF through the online interface, while E-utilities and Python were used in combination with a programmatic web service access to obtain data from the NCBI Nucleotide Database. Results indicate that the American continent, and more specifically the USA, is the top contributor, while Africa and Antarctica are less well represented. This highlights the imbalance of exploration within these areas rather than any reduction in biodiversity. This study describes a novel approach to generating global scale patterns of bacterial biodiversity and biogeography and indicates that the Proteobacteria are the most abundant and widely distributed phylum within both databases.

  15. Database Manager

    Science.gov (United States)

    Martin, Andrew

    2010-01-01

    It is normal practice today for organizations to store large quantities of records of related information as computer-based files or databases. Purposeful information is retrieved by performing queries on the data sets. The purpose of DATABASE MANAGER is to communicate to students the method by which the computer performs these queries. This…

  16. Database Copyright Issues in the Integration of Public Digital Cultural Resources%公共数字文化资源整合中的数据库版权问题

    Institute of Scientific and Technical Information of China (English)

    高峰

    2015-01-01

    公共文化机构存在三种不同类型的数据库:开放存取数据库、自建数据库和商业数据库,在资源整合的过程中,它们分别涉及不同的版权问题.需要规划好资源整合的版权策略,包括强化版权意识,注意保护被整合的数据库的知识产权;充分利用版权例外,最大限度实现资源整合;加强与数据库商的协商,利用约定许可规避整合的版权风险;加强版权法规建设,赋予公共文化机构更多权利以利资源整合;在整合中注意保护自身数据库资源的知识产权等,从而推动公共数字文化资源整合.%There are three different types of databases in public cultural institutions: open access databases, self-built databases, and commercial databases. In the process of resources integration, they are involved in different copyright issues. The copyright strategies of resources integration are needed to be well planned: we should strengthen the copyright awareness, pay attention to the protection of copyrights of the integrated databases and make full use of copyright exceptions to maximize the integration of resources. Meanwhile, it's also recommended to strengthen consultation with the database providers to avoid the copyright risk of resource integration by using the agreed licensing, to strengthen the construction of copyright laws and regulations, and to give the public cultural institutions more rights to facilitate the resources integration and to protect the intellectual property rights of their own database resources, etc. All these measures serve the purpose of the promotion of the integration of public digital cultural resources.

  17. EPIC-DB: a proteomics database for studying Apicomplexan organisms

    Directory of Open Access Journals (Sweden)

    Angeletti Ruth

    2009-01-01

    Full Text Available Abstract Background High throughput proteomics experiments are useful for analyzing the protein expression of an organism, identifying the correct gene structure of a genome, or locating possible post-translational modifications within proteins. High throughput methods necessitate publicly accessible and easily queried databases for efficiently and logically storing, displaying, and analyzing the large volume of data. Description EPICDB is a publicly accessible, queryable, relational database that organizes and displays experimental, high throughput proteomics data for Toxoplasma gondii and Cryptosporidium parvum. Along with detailed information on mass spectrometry experiments, the database also provides antibody experimental results and analysis of functional annotations, comparative genomics, and aligned expressed sequence tag (EST and genomic open reading frame (ORF sequences. The database contains all available alternative gene datasets for each organism, which comprises a complete theoretical proteome for the respective organism, and all data is referenced to these sequences. The database is structured around clusters of protein sequences, which allows for the evaluation of redundancy, protein prediction discrepancies, and possible splice variants. The database can be expanded to include genomes of other organisms for which proteome-wide experimental data are available. Conclusion EPICDB is a comprehensive database of genome-wide T. gondii and C. parvum proteomics data and incorporates many features that allow for the analysis of the entire proteomes and/or annotation of specific protein sequences. EPICDB is complementary to other -genomics- databases of these organisms by offering complete mass spectrometry analysis on a comprehensive set of all available protein sequences.

  18. The Exoplanet Orbit Database

    CERN Document Server

    Wright, Jason T; Marcy, Geoffrey W; Han, Eunkyu; Feng, Ying; Johnson, John Asher; Howard, Andrew W; Valenti, Jeff A; Anderson, Jay; Piskunov, Nikolai

    2010-01-01

    We present a database of well determined orbital parameters of exoplanets. This database comprises spectroscopic orbital elements measured for 421 planets orbiting 357 stars from radial velocity and transit measurements as reported in the literature. We have also compiled fundamental transit parameters, stellar parameters, and the method used for the planets discovery. This Exoplanet Orbit Database includes all planets with robust, well measured orbital parameters reported in peer-reviewed articles. The database is available in a searchable, filterable, and sortable form on the Web at http://exoplanets.org through the Exoplanets Data Explorer Table, and the data can be plotted and explored through the Exoplanets Data Explorer Plotter. We use the Data Explorer to generate publication-ready plots giving three examples of the signatures of exoplanet migration and dynamical evolution: We illustrate the character of the apparent correlation between mass and period in exoplanet orbits, the selection different biase...

  19. The Danish Urogynaecological Database

    DEFF Research Database (Denmark)

    Guldberg, Rikke; Brostrøm, Søren; Hansen, Jesper Kjær

    2013-01-01

    INTRODUCTION AND HYPOTHESIS: The Danish Urogynaecological Database (DugaBase) is a nationwide clinical database established in 2006 to monitor, ensure and improve the quality of urogynaecological surgery. We aimed to describe its establishment and completeness and to validate selected variables....... This is the first study based on data from the DugaBase. METHODS: The database completeness was calculated as a comparison between urogynaecological procedures reported to the Danish National Patient Registry and to the DugaBase. Validity was assessed for selected variables from a random sample of 200 women...... in the DugaBase from 1 January 2009 to 31 October 2010, using medical records as a reference. RESULTS: A total of 16,509 urogynaecological procedures were registered in the DugaBase by 31 December 2010. The database completeness has increased by calendar time, from 38.2 % in 2007 to 93.2 % in 2010 for public...

  20. The Danish Anaesthesia Database

    Directory of Open Access Journals (Sweden)

    Antonsen K

    2016-10-01

    Full Text Available Kristian Antonsen,1 Charlotte Vallentin Rosenstock,2 Lars Hyldborg Lundstrøm2 1Board of Directors, Copenhagen University Hospital, Bispebjerg and Frederiksberg Hospital, Capital Region of Denmark, Denmark; 2Department of Anesthesiology, Copenhagen University Hospital, Nordsjællands Hospital-Hillerød, Capital Region of Denmark, Denmark Aim of database: The aim of the Danish Anaesthesia Database (DAD is the nationwide collection of data on all patients undergoing anesthesia. Collected data are used for quality assurance, quality development, and serve as a basis for research projects. Study population: The DAD was founded in 2004 as a part of Danish Clinical Registries (Regionernes Kliniske Kvalitetsudviklings Program [RKKP]. Patients undergoing general anesthesia, regional anesthesia with or without combined general anesthesia as well as patients under sedation are registered. Data are retrieved from public and private anesthesia clinics, single-centers as well as multihospital corporations across Denmark. In 2014 a total of 278,679 unique entries representing a national coverage of ~70% were recorded, data completeness is steadily increasing. Main variable: Records are aggregated for determining 13 defined quality indicators and eleven defined complications all covering the anesthetic process from the preoperative assessment through anesthesia and surgery until the end of the postoperative recovery period. Descriptive data: Registered variables include patients' individual social security number (assigned to all Danes and both direct patient-related lifestyle factors enabling a quantification of patients' comorbidity as well as variables that are strictly related to the type, duration, and safety of the anesthesia. Data and specific data combinations can be extracted within each department in order to monitor patient treatment. In addition, an annual DAD report is a benchmark for departments nationwide. Conclusion: The DAD is covering the

  1. What is a lexicographical database?

    DEFF Research Database (Denmark)

    Bergenholtz, Henning; Skovgård Nielsen, Jesper

    2013-01-01

    project. Such cooperation will reach the highest level of success if the lexicographer has at least a basic knowledge of the topic presented in this paper: What is a database? This type of knowledge is also needed when the lexicographer describes an ongoing or a finished project. In this article, we......50 years ago, no lexicographer used a database in the work process. Today, almost all dictionary projects incorporate databases. In our opinion, the optimal lexicographical database should be planned in cooperation between a lexicographer and a database specialist in each specific lexicographic...... provide the description of this type of cooperation, using the most important theoretical terms relevant in the planning of a database. It will be made clear that a lexicographical database is like any other database. The only difference is that an optimal lexicographical database is constructed to fulfil...

  2. Journalism, database and the construction of a connected public sphere NEOFLUXO: Jornalismo, base de dados e a construção da esfera pública interconectada

    Directory of Open Access Journals (Sweden)

    Walter Teixeira Lima Junior

    2011-07-01

    Full Text Available The paper aims to reveal the results of researched project research project applied in Conected Social Media Observatory, called Neofluxo. It was approved by the National Council for Scientific and Technological Development (CNPq and its main objective is to identify the behavior of informational flow in social networks during the majority electoral processs in Brazil, in 2010 and demonstrate the possibility to produce Journalism through the intersection and data visualization using APIs. The project stored more than 20,2 million of mentions of candidates, and keywords defined by the researchers. For this, it was elaborated a specific computer program based on an open source that is able to track entries from Twitter users from keywords, collecting and storing them in the database. The Neofluxo also recorded data from official social networks of candidates Jose Serra, Dilma Rousseff and Marina Silva, in order to identify –by these starting points - the informational flows until they have reached Twitter.O presente trabalho visa expor os resultados preliminares do projeto de pesquisa aplicada Observatório de Mídias Sociais Conectadas, batizado de Neofluxo. Aprovado em edital do CNPq, o projeto possui a duração de dois anos, devendo desenvolver-se até junho de 2012. O objetivo principal é identificar o comportamento do fluxo informacional nas redes sociais durante o processo eleitoral majoritário no Brasil, em 2010, e demonstrar a possibilidade de produzir Jornalismo por intermédio do cruzamento e visualização de dados utilizando APIs. O projeto armazenou mais de 20,2 milhões de menções aos candidatos e palavras-chave definidas pelos pesquisadores. Para isso foi elaborado um programa computacional espe¬cífico, baseado em software aberto, capaz de rastrear participações de usuários do Twitter segundo palavras-chave, coletando-as e armazenando-as em banco de dados. Também foram gravados dados das redes sociais oficiais dos

  3. Molecular marker databases.

    Science.gov (United States)

    Lai, Kaitao; Lorenc, Michał Tadeusz; Edwards, David

    2015-01-01

    The detection and analysis of genetic variation plays an important role in plant breeding and this role is increasing with the continued development of genome sequencing technologies. Molecular genetic markers are important tools to characterize genetic variation and assist with genomic breeding. Processing and storing the growing abundance of molecular marker data being produced requires the development of specific bioinformatics tools and advanced databases. Molecular marker databases range from species specific through to organism wide and often host a variety of additional related genetic, genomic, or phenotypic information. In this chapter, we will present some of the features of plant molecular genetic marker databases, highlight the various types of marker resources, and predict the potential future direction of crop marker databases.

  4. Database Replication

    CERN Document Server

    Kemme, Bettina

    2010-01-01

    Database replication is widely used for fault-tolerance, scalability and performance. The failure of one database replica does not stop the system from working as available replicas can take over the tasks of the failed replica. Scalability can be achieved by distributing the load across all replicas, and adding new replicas should the load increase. Finally, database replication can provide fast local access, even if clients are geographically distributed clients, if data copies are located close to clients. Despite its advantages, replication is not a straightforward technique to apply, and

  5. Probabilistic Databases

    CERN Document Server

    Suciu, Dan; Koch, Christop

    2011-01-01

    Probabilistic databases are databases where the value of some attributes or the presence of some records are uncertain and known only with some probability. Applications in many areas such as information extraction, RFID and scientific data management, data cleaning, data integration, and financial risk assessment produce large volumes of uncertain data, which are best modeled and processed by a probabilistic database. This book presents the state of the art in representation formalisms and query processing techniques for probabilistic data. It starts by discussing the basic principles for rep

  6. Querying genomic databases

    Energy Technology Data Exchange (ETDEWEB)

    Baehr, A.; Hagstrom, R.; Joerg, D.; Overbeek, R.

    1991-09-01

    A natural-language interface has been developed that retrieves genomic information by using a simple subset of English. The interface spares the biologist from the task of learning database-specific query languages and computer programming. Currently, the interface deals with the E. coli genome. It can, however, be readily extended and shows promise as a means of easy access to other sequenced genomic databases as well.

  7. SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases.

    Science.gov (United States)

    Schweiger, Dominik; Trajanoski, Zlatko; Pabinger, Stephan

    2014-08-15

    Semantic Web has established itself as a framework for using and sharing data across applications and database boundaries. Here, we present a web-based platform for querying biological Semantic Web databases in a graphical way. SPARQLGraph offers an intuitive drag & drop query builder, which converts the visual graph into a query and executes it on a public endpoint. The tool integrates several publicly available Semantic Web databases, including the databases of the just recently released EBI RDF platform. Furthermore, it provides several predefined template queries for answering biological questions. Users can easily create and save new query graphs, which can also be shared with other researchers. This new graphical way of creating queries for biological Semantic Web databases considerably facilitates usability as it removes the requirement of knowing specific query languages and database structures. The system is freely available at http://sparqlgraph.i-med.ac.at.

  8. Dealer Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The dealer reporting databases contain the primary data reported by federally permitted seafood dealers in the northeast. Electronic reporting was implemented May 1,...

  9. RDD Databases

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This database was established to oversee documents issued in support of fishery research activities including experimental fishing permits (EFP), letters of...

  10. [FY 2014 progress report]: Multi-regional database that documents the specific methods used to reconstruct prairie grasslands for a management unit

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This is an annual report of a project funded in FY14 by the Natural Resource Program Center. The goal of this project is to build a multi-regional database that...

  11. [FY 2015 progress report]: Multi-regional database that documents the specific methods used to reconstruct prairie grasslands for a management unit

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This is the FY2015 annual report of a project funded in FY14 by the Natural Resource Program Center. The goal of this project is to build a multi-regional database...

  12. National database

    DEFF Research Database (Denmark)

    Kristensen, Helen Grundtvig; Stjernø, Henrik

    1995-01-01

    Artikel om national database for sygeplejeforskning oprettet på Dansk Institut for Sundheds- og Sygeplejeforskning. Det er målet med databasen at samle viden om forsknings- og udviklingsaktiviteter inden for sygeplejen.......Artikel om national database for sygeplejeforskning oprettet på Dansk Institut for Sundheds- og Sygeplejeforskning. Det er målet med databasen at samle viden om forsknings- og udviklingsaktiviteter inden for sygeplejen....

  13. Glycoproteomic and glycomic databases.

    Science.gov (United States)

    Baycin Hizal, Deniz; Wolozny, Daniel; Colao, Joseph; Jacobson, Elena; Tian, Yuan; Krag, Sharon S; Betenbaugh, Michael J; Zhang, Hui

    2014-01-01

    Protein glycosylation serves critical roles in the cellular and biological processes of many organisms. Aberrant glycosylation has been associated with many illnesses such as hereditary and chronic diseases like cancer, cardiovascular diseases, neurological disorders, and immunological disorders. Emerging mass spectrometry (MS) technologies that enable the high-throughput identification of glycoproteins and glycans have accelerated the analysis and made possible the creation of dynamic and expanding databases. Although glycosylation-related databases have been established by many laboratories and institutions, they are not yet widely known in the community. Our study reviews 15 different publicly available databases and identifies their key elements so that users can identify the most applicable platform for their analytical needs. These databases include biological information on the experimentally identified glycans and glycopeptides from various cells and organisms such as human, rat, mouse, fly and zebrafish. The features of these databases - 7 for glycoproteomic data, 6 for glycomic data, and 2 for glycan binding proteins are summarized including the enrichment techniques that are used for glycoproteome and glycan identification. Furthermore databases such as Unipep, GlycoFly, GlycoFish recently established by our group are introduced. The unique features of each database, such as the analytical methods used and bioinformatical tools available are summarized. This information will be a valuable resource for the glycobiology community as it presents the analytical methods and glycosylation related databases together in one compendium. It will also represent a step towards the desired long term goal of integrating the different databases of glycosylation in order to characterize and categorize glycoproteins and glycans better for biomedical research.

  14. Chandra Publication Statistics

    CERN Document Server

    Rots, Arnold H; Becker, Glenn

    2011-01-01

    In this study we develop and propose publication metrics, based on an analysis of data from the Chandra bibliographic database, that are more meaningful and less sensitive to observatory-specific characteristics than the traditional metrics. They fall in three main categories: speed of publication; fraction of observing time published; and archival usage. Citation of results is a fourth category, but lends itself less well to definite statements. For Chandra, the median time from observation to publication is 2.36 years; after about 7 years 90% of the observing time is published; and the total annual publication output of the mission is 60-70% of the cumulative observing time available, assuming a two year lag between data retrieval and publication.

  15. Disaster Debris Recovery Database - Recovery

    Data.gov (United States)

    U.S. Environmental Protection Agency — The US EPA Region 5 Disaster Debris Recovery Database includes public datasets of over 6,000 composting facilities, demolition contractors, transfer stations,...

  16. Disaster Debris Recovery Database - Landfills

    Data.gov (United States)

    U.S. Environmental Protection Agency — The US EPA Region 5 Disaster Debris Recovery Database includes public datasets of over 6,000 composting facilities, demolition contractors, transfer stations,...

  17. Human Exposure Database System (HEDS)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Human Exposure Database System (HEDS) provides public access to data sets, documents, and metadata from EPA on human exposure. It is primarily intended for...

  18. Evaluating the impact of different sequence databases on metaproteome analysis: insights from a lab-assembled microbial mixture.

    Science.gov (United States)

    Tanca, Alessandro; Palomba, Antonio; Deligios, Massimo; Cubeddu, Tiziana; Fraumene, Cristina; Biosa, Grazia; Pagnozzi, Daniela; Addis, Maria Filippa; Uzzau, Sergio

    2013-01-01

    Metaproteomics enables the investigation of the protein repertoire expressed by complex microbial communities. However, to unleash its full potential, refinements in bioinformatic approaches for data analysis are still needed. In this context, sequence databases selection represents a major challenge. This work assessed the impact of different databases in metaproteomic investigations by using a mock microbial mixture including nine diverse bacterial and eukaryotic species, which was subjected to shotgun metaproteomic analysis. Then, both the microbial mixture and the single microorganisms were subjected to next generation sequencing to obtain experimental metagenomic- and genomic-derived databases, which were used along with public databases (namely, NCBI, UniProtKB/SwissProt and UniProtKB/TrEMBL, parsed at different taxonomic levels) to analyze the metaproteomic dataset. First, a quantitative comparison in terms of number and overlap of peptide identifications was carried out among all databases. As a result, only 35% of peptides were common to all database classes; moreover, genus/species-specific databases provided up to 17% more identifications compared to databases with generic taxonomy, while the metagenomic database enabled a slight increment in respect to public databases. Then, database behavior in terms of false discovery rate and peptide degeneracy was critically evaluated. Public databases with generic taxonomy exhibited a markedly different trend compared to the counterparts. Finally, the reliability of taxonomic attribution according to the lowest common ancestor approach (using MEGAN and Unipept software) was assessed. The level of misassignments varied among the different databases, and specific thresholds based on the number of taxon-specific peptides were established to minimize false positives. This study confirms that database selection has a significant impact in metaproteomics, and provides critical indications for improving depth and

  19. Public Values

    DEFF Research Database (Denmark)

    Beck Jørgensen, Torben; Rutgers, Mark R.

    2015-01-01

    administration is approached in terms of processes guided or restricted by public values and as public value creating: public management and public policy-making are both concerned with establishing, following and realizing public values. To study public values a broad perspective is needed. The article suggest......This article provides the introduction to a symposium on contemporary public values research. It is argued that the contribution to this symposium represent a Public Values Perspective, distinct from other specific lines of research that also use public value as a core concept. Public...... a research agenda for this encompasing kind of public values research. Finally the contributions to the symposium are introduced....

  20. A Case for Database Filesystems

    Energy Technology Data Exchange (ETDEWEB)

    Adams, P A; Hax, J C

    2009-05-13

    Data intensive science is offering new challenges and opportunities for Information Technology and traditional relational databases in particular. Database filesystems offer the potential to store Level Zero data and analyze Level 1 and Level 3 data within the same database system [2]. Scientific data is typically composed of both unstructured files and scalar data. Oracle SecureFiles is a new database filesystem feature in Oracle Database 11g that is specifically engineered to deliver high performance and scalability for storing unstructured or file data inside the Oracle database. SecureFiles presents the best of both the filesystem and the database worlds for unstructured content. Data stored inside SecureFiles can be queried or written at performance levels comparable to that of traditional filesystems while retaining the advantages of the Oracle database.

  1. Computational Tools and Resources for Metabolism-Related Property Predictions. 1. Overview of Publicly Available (Free and Commercial) Databases and Software

    Science.gov (United States)

    2012-01-01

    models described in the literature have been developed by pharmaceutical companies, on large propri- etary datasets, using proprietary descriptors and...Suite, was created in 2009 with the merger of Pharma Algorithms with ACD/Labs. Initially, the only available metabolism-related model, which had...set of screening hits, or for database filtering prior to sample acquisition or synthesis. Ideally, one would like to be able to predict the rate of

  2. Chemical Kinetics Database

    Science.gov (United States)

    SRD 17 NIST Chemical Kinetics Database (Web, free access)   The NIST Chemical Kinetics Database includes essentially all reported kinetics results for thermal gas-phase chemical reactions. The database is designed to be searched for kinetics data based on the specific reactants involved, for reactions resulting in specified products, for all the reactions of a particular species, or for various combinations of these. In addition, the bibliography can be searched by author name or combination of names. The database contains in excess of 38,000 separate reaction records for over 11,700 distinct reactant pairs. These data have been abstracted from over 12,000 papers with literature coverage through early 2000.

  3. Biological Databases

    Directory of Open Access Journals (Sweden)

    Kaviena Baskaran

    2013-12-01

    Full Text Available Biology has entered a new era in distributing information based on database and this collection of database become primary in publishing information. This data publishing is done through Internet Gopher where information resources easy and affordable offered by powerful research tools. The more important thing now is the development of high quality and professionally operated electronic data publishing sites. To enhance the service and appropriate editorial and policies for electronic data publishing has been established and editors of article shoulder the responsibility.

  4. CERCLIS (Superfund) ASCII Text Format - CPAD Database

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Public Access Database (CPAD) contains a selected set...

  5. Distributed Structure-Searchable Toxicity Database Network

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Distributed Structure-Searchable Toxicity (DSSTox) Database Network provides a public forum for search and publishing downloadable, structure-searchable,...

  6. The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases

    Directory of Open Access Journals (Sweden)

    Sullivan Christopher M

    2007-12-01

    Full Text Available Abstract Background Large molecular sequence databases are fundamental resources for modern bioscientists. Whether for project-specific purposes or sharing data with colleagues, it is often advantageous to maintain smaller sequence databases. However, this is usually not an easy task for the average bench scientist. Results We present the Personal Sequence Database (PSD, a suite of tools to create and maintain small- to medium-sized web-accessible sequence databases. All interactions with PSD tools occur via the internet with a web browser. Users may define sequence groups within their database that can be maintained privately or published to the web for public use. A sequence group can be downloaded, browsed, searched by keyword or searched for sequence similarities using BLAST. Publishing a sequence group extends these capabilities to colleagues and collaborators. In addition to being able to manage their own sequence databases, users can enroll sequences in BLASTAgent, a BLAST hit tracking system, to monitor NCBI databases for new entries displaying a specified level of nucleotide or amino acid similarity. Conclusion The PSD offers a valuable set of resources unavailable elsewhere. In addition to managing sequence data and BLAST search results, it facilitates data sharing with colleagues, collaborators and public users. The PSD is hosted by the authors and is available at http://bioinfo.cgrb.oregonstate.edu/psd/.

  7. USGS Dam Removal Science Database

    Science.gov (United States)

    Bellmore, J. Ryan; Vittum, Katherine; Duda, Jeff J.; Greene, Samantha L.

    2015-01-01

    This database is the result of an extensive literature search aimed at identifying documents relevant to the emerging field of dam removal science. In total the database contains 179 citations that contain empirical monitoring information associated with 130 different dam removals across the United States and abroad. Data includes publications through 2014 and supplemented with the U.S. Army Corps of Engineers National Inventory of Dams database, U.S. Geological Survey National Water Information System and aerial photos to estimate locations when coordinates were not provided. Publications were located using the Web of Science, Google Scholar, and Clearinghouse for Dam Removal Information.

  8. Working with Documents in Databases

    Directory of Open Access Journals (Sweden)

    Marian DARDALA

    2008-01-01

    Full Text Available Using on a larger and larger scale the electronic documents within organizations and public institutions requires their storage and unitary exploitation by the means of databases. The purpose of this article is to present the way of loading, exploitation and visualization of documents in a database, taking as example the SGBD MSSQL Server. On the other hand, the modules for loading the documents in the database and for their visualization will be presented through code sequences written in C#. The interoperability between averages will be carried out by the means of ADO.NET technology of database access.

  9. DMPD: CR3 (CD11b, CD18): a phagocyte and NK cell membrane receptor with multipleligand specificities and functions. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 8485905 CR3 (CD11b, CD18): a phagocyte and NK cell membrane receptor with multipleligand specificities...) (.html) (.csml) Show CR3 (CD11b, CD18): a phagocyte and NK cell membrane receptor with multipleligand specificities...d NK cell membrane receptor with multipleligand specificities and functions. Authors Ross GD, Vetvicka V. Pu

  10. Specific Phobias

    Science.gov (United States)

    ... Mental Health This information in Spanish ( en español ) Specific phobias Treatment More information on specific phobias A specific ... targeted psychotherapy. Return to top More information on Specific phobias Explore other publications and websites Phobias (Copyright © American ...

  11. FishTraits Database

    Science.gov (United States)

    Angermeier, Paul L.; Frimpong, Emmanuel A.

    2009-01-01

    The need for integrated and widely accessible sources of species traits data to facilitate studies of ecology, conservation, and management has motivated development of traits databases for various taxa. In spite of the increasing number of traits-based analyses of freshwater fishes in the United States, no consolidated database of traits of this group exists publicly, and much useful information on these species is documented only in obscure sources. The largely inaccessible and unconsolidated traits information makes large-scale analysis involving many fishes and/or traits particularly challenging. FishTraits is a database of >100 traits for 809 (731 native and 78 exotic) fish species found in freshwaters of the conterminous United States, including 37 native families and 145 native genera. The database contains information on four major categories of traits: (1) trophic ecology, (2) body size and reproductive ecology (life history), (3) habitat associations, and (4) salinity and temperature tolerances. Information on geographic distribution and conservation status is also included. Together, we refer to the traits, distribution, and conservation status information as attributes. Descriptions of attributes are available here. Many sources were consulted to compile attributes, including state and regional species accounts and other databases.

  12. The Danish Depression Database

    Directory of Open Access Journals (Sweden)

    Videbech P

    2016-10-01

    Full Text Available Poul Videbech,1 Anette Deleuran2 1Mental Health Centre Glostrup, Department of Clinical Medicine, University of Copenhagen, Glostrup, 2Psychiatric Centre Amager, Copenhagen S, Denmark Aim of database: The purpose of the Danish Depression Database (DDD is to monitor and facilitate the improvement of the quality of the treatment of depression in Denmark. Furthermore, the DDD has been designed to facilitate research. Study population: Inpatients as well as outpatients with depression, aged above 18 years, and treated in the public psychiatric hospital system were enrolled. Main variables: Variables include whether the patient has been thoroughly somatically examined and has been interviewed about the psychopathology by a specialist in psychiatry. The Hamilton score as well as an evaluation of the risk of suicide are measured before and after treatment. Whether psychiatric aftercare has been scheduled for inpatients and the rate of rehospitalization are also registered. Descriptive data: The database was launched in 2011. Every year since then ~5,500 inpatients and 7,500 outpatients have been registered annually in the database. A total of 24,083 inpatients and 29,918 outpatients have been registered. The DDD produces an annual report published on the Internet. Conclusion: The DDD can become an important tool for quality improvement and research, when the reporting is more complete. Keywords: quality assurance, suicide, somatic diseases, national database

  13. The Chandra Bibliography Database

    Science.gov (United States)

    Rots, A. H.; Winkelman, S. L.; Paltani, S.; Blecksmith, S. E.; Bright, J. D.

    2004-07-01

    Early in the mission, the Chandra Data Archive started the development of a bibliography database, tracking publications in refereed journals and on-line conference proceedings that are based on Chandra observations, allowing our users to link directly to articles in the ADS from our archive, and to link to the relevant data in the archive from the ADS entries. Subsequently, we have been working closely with the ADS and other data centers, in the context of the ADEC-ITWG, on standardizing the literature-data linking. We have also extended our bibliography database to include all Chandra-related articles and we are also keeping track of the number of citations of each paper. Obviously, in addition to providing valuable services to our users, this database allows us to extract a wide variety of statistical information. The project comprises five components: the bibliography database-proper, a maintenance database, an interactive maintenance tool, a user browsing interface, and a web services component for exchanging information with the ADS. All of these elements are nearly mission-independent and we intend make the package as a whole available for use by other data centers. The capabilities thus provided represent support for an essential component of the Virtual Observatory.

  14. ECOTOX database; new additions and future direction

    Science.gov (United States)

    The ECOTOXicology database (ECOTOX) is a comprehensive, publicly available knowledgebase developed and maintained by ORD/NHEERL. It is used for environmental toxicity data on aquatic life, terrestrial plants and wildlife. Publications are identified for potential applicability af...

  15. ECOTOX database; new additions and future direction

    Science.gov (United States)

    The ECOTOXicology database (ECOTOX) is a comprehensive, publicly available knowledgebase developed and maintained by ORD/NHEERL. It is used for environmental toxicity data on aquatic life, terrestrial plants and wildlife. Publications are identified for potential applicability af...

  16. A few problems in the generic nomenclature of insects and amphibians, with recommendations for the publication of new generic nomina in zootaxonomy and comments on taxonomic and nomenclatural databases and websites.

    Science.gov (United States)

    Dubois, Alain

    2017-02-26

    Dahanukar et al. (2016a) proposed the nomen Walkerana for a new genus of amphibians, but shortly after (2016b) they replaced it by the new nomen Sallywalkerana, believing that their nomen Walkerana was preoccupied by a generic nomen of orthopterans. This was unjustified because the orthopteran nomen 'Walkerella' Otte & Perez-Gelabert, 2009a and its new replacement nomen 'Walkerana' Otte & Perez-Gelabert, 2009b were both nomina nuda. These recent examples of nomenclatural errors in generic nomenclature are just a few among many in recent zootaxonomic publications. This opportunity is taken to make some general methodological recommendations, in several domains (availability, homonymy, synonymy, neonymy, length and palatability of nomina), for the publication of new generic nomina in zootaxonomy. However, the absence of a comprehensive database and website providing all the relevant information necessary to establish the nomenclatural status of all zoological generic and subgeneric nomina is a brake on the efforts that can be made to avoid nomenclatural errors in zoological generic nomenclature. The international community of taxonomists should seek at establishing such a database and website.

  17. 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

  18. Specialist Bibliographic Databases.

    Science.gov (United States)

    Gasparyan, Armen Yuri; Yessirkepov, Marlen; Voronov, Alexander A; Trukhachev, Vladimir I; Kostyukova, Elena I; Gerasimov, Alexey N; Kitas, George D

    2016-05-01

    Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls.

  19. Patent Database : A Methodology of Information Retrieval From PDF

    Directory of Open Access Journals (Sweden)

    Pawan Sharma

    2013-10-01

    Full Text Available Patent document holds wealth of information in itself. A brief detail of Indian patent applicationinformation is published as eighteen month publication by Indian patent Office, in electronic gazetteweekly. To date, a proper database of Indian patents specifically for research determination has not beenavailable, making it complicated for researcher to use this data for measuring any kind of researchactivities in terms of patents in India. To facilitate this, we constructed a comprehensive patent databasewhich incorporates the information presented in the electronic gazette. This database includes informationsuch as technology class, applicant, inventor, country of origin etc., of the patent submitted. We present themethodology for the creation of this database, its basic features along with its accuracy and reliability inthis research paper. Patent based database has been developed and can be used for various innovationresearches and activities.

  20. Data Preparation Process for the Buildings Performance Database

    Energy Technology Data Exchange (ETDEWEB)

    Walter, Travis; Dunn, Laurel; Mercado, Andrea; Brown, Richard E.; Mathew, Paul

    2014-06-30

    The Buildings Performance Database (BPD) includes empirically measured data from a variety of data sources with varying degrees of data quality and data availability. The purpose of the data preparation process is to maintain data quality within the database and to ensure that all database entries have sufficient data for meaningful analysis and for the database API. Data preparation is a systematic process of mapping data into the Building Energy Data Exchange Specification (BEDES), cleansing data using a set of criteria and rules of thumb, and deriving values such as energy totals and dominant asset types. The data preparation process takes the most amount of effort and time therefore most of the cleansing process has been automated. The process also needs to adapt as more data is contributed to the BPD and as building technologies over time. The data preparation process is an essential step between data contributed by providers and data published to the public in the BPD.

  1. Intelligence in young adulthood and cause-specific mortality in the Danish Conscription Database – A cohort study of 728,160 men

    DEFF Research Database (Denmark)

    Christensen, G.T.; Mortensen, E.L.; Christensen, K.;

    2016-01-01

    related to all-cause mortality with a 28% higher risk of dying during the study period per 1 standard deviation (SD) decrease in intelligence test score (HR=1.28 95% CI=1.27–1.29). The strength of the observed inverse associations did not vary much across main groups of natural and external causes......An inverse association has been reported between early life intelligence and all-cause mortality. The aim of this study was to investigate whether this well-established association differed according to the underlying cause of death and across different birth cohorts. The associations between young...... adult intelligence and mortality from natural and external causes were investigated in the Danish Conscription Database (DCD), which is a cohort of more than 700,000 men born 1939–1959 and followed in Danish registers from young adulthood until late mid-life. Young adult intelligence was inversely...

  2. 75 FR 50008 - Notice of Availability of a Draft Site-Specific Environmental Assessment and Notice of Public...

    Science.gov (United States)

    2010-08-16

    ..., junction boxes, electric power generation (solar, wind, and/or fuel cell,), and two-way communications...) gives notice of the availability of the Draft SSEA for the OOI, and requests public review and comment... scheduled public hearing at each of the locations listed below and will allow individuals to review...

  3. 77 FR 4586 - Notice of Opportunity for Public Comment on the Proposed Models for Plant-Specific Adoption of...

    Science.gov (United States)

    2012-01-30

    ... Bladey, Chief, Rules, Announcements, and Directives Branch (RADB), Office of Administration, Mail Stop... this page, the public can gain entry into ADAMS, which provides text and image files of the NRC's public documents. If you do not have access to ADAMS or if there are problems in accessing the...

  4. Trends in performance indicators of neuroimaging anatomy research publications: a bibliometric study of major neuroradiology journal output over four decades based on web of science database.

    Science.gov (United States)

    Wing, Louise; Massoud, Tarik F

    2015-01-01

    Quantitative, qualitative, and innovative application of bibliometric research performance indicators to anatomy and radiology research and education can enhance cross-fertilization between the two disciplines. We aim to use these indicators to identify long-term trends in dissemination of publications in neuroimaging anatomy (including both productivity and citation rates), which has subjectively waned in prestige during recent years. We examined publications over the last 40 years in two neuroradiological journals, AJNR and Neuroradiology, and selected and categorized all neuroimaging anatomy research articles according to theme and type. We studied trends in their citation activity over time, and mathematically analyzed these trends for 1977, 1987, and 1997 publications. We created a novel metric, "citation half-life at 10 years postpublication" (CHL-10), and used this to examine trends in the skew of citation numbers for anatomy articles each year. We identified 367 anatomy articles amongst a total of 18,110 in these journals: 74.2% were original articles, with study of normal anatomy being the commonest theme (46.7%). We recorded a mean of 18.03 citations for each anatomy article, 35% higher than for general neuroradiology articles. Graphs summarizing the rise (upslope) in citation rates after publication revealed similar trends spanning two decades. CHL-10 trends demonstrated that more recently published anatomy articles were likely to take longer to reach peak citation rate. Bibliometric analysis suggests that anatomical research in neuroradiology is not languishing. This novel analytical approach can be applied to other aspects of neuroimaging research, and within other subspecialties in radiology and anatomy, and also to foster anatomical education. © 2014 Wiley Periodicals, Inc.

  5. The Gene Expression Omnibus database

    Science.gov (United States)

    Clough, Emily; Barrett, Tanya

    2016-01-01

    The Gene Expression Omnibus (GEO) database is an international public repository that archives and freely distributes high-throughput gene expression and other functional genomics data sets. Created in 2000 as a worldwide resource for gene expression studies, GEO has evolved with rapidly changing technologies and now accepts high-throughput data for many other data applications, including those that examine genome methylation, chromatin structure, and genome–protein interactions. GEO supports community-derived reporting standards that specify provision of several critical study elements including raw data, processed data, and descriptive metadata. The database not only provides access to data for tens of thousands of studies, but also offers various Web-based tools and strategies that enable users to locate data relevant to their specific interests, as well as to visualize and analyze the data. This chapter includes detailed descriptions of methods to query and download GEO data and use the analysis and visualization tools. The GEO homepage is at http://www.ncbi.nlm.nih.gov/geo/. PMID:27008011

  6. The RIKEN integrated database of mammals.

    Science.gov (United States)

    Masuya, Hiroshi; Makita, Yuko; Kobayashi, Norio; Nishikata, Koro; Yoshida, Yuko; Mochizuki, Yoshiki; Doi, Koji; Takatsuki, Terue; Waki, Kazunori; Tanaka, Nobuhiko; Ishii, Manabu; Matsushima, Akihiro; Takahashi, Satoshi; Hijikata, Atsushi; Kozaki, Kouji; Furuichi, Teiichi; Kawaji, Hideya; Wakana, Shigeharu; Nakamura, Yukio; Yoshiki, Atsushi; Murata, Takehide; Fukami-Kobayashi, Kaoru; Mohan, Sujatha; Ohara, Osamu; Hayashizaki, Yoshihide; Mizoguchi, Riichiro; Obata, Yuichi; Toyoda, Tetsuro

    2011-01-01

    The RIKEN integrated database of mammals (http://scinets.org/db/mammal) is the official undertaking to integrate its mammalian databases produced from multiple large-scale programs that have been promoted by the institute. The database integrates not only RIKEN's original databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. Our integrated database has been implemented on the infrastructure of publication medium for databases, termed SciNetS/SciNeS, or the Scientists' Networking System, where the data and metadata are structured as a semantic web and are downloadable in various standardized formats. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations. Through the development of this database, we propose a novel methodology for the development of standardized comprehensive management of heterogeneous data sets in multiple databases to improve the sustainability, accessibility, utility and publicity of the data of biomedical information.

  7. Analysis of Coordinating Acquisition of Multimedia Database and Audiovisual Publication%浅析多媒体数据库与音像出版物协调采访

    Institute of Scientific and Technical Information of China (English)

    刘薇

    2012-01-01

    After the newborn multimedia database came into appearance,it has had a great attack on traditional audiovisual publication industry;however,it still cannot take the place of those multimedia publications seeing in the long run.Based on a comparison of multimedia database and audiovisual publication,the author discussed the necessities and feasibilities of coordinate acquisition for these two types of resources;besides,this essay introduced some exploration and achievements of coordinate acquisition in National Library of China,and finally provides some strategies for coordinate acquisition in library,from the angle of library status,technology,user types and human resources.%多媒体数据库这一新的资源类型出现后,对传统的音像出版物造成了一定的冲击,但在相当长一段时间内还无法替代音像出版物。在对比多媒体数据库和音像出版物这两种载体资源特点的基础上,论述了二者协调采访的必要性和可行性,并结合国家图书馆在协调采访方面的探索和成效,从馆情、技术条件、用户、人才等方面提出图书馆多媒体数据库与音像出版物协调采访的策略。

  8. Professional competencies in health promotion and public health: what is common and what is specific? Review of the European debate and perspectives for professional development.

    Science.gov (United States)

    Mereu, Alessandra; Sotgiu, Alessandra; Buja, Alessandra; Casuccio, Alessandra; Cecconi, Rosaria; Fabiani, Leila; Guberti, Emilia; Lorini, Chiara; Minelli, Liliana; Pocetta, Giancarlo; Contu, Paolo

    2015-01-01

    According to the Nairobi Call to Action, the growth of practitioners' skills can be favoured by setting accreditation standards and by reorienting professional competencies of current and future health workers. This will make it possible to develop a critical mass of competent practitioners, foster training, and increase visibility of the professional field. Through a review of the literature, the authors offer an overview of competency-based strategies for professional development in health promotion. The main research questions discussed were as follows: Is there a shared definition of public health?; Is there a shared definition of health promotion?; Who are the main stakeholders for public health and health promotion in Europe?; What is the meaning of professional competencies in education and practice for public health and health promotion?; Is there a shared system of professional core competencies in public health and health promotion?;What is common and what is specific between the two systems of professional competencies?; Is it useful and feasible to create specific strategies of professional development for public health and health promotion? A transformative use of competencies makes it possible to inform students, professionals, employers, and political decision-makers about what is expected from a specific profession and its values.

  9. The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database

    OpenAIRE

    Okba Selama; Phillip James; Farida Nateche; Wellington, Elizabeth M. H.; Hocine Hacène

    2013-01-01

    Databases are an essential tool and resource within the field of bioinformatics. The primary aim of this study was to generate an overview of global bacterial biodiversity and biogeography using available data from the two largest public online databases, NCBI Nucleotide and GBIF. The secondary aim was to highlight the contribution each geographic area has to each database. The basis for data analysis of this study was the metadata provided by both databases, mainly, the taxonomy and the geog...

  10. MetaBase—the wiki-database of biological databases

    Science.gov (United States)

    Bolser, Dan M.; Chibon, Pierre-Yves; Palopoli, Nicolas; Gong, Sungsam; Jacob, Daniel; Angel, Victoria Dominguez Del; Swan, Dan; Bassi, Sebastian; González, Virginia; Suravajhala, Prashanth; Hwang, Seungwoo; Romano, Paolo; Edwards, Rob; Bishop, Bryan; Eargle, John; Shtatland, Timur; Provart, Nicholas J.; Clements, Dave; Renfro, Daniel P.; Bhak, Daeui; Bhak, Jong

    2012-01-01

    Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project. PMID:22139927

  11. Lack of proportionality. Seven specifications of public interest that override post-approval commercial interests on limited access to clinical data

    Directory of Open Access Journals (Sweden)

    Strech Daniel

    2012-07-01

    Full Text Available Abstract For the protection of commercial interests, licensing bodies such as the EMA and health technology assessment institutions such as NICE restrict full access to unpublished evidence. Their respective policies on data transparency, however, lack a systematic account of (1 what kinds of commercial interests remain relevant after market approval has been granted, (2 what the specific types of public interest are that may override these commercial interests post approval, and, most importantly, (3 what criteria guide the trade-off between public interest and legitimate measures for the protection of commercial interest. Comparing potential commercial interests with seven specifications of relevant public interest reveals the lack of proportionality inherent in the current practices of EMA and NICE.

  12. Hanford Site technical baseline database

    Energy Technology Data Exchange (ETDEWEB)

    Porter, P.E.

    1996-09-30

    This document includes a cassette tape that contains the Hanford specific files that make up the Hanford Site Technical Baseline Database as of September 30, 1996. The cassette tape also includes the delta files that dellinate the differences between this revision and revision 4 (May 10, 1996) of the Hanford Site Technical Baseline Database.

  13. Hanford Site technical baseline database

    Energy Technology Data Exchange (ETDEWEB)

    Porter, P.E., Westinghouse Hanford

    1996-05-10

    This document includes a cassette tape that contains the Hanford specific files that make up the Hanford Site Technical Baseline Database as of May 10, 1996. The cassette tape also includes the delta files that delineate the differences between this revision and revision 3 (April 10, 1996) of the Hanford Site Technical Baseline Database.

  14. Medical database security evaluation.

    Science.gov (United States)

    Pangalos, G J

    1993-01-01

    Users of medical information systems need confidence in the security of the system they are using. They also need a method to evaluate and compare its security capabilities. Every system has its own requirements for maintaining confidentiality, integrity and availability. In order to meet these requirements a number of security functions must be specified covering areas such as access control, auditing, error recovery, etc. Appropriate confidence in these functions is also required. The 'trust' in trusted computer systems rests on their ability to prove that their secure mechanisms work as advertised and cannot be disabled or diverted. The general framework and requirements for medical database security and a number of parameters of the evaluation problem are presented and discussed. The problem of database security evaluation is then discussed, and a number of specific proposals are presented, based on a number of existing medical database security systems.

  15. Musical Structural Analysis Database Based on GTTM

    OpenAIRE

    Hamanaka, Masatoshi; Hirata, Keiji; Tojo, Satoshi

    2014-01-01

    This paper, we present the publication of our analysis data and analyzing tool based on the generative theory of tonal music (GTTM). Musical databases such as score databases, instrument sound databases, and musical pieces with standard MIDI files and annotated data are key to advancements in the field of music information technology. We started implementing the GTTM on a computer in 2004 and ever since have collected and publicized test data by musicologists in a step-by-step manner. In our ...

  16. A user-friendly phytoremediation database: creating the searchable database, the users, and the broader implications.

    Science.gov (United States)

    Famulari, Stevie; Witz, Kyla

    2015-01-01

    Designers, students, teachers, gardeners, farmers, landscape architects, architects, engineers, homeowners, and others have uses for the practice of phytoremediation. This research looks at the creation of a phytoremediation database which is designed for ease of use for a non-scientific user, as well as for students in an educational setting ( http://www.steviefamulari.net/phytoremediation ). During 2012, Environmental Artist & Professor of Landscape Architecture Stevie Famulari, with assistance from Kyla Witz, a landscape architecture student, created an online searchable database designed for high public accessibility. The database is a record of research of plant species that aid in the uptake of contaminants, including metals, organic materials, biodiesels & oils, and radionuclides. The database consists of multiple interconnected indexes categorized into common and scientific plant name, contaminant name, and contaminant type. It includes photographs, hardiness zones, specific plant qualities, full citations to the original research, and other relevant information intended to aid those designing with phytoremediation search for potential plants which may be used to address their site's need. The objective of the terminology section is to remove uncertainty for more inexperienced users, and to clarify terms for a more user-friendly experience. Implications of the work, including education and ease of browsing, as well as use of the database in teaching, are discussed.

  17. The AMMA database

    Science.gov (United States)

    Boichard, Jean-Luc; Brissebrat, Guillaume; Cloche, Sophie; Eymard, Laurence; Fleury, Laurence; Mastrorillo, Laurence; Moulaye, Oumarou; Ramage, Karim

    2010-05-01

    The AMMA project includes aircraft, ground-based and ocean measurements, an intensive use of satellite data and diverse modelling studies. Therefore, the AMMA database aims at storing a great amount and a large variety of data, and at providing the data as rapidly and safely as possible to the AMMA research community. In order to stimulate the exchange of information and collaboration between researchers from different disciplines or using different tools, the database provides a detailed description of the products and uses standardized formats. The AMMA database contains: - AMMA field campaigns datasets; - historical data in West Africa from 1850 (operational networks and previous scientific programs); - satellite products from past and future satellites, (re-)mapped on a regular latitude/longitude grid and stored in NetCDF format (CF Convention); - model outputs from atmosphere or ocean operational (re-)analysis and forecasts, and from research simulations. The outputs are processed as the satellite products are. Before accessing the data, any user has to sign the AMMA data and publication policy. This chart only covers the use of data in the framework of scientific objectives and categorically excludes the redistribution of data to third parties and the usage for commercial applications. Some collaboration between data producers and users, and the mention of the AMMA project in any publication is also required. The AMMA database and the associated on-line tools have been fully developed and are managed by two teams in France (IPSL Database Centre, Paris and OMP, Toulouse). Users can access data of both data centres using an unique web portal. This website is composed of different modules : - Registration: forms to register, read and sign the data use chart when an user visits for the first time - Data access interface: friendly tool allowing to build a data extraction request by selecting various criteria like location, time, parameters... The request can

  18. Native Pig and Chicken Breed Database: NPCDB

    Directory of Open Access Journals (Sweden)

    Hyeon-Soo Jeong

    2014-10-01

    Full Text Available Indigenous (native breeds of livestock have higher disease resistance and adaptation to the environment due to high genetic diversity. Even though their extinction rate is accelerated due to the increase of commercial breeds, natural disaster, and civil war, there is a lack of well-established databases for the native breeds. Thus, we constructed the native pig and chicken breed database (NPCDB which integrates available information on the breeds from around the world. It is a nonprofit public database aimed to provide information on the genetic resources of indigenous pig and chicken breeds for their conservation. The NPCDB (http://npcdb.snu.ac.kr/ provides the phenotypic information and population size of each breed as well as its specific habitat. In addition, it provides information on the distribution of genetic resources across the country. The database will contribute to understanding of the breed’s characteristics such as disease resistance and adaptation to environmental changes as well as the conservation of indigenous genetic resources.

  19. Cooperative Project To Develop a Database of Discipline-Specific Workbook Exercises for Agricultural and Biological Engineering, Entomology, and Biological Sciences Courses.

    Science.gov (United States)

    Ellsbury, Susan H.; And Others

    A two-part text, "Science Resources: A Self-Paced Instructional Workbook," was designed to provide science students at Mississippi State University with: (1) instruction on basic library usage and reference tools common to most scientific disciplines; (2) materials adapted to specific disciplines; and (3) services available to them from the…

  20. BBGD: an online database for blueberry genomic data

    Directory of Open Access Journals (Sweden)

    Matthews Benjamin F

    2007-01-01

    Full Text Available Abstract Background Blueberry is a member of the Ericaceae family, which also includes closely related cranberry and more distantly related rhododendron, azalea, and mountain laurel. Blueberry is a major berry crop in the United States, and one that has great nutritional and economical value. Extreme low temperatures, however, reduce crop yield and cause major losses to US farmers. A better understanding of the genes and biochemical pathways that are up- or down-regulated during cold acclimation is needed to produce blueberry cultivars with enhanced cold hardiness. To that end, the blueberry genomics database (BBDG was developed. Along with the analysis tools and web-based query interfaces, the database serves both the broader Ericaceae research community and the blueberry research community specifically by making available ESTs and gene expression data in searchable formats and in elucidating the underlying mechanisms of cold acclimation and freeze tolerance in blueberry. Description BBGD is the world's first database for blueberry genomics. BBGD is both a sequence and gene expression database. It stores both EST and microarray data and allows scientists to correlate expression profiles with gene function. BBGD is a public online database. Presently, the main focus of the database is the identification of genes in blueberry that are significantly induced or suppressed after low temperature exposure. Conclusion By using the database, researchers have developed EST-based markers for mapping and have identified a number of "candidate" cold tolerance genes that are highly expressed in blueberry flower buds after exposure to low temperatures.

  1. BBGD: an online database for blueberry genomic data.

    Science.gov (United States)

    Alkharouf, Nadim W; Dhanaraj, Anik L; Naik, Dhananjay; Overall, Chris; Matthews, Benjamin F; Rowland, Lisa J

    2007-01-30

    Blueberry is a member of the Ericaceae family, which also includes closely related cranberry and more distantly related rhododendron, azalea, and mountain laurel. Blueberry is a major berry crop in the United States, and one that has great nutritional and economical value. Extreme low temperatures, however, reduce crop yield and cause major losses to US farmers. A better understanding of the genes and biochemical pathways that are up- or down-regulated during cold acclimation is needed to produce blueberry cultivars with enhanced cold hardiness. To that end, the blueberry genomics database (BBDG) was developed. Along with the analysis tools and web-based query interfaces, the database serves both the broader Ericaceae research community and the blueberry research community specifically by making available ESTs and gene expression data in searchable formats and in elucidating the underlying mechanisms of cold acclimation and freeze tolerance in blueberry. BBGD is the world's first database for blueberry genomics. BBGD is both a sequence and gene expression database. It stores both EST and microarray data and allows scientists to correlate expression profiles with gene function. BBGD is a public online database. Presently, the main focus of the database is the identification of genes in blueberry that are significantly induced or suppressed after low temperature exposure. By using the database, researchers have developed EST-based markers for mapping and have identified a number of "candidate" cold tolerance genes that are highly expressed in blueberry flower buds after exposure to low temperatures.

  2. 50 CFR 32.6 - What are the procedures for publication of refuge-specific sport fishing regulations?

    Science.gov (United States)

    2010-10-01

    ... refuge-specific sport fishing regulations? 32.6 Section 32.6 Wildlife and Fisheries UNITED STATES FISH... sport fishing regulations? (a) Refuge-specific fishing regulations are issued only at the time of or after the opening of a wildlife refuge area to sport fishing. (b) Refuge-specific fishing...

  3. Phylogenetic associations with demographic, epidemiological and drug resistance characteristics of Mycobacterium tuberculosis lineages in the SITVIT2 database: Macro- and micro-geographical cleavages and phylogeographical specificities

    Directory of Open Access Journals (Sweden)

    Nalin Rastogi

    2015-01-01

    Conclusions: This research was focused to improve the in-depth phylogenetic characterization of MTBC lineages in conjunction with epidemiological analysis of circulating clones to generate evidence-based geographical mapping of predominant clinical isolates of tubercle bacilli causing the bulk of the disease both at the country and regional levels. Further superimposition of these maps with socio-political, economical, and demographical characteristics available through Geographic Information Systems (GIS allows access to a precise view of prevailing disparities as seen at the level of the United Nation's sub-regional stratification. An in-depth comprehension of these disparities and drawbacks is important to take appropriate actions by decision-makers and public health authorities alike, in order to better monitor, understand and control the tuberculosis epidemic worldwide.

  4. The Specification of Science Education Programs in the Local Public Library: Focusing on the Programs In G-city

    Directory of Open Access Journals (Sweden)

    In-Ja Ahn*

    2012-06-01

    Full Text Available The city of 'G' has been made a number of achievements with its science program as a part of public library's cultural program during the last 5 years. Recently, the national science centre has been established in the same city, the debate is now needed whether the science program in the public library have reasons to be maintained or to be reduced. The aim of this research is on the operating strategies of the science program in the public library. The research methods include case studies of operational strategies in domestic and foreign science centre, the level of satisfaction of local citizen on the science program, the vision of science program in the advancement of public library in the century. In results, the research proposes that the science program in public library should be maintained, but with locally characterised programs. In addition, the study also advised on the provision of scientific information, the strengthened search functions, and the development of user-centred services for those in science fields.

  5. Database of recent tsunami deposits

    Science.gov (United States)

    Peters, Robert; Jaffe, Bruce E.

    2010-01-01

    This report describes a database of sedimentary characteristics of tsunami deposits derived from published accounts of tsunami deposit investigations conducted shortly after the occurrence of a tsunami. The database contains 228 entries, each entry containing data from up to 71 categories. It includes data from 51 publications covering 15 tsunamis distributed between 16 countries. The database encompasses a wide range of depositional settings including tropical islands, beaches, coastal plains, river banks, agricultural fields, and urban environments. It includes data from both local tsunamis and teletsunamis. The data are valuable for interpreting prehistorical, historical, and modern tsunami deposits, and for the development of criteria to identify tsunami deposits in the geologic record.

  6. Protein Model Database

    Energy Technology Data Exchange (ETDEWEB)

    Fidelis, K; Adzhubej, A; Kryshtafovych, A; Daniluk, P

    2005-02-23

    The phenomenal success of the genome sequencing projects reveals the power of completeness in revolutionizing biological science. Currently it is possible to sequence entire organisms at a time, allowing for a systemic rather than fractional view of their organization and the various genome-encoded functions. There is an international plan to move towards a similar goal in the area of protein structure. This will not be achieved by experiment alone, but rather by a combination of efforts in crystallography, NMR spectroscopy, and computational modeling. Only a small fraction of structures are expected to be identified experimentally, the remainder to be modeled. Presently there is no organized infrastructure to critically evaluate and present these data to the biological community. The goal of the Protein Model Database project is to create such infrastructure, including (1) public database of theoretically derived protein structures; (2) reliable annotation of protein model quality, (3) novel structure analysis tools, and (4) access to the highest quality modeling techniques available.

  7. Teaching Case: Adapting the Access Northwind Database to Support a Database Course

    Science.gov (United States)

    Dyer, John N.; Rogers, Camille

    2015-01-01

    A common problem encountered when teaching database courses is that few large illustrative databases exist to support teaching and learning. Most database textbooks have small "toy" databases that are chapter objective specific, and thus do not support application over the complete domain of design, implementation and management concepts…

  8. Political Incongruity between Students' Ideological Identity and Stance on Specific Public Policies in a Predominantly White Southeastern State Institution

    Science.gov (United States)

    Coles, Jeremy T.; Carstens, Brittany A.; Wright, Jennifer M.; Williams, Robert L.

    2015-01-01

    The study determined whether or not a predominantly Caucasian sample (N = 187) attending a southeastern state's major public university embraced political policies consistent with their self-identified political ideology. The findings showed that the highest percentage of students identified with a conservative ideology and that a much lower…

  9. 75 FR 52555 - Notice of Availability of a Draft Site-Specific Environmental Assessment and Notice of Public...

    Science.gov (United States)

    2010-08-26

    ..., junction boxes, electric power generation (solar, wind, and/or fuel cell,), and two-way communications... the availability of the Draft SSEA for the OOI, and requests public review and comment on the document... hearing at each of the locations listed below and will allow individuals to review the...

  10. Political Incongruity between Students' Ideological Identity and Stance on Specific Public Policies in a Predominantly White Southeastern State Institution

    Science.gov (United States)

    Coles, Jeremy T.; Carstens, Brittany A.; Wright, Jennifer M.; Williams, Robert L.

    2015-01-01

    The study determined whether or not a predominantly Caucasian sample (N = 187) attending a southeastern state's major public university embraced political policies consistent with their self-identified political ideology. The findings showed that the highest percentage of students identified with a conservative ideology and that a much lower…

  11. The Danish Sarcoma Database

    Directory of Open Access Journals (Sweden)

    Jorgensen PH

    2016-10-01

    Full Text Available Peter Holmberg Jørgensen,1 Gunnar Schwarz Lausten,2 Alma B Pedersen3 1Tumor Section, Department of Orthopedic Surgery, Aarhus University Hospital, Aarhus, 2Tumor Section, Department of Orthopedic Surgery, Rigshospitalet, Copenhagen, 3Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark Aim: The aim of the database is to gather information about sarcomas treated in Denmark in order to continuously monitor and improve the quality of sarcoma treatment in a local, a national, and an international perspective. Study population: Patients in Denmark diagnosed with a sarcoma, both skeletal and ekstraskeletal, are to be registered since 2009. Main variables: The database contains information about appearance of symptoms; date of receiving referral to a sarcoma center; date of first visit; whether surgery has been performed elsewhere before referral, diagnosis, and treatment; tumor characteristics such as location, size, malignancy grade, and growth pattern; details on treatment (kind of surgery, amount of radiation therapy, type and duration of chemotherapy; complications of treatment; local recurrence and metastases; and comorbidity. In addition, several quality indicators are registered in order to measure the quality of care provided by the hospitals and make comparisons between hospitals and with international standards. Descriptive data: Demographic patient-specific data such as age, sex, region of living, comorbidity, World Health Organization's International Classification of Diseases – tenth edition codes and TNM Classification of Malignant Tumours, and date of death (after yearly coupling to the Danish Civil Registration System. Data quality and completeness are currently secured. Conclusion: The Danish Sarcoma Database is population based and includes sarcomas occurring in Denmark since 2009. It is a valuable tool for monitoring sarcoma incidence and quality of treatment and its improvement, postoperative

  12. 新立法对公共设施经营机构的数据库设计和维护的影响(英文)%Impact of Legislation on Database Design and Maintenance in Public Administration and Utilities

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    正如在其它欧洲国家所发生的一样,目前欧共体关于经济和货币一体化的政策对意大利的公共设施运营机构产生了戏剧性的影响.一方面,这些机构必须提供有效的服务,甚至通过互联网来提供给公民和企业,另一方面,市场的不合常规目的是促进更强的竞争:如今那些垄断的行业,如能源、汽油、水和电信,不得不进行竞争.这个新的范型需要组织方式的变化,它对信息系统以及其中最为重要的部分--数据库将产生重大的影响.通过两个案例研究来说明欧洲的政策对数据库所产生的影响.这两个案例分别是,一个坐落在意大利米兰的地方性的公共设施经营机构Regione Lombardia,另一个是在意大利罗马的能源企业ACEA.关于新立法对数据库设计和维护的影响,将介绍一些基本的观点.还将特别讨论,作为新法律环境下的一个产物,数据库重新设计所进行联合和分裂的一些问题.%Analogously to what occurs in other European Countries,the current policy of the European Union concerning the economic and monetary union is having a dramatic impact on Public Administration and utilities in Italy.As for Public Administrations,efficient services have to be provided,and even distributed via the Internet,to citizens and enterprises.On the other hand,the deregulation of the market is aimed at promoting a higher level of competitiveness:today also "natural" monopolies (like energy,gas,water,and telecommunications) are forced to competition.This new paradigm requires an organizational change which has a significant impact on information systems and on their most valuable component:the database.In this paper,the authors present the impact of the European policy on databases in two case studies:Regione Lombardia,an Italian Local Public Administration located in Milan,and ACEA,an Italian Energy Undertaking located in Rome.The authors show common issues related to the impact of the

  13. A systematic review of administrative and clinical databases of infants admitted to neonatal units.

    Science.gov (United States)

    Statnikov, Yevgeniy; Ibrahim, Buthaina; Modi, Neena

    2017-05-01

    High quality information, increasingly captured in clinical databases, is a useful resource for evaluating and improving newborn care. We conducted a systematic review to identify neonatal databases, and define their characteristics. We followed a preregistered protocol using MesH terms to search MEDLINE, EMBASE, CINAHL, Web of Science and OVID Maternity and Infant Care Databases for articles identifying patient level databases covering more than one neonatal unit. Full-text articles were reviewed and information extracted on geographical coverage, criteria for inclusion, data source, and maternal and infant characteristics. We identified 82 databases from 2037 publications. Of the country-specific databases there were 39 regional and 39 national. Sixty databases restricted entries to neonatal unit admissions by birth characteristic or insurance cover; 22 had no restrictions. Data were captured specifically for 53 databases; 21 administrative sources; 8 clinical sources. Two clinical databases hold the largest range of data on patient characteristics, USA's Pediatrix BabySteps Clinical Data Warehouse and UK's National Neonatal Research Database. A number of neonatal databases exist that have potential to contribute to evaluating neonatal care. The majority is created by entering data specifically for the database, duplicating information likely already captured in other administrative and clinical patient records. This repetitive data entry represents an unnecessary burden in an environment where electronic patient records are increasingly used. Standardisation of data items is necessary to facilitate linkage within and between countries. 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/.

  14. Addition of a breeding database in the Genome Database for Rosaceae.

    Science.gov (United States)

    Evans, Kate; Jung, Sook; Lee, Taein; Brutcher, Lisa; Cho, Ilhyung; Peace, Cameron; Main, Dorrie

    2013-01-01

    Breeding programs produce large datasets that require efficient management systems to keep track of performance, pedigree, geographical and image-based data. With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation. The integration of breeding data with other genomic and genetic data is instrumental for the refinement of marker-assisted breeding tools, enhances genetic understanding of important crop traits and maximizes access and utility by crop breeders and allied scientists. Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington State University apple breeding program and subsequently expanded to fit datasets from other Rosaceae breeders. The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data. Breeders can search accessions within the GDR to identify individuals with specific trait combinations. Results from Search by Parentage lists individuals with parents in common and results from Individual Variety pages link to all data available on each chosen individual including pedigree, phenotypic and genotypic information. Genotypic data are searchable by markers and alleles; results are linked to other pages in the GDR to enable the user to access tools such as GBrowse and CMap. This breeding database provides users with the opportunity to search datasets in a fully targeted manner and retrieve and compare performance data from multiple selections, years and sites, and to output the data needed for variety release publications and patent applications. The breeding database facilitates efficient program management. Storing publicly available breeding data in a database together with genomic and genetic data will

  15. A Comparative Analysis Among the SRS M&M, NIS, and KID Databases for the Adolescent Idiopathic Scoliosis.

    Science.gov (United States)

    Lee, Nathan J; Guzman, Javier Z; Kim, Jun; Skovrlj, Branko; Martin, Christopher T; Pugely, Andrew J; Gao, Yubo; Caridi, John M; Mendoza-Lattes, Sergio; Cho, Samuel K

    2016-11-01

    Retrospective cohort analysis. A growing number of publications have utilized the Scoliosis Research Society (SRS) Morbidity and Mortality (M&M) database, but none have compared it to other large databases. The objective of this study was to compare SRS complications with those in administrative databases. The Nationwide Inpatient Sample (NIS) and Kid's Inpatient Database (KID) captured a greater number of overall complications while the SRS M&M data provided a greater incidence of spine-related complications following adolescent idiopathic scoliosis (AIS) surgery. Chi-square was used to obtain statistical significance, with p databases were analyzed for AIS patients who underwent fusion. Comparable variables were queried in all three databases, including patient demographics, surgical variables, and complications. Patients undergoing AIS in the SRS database were slightly older (SRS 14.4 years vs. NIS 13.8 years, p database. The SRS database reported fewer overall complications (SRS 3.9% vs. NIS 7.3%, p databases. In contrast, SRS reported higher spine-specific complication rates. Mortality rates were similar between SRS versus NIS (p = .280) and SRS versus KID (p = .08) databases. There are similarities and differences between the three databases. These discrepancies are likely due to the varying data-gathering methods each organization uses to collect their morbidity data. Level IV. Copyright © 2016 Scoliosis Research Society. Published by Elsevier Inc. All rights reserved.

  16. The Cambridge Structural Database.

    Science.gov (United States)

    Groom, Colin R; Bruno, Ian J; Lightfoot, Matthew P; Ward, Suzanna C

    2016-04-01

    The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal-organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.

  17. The NEI/NCBI dbGAP database: Genotypes and haplotypes that may specifically predispose to risk of neovascular age-related macular degeneration

    Directory of Open Access Journals (Sweden)

    Miller Joan W

    2008-06-01

    Full Text Available Abstract Background To examine if the significantly associated SNPs derived from the genome wide allelic association study on the AREDS cohort at the NEI (dbGAP specifically confer risk for neovascular age-related macular degeneration (AMD. We ascertained 134 unrelated patients with AMD who had one sibling with an AREDS classification 1 or less and was past the age at which the affected sibling was diagnosed (268 subjects. Genotyping was performed by both direct sequencing and Sequenom iPLEX system technology. Single SNP analyses were conducted with McNemar's Test (both 2 × 2 and 3 × 3 tests and likelihood ratio tests (LRT. Conditional logistic regression was used to determine significant gene-gene interactions. LRT was used to determine the best fit for each genotypic model tested (additive, dominant or recessive. Results Before release of individual data, p-value information was obtained directly from the AREDS dbGAP website. Of the 35 variants with P -6 examined, 23 significantly modified risk of neovascular AMD. Many variants located in tandem on 1q32-q22 including those in CFH, CFHR4, CFHR2, CFHR5, F13B, ASPM and ZBTB were significantly associated with AMD risk. Of these variants, single SNP analysis revealed that CFH rs572515 was the most significantly associated with AMD risk (P -6. Haplotype analysis supported our findings of single SNP association, demonstrating that the most significant haplotype, GATAGTTCTC, spanning CFH, CFHR4, and CFHR2 was associated with the greatest risk of developing neovascular AMD (P -6. Other than variants on 1q32-q22, only two SNPs, rs9288410 (MAP2 on 2q34-q35 and rs2014307 (PLEKHA1/HTRA1 on 10q26 were significantly associated with AMD status (P = .03 and P -6 respectively. After controlling for smoking history, gender and age, the most significant gene-gene interaction appears to be between rs10801575 (CFH and rs2014307 (PLEKHA1/HTRA1 (P -11. The best genotypic fit for rs10801575 and rs2014307 was an

  18. VIRTUAL MUSEUMS OF PUBLIC ART: GENERAL CONSIDERATIONS AND SPECIFICITIES OF THE PROJECT FOR THE MUNICIPAL WEB OF ZARAGOZA

    Directory of Open Access Journals (Sweden)

    Jesús Pedro Lorente

    2008-10-01

    Full Text Available This paper gives a foretaste of the catalogue of public art currently being carried out by a multidisciplinary team of researchers for the web site of Saragossa City Council. It will be produced in collaboration with that of Barcelona, within a network of research projects financed by the Spanish Ministry of Education. We like to call it “virtual museum”, because it is going to be not just a register of schedules, but also a combination of itineraries and curatorial explanations. A first stage of the work will be available in internet by May 2008 at the following address: http://www.zaragoza.es/artepublico

  19. 推动征信标准实施 规范数据库用户管理——《金融信用信息基础数据库用户管理规范》解读%Promote the Implementation of Credit Reporting Standardization and Normalize Database User Management——An Interpretation of"Financial Credit Information Database User Management Specification"

    Institute of Scientific and Technical Information of China (English)

    王俊山

    2015-01-01

    The "Financial Credit Information Database User Management Specification" imposes the constraints on various users of financial credit information database from different institutions.The promotion and implementation of the "Specification" will help safeguard the legitimate rights and interests of the information subjects, and guarantee the smooth operation of the financial credit information database.%《金融信用信息基础数据库用户管理规范》对不同机构在金融信用信息基础数据库上的各类用户做出了约束. 其推广和实施有助于维护信息主体的合法权益,保障金融信用信息基础数据库平稳运行.

  20. The LAILAPS search engine: relevance ranking in life science databases.

    Science.gov (United States)

    Lange, Matthias; Spies, Karl; Bargsten, Joachim; Haberhauer, Gregor; Klapperstück, Matthias; Leps, Michael; Weinel, Christian; Wünschiers, Röbbe; Weissbach, Mandy; Stein, Jens; Scholz, Uwe

    2010-01-15

    Search engines and retrieval systems are popular tools at a life science desktop. The manual inspection of hundreds of database entries, that reflect a life science concept or fact, is a time intensive daily work. Hereby, not the number of query results matters, but the relevance does. In this paper, we present the LAILAPS search engine for life science databases. The concept is to combine a novel feature model for relevance ranking, a machine learning approach to model user relevance profiles, ranking improvement by user feedback tracking and an intuitive and slim web user interface, that estimates relevance rank by tracking user interactions. Queries are formulated as simple keyword lists and will be expanded by synonyms. Supporting a flexible text index and a simple data import format, LAILAPS can easily be used both as search engine for comprehensive integrated life science databases and for small in-house project databases. With a set of features, extracted from each database hit in combination with user relevance preferences, a neural network predicts user specific relevance scores. Using expert knowledge as training data for a predefined neural network or using users own relevance training sets, a reliable relevance ranking of database hits has been implemented. In this paper, we present the LAILAPS system, the concepts, benchmarks and use cases. LAILAPS is public available for SWISSPROT data at http://lailaps.ipk-gatersleben.de.

  1. Computerized comprehensive data analysis of Lung Imaging Database Consortium (LIDC)

    OpenAIRE

    Tan, Jun; Pu, Jiantao; Zheng, Bin; Wang, Xingwei; Leader, Joseph K.

    2010-01-01

    Purpose: Lung Image Database Consortium (LIDC) is the largest public CT image database of lung nodules. In this study, the authors present a comprehensive and the most updated analysis of this dynamically growing database under the help of a computerized tool, aiming to assist researchers to optimally use this database for lung cancer related investigations.

  2. Database development and management

    CERN Document Server

    Chao, Lee

    2006-01-01

    Introduction to Database Systems Functions of a DatabaseDatabase Management SystemDatabase ComponentsDatabase Development ProcessConceptual Design and Data Modeling Introduction to Database Design Process Understanding Business ProcessEntity-Relationship Data Model Representing Business Process with Entity-RelationshipModelTable Structure and NormalizationIntroduction to TablesTable NormalizationTransforming Data Models to Relational Databases .DBMS Selection Transforming Data Models to Relational DatabasesEnforcing ConstraintsCreating Database for Business ProcessPhysical Design and Database

  3. Development and validation of a Database Forensic Metamodel (DBFM)

    Science.gov (United States)

    Al-dhaqm, Arafat; Razak, Shukor; Othman, Siti Hajar; Ngadi, Asri; Ahmed, Mohammed Nazir; Ali Mohammed, Abdulalem

    2017-01-01

    Database Forensics (DBF) is a widespread area of knowledge. It has many complex features and is well known amongst database investigators and practitioners. Several models and frameworks have been created specifically to allow knowledge-sharing and effective DBF activities. However, these are often narrow in focus and address specified database incident types. We have analysed 60 such models in an attempt to uncover how numerous DBF activities are really public even when the actions vary. We then generate a unified abstract view of DBF in the form of a metamodel. We identified, extracted, and proposed a common concept and reconciled concept definitions to propose a metamodel. We have applied a metamodelling process to guarantee that this metamodel is comprehensive and consistent. PMID:28146585

  4. Mammalian Mitochondrial ncRNA Database.

    Science.gov (United States)

    Anandakumar, Shanmugam; Vijayakumar, Saravanan; Arumugam, Nagarajan; Gromiha, M Michael

    2015-01-01

    Mammalian Mitochondrial ncRNA is a web-based database, which provides specific information on non-coding RNA in mammals. This database includes easy searching, comparing with BLAST and retrieving information on predicted structure and its function about mammalian ncRNAs. The database is available for free at http://www.iitm.ac.in/bioinfo/mmndb/.

  5. Bisphosphonate adverse effects, lessons from large databases

    DEFF Research Database (Denmark)

    Abrahamsen, Bo

    2010-01-01

    PURPOSE OF REVIEW: To review the latest findings on bisphosphonate safety from health databases, in particular sources that can provide incidence rates for stress fractures, osteonecrosis of the jaw (ONJ), atrial fibrillation and gastrointestinal lesions including esophageal cancer. The main focus...... health databases. However, database studies have limited specificity and sensitivity for atypical fractures and ONJ. Clinical case control studies are recommended....

  6. Immune epitope database analysis resource

    DEFF Research Database (Denmark)

    Kim, Yohan; Ponomarenko, Julia; Zhu, Zhanyang

    2012-01-01

    The immune epitope database analysis resource (IEDB-AR: http://tools.iedb.org) is a collection of tools for prediction and analysis of molecular targets of T- and B-cell immune responses (i.e. epitopes). Since its last publication in the NAR webserver issue in 2008, a new generation of peptide:MH...

  7. The COMPADRE Plant Matrix Database

    DEFF Research Database (Denmark)

    2014-01-01

    COMPADRE contains demographic information on hundreds of plant species. The data in COMPADRE are in the form of matrix population models and our goal is to make these publicly available to facilitate their use for research and teaching purposes. COMPADRE is an open-access database. We only request...

  8. The COMPADRE Plant Matrix Database

    DEFF Research Database (Denmark)

    2014-01-01

    COMPADRE contains demographic information on hundreds of plant species. The data in COMPADRE are in the form of matrix population models and our goal is to make these publicly available to facilitate their use for research and teaching purposes. COMPADRE is an open-access database. We only request...

  9. The magnet components database system

    Energy Technology Data Exchange (ETDEWEB)

    Baggett, M.J. (Brookhaven National Lab., Upton, NY (USA)); Leedy, R.; Saltmarsh, C.; Tompkins, J.C. (Superconducting Supercollider Lab., Dallas, TX (USA))

    1990-01-01

    The philosophy, structure, and usage MagCom, the SSC magnet components database, are described. The database has been implemented in Sybase (a powerful relational database management system) on a UNIX-based workstation at the Superconducting Super Collider Laboratory (SSCL); magnet project collaborators can access the database via network connections. The database was designed to contain the specifications and measured values of important properties for major materials, plus configuration information (specifying which individual items were used in each cable, coil, and magnet) and the test results on completed magnets. These data will facilitate the tracking and control of the production process as well as the correlation of magnet performance with the properties of its constituents. 3 refs., 10 figs.

  10. Building Database-Powered Mobile Applications

    Directory of Open Access Journals (Sweden)

    Paul POCATILU

    2012-01-01

    Full Text Available Almost all mobile applications use persistency for their data. A common way for complex mobile applications is to store data in local relational databases. Almost all major mobile platforms include a relational database engine. These databases engines expose specific API (Application Programming Interface to be used by mobile applications developers for data definition and manipulation. This paper focus on database-based application models for several mobile platforms (Android, Symbian, Windows CE/Mobile and Windows Phone. For each selected platform the API and specific database operations are presented.

  11. Gender-gaps and glass ceilings: A survey of gender-specific publication trends in Psychiatry between 1994 and 2014.

    Science.gov (United States)

    Süßenbacher, S; Amering, M; Gmeiner, A; Schrank, B

    2017-07-01

    Within academic psychiatry, women are underrepresented in the higher academic ranks. However, basic determinants of women's lack of academic advancement such as publication activity are poorly understood. The present study examines women's publication activity in high-impact psychiatry journals over two decades and reports developments in the numbers of male and female authorship over time and across cultural areas. We conducted a retrospective bibliometric review of all articles published in 2004 and 2014 in three high-ranking general psychiatry journals. Statistical comparisons were made between the two years and with results from a baseline assessment in 1994. The overall percentage of female authors increased from 24.6% in 1994 to 33.2% in 2004 to 38.9% in 2014. Though increases in female authorship were statistically significant for both decades, there was less difference between 2004 and 2014, indicating a possible ceiling effect. Rates of female first authors increased between 1994 and 2014, though to a lesser degree between 2004 and 2014. Numbers of female corresponding authors plateaued between 2004 and 2014. Within Europe, Scandinavia displayed the most balanced gender-wise first author ratios. Western European and Central European countries increased their rates of female first authors substantially between 2004 and 2014. Despite gains in some areas, our study reveals considerable deficits in the diversity of the current academic psychiatric landscape. Ongoing efforts and interventions to enhance the participation of underrepresented groups on institutional, political and editorial levels are necessary to diversify psychiatric research. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  12. A New Database for Speaker Recognition

    DEFF Research Database (Denmark)

    Feng, Ling; Hansen, Lars Kai

    2005-01-01

    In this paper we discuss properties of speech databases used for speaker recognition research and evaluation, and we characterize some popular standard databases. The paper presents a new database called ELSDSR dedicated to speaker recognition applications. The main characteristics of this database...... are: English spoken by non-native speakers, a single session of sentence reading and relatively extensive speech samples suitable for learning person specific speech characteristics....

  13. Summary of comments received at workshop on use of a Site Specific Advisory Board (SSAB) to facilitate public participation in decommissioning cases

    Energy Technology Data Exchange (ETDEWEB)

    Caplin, J.; Padge, G.; Smith, D.; Wiblin, C. [Advanced Systems Technology, Inc., Rockville, MD (United States)

    1995-06-01

    The Nuclear Regulatory Commission (NRC) is conducting an enhanced participatory rulemaking to establish radiological criteria for the decommissioning of NRC-licensed facilities. As part of this rulemaking, On August 20, 1994 the NRC published a proposed rule for public comment. Paragraph 20.1406(b) of the proposed rule would require that the licensee convene a Site Specific Advisory Board (SSAB) if the licensee proposed release of the site for restricted use after decommissioning. To encourage comment the NRC held a workshop on the subject of $SABs on December 6, 7, and 8, 1994. This report summarizes the 567 comments categorized from the transcript of the workshop. The commenters at the workshop generally supported public participation in decommissioning cases. Many participants favored promulgating requirements in the NRC`s rules. Some industry participants favored relying on voluntary exchanges between the public and the licensees. Many participants indicated that a SSAB or something functionally equivalent is needed in controversial decommissioning cases, but that some lesser undertaking can achieve meaningful public participation in other cases. No analysis or response to the comments is included in this report.

  14. Quality Control of EUVE Databases

    Science.gov (United States)

    John, Linda M.

    1993-01-01

    The publicly accessible databases for the Extreme Ultraviolet Explorer (EUVE) include: the EUVE Archive Mailserver, the Center for EUV Astrophysics ftp site, the EUVE Guest Observer Mailserver, and the Astronomical Data System node. The EUVE Performance Assurance team is responsible for verifying that these public databases are working properly and that the public availability of EUVE data contained therein does not infringe any data rights which may have been assigned. In this paper, we describe the quality assurance (QA) procedures we have developed from approaching QA as a service organization; this approach reflects the overall EUVE philosophy of QA integrated into normal operating procedures, rather than imposed as an external, post-facto, control mechanism.

  15. Engaging general practitioners in public-private mix tuberculosis DOTS program in an urban area in Pakistan: need for context-specific approach.

    Science.gov (United States)

    Pethani, Amin; Zafar, Mubashir; Khan, Adeel Ahmed; Rabbani Sana, Unaib; Ahmed, Sana; Fatmi, Zafar

    2015-03-01

    A public-private mix tuberculosis (TB) DOTS project was implemented to enhance coverage and collaboration between the public and private sectors, with an objective to increase case detection and to improve TB case management in a large urban area. General practitioners (GPs) were trained to provide DOTS services. Patients were diagnosed and treated as per national guidelines and outcomes were reported to national TB control program. Treatment and sputum microscopy were provided free of cost. A total of 94 GPs were trained. In all, 57.4% of trained GPs remained actively involved in the project. Overall treatment success rate of the patients enrolled with the project was 86.3% with 8.7% default patients. Experience suggests that a more stringent selection criteria need to be followed for inclusion of GPs in the program to improve the success of the program. A multifaceted context specific approach is needed while working with private health care providers.

  16. PLANEX: the plant co-expression database

    OpenAIRE

    Yim, Won Cheol; Yu, YongBin; Song, Kitae; Jang, Cheol Seong; Lee, Byung-Moo

    2013-01-01

    Background The PLAnt co-EXpression database (PLANEX) is a new internet-based database for plant gene analysis. PLANEX (http://planex.plantbioinformatics.org) contains publicly available GeneChip data obtained from the Gene Expression Omnibus (GEO) of the National Center for Biotechnology Information (NCBI). PLANEX is a genome-wide co-expression database, which allows for the functional identification of genes from a wide variety of experimental designs. It can be used for the characterization...

  17. Ethical guideposts for allelic variation databases.

    Science.gov (United States)

    Knoppers, B M; Laberge, C M

    2000-01-01

    Basically, a mutation database (MDB) is a repository where allelic variations are described and assigned within a specific gene locus. The purposes of an MDB may vary greatly and have different content and structure. The curator of an electronic and computer-based MDB will provide expert feedback (clinical and research). This requires ethical guideposts. Going to direct on-line public access for the content of an MDB or to interactive communication also raises other considerations. Currently, HUGO's MDI (Mutation Database Initiative) is the only integrated effort supporting and guiding the coordinated deployment of MDBs devoted to genetic diversity. Thus, HUGO's ethical "Statements" are applicable. Among the ethical principles, the obligation of preserving the confidentiality of information transferred by a collaborator to the curator is particularly important. Thus, anonymization of such data prior to transmission is essential. The 1997 Universal Declaration on the Human Genome and Human Rights of UNESCO addresses the participation of vulnerable persons. Researchers in charge of MDBs should ensure that information received on the testing of children or incompetent adults is subject to ethical review and approval in the country of origin. Caution should be taken against the involuntary consequences of public disclosure of results without complete explanation. Clear and enforceable regulations must be developed to protect the public against misuse of genetic databanks. Interaction with a databank could be seen as creating a "virtual" physician-patient relationship. However, interactive public MDBs should not give medical advice. We have identified new social ethical principles to govern different levels of complexity of genetic information. They are: reciprocity, mutuality, solidarity, and universality. Finally, precaution and prudence at this early stage of the MDI may not only avoid ethically inextricable conundrums but also provide for the respect for the rights

  18. Databases of the marine metagenomics

    KAUST Repository

    Mineta, Katsuhiko

    2015-10-28

    The metagenomic data obtained from marine environments is significantly useful for understanding marine microbial communities. In comparison with the conventional amplicon-based approach of metagenomics, the recent shotgun sequencing-based approach has become a powerful tool that provides an efficient way of grasping a diversity of the entire microbial community at a sampling point in the sea. However, this approach accelerates accumulation of the metagenome data as well as increase of data complexity. Moreover, when metagenomic approach is used for monitoring a time change of marine environments at multiple locations of the seawater, accumulation of metagenomics data will become tremendous with an enormous speed. Because this kind of situation has started becoming of reality at many marine research institutions and stations all over the world, it looks obvious that the data management and analysis will be confronted by the so-called Big Data issues such as how the database can be constructed in an efficient way and how useful knowledge should be extracted from a vast amount of the data. In this review, we summarize the outline of all the major databases of marine metagenome that are currently publically available, noting that database exclusively on marine metagenome is none but the number of metagenome databases including marine metagenome data are six, unexpectedly still small. We also extend our explanation to the databases, as reference database we call, that will be useful for constructing a marine metagenome database as well as complementing important information with the database. Then, we would point out a number of challenges to be conquered in constructing the marine metagenome database.

  19. Databases of the marine metagenomics.

    Science.gov (United States)

    Mineta, Katsuhiko; Gojobori, Takashi

    2016-02-01

    The metagenomic data obtained from marine environments is significantly useful for understanding marine microbial communities. In comparison with the conventional amplicon-based approach of metagenomics, the recent shotgun sequencing-based approach has become a powerful tool that provides an efficient way of grasping a diversity of the entire microbial community at a sampling point in the sea. However, this approach accelerates accumulation of the metagenome data as well as increase of data complexity. Moreover, when metagenomic approach is used for monitoring a time change of marine environments at multiple locations of the seawater, accumulation of metagenomics data will become tremendous with an enormous speed. Because this kind of situation has started becoming of reality at many marine research institutions and stations all over the world, it looks obvious that the data management and analysis will be confronted by the so-called Big Data issues such as how the database can be constructed in an efficient way and how useful knowledge should be extracted from a vast amount of the data. In this review, we summarize the outline of all the major databases of marine metagenome that are currently publically available, noting that database exclusively on marine metagenome is none but the number of metagenome databases including marine metagenome data are six, unexpectedly still small. We also extend our explanation to the databases, as reference database we call, that will be useful for constructing a marine metagenome database as well as complementing important information with the database. Then, we would point out a number of challenges to be conquered in constructing the marine metagenome database.

  20. Public Budget Database - Governmental receipts 1962-Current

    Data.gov (United States)

    Executive Office of the President — This file contains governmental receipts for 1962 through the current budget year, as well as four years of projections. It can be used to reproduce many of the...

  1. Maize microarray annotation database

    Directory of Open Access Journals (Sweden)

    Berger Dave K

    2011-10-01

    Full Text Available Abstract Background Microarray technology has matured over the past fifteen years into a cost-effective solution with established data analysis protocols for global gene expression profiling. The Agilent-016047 maize 44 K microarray was custom-designed from EST sequences, but only reporter sequences with EST accession numbers are publicly available. The following information is lacking: (a reporter - gene model match, (b number of reporters per gene model, (c potential for cross hybridization, (d sense/antisense orientation of reporters, (e position of reporter on B73 genome sequence (for eQTL studies, and (f functional annotations of genes represented by reporters. To address this, we developed a strategy to annotate the Agilent-016047 maize microarray, and built a publicly accessible annotation database. Description Genomic annotation of the 42,034 reporters on the Agilent-016047 maize microarray was based on BLASTN results of the 60-mer reporter sequences and their corresponding ESTs against the maize B73 RefGen v2 "Working Gene Set" (WGS predicted transcripts and the genome sequence. The agreement between the EST, WGS transcript and gDNA BLASTN results were used to assign the reporters into six genomic annotation groups. These annotation groups were: (i "annotation by sense gene model" (23,668 reporters, (ii "annotation by antisense gene model" (4,330; (iii "annotation by gDNA" without a WGS transcript hit (1,549; (iv "annotation by EST", in which case the EST from which the reporter was designed, but not the reporter itself, has a WGS transcript hit (3,390; (v "ambiguous annotation" (2,608; and (vi "inconclusive annotation" (6,489. Functional annotations of reporters were obtained by BLASTX and Blast2GO analysis of corresponding WGS transcripts against GenBank. The annotations are available in the Maize Microarray Annotation Database http://MaizeArrayAnnot.bi.up.ac.za/, as well as through a GBrowse annotation file that can be uploaded to

  2. Large-scale Health Information Database and Privacy Protection*1

    Science.gov (United States)

    YAMAMOTO, Ryuichi

    2016-01-01

    Japan was once progressive in the digitalization of healthcare fields but unfortunately has fallen behind in terms of the secondary use of data for public interest. There has recently been a trend to establish large-scale health databases in the nation, and a conflict between data use for public interest and privacy protection has surfaced as this trend has progressed. Databases for health insurance claims or for specific health checkups and guidance services were created according to the law that aims to ensure healthcare for the elderly; however, there is no mention in the act about using these databases for public interest in general. Thus, an initiative for such use must proceed carefully and attentively. The PMDA*2 projects that collect a large amount of medical record information from large hospitals and the health database development project that the Ministry of Health, Labour and Welfare (MHLW) is working on will soon begin to operate according to a general consensus; however, the validity of this consensus can be questioned if issues of anonymity arise. The likelihood that researchers conducting a study for public interest would intentionally invade the privacy of their subjects is slim. However, patients could develop a sense of distrust about their data being used since legal requirements are ambiguous. Nevertheless, without using patients’ medical records for public interest, progress in medicine will grind to a halt. Proper legislation that is clear for both researchers and patients will therefore be highly desirable. A revision of the Act on the Protection of Personal Information is currently in progress. In reality, however, privacy is not something that laws alone can protect; it will also require guidelines and self-discipline. We now live in an information capitalization age. I will introduce the trends in legal reform regarding healthcare information and discuss some basics to help people properly face the issue of health big data and privacy

  3. Large-scale Health Information Database and Privacy Protection.

    Science.gov (United States)

    Yamamoto, Ryuichi

    2016-09-01

    Japan was once progressive in the digitalization of healthcare fields but unfortunately has fallen behind in terms of the secondary use of data for public interest. There has recently been a trend to establish large-scale health databases in the nation, and a conflict between data use for public interest and privacy protection has surfaced as this trend has progressed. Databases for health insurance claims or for specific health checkups and guidance services were created according to the law that aims to ensure healthcare for the elderly; however, there is no mention in the act about using these databases for public interest in general. Thus, an initiative for such use must proceed carefully and attentively. The PMDA projects that collect a large amount of medical record information from large hospitals and the health database development project that the Ministry of Health, Labour and Welfare (MHLW) is working on will soon begin to operate according to a general consensus; however, the validity of this consensus can be questioned if issues of anonymity arise. The likelihood that researchers conducting a study for public interest would intentionally invade the privacy of their subjects is slim. However, patients could develop a sense of distrust about their data being used since legal requirements are ambiguous. Nevertheless, without using patients' medical records for public interest, progress in medicine will grind to a halt. Proper legislation that is clear for both researchers and patients will therefore be highly desirable. A revision of the Act on the Protection of Personal Information is currently in progress. In reality, however, privacy is not something that laws alone can protect; it will also require guidelines and self-discipline. We now live in an information capitalization age. I will introduce the trends in legal reform regarding healthcare information and discuss some basics to help people properly face the issue of health big data and privacy

  4. World Ocean Database 2013 (NCEI Accession 0117075)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The World Ocean Database (WOD) is the World’s largest publicly available uniform format quality controlled ocean profile dataset. Ocean profile data are sets of...

  5. Protected Areas Database for New Mexico

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — The Protected Areas Database of the United States (PAD-US) is a geodatabase, managed by USGS GAP, that illustrates and describes public land ownership, management...

  6. Pacific Northwest Salmon Habitat Project Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — In the Pacific Northwest Salmon Habitat Project Database Across the Pacific Northwest, both public and private agents are working to improve riverine habitat for a...

  7. A Novel Approach: Chemical Relational Databases, and the Role of the ISSCAN Database on Assessing Chemical Carcinogenity

    Science.gov (United States)

    Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as "look-up-tables" of existing data, and most often did no...

  8. Breast Cancer: subgroups specific blood-biomarkers for early / predictive diagnosis and personalized treatment — EDRN Public Portal

    Science.gov (United States)

    Breast-conserving lumpectomy followed by radiation therapy has been shown to be an alternative strategy, competitive to mastectomy, in preventing mortality caused by breast cancer. However, besides negative short-term effects (blood flow disturbances, painful erythema, etc.) breast irradiation causes severe long-term side-effects (leucopenia, anemia, breast edema, fibrosis, increase of angiosarcoma, leukemia, myelodysplastic syndromes). Therefore, the identification of individual susceptibility to radiation and improved patient-specific radiotherapy planning are highly desirable for personalised treatment in breast cancer. Why early and predictive diagnosis is crucial for long-term outcomes of breast cancer? Breast cancer is the most common cause of cancer death among women with an average incidence rate of 10-12 per 100 women. In 2005, breast cancer led to 502,000 deaths worldwide. Advanced stages of breast cancer lead to the development of metastasis predominantly in the lymph nodes, bone, lung, skin, brain, and liver. Although breast-MRI is currently the most sensitive diagnostic tool for breast imaging, its specificity is limited resulting in a negative impact for surgical management in approximately 9 % of cases. Early diagnosis has been demonstrated to be highly beneficial, enabling significantly enhanced therapy efficiency and possibly full recovery.

  9. Library Instruction and Online Database Searching.

    Science.gov (United States)

    Mercado, Heidi

    1999-01-01

    Reviews changes in online database searching in academic libraries. Topics include librarians conducting all searches; the advent of end-user searching and the need for user instruction; compact disk technology; online public catalogs; the Internet; full text databases; electronic information literacy; user education and the remote library user;…

  10. Correlates of Access to Business Research Databases

    Science.gov (United States)

    Gottfried, John C.

    2010-01-01

    This study examines potential correlates of business research database access through academic libraries serving top business programs in the United States. Results indicate that greater access to research databases is related to enrollment in graduate business programs, but not to overall enrollment or status as a public or private institution.…

  11. Managing Multiuser Database Buffers Using Data Mining Techniques

    NARCIS (Netherlands)

    Feng, L.; Lu, H.J.

    2004-01-01

    In this paper, we propose a data-mining-based approach to public buffer management for a multiuser database system, where database buffers are organized into two areas – public and private. While the private buffer areas contain pages to be updated by particular users, the public buffe

  12. Advancements in web-database applications for rabies surveillance

    Directory of Open Access Journals (Sweden)

    Bélanger Denise

    2011-08-01

    Full Text Available Abstract Background Protection of public health from rabies is informed by the analysis of surveillance data from human and animal populations. In Canada, public health, agricultural and wildlife agencies at the provincial and federal level are responsible for rabies disease control, and this has led to multiple agency-specific data repositories. Aggregation of agency-specific data into one database application would enable more comprehensive data analyses and effective communication among participating agencies. In Québec, RageDB was developed to house surveillance data for the raccoon rabies variant, representing the next generation in web-based database applications that provide a key resource for the protection of public health. Results RageDB incorporates data from, and grants access to, all agencies responsible for the surveillance of raccoon rabies in Québec. Technological advancements of RageDB to rabies surveillance databases include 1 automatic integration of multi-agency data and diagnostic results on a daily basis; 2 a web-based data editing interface that enables authorized users to add, edit and extract data; and 3 an interactive dashboard to help visualize data simply and efficiently, in table, chart, and cartographic formats. Furthermore, RageDB stores data from citizens who voluntarily report sightings of rabies suspect animals. We also discuss how sightings data can indicate public perception to the risk of racoon rabies and thus aid in directing the allocation of disease control resources for protecting public health. Conclusions RageDB provides an example in the evolution of spatio-temporal database applications for the storage, analysis and communication of disease surveillance data. The database was fast and inexpensive to develop by using open-source technologies, simple and efficient design strategies, and shared web hosting. The database increases communication among agencies collaborating to protect human health from

  13. Dietary Supplement Ingredient Database

    Science.gov (United States)

    ... and US Department of Agriculture Dietary Supplement Ingredient Database Toggle navigation Menu Home About DSID Mission Current ... values can be saved to build a small database or add to an existing database for national, ...

  14. Obesity and oncological outcome after radical prostatectomy: impact of prostate-specific antigen-based prostate cancer screening: results from the Shared Equal Access Regional Cancer Hospital and Duke Prostate Center databases.

    Science.gov (United States)

    Freedland, Stephen J; Sun, Leon; Kane, Christopher J; Presti, Joseph C; Terris, Martha K; Amling, Christopher L; Moul, Judd W; Aronson, William J

    2008-09-01

    To indirectly test the hypothesis that prostate-specific antigen (PSA)-based screening is biased against obese men due to haemodilution of PSA, and thus results in delayed diagnosis and poorer outcome beyond the biological link between obesity and aggressive prostate cancer. We sought to examine the association between body mass index (BMI) and the outcome of radical prostatectomy (RP) separately for men with PSA-detected cancers (cT1c) or with abnormal digital rectal examination (DRE) findings (cT2/T3), and stratified by year of treatment, using two large databases. We conducted a retrospective cohort study of 1375 and 2014 men treated by RP between 1988 and 2007 using the Shared Equal Access Regional Cancer Hospital (SEARCH) and Duke Prostate Center (DPC) databases. We evaluated the association between BMI and adverse pathological features and biochemical progression, using logistic regression and Cox proportional hazards models, adjusting for several clinical characteristics, respectively. Data were examined as a whole and as stratified by clinical stage (cT1c vs cT2/T3) and year of surgery (>or=2000 vs obesity was significantly related to progression in both cohorts among men with T1c cancers (P cancers (P > 0.3). Among men with T1c disease, the association between BMI and biochemical progression was limited to men treated in 2000 or later (P 0.4). Obese men with PSA-detected cancers and treated with RP since 2000 were at significantly greater risk of biochemical progression, while obese men treated before 2000 or diagnosed with an abnormal DRE were not at significantly greater risk of progression. These findings support the hypothesis that current PSA-based screening is less effective at finding cancers in obese men, leading to more aggressive tumours at diagnosis. Lowering the PSA threshold for biopsy among obese men might help to improve outcomes among this high-risk group.

  15. Legume and Lotus japonicus Databases

    DEFF Research Database (Denmark)

    Hirakawa, Hideki; Mun, Terry; Sato, Shusei

    2014-01-01

    Since the genome sequence of Lotus japonicus, a model plant of family Fabaceae, was determined in 2008 (Sato et al. 2008), the genomes of other members of the Fabaceae family, soybean (Glycine max) (Schmutz et al. 2010) and Medicago truncatula (Young et al. 2011), have been sequenced. In this sec....... In this section, we introduce representative, publicly accessible online resources related to plant materials, integrated databases containing legume genome information, and databases for genome sequence and derived marker information of legume species including L. japonicus...

  16. The Danish Inguinal Hernia Database

    Directory of Open Access Journals (Sweden)

    Friis-Andersen H

    2016-10-01

    Full Text Available Hans Friis-Andersen1,2, Thue Bisgaard2,3 1Surgical Department, Horsens Regional Hospital, Horsens, Denmark; 2Steering Committee, Danish Hernia Database, 3Surgical Gastroenterological Department 235, Copenhagen University Hospital, Hvidovre, Denmark Aim of database: To monitor and improve nation-wide surgical outcome after groin hernia repair based on scientific evidence-based surgical strategies for the national and international surgical community. Study population: Patients ≥18 years operated for groin hernia. Main variables: Type and size of hernia, primary or recurrent, type of surgical repair procedure, mesh and mesh fixation methods. Descriptive data: According to the Danish National Health Act, surgeons are obliged to register all hernia repairs immediately after surgery (3 minute registration time. All institutions have continuous access to their own data stratified on individual surgeons. Registrations are based on a closed, protected Internet system requiring personal codes also identifying the operating institution. A national steering committee consisting of 13 voluntary and dedicated surgeons, 11 of whom are unpaid, handles the medical management of the database. Results: The Danish Inguinal Hernia Database comprises intraoperative data from >130,000 repairs (May 2015. A total of 49 peer-reviewed national and international publications have been published from the database (June 2015. Conclusion: The Danish Inguinal Hernia Database is fully active monitoring surgical quality and contributes to the national and international surgical society to improve outcome after groin hernia repair. Keywords: nation-wide, recurrence, chronic pain, femoral hernia, surgery, quality improvement

  17. NoSQL Databases

    OpenAIRE

    2013-01-01

    This thesis deals with database systems referred to as NoSQL databases. In the second chapter, I explain basic terms and the theory of database systems. A short explanation is dedicated to database systems based on the relational data model and the SQL standardized query language. Chapter Three explains the concept and history of the NoSQL databases, and also presents database models, major features and the use of NoSQL databases in comparison with traditional database systems. In the fourth ...

  18. USAID Anticorruption Projects Database

    Data.gov (United States)

    US Agency for International Development — The Anticorruption Projects Database (Database) includes information about USAID projects with anticorruption interventions implemented worldwide between 2007 and...

  19. Collecting Taxes Database

    Data.gov (United States)

    US Agency for International Development — The Collecting Taxes Database contains performance and structural indicators about national tax systems. The database contains quantitative revenue performance...

  20. Too much data, but little inter-changeability: a lesson learned from mining public data on tissue specificity of gene expression

    Directory of Open Access Journals (Sweden)

    Duffin Kevin

    2006-10-01

    Full Text Available Abstract Background The tissue expression pattern of a gene often provides an important clue to its potential role in a biological process. A vast amount of gene expression data have been and are being accumulated in public repository through different technology platforms. However, exploitations of these rich data sources remain limited in part due to issues of technology standardization. Our objective is to test the data comparability between SAGE and microarray technologies, through examining the expression pattern of genes under normal physiological states across variety of tissues. Results There are 42–54% of genes showing significant correlations in tissue expression patterns between SAGE and GeneChip, with 30–40% of genes whose expression patterns are positively correlated and 10–15% of genes whose expression patterns are negatively correlated at a statistically significant level (p = 0.05. Our analysis suggests that the discrepancy on the expression patterns derived from technology platforms is not likely from the heterogeneity of tissues used in these technologies, or other spurious correlations resulting from microarray probe design, abundance of genes, or gene function. The discrepancy can be partially explained by errors in the original assignment of SAGE tags to genes due to the evolution of sequence databases. In addition, sequence analysis has indicated that many SAGE tags and Affymetrix array probe sets are mapped to different splice variants or different sequence regions although they represent the same gene, which also contributes to the observed discrepancies between SAGE and array expression data. Conclusion To our knowledge, this is the first report attempting to mine gene expression patterns across tissues using public data from different technology platforms. Unlike previous similar studies that only demonstrated the discrepancies between the two gene expression platforms, we carried out in-depth analysis to further

  1. Genomic Database Searching.

    Science.gov (United States)

    Hutchins, James R A

    2017-01-01

    The availability of reference genome sequences for virtually all species under active research has revolutionized biology. Analyses of genomic variations in many organisms have provided insights into phenotypic traits, evolution and disease, and are transforming medicine. All genomic data from publicly funded projects are freely available in Internet-based databases, for download or searching via genome browsers such as Ensembl, Vega, NCBI's Map Viewer, and the UCSC Genome Browser. These online tools generate interactive graphical outputs of relevant chromosomal regions, showing genes, transcripts, and other genomic landmarks, and epigenetic features mapped by projects such as ENCODE.This chapter provides a broad overview of the major genomic databases and browsers, and describes various approaches and the latest resources for searching them. Methods are provided for identifying genomic locus and sequence information using gene names or codes, identifiers for DNA and RNA molecules and proteins; also from karyotype bands, chromosomal coordinates, sequences, motifs, and matrix-based patterns. Approaches are also described for batch retrieval of genomic information, performing more complex queries, and analyzing larger sets of experimental data, for example from next-generation sequencing projects.

  2. SoyFN: a knowledge database of soybean functional networks.

    Science.gov (United States)

    Xu, Yungang; Guo, Maozu; Liu, Xiaoyan; Wang, Chunyu; Liu, Yang

    2014-01-01

    Many databases for soybean genomic analysis have been built and made publicly available, but few of them contain knowledge specifically targeting the omics-level gene-gene, gene-microRNA (miRNA) and miRNA-miRNA interactions. Here, we present SoyFN, a knowledge database of soybean functional gene networks and miRNA functional networks. SoyFN provides user-friendly interfaces to retrieve, visualize, analyze and download the functional networks of soybean genes and miRNAs. In addition, it incorporates much information about KEGG pathways, gene ontology annotations and 3'-UTR sequences as well as many useful tools including SoySearch, ID mapping, Genome Browser, eFP Browser and promoter motif scan. SoyFN is a schema-free database that can be accessed as a Web service from any modern programming language using a simple Hypertext Transfer Protocol call. The Web site is implemented in Java, JavaScript, PHP, HTML and Apache, with all major browsers supported. We anticipate that this database will be useful for members of research communities both in soybean experimental science and bioinformatics. Database URL: http://nclab.hit.edu.cn/SoyFN.

  3. Asbestos Exposure Assessment Database

    Science.gov (United States)

    Arcot, Divya K.

    2010-01-01

    Exposure to particular hazardous materials in a work environment is dangerous to the employees who work directly with or around the materials as well as those who come in contact with them indirectly. In order to maintain a national standard for safe working environments and protect worker health, the Occupational Safety and Health Administration (OSHA) has set forth numerous precautionary regulations. NASA has been proactive in adhering to these regulations by implementing standards which are often stricter than regulation limits and administering frequent health risk assessments. The primary objective of this project is to create the infrastructure for an Asbestos Exposure Assessment Database specific to NASA Johnson Space Center (JSC) which will compile all of the exposure assessment data into a well-organized, navigable format. The data includes Sample Types, Samples Durations, Crafts of those from whom samples were collected, Job Performance Requirements (JPR) numbers, Phased Contrast Microscopy (PCM) and Transmission Electron Microscopy (TEM) results and qualifiers, Personal Protective Equipment (PPE), and names of industrial hygienists who performed the monitoring. This database will allow NASA to provide OSHA with specific information demonstrating that JSC s work procedures are protective enough to minimize the risk of future disease from the exposures. The data has been collected by the NASA contractors Computer Sciences Corporation (CSC) and Wyle Laboratories. The personal exposure samples were collected from devices worn by laborers working at JSC and by building occupants located in asbestos-containing buildings.

  4. Large Catalogue Query Performance in Relational Databases

    Science.gov (United States)

    Power, Robert A.

    2007-05-01

    The performance of the mysql and oracle database systems have been compared for a selection of astronomy queries using large catalogues of up to a billion objects. The queries tested are those expected from the astronomy community: general database queries, cone searches, neighbour finding and cross matching. The catalogue preparation, sql query formulation and database performance is presented. Most of the general queries perform adequately when appropriate indexes are present in the database. Each system performs well for cone search queries when the Hierarchical Triangular Mesh spatial index is used. Neighbour finding and cross matching are not well supported in a database environment when compared to software specifically developed to solve these problems.

  5. Accessing and using chemical property databases.

    Science.gov (United States)

    Hastings, Janna; Josephs, Zara; Steinbeck, Christoph

    2012-01-01

    Chemical compounds participate in all the processes of life. Understanding the complex interactions of small molecules such as metabolites and drugs and the biological macromolecules that consume and produce them is key to gaining a wider understanding in a systemic context. Chemical property databases collect information on the biological effects and physicochemical properties of chemical entities. Accessing and using such databases is key to understanding the chemistry of toxic molecules. In this chapter, we present methods to search, understand, download, and manipulate the wealth of information available in public chemical property databases, with particular focus on the database of Chemical Entities of Biological Interest (ChEBI).

  6. The Danish Inguinal Hernia database

    DEFF Research Database (Denmark)

    Friis-Andersen, Hans; Bisgaard, Thue

    2016-01-01

    of hernia, primary or recurrent, type of surgical repair procedure, mesh and mesh fixation methods. DESCRIPTIVE DATA: According to the Danish National Health Act, surgeons are obliged to register all hernia repairs immediately after surgery (3 minute registration time). All institutions have continuous...... access to their own data stratified on individual surgeons. Registrations are based on a closed, protected Internet system requiring personal codes also identifying the operating institution. A national steering committee consisting of 13 voluntary and dedicated surgeons, 11 of whom are unpaid, handles...... the medical management of the database. RESULTS: The Danish Inguinal Hernia Database comprises intraoperative data from >130,000 repairs (May 2015). A total of 49 peer-reviewed national and international publications have been published from the database (June 2015). CONCLUSION: The Danish Inguinal Hernia...

  7. Searching NCBI Databases Using Entrez.

    Science.gov (United States)

    Gibney, Gretchen; Baxevanis, Andreas D

    2011-10-01

    One of the most widely used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre-existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two basic protocols describe simple, text-based searches, illustrating the types of information that can be retrieved through the Entrez system. An alternate protocol builds upon the first basic protocol, using additional, built-in features of the Entrez system, and providing alternative ways to issue the initial query. The support protocol reviews how to save frequently issued queries. Finally, Cn3D, a structure visualization tool, is also discussed.

  8. Quantifying the consistency of scientific databases

    CERN Document Server

    Šubelj, Lovro; Boshkoska, Biljana Mileva; Kastrin, Andrej; Levnajić, Zoran

    2015-01-01

    Science is a social process with far-reaching impact on our modern society. In the recent years, for the first time we are able to scientifically study the science itself. This is enabled by massive amounts of data on scientific publications that is increasingly becoming available. The data is contained in several databases such as Web of Science or PubMed, maintained by various public and private entities. Unfortunately, these databases are not always consistent, which considerably hinders this study. Relying on the powerful framework of complex networks, we conduct a systematic analysis of the consistency among six major scientific databases. We found that identifying a single "best" database is far from easy. Nevertheless, our results indicate appreciable differences in mutual consistency of different databases, which we interpret as recipes for future bibliometric studies.

  9. Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

    Energy Technology Data Exchange (ETDEWEB)

    Omenn, Gilbert; States, David J.; Adamski, Marcin; Blackwell, Thomas W.; Menon, Rajasree; Hermjakob, Henning; Apweiler, Rolf; Haab, Brian B.; Simpson, Richard; Eddes, James; Kapp, Eugene; Moritz, Rod; Chan, Daniel W.; Rai, Alex J.; Admon, Arie; Aebersold, Ruedi; Eng, Jimmy K.; Hancock, William S.; Hefta, Stanley A.; Meyer, Helmut; Paik, Young-Ki; Yoo, Jong-Shin; Ping, Peipei; Pounds, Joel G.; Adkins, Joshua N.; Qian, Xiaohong; Wang, Rong; Wasinger, Valerie; Wu, Chi Yue; Zhao, Xiaohang; Zeng, Rong; Archakov, Alexander; Tsugita, Akira; Beer, Ilan; Pandey, Akhilesh; Pisano, Michael; Andrews, Philip; Tammen, Harald; Speicher, David W.; Hanash, Samir M.

    2005-08-13

    HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anticoagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics. med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan

  10. The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection.

    Science.gov (United States)

    Fernández-Suárez, Xosé M; Galperin, Michael Y

    2013-01-01

    The 20th annual Database Issue of Nucleic Acids Research includes 176 articles, half of which describe new online molecular biology databases and the other half provide updates on the databases previously featured in NAR and other journals. This year's highlights include two databases of DNA repeat elements; several databases of transcriptional factors and transcriptional factor-binding sites; databases on various aspects of protein structure and protein-protein interactions; databases for metagenomic and rRNA sequence analysis; and four databases specifically dedicated to Escherichia coli. The increased emphasis on using the genome data to improve human health is reflected in the development of the databases of genomic structural variation (NCBI's dbVar and EBI's DGVa), the NIH Genetic Testing Registry and several other databases centered on the genetic basis of human disease, potential drugs, their targets and the mechanisms of protein-ligand binding. Two new databases present genomic and RNAseq data for monkeys, providing wealth of data on our closest relatives for comparative genomics purposes. The NAR online Molecular Biology Database Collection, available at http://www.oxfordjournals.org/nar/database/a/, has been updated and currently lists 1512 online databases. The full content of the Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/).

  11. Multi databases in Health Care Networks

    CERN Document Server

    Salih, Nadir K; Sun, Mingrui

    2011-01-01

    E-Health is a relatively recent term for healthcare practice supported by electronic processes and communication, dating back to at least 1999. E-Health is greatly impacting on information distribution and availability within the health services, hospitals and to the public. E-health was introduced as the death of telemedicine, because - in the context of a broad availability of medical information systems that can interconnect and communicate - telemedicine will no longer exist as a specific field. The same could also be said for any other traditional field in medical informatics, including information systems and electronic patient records. E-health presents itself as a common name for all such technological fields. In this paper we focuses in multi database by determined some sites and distributed it in Homogenous way. This will be followed by an illustrative example as related works. Finally, the paper concludes with general remarks and a statement of further work.

  12. Cloud Databases: A Paradigm Shift in Databases

    Directory of Open Access Journals (Sweden)

    Indu Arora

    2012-07-01

    Full Text Available Relational databases ruled the Information Technology (IT industry for almost 40 years. But last few years have seen sea changes in the way IT is being used and viewed. Stand alone applications have been replaced with web-based applications, dedicated servers with multiple distributed servers and dedicated storage with network storage. Cloud computing has become a reality due to its lesser cost, scalability and pay-as-you-go model. It is one of the biggest changes in IT after the rise of World Wide Web. Cloud databases such as Big Table, Sherpa and SimpleDB are becoming popular. They address the limitations of existing relational databases related to scalability, ease of use and dynamic provisioning. Cloud databases are mainly used for data-intensive applications such as data warehousing, data mining and business intelligence. These applications are read-intensive, scalable and elastic in nature. Transactional data management applications such as banking, airline reservation, online e-commerce and supply chain management applications are write-intensive. Databases supporting such applications require ACID (Atomicity, Consistency, Isolation and Durability properties, but these databases are difficult to deploy in the cloud. The goal of this paper is to review the state of the art in the cloud databases and various architectures. It further assesses the challenges to develop cloud databases that meet the user requirements and discusses popularly used Cloud databases.

  13. Human genetic variation database, a reference database of genetic variations in the Japanese population

    Science.gov (United States)

    Higasa, Koichiro; Miyake, Noriko; Yoshimura, Jun; Okamura, Kohji; Niihori, Tetsuya; Saitsu, Hirotomo; Doi, Koichiro; Shimizu, Masakazu; Nakabayashi, Kazuhiko; Aoki, Yoko; Tsurusaki, Yoshinori; Morishita, Shinichi; Kawaguchi, Takahisa; Migita, Osuke; Nakayama, Keiko; Nakashima, Mitsuko; Mitsui, Jun; Narahara, Maiko; Hayashi, Keiko; Funayama, Ryo; Yamaguchi, Daisuke; Ishiura, Hiroyuki; Ko, Wen-Ya; Hata, Kenichiro; Nagashima, Takeshi; Yamada, Ryo; Matsubara, Yoichi; Umezawa, Akihiro; Tsuji, Shoji; Matsumoto, Naomichi; Matsuda, Fumihiko

    2016-01-01

    Whole-genome and -exome resequencing using next-generation sequencers is a powerful approach for identifying genomic variations that are associated with diseases. However, systematic strategies for prioritizing causative variants from many candidates to explain the disease phenotype are still far from being established, because the population-specific frequency spectrum of genetic variation has not been characterized. Here, we have collected exomic genetic variation from 1208 Japanese individuals through a collaborative effort, and aggregated the data into a prevailing catalog. In total, we identified 156 622 previously unreported variants. The allele frequencies for the majority (88.8%) were lower than 0.5% in allele frequency and predicted to be functionally deleterious. In addition, we have constructed a Japanese-specific major allele reference genome by which the number of unique mapping of the short reads in our data has increased 0.045% on average. Our results illustrate the importance of constructing an ethnicity-specific reference genome for identifying rare variants. All the collected data were centralized to a newly developed database to serve as useful resources for exploring pathogenic variations. Public access to the database is available at http://www.genome.med.kyoto-u.ac.jp/SnpDB/. PMID:26911352

  14. Interactive bibliographical database on color

    Science.gov (United States)

    Caivano, Jose L.

    2002-06-01

    The paper describes the methodology and results of a project under development, aimed at the elaboration of an interactive bibliographical database on color in all fields of application: philosophy, psychology, semiotics, education, anthropology, physical and natural sciences, biology, medicine, technology, industry, architecture and design, arts, linguistics, geography, history. The project is initially based upon an already developed bibliography, published in different journals, updated in various opportunities, and now available at the Internet, with more than 2,000 entries. The interactive database will amplify that bibliography, incorporating hyperlinks and contents (indexes, abstracts, keywords, introductions, or eventually the complete document), and devising mechanisms for information retrieval. The sources to be included are: books, doctoral dissertations, multimedia publications, reference works. The main arrangement will be chronological, but the design of the database will allow rearrangements or selections by different fields: subject, Decimal Classification System, author, language, country, publisher, etc. A further project is to develop another database, including color-specialized journals or newsletters, and articles on color published in international journals, arranged in this case by journal name and date of publication, but allowing also rearrangements or selections by author, subject and keywords.

  15. Logical database design principles

    CERN Document Server

    Garmany, John; Clark, Terry

    2005-01-01

    INTRODUCTION TO LOGICAL DATABASE DESIGNUnderstanding a Database Database Architectures Relational Databases Creating the Database System Development Life Cycle (SDLC)Systems Planning: Assessment and Feasibility System Analysis: RequirementsSystem Analysis: Requirements Checklist Models Tracking and Schedules Design Modeling Functional Decomposition DiagramData Flow Diagrams Data Dictionary Logical Structures and Decision Trees System Design: LogicalSYSTEM DESIGN AND IMPLEMENTATION The ER ApproachEntities and Entity Types Attribute Domains AttributesSet-Valued AttributesWeak Entities Constraint

  16. An Interoperable Cartographic Database

    OpenAIRE

    Slobodanka Ključanin; Zdravko Galić

    2007-01-01

    The concept of producing a prototype of interoperable cartographic database is explored in this paper, including the possibilities of integration of different geospatial data into the database management system and their visualization on the Internet. The implementation includes vectorization of the concept of a single map page, creation of the cartographic database in an object-relation database, spatial analysis, definition and visualization of the database content in the form of a map on t...

  17. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata

    Energy Technology Data Exchange (ETDEWEB)

    Fenner, Marsha W; Liolios, Konstantinos; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Kyrpides, Nikos C.

    2007-12-31

    The Genomes On Line Database (GOLD) is a comprehensive resource of information for genome and metagenome projects world-wide. GOLD provides access to complete and ongoing projects and their associated metadata through pre-computed lists and a search page. The database currently incorporates information for more than 2900 sequencing projects, of which 639 have been completed and the data deposited in the public databases. GOLD is constantly expanding to provide metadata information related to the project and the organism and is compliant with the Minimum Information about a Genome Sequence (MIGS) specifications.

  18. Evolution of Relational Database to Object-Relational Database in Abstract Level

    OpenAIRE

    Yugopuspito, Pujianto; Araki, Keijiro

    1999-01-01

    Relational Database is a mature database with a rigorous specification and is broadly applicable. The deficient in data representation has been known since the software application changed to object oriented. An effort should be taken to encounter the connection between existing Relational Database with a new software application that is object oriented. In a case where a complete migration is not the choice of solution since the existing Relational Database should be preserved, then an Objec...

  19. On-Line Databases in Mexico.

    Science.gov (United States)

    Molina, Enzo

    1986-01-01

    Use of online bibliographic databases in Mexico is provided through Servicio de Consulta a Bancos de Informacion, a public service that provides information retrieval, document delivery, translation, technical support, and training services. Technical infrastructure is based on a public packet-switching network and institutional users may receive…

  20. Village Green Project: Web-accessible Database

    Science.gov (United States)

    The purpose of this web-accessible database is for the public to be able to view instantaneous readings from a solar-powered air monitoring station located in a public location (prototype pilot test is outside of a library in Durham County, NC). The data are wirelessly transmitte...

  1. Depression and Psychological Trauma: An Overview Integrating Current Research and Specific Evidence of Studies in the Treatment of Depression in Public Mental Health Services in Chile

    Directory of Open Access Journals (Sweden)

    Verónica Vitriol

    2014-01-01

    Full Text Available In the last two decades, different research has demonstrated the high prevalence of childhood trauma, including sexual abuse, among depressive women. These findings are associated with a complex, severe, and chronic psychopathology. This can be explained considering the neurobiological changes secondary to early trauma that can provoke a neuroendocrine failure to compensate in response to challenge. It suggests the existence of a distinguishable clinical-neurobiological subtype of depression as a function of childhood trauma that requires specific treatments. Among women with depression and early trauma receiving treatment in a public mental health service in Chile, it was demonstrated that a brief outpatient intervention (that screened for and focused on childhood trauma and helped patients to understand current psychosocial difficulties as a repetition of past trauma was effective in reducing psychiatric symptoms and improving interpersonal relationships. However, in this population, this intervention did not prevent posttraumatic stress disorder secondary to the extreme earthquake that occurred in February 2010. Therefore in adults with depression and early trauma, it is necessary to evaluate prolonged multimodal treatments that integrate pharmacotherapy, social support, and interpersonal psychotherapies with trauma focused interventions (specific interventions for specific traumas.

  2. The Danish Inguinal Hernia database

    Science.gov (United States)

    Friis-Andersen, Hans; Bisgaard, Thue

    2016-01-01

    Aim of database To monitor and improve nation-wide surgical outcome after groin hernia repair based on scientific evidence-based surgical strategies for the national and international surgical community. Study population Patients ≥18 years operated for groin hernia. Main variables Type and size of hernia, primary or recurrent, type of surgical repair procedure, mesh and mesh fixation methods. Descriptive data According to the Danish National Health Act, surgeons are obliged to register all hernia repairs immediately after surgery (3 minute registration time). All institutions have continuous access to their own data stratified on individual surgeons. Registrations are based on a closed, protected Internet system requiring personal codes also identifying the operating institution. A national steering committee consisting of 13 voluntary and dedicated surgeons, 11 of whom are unpaid, handles the medical management of the database. Results The Danish Inguinal Hernia Database comprises intraoperative data from >130,000 repairs (May 2015). A total of 49 peer-reviewed national and international publications have been published from the database (June 2015). Conclusion The Danish Inguinal Hernia Database is fully active monitoring surgical quality and contributes to the national and international surgical society to improve outcome after groin hernia repair. PMID:27822094

  3. Object-oriented modeling and design of database federations

    NARCIS (Netherlands)

    Balsters, H.

    2003-01-01

    We describe a logical architecture and a general semantic framework for precise specification of so-called database federations. A database federation provides for tight coupling of a collection of heterogeneous component databases into a global integrated system. Our approach to database federation

  4. Object-oriented modeling and design of database federations

    NARCIS (Netherlands)

    Balsters, H.

    2003-01-01

    We describe a logical architecture and a general semantic framework for precise specification of so-called database federations. A database federation provides for tight coupling of a collection of heterogeneous component databases into a global integrated system. Our approach to database federation

  5. REDIdb: the RNA editing database.

    Science.gov (United States)

    Picardi, Ernesto; Regina, Teresa Maria Rosaria; Brennicke, Axel; Quagliariello, Carla

    2007-01-01

    The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing information is available either by experimental inspection (in vitro) or by computational detection (in silico). Each record of REDIdb is organized in a specific flat-file containing a description of the main characteristics of the entry, a feature table with the editing events and related details and a sequence zone with both the genomic sequence and the corresponding edited transcript. REDIdb is a relational database in which the browsing and identification of editing sites has been simplified by means of two facilities to either graphically display genomic or cDNA sequences or to show the corresponding alignment. In both cases, all editing sites are highlighted in colour and their relative positions are detailed by mousing over. New editing positions can be directly submitted to REDIdb after a user-specific registration to obtain authorized secure access. This first version of REDIdb database stores 9964 editing events and can be freely queried at http://biologia.unical.it/py_script/search.html.

  6. Database Description - RMOS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us RMOS Database Description General information of database Database name RMOS Alternative nam...arch Unit Shoshi Kikuchi E-mail : Database classification Plant databases - Rice Microarray Data and other Gene Expression Database...s Organism Taxonomy Name: Oryza sativa Taxonomy ID: 4530 Database description The Ric...e Microarray Opening Site is a database of comprehensive information for Rice Mic...es and manner of utilization of database You can refer to the information of the

  7. 40 CFR 1400.13 - Read-only database.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 32 2010-07-01 2010-07-01 false Read-only database. 1400.13 Section... INFORMATION Other Provisions § 1400.13 Read-only database. The Administrator is authorized to establish... public off-site consequence analysis information by means of a central database under the control of...

  8. Vector database for vehicle road navigation

    OpenAIRE

    Kenda, Lian

    2007-01-01

    Vehicle navigation devices use vector cartographic view, which is designed as a vector database. Database creation begins by setting up a landscape model which includes all the graphical and descriptive data required for accurate vehicle navigation. This paper presents the creation of a database part called StreetConnect, which is used for road navigation. Data obtained using distinct specifications have been transformed into the format compatible with Garmin GPS devices. Data have been obtai...

  9. Incorporating Database Design in Warnier Method

    Directory of Open Access Journals (Sweden)

    Donald Chand

    2000-11-01

    Full Text Available The Warnier method, a highly prescriptive program design approach for file-oriented solutions, has been criticized for its lack of a database design component. This paper addresses this weakness by incorporating a logical database design step in Warnier method. Specifically, the paper presents rules for transforming the information in a Warnier diagram into a set of relations. With this extension the Wamier method complements the entity-relationship approach for data analysis and logical database design.

  10. DASHR: database of small human noncoding RNAs.

    Science.gov (United States)

    Leung, Yuk Yee; Kuksa, Pavel P; Amlie-Wolf, Alexandre; Valladares, Otto; Ungar, Lyle H; Kannan, Sampath; Gregory, Brian D; Wang, Li-San

    2016-01-01

    Small non-coding RNAs (sncRNAs) are highly abundant RNAs, typically database provides searchable, unified annotation, and expression information for full sncRNA transcripts and mature RNA products derived from these larger RNAs. Here, we present the Database of small human noncoding RNAs (DASHR). DASHR contains the most comprehensive information to date on human sncRNA genes and mature sncRNA products. DASHR provides a simple user interface for researchers to view sequence and secondary structure, compare expression levels, and evidence of specific processing across all sncRNA genes and mature sncRNA products in various human tissues. DASHR annotation and expression data covers all major classes of sncRNAs including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear, nucleolar, cytoplasmic (sn-, sno-, scRNAs, respectively), transfer (tRNAs), and ribosomal RNAs (rRNAs). Currently, DASHR (v1.0) integrates 187 smRNA high-throughput sequencing (smRNA-seq) datasets with over 2.5 billion reads and annotation data from multiple public sources. DASHR contains annotations for ∼ 48,000 human sncRNA genes and mature sncRNA products, 82% of which are expressed in one or more of the curated tissues. DASHR is available at http://lisanwanglab.org/DASHR.

  11. Danish Palliative Care Database

    Directory of Open Access Journals (Sweden)

    Groenvold M

    2016-10-01

    Full Text Available Mogens Groenvold,1,2 Mathilde Adsersen,1 Maiken Bang Hansen1 1The Danish Palliative Care Database (DPD Secretariat, Research Unit, Department of Palliative Medicine, Bispebjerg Hospital, 2Department of Public Health, University of Copenhagen, Copenhagen, Denmark Aims: The aim of the Danish Palliative Care Database (DPD is to monitor, evaluate, and improve the clinical quality of specialized palliative care (SPC (ie, the activity of hospital-based palliative care teams/departments and hospices in Denmark. Study population: The study population is all patients in Denmark referred to and/or in contact with SPC after January 1, 2010. Main variables: The main variables in DPD are data about referral for patients admitted and not admitted to SPC, type of the first SPC contact, clinical and sociodemographic factors, multidisciplinary conference, and the patient-reported European Organisation for Research and Treatment of Cancer Quality of Life Questionaire-Core-15-Palliative Care questionnaire, assessing health-related quality of life. The data support the estimation of currently five quality of care indicators, ie, the proportions of 1 referred and eligible patients who were actually admitted to SPC, 2 patients who waited <10 days before admission to SPC, 3 patients who died from cancer and who obtained contact with SPC, 4 patients who were screened with European Organisation for Research and Treatment of Cancer Quality of Life Questionaire-Core-15-Palliative Care at admission to SPC, and 5 patients who were discussed at a multidisciplinary conference. Descriptive data: In 2014, all 43 SPC units in Denmark reported their data to DPD, and all 9,434 cancer patients (100% referred to SPC were registered in DPD. In total, 41,104 unique cancer patients were registered in DPD during the 5 years 2010–2014. Of those registered, 96% had cancer. Conclusion: DPD is a national clinical quality database for SPC having clinically relevant variables and high data

  12. Curation accuracy of model organism databases.

    Science.gov (United States)

    Keseler, Ingrid M; Skrzypek, Marek; Weerasinghe, Deepika; Chen, Albert Y; Fulcher, Carol; Li, Gene-Wei; Lemmer, Kimberly C; Mladinich, Katherine M; Chow, Edmond D; Sherlock, Gavin; Karp, Peter D

    2014-01-01

    Manual extraction of information from the biomedical literature-or biocuration-is the central methodology used to construct many biological databases. For example, the UniProt protein database, the EcoCyc Escherichia coli database and the Candida Genome Database (CGD) are all based on biocuration. Biological databases are used extensively by life science researchers, as online encyclopedias, as aids in the interpretation of new experimental data and as golden standards for the development of new bioinformatics algorithms. Although manual curation has been assumed to be highly accurate, we are aware of only one previous study of biocuration accuracy. We assessed the accuracy of EcoCyc and CGD by manually selecting curated assertions within randomly chosen EcoCyc and CGD gene pages and by then validating that the data found in the referenced publications supported those assertions. A database assertion is considered to be in error if that assertion could not be found in the publication cited for that assertion. We identified 10 errors in the 633 facts that we validated across the two databases, for an overall error rate of 1.58%, and individual error rates of 1.82% for CGD and 1.40% for EcoCyc. These data suggest that manual curation of the experimental literature by Ph.D-level scientists is highly accurate. Database URL: http://ecocyc.org/, http://www.candidagenome.org//

  13. XTalkDB: a database of signaling pathway crosstalk

    Science.gov (United States)

    Sam, Sarah A.; Teel, Joelle; Tegge, Allison N.; Bharadwaj, Aditya; Murali, T.M.

    2017-01-01

    Analysis of signaling pathways and their crosstalk is a cornerstone of systems biology. Thousands of papers have been published on these topics. Surprisingly, there is no database that carefully and explicitly documents crosstalk between specific pairs of signaling pathways. We have developed XTalkDB (http://www.xtalkdb.org) to fill this very important gap. XTalkDB contains curated information for 650 pairs of pathways from over 1600 publications. In addition, the database reports the molecular components (e.g. proteins, hormones, microRNAs) that mediate crosstalk between a pair of pathways and the species and tissue in which the crosstalk was observed. The XTalkDB website provides an easy-to-use interface for scientists to browse crosstalk information by querying one or more pathways or molecules of interest. PMID:27899583

  14. E3 Staff Database

    Data.gov (United States)

    US Agency for International Development — E3 Staff database is maintained by E3 PDMS (Professional Development & Management Services) office. The database is Mysql. It is manually updated by E3 staff as...

  15. Physiological Information Database (PID)

    Science.gov (United States)

    EPA has developed a physiological information database (created using Microsoft ACCESS) intended to be used in PBPK modeling. The database contains physiological parameter values for humans from early childhood through senescence as well as similar data for laboratory animal spec...

  16. Cell Centred Database (CCDB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Cell Centered Database (CCDB) is a web accessible database for high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging.

  17. Database Urban Europe

    NARCIS (Netherlands)

    Sleutjes, B.; de Valk, H.A.G.

    2016-01-01

    Database Urban Europe: ResSegr database on segregation in The Netherlands. Collaborative research on residential segregation in Europe 2014–2016 funded by JPI Urban Europe (Joint Programming Initiative Urban Europe).

  18. Danish Colorectal Cancer Group Database

    Directory of Open Access Journals (Sweden)

    Ingeholm P

    2016-10-01

    Full Text Available Peter Ingeholm,1,2 Ismail Gögenur,1,3 Lene H Iversen1,4 1Danish Colorectal Cancer Group Database, Copenhagen, 2Department of Pathology, Herlev University Hospital, Herlev, 3Department of Surgery, Roskilde University Hospital, Roskilde, 4Department of Surgery P, Aarhus University Hospital, Aarhus C, Denmark Aim of database: The aim of the database, which has existed for registration of all patients with colorectal cancer in Denmark since 2001, is to improve the prognosis for this patient group. Study population: All Danish patients with newly diagnosed colorectal cancer who are either diagnosed or treated in a surgical department of a public Danish hospital. Main variables: The database comprises an array of surgical, radiological, oncological, and pathological variables. The surgeons record data such as diagnostics performed, including type and results of radiological examinations, lifestyle factors, comorbidity and performance, treatment including the surgical procedure, urgency of surgery, and intra- and postoperative complications within 30 days after surgery. The pathologists record data such as tumor type, number of lymph nodes and metastatic lymph nodes, surgical margin status, and other pathological risk factors. Descriptive data: The database has had >95% completeness in including patients with colorectal adenocarcinoma with >54,000 patients registered so far with approximately one-third rectal cancers and two-third colon cancers and an overrepresentation of men among rectal cancer patients. The stage distribution has been more or less constant until 2014 with a tendency toward a lower rate of stage IV and higher rate of stage I after introduction of the national screening program in 2014. The 30-day mortality rate after elective surgery has been reduced from >7% in 2001–2003 to <2% since 2013. Conclusion: The database is a national population-based clinical database with high patient and data completeness for the perioperative period

  19. Using Classifiers to Find Domain-Specific Online Databases Automatically%使用分类器自动发现特定领域的深度网入口

    Institute of Scientific and Technical Information of China (English)

    王辉; 刘艳威; 左万利

    2008-01-01

    在深度网研究领域,通用搜索引擎(比如Google和Yahoo)具有许多不足之处:它们各自所能覆盖的数据量与整个深度网数据总量的比值小于1/3;与表层网中的情况不同,几个搜索引擎相结合所能覆盖的数据量基本没有发生变化.许多深度网站点能够提供大量高质量的信息,并且,深度网正在逐渐成为一个最重要的信息资源.提出了一个三分类器的框架,用于自动识别特定领域的深度网入口.查询接口得到以后,可以将它们进行集成,然后将一个统一的接口提交给用户以方便他们查询信息.通过8组大规模的实验,验证了所提出的方法可以准确高效地发现特定领域的深度网入口.%In hidden Web domain, general-purpose search engines (i.e., Google and Yahoo) have their shortcomings. They cover less than one-third of the data stored in document databases. Unlike the surface Web, if combined, they cover roughly the same data. Hidden Web is a highly important information source since the content provided by many hidden Web sites is often of very high quality. This paper proposes a three-step framework to automatically identify domain-specific hidden Web entries. With those obtained query interfaces, they can be integrated to obtain a unified interface which is given to users to query. Eight large-scale experiments demonstrate that the technique can find domain-specific hidden Web entries accurately and efficiently.

  20. Scopus database: a review.

    Science.gov (United States)

    Burnham, Judy F

    2006-03-08

    The Scopus database provides access to STM journal articles and the references included in those articles, allowing the searcher to search both forward and backward in time. The database can be used for collection development as well as for research. This review provides information on the key points of the database and compares it to Web of Science. Neither database is inclusive, but complements each other. If a library can only afford one, choice must be based in institutional needs.

  1. Future database machine architectures

    OpenAIRE

    Hsiao, David K.

    1984-01-01

    There are many software database management systems available on many general-purpose computers ranging from micros to super-mainframes. Database machines as backened computers can offload the database management work from the mainframe so that we can retain the same mainframe longer. However, the database backend must also demonstrate lower cost, higher performance, and newer functionality. Some of the fundamental architecture issues in the design of high-performance and great-capacity datab...

  2. MPlus Database system

    Energy Technology Data Exchange (ETDEWEB)

    1989-01-20

    The MPlus Database program was developed to keep track of mail received. This system was developed by TRESP for the Department of Energy/Oak Ridge Operations. The MPlus Database program is a PC application, written in dBase III+'' and compiled with Clipper'' into an executable file. The files you need to run the MPLus Database program can be installed on a Bernoulli, or a hard drive. This paper discusses the use of this database.

  3. Reduction in camera-specific variability in [{sup 123}I]FP-CIT SPECT outcome measures by image reconstruction optimized for multisite settings: impact on age-dependence of the specific binding ratio in the ENC-DAT database of healthy controls

    Energy Technology Data Exchange (ETDEWEB)

    Buchert, Ralph; Lange, Catharina [Charite - Universitaetsmedizin Berlin, Department of Nuclear Medicine, Berlin (Germany); Kluge, Andreas; Bronzel, Marcus [ABX-CRO advanced pharmaceutical services Forschungsgesellschaft m.b.H., Dresden (Germany); Tossici-Bolt, Livia [University Hospital Southampton NHS Foundation Trust, Department of Medical Physics, Southampton (United Kingdom); Dickson, John [University College London Hospital NHS Foundation Trust, Institute of Nuclear Medicine, London (United Kingdom); Asenbaum, Susanne [Medical University of Vienna, Department of Nuclear Medicine, Vienna (Austria); Booij, Jan [University of Amsterdam, Department of Nuclear Medicine, Academic Medical Centre, Amsterdam (Netherlands); Kapucu, L. Oezlem Atay [Gazi University, Department of Nuclear Medicine, Faculty of Medicine, Ankara (Turkey); Svarer, Claus [Rigshospitalet and University of Copenhagen, Neurobiology Research Unit, Copenhagen (Denmark); Koulibaly, Pierre-Malick [University of Nice-Sophia Antipolis, Nuclear Medicine Department, Centre Antoine Lacassagne, Nice (France); Nobili, Flavio [University of Genoa, Department of Neuroscience (DINOGMI), Clinical Neurology Unit, Genoa (Italy); Pagani, Marco [CNR, Institute of Cognitive Sciences and Technologies, Rome (Italy); Karolinska Hospital, Department of Nuclear Medicine, Stockholm (Sweden); Sabri, Osama [University of Leipzig, Department of Nuclear Medicine, Leipzig (Germany); Sera, Terez [University of Szeged, Department of Nuclear Medicine and Euromedic Szeged, Szeged (Hungary); Tatsch, Klaus [Municipal Hospital of Karlsruhe Inc, Department of Nuclear Medicine, Karlsruhe (Germany); Borght, Thierry vander [CHU Namur, IREC, Nuclear Medicine Division, Universite catholique de Louvain, Yvoir (Belgium); Laere, Koen van [University Hospital and K.U. Leuven, Nuclear Medicine, Leuven (Belgium); Varrone, Andrea [Karolinska University Hospital, Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet, Stockholm (Sweden); Iida, Hidehiro [National Cerebral and Cardiovascular Center - Research Institute, Osaka (Japan)

    2016-07-15

    Quantitative estimates of dopamine transporter availability, determined with [{sup 123}I]FP-CIT SPECT, depend on the SPECT equipment, including both hardware and (reconstruction) software, which limits their use in multicentre research and clinical routine. This study tested a dedicated reconstruction algorithm for its ability to reduce camera-specific intersubject variability in [{sup 123}I]FP-CIT SPECT. The secondary aim was to evaluate binding in whole brain (excluding striatum) as a reference for quantitative analysis. Of 73 healthy subjects from the European Normal Control Database of [{sup 123}I]FP-CIT recruited at six centres, 70 aged between 20 and 82 years were included. SPECT images were reconstructed using the QSPECT software package which provides fully automated detection of the outer contour of the head, camera-specific correction for scatter and septal penetration by transmission-dependent convolution subtraction, iterative OSEM reconstruction including attenuation correction, and camera-specific ''to kBq/ml'' calibration. LINK and HERMES reconstruction were used for head-to-head comparison. The specific striatal [{sup 123}I]FP-CIT binding ratio (SBR) was computed using the Southampton method with binding in the whole brain, occipital cortex or cerebellum as the reference. The correlation between SBR and age was used as the primary quality measure. The fraction of SBR variability explained by age was highest (1) with QSPECT, independently of the reference region, and (2) with whole brain as the reference, independently of the reconstruction algorithm. QSPECT reconstruction appears to be useful for reduction of camera-specific intersubject variability of [{sup 123}I]FP-CIT SPECT in multisite and single-site multicamera settings. Whole brain excluding striatal binding as the reference provides more stable quantitative estimates than occipital or cerebellar binding. (orig.)

  4. Reverse engineering of relational database applications

    NARCIS (Netherlands)

    Vermeer, W.W.M.; Apers, P.M.G.

    1995-01-01

    This paper presents techniques for reverse engineering of relational database applications. The target of such an effort is the definition of a fully equipped object-oriented view of the relational database, including methods and constraints. Such views can be seen as a full specification of the dat

  5. CTD_DATABASE - Cascadia tsunami deposit database

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The Cascadia Tsunami Deposit Database contains data on the location and sedimentological properties of tsunami deposits found along the Cascadia margin. Data have...

  6. Steviol glycoside safety: is the genotoxicity database sufficient?

    Science.gov (United States)

    Urban, J D; Carakostas, M C; Brusick, D J

    2013-01-01

    The safety of steviol glycoside sweeteners has been extensively reviewed in the literature. National and international food safety agencies and approximately 20 expert panels have concluded that steviol glycosides, including the widely used sweeteners stevioside and rebaudioside A, are not genotoxic. However, concern has been expressed in recent publications that steviol glycosides may be mutagenic based on select studies representing a small fraction of the overall database, and it has been suggested that further in vivo genotoxicity studies are required to complete their safety profiles. To address the utility of conducting additional in vivo genotoxicity studies, this review evaluates the specific genotoxicity studies that are the sources of concern, and evaluates the adequacy of the database including more recent genotoxicity data not mentioned in those publications. The current database of in vitro and in vivo studies for steviol glycosides is robust and does not indicate that either stevioside or rebaudioside A are genotoxic. This, combined with a lack of evidence for neoplasm development in rat bioassays, establish the safety of all steviol glycosides with respect to their genotoxic/carcinogenic potential.

  7. Database Description - Trypanosomes Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us Trypanosomes Database... Database Description General information of database Database name Trypanosomes Database...rmation and Systems Yata 1111, Mishima, Shizuoka 411-8540, JAPAN E mail: Database... classification Protein sequence databases Organism Taxonomy Name: Trypanosoma Taxonomy ID: 5690 Taxonomy Na...me: Homo sapiens Taxonomy ID: 9606 Database description The Trypanosomes database is a database providing th

  8. Maternal Deaths Databases Analysis: Ecuador 2003-2013.

    Science.gov (United States)

    Pino, Antonio; Albán, María; Rivas, Alejandra; Rodríguez, Erika

    2016-08-19

    Background: Maternal mortality ratio in Ecuador is the only millennium goal on which national agencies are still making strong efforts to reach 2015 target. The purpose of the study was to process national maternal death databases to identify a specific association pattern of variable included in the death certificate. Design and methods: The study processed mortality databases published yearly by the National Census and Statistics Institute (INEC). Data analysed were exclusively maternal deaths. Data corresponds to the 2003-2013 period, accessible through INEC's website. Comparisons are based on number of deaths and use an ecological approach for geographical coincidences. Results: The study identified variable association into the maternal mortality national databases showing that to die at home or in a different place than a hospital is closely related to women's socioeconomic characteristics; there was an association with the absence of a public health facility. Also, to die in a different place than the usual residence could mean that women and families are searching for or were referred to a higher level of attention when they face complications. Conclusions: Ecuadorian maternal deaths showed Patterns of inequity in health status, health care provision and health risks. A predominant factor seems unclear to explain the variable association found processing national databases; perhaps every pattern of health systems development played a role in maternal mortality or factors different from those registered by the statistics system may remain hidden. Some random influences might not be even considered in an explanatory model yet.

  9. The BioGRID interaction database: 2017 update

    Science.gov (United States)

    Chatr-aryamontri, Andrew; Oughtred, Rose; Boucher, Lorrie; Rust, Jennifer; Chang, Christie; Kolas, Nadine K.; O'Donnell, Lara; Oster, Sara; Theesfeld, Chandra; Sellam, Adnane; Stark, Chris; Breitkreutz, Bobby-Joe; Dolinski, Kara; Tyers, Mike

    2017-01-01

    The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the annotation and archival of protein, genetic and chemical interactions for all major model organism species and humans. As of September 2016 (build 3.4.140), the BioGRID contains 1 072 173 genetic and protein interactions, and 38 559 post-translational modifications, as manually annotated from 48 114 publications. This dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 BioGRID update. BioGRID curates the biomedical literature for major model organism species, including humans, with a recent emphasis on central biological processes and specific human diseases. To facilitate network-based approaches to drug discovery, BioGRID now incorporates 27 501 chemical–protein interactions for human drug targets, as drawn from the DrugBank database. A new dynamic interaction network viewer allows the easy navigation and filtering of all genetic and protein interaction data, as well as for bioactive compounds and their established targets. BioGRID data are directly downloadable without restriction in a variety of standardized formats and are freely distributed through partner model organism databases and meta-databases. PMID:27980099

  10. The BioGRID interaction database: 2017 update.

    Science.gov (United States)

    Chatr-Aryamontri, Andrew; Oughtred, Rose; Boucher, Lorrie; Rust, Jennifer; Chang, Christie; Kolas, Nadine K; O'Donnell, Lara; Oster, Sara; Theesfeld, Chandra; Sellam, Adnane; Stark, Chris; Breitkreutz, Bobby-Joe; Dolinski, Kara; Tyers, Mike

    2017-01-04

    The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the annotation and archival of protein, genetic and chemical interactions for all major model organism species and humans. As of September 2016 (build 3.4.140), the BioGRID contains 1 072 173 genetic and protein interactions, and 38 559 post-translational modifications, as manually annotated from 48 114 publications. This dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 BioGRID update. BioGRID curates the biomedical literature for major model organism species, including humans, with a recent emphasis on central biological processes and specific human diseases. To facilitate network-based approaches to drug discovery, BioGRID now incorporates 27 501 chemical-protein interactions for human drug targets, as drawn from the DrugBank database. A new dynamic interaction network viewer allows the easy navigation and filtering of all genetic and protein interaction data, as well as for bioactive compounds and their established targets. BioGRID data are directly downloadable without restriction in a variety of standardized formats and are freely distributed through partner model organism databases and meta-databases. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Maternal deaths databases analysis: Ecuador 2003-2013

    Directory of Open Access Journals (Sweden)

    Antonio Pino

    2016-08-01

    Full Text Available Background: Maternal mortality ratio in Ecuador is the only millennium goal on which national agencies are still making strong efforts to reach 2015 target. The purpose of the study was to process national maternal death databases to identify a specific association pattern of variable included in the death certificate. Design and methods: The study processed mortality databases published yearly by the National Census and Statistics Institute (INEC. Data analysed were exclusively maternal deaths. Data corresponds to the 2003-2013 period, accessible through INEC’s website. Comparisons are based on number of deaths and use an ecological approach for geographical coincidences. Results: The study identified variable association into the maternal mortality national databases showing that to die at home or in a different place than a hospital is closely related to women’s socioeconomic characteristics; there was an association with the absence of a public health facility. Also, to die in a different place than the usual residence could mean that women and families are searching for or were referred to a higher level of attention when they face complications. Conclusions: Ecuadorian maternal deaths showed Patterns of inequity in health status, health care provision and health risks. A predominant factor seems unclear to explain the variable association found processing national databases; perhaps every pattern of health systems development played a role in maternal mortality or factors different from those registered by the statistics system may remain hidden. Some random influences might not be even considered in an explanatory model yet.

  12. Database Description - PLACE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PLACE Database... Description General information of database Database name A Database of Plant Cis-acting Regu...araki 305-8602, Japan National Institute of Agrobiological Sciences E-mail : Database classification Plant database...s Organism Taxonomy Name: Tracheophyta Taxonomy ID: 58023 Database description PLACE is a database of... motifs found in plant cis-acting regulatory DNA elements based on previously pub

  13. Electronic database of arterial aneurysms

    Directory of Open Access Journals (Sweden)

    Fabiano Luiz Erzinger

    2014-12-01

    Full Text Available Background:The creation of an electronic database facilitates the storage of information, as well as streamlines the exchange of data, making easier the exchange of knowledge for future research.Objective:To construct an electronic database containing comprehensive and up-to-date clinical and surgical data on the most common arterial aneurysms, to help advance scientific research.Methods:The most important specialist textbooks and articles found in journals and on internet databases were reviewed in order to define the basic structure of the protocol. Data were computerized using the SINPE© system for integrated electronic protocols and tested in a pilot study.Results:The data entered onto the system was first used to create a Master protocol, organized into a structure of top-level directories covering a large proportion of the content on vascular diseases as follows: patient history; physical examination; supplementary tests and examinations; diagnosis; treatment; and clinical course. By selecting items from the Master protocol, Specific protocols were then created for the 22 arterial sites most often involved by aneurysms. The program provides a method for collection of data on patients including clinical characteristics (patient history and physical examination, supplementary tests and examinations, treatments received and follow-up care after treatment. Any information of interest on these patients that is contained in the protocol can then be used to query the database and select data for studies.Conclusions:It proved possible to construct a database of clinical and surgical data on the arterial aneurysms of greatest interest and, by adapting the data to specific software, the database was integrated into the SINPE© system, thereby providing a standardized method for collection of data on these patients and tools for retrieving this information in an organized manner for use in scientific studies.

  14. An Alaska Soil Carbon Database

    Science.gov (United States)

    Johnson, Kristofer; Harden, Jennifer

    2009-05-01

    Database Collaborator's Meeting; Fairbanks, Alaska, 4 March 2009; Soil carbon pools in northern high-latitude regions and their response to climate changes are highly uncertain, and collaboration is required from field scientists and modelers to establish baseline data for carbon cycle studies. The Global Change Program at the U.S. Geological Survey has funded a 2-year effort to establish a soil carbon network and database for Alaska based on collaborations from numerous institutions. To initiate a community effort, a workshop for the development of an Alaska soil carbon database was held at the University of Alaska Fairbanks. The database will be a resource for spatial and biogeochemical models of Alaska ecosystems and will serve as a prototype for a nationwide community project: the National Soil Carbon Network (http://www.soilcarb.net). Studies will benefit from the combination of multiple academic and government data sets. This collaborative effort is expected to identify data gaps and uncertainties more comprehensively. Future applications of information contained in the database will identify specific vulnerabilities of soil carbon in Alaska to climate change, disturbance, and vegetation change.

  15. Keyword Search in Databases

    CERN Document Server

    Yu, Jeffrey Xu; Chang, Lijun

    2009-01-01

    It has become highly desirable to provide users with flexible ways to query/search information over databases as simple as keyword search like Google search. This book surveys the recent developments on keyword search over databases, and focuses on finding structural information among objects in a database using a set of keywords. Such structural information to be returned can be either trees or subgraphs representing how the objects, that contain the required keywords, are interconnected in a relational database or in an XML database. The structural keyword search is completely different from

  16. An Interoperable Cartographic Database

    Directory of Open Access Journals (Sweden)

    Slobodanka Ključanin

    2007-05-01

    Full Text Available The concept of producing a prototype of interoperable cartographic database is explored in this paper, including the possibilities of integration of different geospatial data into the database management system and their visualization on the Internet. The implementation includes vectorization of the concept of a single map page, creation of the cartographic database in an object-relation database, spatial analysis, definition and visualization of the database content in the form of a map on the Internet. 

  17. 1962 Satellite High Altitude Radiation Belt Database

    Science.gov (United States)

    2014-03-01

    TR-14-18 1962 Satellite High Altitude Radiation Belt Database Approved for public release; distribution is unlimited. March...the Status of the High Altitude Nuclear Explosion (HANE) Trapped Radiation Belt Database”, AFRL-VS-PS-TR- 2006-1079, Air Force Research Laboratory...Roth, B., “Blue Ribbon Panel and Support Work Assessing the Status of the High Altitude Nuclear Explosion (HANE) Trapped Radiation Belt Database

  18. A High Energy Nuclear Database Proposal

    CERN Document Server

    Brown, D A; Brown, David A.; Vogt, Ramona

    2005-01-01

    We propose to develop a high-energy heavy-ion experimental database and make it accessible to the scientific community through an on-line interace. This database will be searchable and cross-indexed with relevant publications, including published detector descriptions. Since this database will be a community resource, it requires the high-energy nuclear physics community's financial and manpower support. This database should eventually contain all published data from the Bevalac, AGS and SPS to RHIC and LHC energies, proton-proton to nucleus-nucleus collisions as well as other relevant systems and all measured observables. Such a database would have tremendous scientific payoff as it makes systematic studies easier and allows simpler benchmarking of theoretical models to a broad range of old and new experiments. Furthermore, there is a growing need for compilations of high-energy nuclear data for applications including stockpile stewardship, technology development for intertial confinement fusion and target a...

  19. Proposal for a High Energy Nuclear Database

    CERN Document Server

    Vogt, D A B R

    2005-01-01

    We propose to develop a high-energy heavy-ion experimental database and make it accessible to the scientific community through an on-line interface. This database will be searchable and cross-indexed with relevant publications, including published detector descriptions. Since this database will be a community resource, it requires the high-energy nuclear physics community's financial and manpower support. This database should eventually contain all published data from Bevalac, AGS and SPS to RHIC and LHC energies, proton-proton to nucleus-nucleus collisions as well as other relevant systems, and all measured observables. Such a database would have tremendous scientific payoff as it makes systematic studies easier and allows simpler benchmarking of theoretical models to a broad range of old and new experiments. Furthermore, there is a growing need for compilations of high-energy nuclear data for applications including stockpile stewardship, technology development for inertial confinement fusion and target and ...

  20. Indexed University presses: overlap and geographical distribution in five book assessment databases

    Energy Technology Data Exchange (ETDEWEB)

    Mañana-Rodriguez, J.; Gimenez-Toledo, E

    2016-07-01

    Scholarly books have been a periphery among the objects of study of bibliometrics until recent developments provided tools for assessment purposes. Among scholarly book publishers, University Presses (UPs hereinafter), subject to specific ends and constrains in their publishing activity, might also remain on a second-level periphery despite their relevance as scholarly book publishers. In this study the authors analyze the absolute and relative presence, overlap and uniquely-indexed cases of 503 UPs by country, among five assessment-oriented databases containing data on scholarly book publishers: Book Citation Index, Scopus, Scholarly Publishers Indicators (Spain), the lists of publishers from the Norwegian System (CRISTIN) and the lists of publishers from the Finnish System (JUFO). The comparison between commercial databases and public, national databases points towards a differential pattern: prestigious UPs in the English Speaking world represent larger shares and there is a higher overall percentage of UPs in the commercial databases, while the richness and diversity is higher in the case of national databases. Explicit or de facto biases towards production in English by commercial databases, as well as diverse indexation criteria might explain the differences observed. The analysis of the presence of UPs in different numbers of databases by country also provides a general picture of the average degree of diffusion of UPs among information systems. The analysis of ‘endemic’ UPs, those indexed only in one of the five databases points out to strongly different compositions of UPs in commercial and non-commercial databases. A combination of commercial and non commercial databases seems to be the optimal option for assessment purposes while the validity and desirability of the ongoing debate on the role of UPs can be also concluded. (Author)

  1. HIERARCHICAL ORGANIZATION OF INFORMATION, IN RELATIONAL DATABASES

    Directory of Open Access Journals (Sweden)

    Demian Horia

    2008-05-01

    Full Text Available In this paper I will present different types of representation, of hierarchical information inside a relational database. I also will compare them to find the best organization for specific scenarios.

  2. The National Land Cover Database

    Science.gov (United States)

    Homer, Collin H.; Fry, Joyce A.; Barnes, Christopher A.

    2012-01-01

    The National Land Cover Database (NLCD) serves as the definitive Landsat-based, 30-meter resolution, land cover database for the Nation. NLCD provides spatial reference and descriptive data for characteristics of the land surface such as thematic class (for example, urban, agriculture, and forest), percent impervious surface, and percent tree canopy cover. NLCD supports a wide variety of Federal, State, local, and nongovernmental applications that seek to assess ecosystem status and health, understand the spatial patterns of biodiversity, predict effects of climate change, and develop land management policy. NLCD products are created by the Multi-Resolution Land Characteristics (MRLC) Consortium, a partnership of Federal agencies led by the U.S. Geological Survey. All NLCD data products are available for download at no charge to the public from the MRLC Web site: http://www.mrlc.gov.

  3. Integrating Variances into an Analytical Database

    Science.gov (United States)

    Sanchez, Carlos

    2010-01-01

    For this project, I enrolled in numerous SATERN courses that taught the basics of database programming. These include: Basic Access 2007 Forms, Introduction to Database Systems, Overview of Database Design, and others. My main job was to create an analytical database that can handle many stored forms and make it easy to interpret and organize. Additionally, I helped improve an existing database and populate it with information. These databases were designed to be used with data from Safety Variances and DCR forms. The research consisted of analyzing the database and comparing the data to find out which entries were repeated the most. If an entry happened to be repeated several times in the database, that would mean that the rule or requirement targeted by that variance has been bypassed many times already and so the requirement may not really be needed, but rather should be changed to allow the variance's conditions permanently. This project did not only restrict itself to the design and development of the database system, but also worked on exporting the data from the database to a different format (e.g. Excel or Word) so it could be analyzed in a simpler fashion. Thanks to the change in format, the data was organized in a spreadsheet that made it possible to sort the data by categories or types and helped speed up searches. Once my work with the database was done, the records of variances could be arranged so that they were displayed in numerical order, or one could search for a specific document targeted by the variances and restrict the search to only include variances that modified a specific requirement. A great part that contributed to my learning was SATERN, NASA's resource for education. Thanks to the SATERN online courses I took over the summer, I was able to learn many new things about computers and databases and also go more in depth into topics I already knew about.

  4. PDS: A Performance Database Server

    Directory of Open Access Journals (Sweden)

    Michael W. Berry

    1994-01-01

    Full Text Available The process of gathering, archiving, and distributing computer benchmark data is a cumbersome task usually performed by computer users and vendors with little coordination. Most important, there is no publicly available central depository of performance data for all ranges of machines from personal computers to supercomputers. We present an Internet-accessible performance database server (PDS that can be used to extract current benchmark data and literature. As an extension to the X-Windows-based user interface (Xnetlib to the Netlib archival system, PDS provides an on-line catalog of public domain computer benchmarks such as the LINPACK benchmark, Perfect benchmarks, and the NAS parallel benchmarks. PDS does not reformat or present the benchmark data in any way that conflicts with the original methodology of any particular benchmark; it is thereby devoid of any subjective interpretations of machine performance. We believe that all branches (research laboratories, academia, and industry of the general computing community can use this facility to archive performance metrics and make them readily available to the public. PDS can provide a more manageable approach to the development and support of a large dynamic database of published performance metrics.

  5. Impact of public programs on fertility and gender specific investment in human capital of children in rural India: cross sectional and time series analyses.

    Science.gov (United States)

    Duraisamy, P; Malathy, R

    1991-01-01

    Cross sectional and time series analyses are conducted with 1971 and 1981 rural district level data for India in order to estimate variations in program impacts on household decisionmaking concerning fertility, child mortality, and schooling; to analyze how the variation in public program subsidies and services influences sex specific investments in schooling; and to examine the bias in cross sectional estimates by employing fixed effects methodology. The theory of household production uses the framework development by Rosenzweig and Wolpin. The utility function is expressed as a function of families' desired number of children, sex specific investment in human capital of children measured by schooling of males and females, and a composite consumption good. Budget constraints are characterized in terms of the biological supply of births or natural fertility, the number of births averted by fertility control, exogenous money income, the prices of number of children, contraceptives, child schooling, and consumption of goods. Demand functions are constructed from maximizing the utility function subject to the budget constraint. Data constitute 40% of the total districts and 50% of the rural population. The empirical specification of the linear model and variable description are provided. Other explanatory variables included are adult educational attainment; % of scheduled castes and tribes and % Muslim; and % rural population. Estimation methods are described and justification is provided for the use of ordinary least squares and fixed effects methods. The results of the cross sectional analysis reveal that own-program effects of family planning and primary health centers reduced family size in 1971 and 81. The increase in secondary school enrollment is evidenced in only 1971. There is a significant effect of family planning (FP) clinics on the demand for surviving children only in 1971. The presence of a seconary school in a village reduces the demand for children in

  6. Characterization of the Scientific Output of Health Professionals from Cienfuegos Visible in the Scopus Database

    Directory of Open Access Journals (Sweden)

    Yuniet Rojas Mesa

    2014-08-01

    Full Text Available Background: the publication of the results from scientific research and projects ensures dissemination of science, exchange, feedback and update of its trends.Objective: to characterize the scientific output of health professionals from Cienfuegos visible in the Scopus database. Methods: a descriptive study was conducted in the Provincial Medical Sciences Information Center including the publications by health professionals from Cienfuegos visible in the Scopus database from January 2007 to September 2013. The variables analyzed were: publications per year, topics discussed in the publications, most prolific authors, collaboration among institutions and countries as well as institutions according to the authors' affiliation. Results: 102 papers were retrieved, mostly by authors working in secondary care, specifically at the Gustavo Aldereguía Lima Provincial Hospital. A total of 141 authors are represented, 82 times as first authors and 230 as co-authors. Only 9.2 % appears five or more times. Most common topics are: cardiovascular diseases and public health. Collaboration with 13 institutions (nine papers with four national institutes and 30 with foreign institutions was observed. Conclusions: scientific output of health professionals from Cienfuegos visible in the Scopus database is still scant.

  7. Update History of This Database - Arabidopsis Phenome Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Arabidopsis Phenome Database Update History of This Database Date Update contents 2017/02/27... Arabidopsis Phenome Database English archive site is opened. - Arabidopsis Phenome Database (http://jphenom...e.info/?page_id=95) is opened. About This Database Database Description Download License Update History of This Database... Site Policy | Contact Us Update History of This Database - Arabidopsis Phenome Database | LSDB Archive ...

  8. Update History of This Database - SKIP Stemcell Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us SKIP Stemcell Database Update History of This Database Date Update contents 2017/03/13 SKIP Stemcell Database... English archive site is opened. 2013/03/29 SKIP Stemcell Database ( https://www.skip.med.k...eio.ac.jp/SKIPSearch/top?lang=en ) is opened. About This Database Database Description Download License Upda...te History of This Database Site Policy | Contact Us Update History of This Database - SKIP Stemcell Database | LSDB Archive ...

  9. Database Description - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us RMG Database... Description General information of database Database name RMG Alternative name Rice Mitochondri...ational Institute of Agrobiological Sciences E-mail : Database classification Nucleotide Sequence Databases ...Organism Taxonomy Name: Oryza sativa Japonica Group Taxonomy ID: 39947 Database description This database co...e of rice mitochondrial genome and information on the analysis results. Features and manner of utilization of database

  10. The EcoCyc Database

    Science.gov (United States)

    Karp, Peter D.; Riley, Monica; Saier, Milton; Paulsen, Ian T.; Collado-Vides, Julio; Paley, Suzanne M.; Pellegrini-Toole, Alida; Bonavides, César; Gama-Castro, Socorro

    2002-01-01

    EcoCyc is an organism-specific pathway/genome database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, its transport proteins and its mechanisms of transcriptional control of gene expression. EcoCyc is queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools. EcoCyc is available at http://ecocyc.org/. PMID:11752253

  11. Stockpile Dismantlement Database Training Materials

    Energy Technology Data Exchange (ETDEWEB)

    1993-11-01

    This document, the Stockpile Dismantlement Database (SDDB) training materials is designed to familiarize the user with the SDDB windowing system and the data entry steps for Component Characterization for Disposition. The foundation of information required for every part is depicted by using numbered graphic and text steps. The individual entering data is lead step by step through generic and specific examples. These training materials are intended to be supplements to individual on-the-job training.

  12. Hazard Analysis Database Report

    CERN Document Server

    Grams, W H

    2000-01-01

    The Hazard Analysis Database was developed in conjunction with the hazard analysis activities conducted in accordance with DOE-STD-3009-94, Preparation Guide for U S . Department of Energy Nonreactor Nuclear Facility Safety Analysis Reports, for HNF-SD-WM-SAR-067, Tank Farms Final Safety Analysis Report (FSAR). The FSAR is part of the approved Authorization Basis (AB) for the River Protection Project (RPP). This document describes, identifies, and defines the contents and structure of the Tank Farms FSAR Hazard Analysis Database and documents the configuration control changes made to the database. The Hazard Analysis Database contains the collection of information generated during the initial hazard evaluations and the subsequent hazard and accident analysis activities. The Hazard Analysis Database supports the preparation of Chapters 3 ,4 , and 5 of the Tank Farms FSAR and the Unreviewed Safety Question (USQ) process and consists of two major, interrelated data sets: (1) Hazard Analysis Database: Data from t...

  13. Conditioning Probabilistic Databases

    CERN Document Server

    Koch, Christoph

    2008-01-01

    Past research on probabilistic databases has studied the problem of answering queries on a static database. Application scenarios of probabilistic databases however often involve the conditioning of a database using additional information in the form of new evidence. The conditioning problem is thus to transform a probabilistic database of priors into a posterior probabilistic database which is materialized for subsequent query processing or further refinement. It turns out that the conditioning problem is closely related to the problem of computing exact tuple confidence values. It is known that exact confidence computation is an NP-hard problem. This has lead researchers to consider approximation techniques for confidence computation. However, neither conditioning nor exact confidence computation can be solved using such techniques. In this paper we present efficient techniques for both problems. We study several problem decomposition methods and heuristics that are based on the most successful search techn...

  14. Database design and database administration for a kindergarten

    OpenAIRE

    Vítek, Daniel

    2009-01-01

    The bachelor thesis deals with creation of database design for a standard kindergarten, installation of the designed database into the database system Oracle Database 10g Express Edition and demonstration of the administration tasks in this database system. The verification of the database was proved by a developed access application.

  15. ITS-90 Thermocouple Database

    Science.gov (United States)

    SRD 60 NIST ITS-90 Thermocouple Database (Web, free access)   Web version of Standard Reference Database 60 and NIST Monograph 175. The database gives temperature -- electromotive force (emf) reference functions and tables for the letter-designated thermocouple types B, E, J, K, N, R, S and T. These reference functions have been adopted as standards by the American Society for Testing and Materials (ASTM) and the International Electrotechnical Commission (IEC).

  16. Searching Databases with Keywords

    Institute of Scientific and Technical Information of China (English)

    Shan Wang; Kun-Long Zhang

    2005-01-01

    Traditionally, SQL query language is used to search the data in databases. However, it is inappropriate for end-users, since it is complex and hard to learn. It is the need of end-user, searching in databases with keywords, like in web search engines. This paper presents a survey of work on keyword search in databases. It also includes a brief introduction to the SEEKER system which has been developed.

  17. The design and implementation of pedagogical software for multi-backend/multi-lingual database system.

    OpenAIRE

    Little, Craig W.

    1987-01-01

    Approved for public release; distribution is unlimited Traditionally, courses in database systems do not use pedagogical software for the purpose of instructing the database systems, despite the progress made in modem database architecture. In this thesis, we present a working document to assist in the instruction of a new database system, the Multi-Backend Database System (MBDS)-and the Multi-Lingual Database System (MLDS). As the course of instruction describes the creatio...

  18. Smart Location Database - Download

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Smart Location Database (SLD) summarizes over 80 demographic, built environment, transit service, and destination accessibility attributes for every census block...

  19. Database principles programming performance

    CERN Document Server

    O'Neil, Patrick

    2014-01-01

    Database: Principles Programming Performance provides an introduction to the fundamental principles of database systems. This book focuses on database programming and the relationships between principles, programming, and performance.Organized into 10 chapters, this book begins with an overview of database design principles and presents a comprehensive introduction to the concepts used by a DBA. This text then provides grounding in many abstract concepts of the relational model. Other chapters introduce SQL, describing its capabilities and covering the statements and functions of the programmi

  20. Smart Location Database - Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Smart Location Database (SLD) summarizes over 80 demographic, built environment, transit service, and destination accessibility attributes for every census block...

  1. The Danish Melanoma Database

    DEFF Research Database (Denmark)

    Hölmich, Lisbet Rosenkrantz; Klausen, Siri; Spaun, Eva

    2016-01-01

    AIM OF DATABASE: The aim of the database is to monitor and improve the treatment and survival of melanoma patients. STUDY POPULATION: All Danish patients with cutaneous melanoma and in situ melanomas must be registered in the Danish Melanoma Database (DMD). In 2014, 2,525 patients with invasive......, nature, and treatment hereof is registered. In case of death, the cause and date are included. Currently, all data are entered manually; however, data catchment from the existing registries is planned to be included shortly. DESCRIPTIVE DATA: The DMD is an old research database, but new as a clinical...

  2. Danish Gynecological Cancer Database

    DEFF Research Database (Denmark)

    Sørensen, Sarah Mejer; Bjørn, Signe Frahm; Jochumsen, Kirsten Marie

    2016-01-01

    AIM OF DATABASE: The Danish Gynecological Cancer Database (DGCD) is a nationwide clinical cancer database and its aim is to monitor the treatment quality of Danish gynecological cancer patients, and to generate data for scientific purposes. DGCD also records detailed data on the diagnostic measures...... is the registration of oncological treatment data, which is incomplete for a large number of patients. CONCLUSION: The very complete collection of available data from more registries form one of the unique strengths of DGCD compared to many other clinical databases, and provides unique possibilities for validation...

  3. Transporter Classification Database (TCDB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Transporter Classification Database details a comprehensive classification system for membrane transport proteins known as the Transporter Classification (TC)...

  4. The Relational Database Dictionary

    CERN Document Server

    J, C

    2006-01-01

    Avoid misunderstandings that can affect the design, programming, and use of database systems. Whether you're using Oracle, DB2, SQL Server, MySQL, or PostgreSQL, The Relational Database Dictionary will prevent confusion about the precise meaning of database-related terms (e.g., attribute, 3NF, one-to-many correspondence, predicate, repeating group, join dependency), helping to ensure the success of your database projects. Carefully reviewed for clarity, accuracy, and completeness, this authoritative and comprehensive quick-reference contains more than 600 terms, many with examples, covering i

  5. IVR EFP Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This database contains trip-level reports submitted by vessels participating in Exempted Fishery projects with IVR reporting requirements.

  6. Databases for Microbiologists

    Science.gov (United States)

    2015-01-01

    Databases play an increasingly important role in biology. They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways. All these data are critically important to microbiologists. Furthermore, microbiology has its own databases that deal with model microorganisms, microbial diversity, physiology, and pathogenesis. Thousands of biological databases are currently available, and it becomes increasingly difficult to keep up with their development. The purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists. PMID:26013493

  7. Veterans Administration Databases

    Science.gov (United States)

    The Veterans Administration Information Resource Center provides database and informatics experts, customer service, expert advice, information products, and web technology to VA researchers and others.

  8. Residency Allocation Database

    Data.gov (United States)

    Department of Veterans Affairs — The Residency Allocation Database is used to determine allocation of funds for residency programs offered by Veterans Affairs Medical Centers (VAMCs). Information...

  9. Tools and Databases of the KOMICS Web Portal for Preprocessing, Mining, and Dissemination of Metabolomics Data

    Directory of Open Access Journals (Sweden)

    Nozomu Sakurai

    2014-01-01

    Full Text Available A metabolome—the collection of comprehensive quantitative data on metabolites in an organism—has been increasingly utilized for applications such as data-intensive systems biology, disease diagnostics, biomarker discovery, and assessment of food quality. A considerable number of tools and databases have been developed to date for the analysis of data generated by various combinations of chromatography and mass spectrometry. We report here a web portal named KOMICS (The Kazusa Metabolomics Portal, where the tools and databases that we developed are available for free to academic users. KOMICS includes the tools and databases for preprocessing, mining, visualization, and publication of metabolomics data. Improvements in the annotation of unknown metabolites and dissemination of comprehensive metabolomic data are the primary aims behind the development of this portal. For this purpose, PowerGet and FragmentAlign include a manual curation function for the results of metabolite feature alignments. A metadata-specific wiki-based database, Metabolonote, functions as a hub of web resources related to the submitters' work. This feature is expected to increase citation of the submitters' work, thereby promoting data publication. As an example of the practical use of KOMICS, a workflow for a study on Jatropha curcas is presented. The tools and databases available at KOMICS should contribute to enhanced production, interpretation, and utilization of metabolomic Big Data.

  10. Tools and databases of the KOMICS web portal for preprocessing, mining, and dissemination of metabolomics data.

    Science.gov (United States)

    Sakurai, Nozomu; Ara, Takeshi; Enomoto, Mitsuo; Motegi, Takeshi; Morishita, Yoshihiko; Kurabayashi, Atsushi; Iijima, Yoko; Ogata, Yoshiyuki; Nakajima, Daisuke; Suzuki, Hideyuki; Shibata, Daisuke

    2014-01-01

    A metabolome--the collection of comprehensive quantitative data on metabolites in an organism--has been increasingly utilized for applications such as data-intensive systems biology, disease diagnostics, biomarker discovery, and assessment of food quality. A considerable number of tools and databases have been developed to date for the analysis of data generated by various combinations of chromatography and mass spectrometry. We report here a web portal named KOMICS (The Kazusa Metabolomics Portal), where the tools and databases that we developed are available for free to academic users. KOMICS includes the tools and databases for preprocessing, mining, visualization, and publication of metabolomics data. Improvements in the annotation of unknown metabolites and dissemination of comprehensive metabolomic data are the primary aims behind the development of this portal. For this purpose, PowerGet and FragmentAlign include a manual curation function for the results of metabolite feature alignments. A metadata-specific wiki-based database, Metabolonote, functions as a hub of web resources related to the submitters' work. This feature is expected to increase citation of the submitters' work, thereby promoting data publication. As an example of the practical use of KOMICS, a workflow for a study on Jatropha curcas is presented. The tools and databases available at KOMICS should contribute to enhanced production, interpretation, and utilization of metabolomic Big Data.

  11. Standards for Clinical Grade Genomic Databases.

    Science.gov (United States)

    Yohe, Sophia L; Carter, Alexis B; Pfeifer, John D; Crawford, James M; Cushman-Vokoun, Allison; Caughron, Samuel; Leonard, Debra G B

    2015-11-01

    Next-generation sequencing performed in a clinical environment must meet clinical standards, which requires reproducibility of all aspects of the testing. Clinical-grade genomic databases (CGGDs) are required to classify a variant and to assist in the professional interpretation of clinical next-generation sequencing. Applying quality laboratory standards to the reference databases used for sequence-variant interpretation presents a new challenge for validation and curation. To define CGGD and the categories of information contained in CGGDs and to frame recommendations for the structure and use of these databases in clinical patient care. Members of the College of American Pathologists Personalized Health Care Committee reviewed the literature and existing state of genomic databases and developed a framework for guiding CGGD development in the future. Clinical-grade genomic databases may provide different types of information. This work group defined 3 layers of information in CGGDs: clinical genomic variant repositories, genomic medical data repositories, and genomic medicine evidence databases. The layers are differentiated by the types of genomic and medical information contained and the utility in assisting with clinical interpretation of genomic variants. Clinical-grade genomic databases must meet specific standards regarding submission, curation, and retrieval of data, as well as the maintenance of privacy and security. These organizing principles for CGGDs should serve as a foundation for future development of specific standards that support the use of such databases for patient care.

  12. NESHAP Area-Specific Dose-Release Factors for Potential Onsite Member-of-the-Public Locations at SRS using CAP88-PC Version 4.0

    Energy Technology Data Exchange (ETDEWEB)

    Trimor, P. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2017-08-09

    The Environmental Protection Agency (EPA) requires the use of the computer model CAP88-PC to estimate the total effective doses (TED) for demonstrating compliance with 40 CFR 61, Subpart H (EPA 2006), the National Emission Standards for Hazardous Air Pollutants (NESHAP) regulations. As such, CAP88 Version 4.0 was used to calculate the receptor dose due to routine atmospheric releases at the Savannah River Site (SRS). For estimation, NESHAP dose-release factors (DRFs) have been supplied to Environmental Compliance and Area Closure Projects (EC&ACP) for many years. DRFs represent the dose to a maximum receptor exposed to 1 Ci of a specified radionuclide being released into the atmosphere. They are periodically updated to include changes in the CAP88 version, input parameter values, site meteorology, and location of the maximally exposed individual (MEI). In this report, the DRFs were calculated for potential radionuclide atmospheric releases from 13 SRS release points. The three potential onsite MEI locations to be evaluated are B-Area, Three Rivers Landfill (TRL), and Savannah River Ecology Lab Conference Center (SRELCC) with TRL’s onsite workers considered as members-of-the-public, and the potential future constructions of dormitories at SRELCC and Barracks at B-Area. Each MEI location was evaluated at a specified compass sector with different area to receptor distances and was conducted for both ground-level and elevated release points. The analysis makes use of area-specific meteorological data (Viner 2014). The resulting DRFs are compared to the 2014 NESHAP offsite MEI DRFs for three operational areas; A-Area, H-Area, and COS for a release rate of 1 Ci of tritium oxide at 0 ft. elevation. CAP88 was executed again using the 2016 NESHAP MEI release rates for 0 and 61 m stack heights to determine the radionuclide dose at TRL from the center-of-site (COS).

  13. Publicity and public relations

    Science.gov (United States)

    Fosha, Charles E.

    1990-01-01

    This paper addresses approaches to using publicity and public relations to meet the goals of the NASA Space Grant College. Methods universities and colleges can use to publicize space activities are presented.

  14. License - Trypanosomes Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Trypanosomes Database License License to Use This Database Last updated : 2014/02/04 You may use this database...pecifies the license terms regarding the use of this database and the requirements you must follow in using this database.... The license for this database is specified in the Creative Commons... Attribution-Share Alike 2.1 Japan . If you use data from this database, please be sure attribute this database...pan is found here . With regard to this database, you are licensed to: freely access part or whole of this database

  15. Croatian Cadastre Database Modelling

    Directory of Open Access Journals (Sweden)

    Zvonko Biljecki

    2013-04-01

    Full Text Available The Cadastral Data Model has been developed as a part of a larger programme to improve products and production environment of the Croatian Cadastral Service of the State Geodetic Administration (SGA. The goal of the project was to create a cadastral data model conforming to relevant standards and specifications in the field of geoinformation (GI adapted by international organisations for standardisation under the competence of GI (ISO TC211 and OpenGIS and it implementations.The main guidelines during the project have been object-oriented conceptual modelling of the updated users' requests and a "new" cadastral data model designed by SGA - Faculty of Geodesy - Geofoto LLC project team. The UML of the conceptual model is given per all feature categories and is described only at class level. The next step was the UML technical model, which was developed from the UML conceptual model. The technical model integrates different UML schemas in one united schema.XML (eXtensible Markup Language was applied for XML description of UML models, and then the XML schema was transferred into GML (Geography Markup Language application schema. With this procedure we have completely described the behaviour of each cadastral feature and rules for the transfer and storage of cadastral features into the database.

  16. Intra-disciplinary differences in database coverage and the consequences for bibliometric research

    DEFF Research Database (Denmark)

    Faber Frandsen, Tove; Nicolaisen, Jeppe

    2008-01-01

    disciplines focusing on interdisciplinary differences; however, little is known about the potential existence of intradisciplinary differences in database coverage. Focusing on intradisciplinary differences, the article documents large database-coverage differences within two disciplines (economics......Bibliographic databases (including databases based on open access) are routinely used for bibliometric research. The value of a specific database depends to a large extent on the coverage of the discipline(s) under study. A number of studies have determined the coverage of databases in specific...

  17. IDBD: infectious disease biomarker database.

    Science.gov (United States)

    Yang, In Seok; Ryu, Chunsun; Cho, Ki Joon; Kim, Jin Kwang; Ong, Swee Hoe; Mitchell, Wayne P; Kim, Bong Su; Oh, Hee-Bok; Kim, Kyung Hyun

    2008-01-01

    Biomarkers enable early diagnosis, guide molecularly targeted therapy and monitor the activity and therapeutic responses across a variety of diseases. Despite intensified interest and research, however, the overall rate of development of novel biomarkers has been falling. Moreover, no solution is yet available that efficiently retrieves and processes biomarker information pertaining to infectious diseases. Infectious Disease Biomarker Database (IDBD) is one of the first efforts to build an easily accessible and comprehensive literature-derived database covering known infectious disease biomarkers. IDBD is a community annotation database, utilizing collaborative Web 2.0 features, providing a convenient user interface to input and revise data online. It allows users to link infectious diseases or pathogens to protein, gene or carbohydrate biomarkers through the use of search tools. It supports various types of data searches and application tools to analyze sequence and structure features of potential and validated biomarkers. Currently, IDBD integrates 611 biomarkers for 66 infectious diseases and 70 pathogens. It is publicly accessible at http://biomarker.cdc.go.kr and http://biomarker.korea.ac.kr.

  18. Neutrosophic Relational Database Decomposition

    OpenAIRE

    Meena Arora; Ranjit Biswas; Dr. U.S.Pandey

    2011-01-01

    In this paper we present a method of decomposing a neutrosophic database relation with Neutrosophic attributes into basic relational form. Our objective is capable of manipulating incomplete as well as inconsistent information. Fuzzy relation or vague relation can only handle incomplete information. Authors are taking the Neutrosophic Relational database [8],[2] to show how imprecise data can be handled in relational schema.

  19. HIV Structural Database

    Science.gov (United States)

    SRD 102 HIV Structural Database (Web, free access)   The HIV Protease Structural Database is an archive of experimentally determined 3-D structures of Human Immunodeficiency Virus 1 (HIV-1), Human Immunodeficiency Virus 2 (HIV-2) and Simian Immunodeficiency Virus (SIV) Proteases and their complexes with inhibitors or products of substrate cleavage.

  20. Structural Ceramics Database

    Science.gov (United States)

    SRD 30 NIST Structural Ceramics Database (Web, free access)   The NIST Structural Ceramics Database (WebSCD) provides evaluated materials property data for a wide range of advanced ceramics known variously as structural ceramics, engineering ceramics, and fine ceramics.

  1. Odense Pharmacoepidemiological Database (OPED)

    DEFF Research Database (Denmark)

    Hallas, Jesper; Poulsen, Maja Hellfritzsch; Hansen, Morten Rix

    2017-01-01

    The Odense University Pharmacoepidemiological Database (OPED) is a prescription database established in 1990 by the University of Southern Denmark, covering reimbursed prescriptions from the county of Funen in Denmark and the region of Southern Denmark (1.2 million inhabitants). It is still active...

  2. The Danish Anaesthesia Database

    DEFF Research Database (Denmark)

    Antonsen, Kristian; Rosenstock, Charlotte Vallentin; Lundstrøm, Lars Hyldborg

    2016-01-01

    AIM OF DATABASE: The aim of the Danish Anaesthesia Database (DAD) is the nationwide collection of data on all patients undergoing anesthesia. Collected data are used for quality assurance, quality development, and serve as a basis for research projects. STUDY POPULATION: The DAD was founded in 2004...

  3. World Database of Happiness

    NARCIS (Netherlands)

    R. Veenhoven (Ruut)

    1995-01-01

    textabstractABSTRACT The World Database of Happiness is an ongoing register of research on subjective appreciation of life. Its purpose is to make the wealth of scattered findings accessible, and to create a basis for further meta-analytic studies. The database involves four sections:
    1.

  4. Balkan Vegetation Database

    NARCIS (Netherlands)

    Vassilev, Kiril; Pedashenko, Hristo; Alexandrova, Alexandra; Tashev, Alexandar; Ganeva, Anna; Gavrilova, Anna; Gradevska, Asya; Assenov, Assen; Vitkova, Antonina; Grigorov, Borislav; Gussev, Chavdar; Filipova, Eva; Aneva, Ina; Knollová, Ilona; Nikolov, Ivaylo; Georgiev, Georgi; Gogushev, Georgi; Tinchev, Georgi; Pachedjieva, Kalina; Koev, Koycho; Lyubenova, Mariyana; Dimitrov, Marius; Apostolova-Stoyanova, Nadezhda; Velev, Nikolay; Zhelev, Petar; Glogov, Plamen; Natcheva, Rayna; Tzonev, Rossen; Boch, Steffen; Hennekens, Stephan M.; Georgiev, Stoyan; Stoyanov, Stoyan; Karakiev, Todor; Kalníková, Veronika; Shivarov, Veselin; Russakova, Veska; Vulchev, Vladimir

    2016-01-01

    The Balkan Vegetation Database (BVD; GIVD ID: EU-00-019; http://www.givd.info/ID/EU-00- 019) is a regional database that consists of phytosociological relevés from different vegetation types from six countries on the Balkan Peninsula (Albania, Bosnia and Herzegovina, Bulgaria, Kosovo, Montenegro

  5. Balkan Vegetation Database

    NARCIS (Netherlands)

    Vassilev, Kiril; Pedashenko, Hristo; Alexandrova, Alexandra; Tashev, Alexandar; Ganeva, Anna; Gavrilova, Anna; Gradevska, Asya; Assenov, Assen; Vitkova, Antonina; Grigorov, Borislav; Gussev, Chavdar; Filipova, Eva; Aneva, Ina; Knollová, Ilona; Nikolov, Ivaylo; Georgiev, Georgi; Gogushev, Georgi; Tinchev, Georgi; Pachedjieva, Kalina; Koev, Koycho; Lyubenova, Mariyana; Dimitrov, Marius; Apostolova-Stoyanova, Nadezhda; Velev, Nikolay; Zhelev, Petar; Glogov, Plamen; Natcheva, Rayna; Tzonev, Rossen; Boch, Steffen; Hennekens, Stephan M.; Georgiev, Stoyan; Stoyanov, Stoyan; Karakiev, Todor; Kalníková, Veronika; Shivarov, Veselin; Russakova, Veska; Vulchev, Vladimir

    2016-01-01

    The Balkan Vegetation Database (BVD; GIVD ID: EU-00-019; http://www.givd.info/ID/EU-00- 019) is a regional database that consists of phytosociological relevés from different vegetation types from six countries on the Balkan Peninsula (Albania, Bosnia and Herzegovina, Bulgaria, Kosovo, Montenegro

  6. Biological Macromolecule Crystallization Database

    Science.gov (United States)

    SRD 21 Biological Macromolecule Crystallization Database (Web, free access)   The Biological Macromolecule Crystallization Database and NASA Archive for Protein Crystal Growth Data (BMCD) contains the conditions reported for the crystallization of proteins and nucleic acids used in X-ray structure determinations and archives the results of microgravity macromolecule crystallization studies.

  7. A Quality System Database

    Science.gov (United States)

    Snell, William H.; Turner, Anne M.; Gifford, Luther; Stites, William

    2010-01-01

    A quality system database (QSD), and software to administer the database, were developed to support recording of administrative nonconformance activities that involve requirements for documentation of corrective and/or preventive actions, which can include ISO 9000 internal quality audits and customer complaints.

  8. An organic database system

    NARCIS (Netherlands)

    M.L. Kersten (Martin); A.P.J.M. Siebes (Arno)

    1999-01-01

    textabstractThe pervasive penetration of database technology may suggest that we have reached the end of the database research era. The contrary is true. Emerging technology, in hardware, software, and connectivity, brings a wealth of opportunities to push technology to a new level of maturity.

  9. Atomic Spectra Database (ASD)

    Science.gov (United States)

    SRD 78 NIST Atomic Spectra Database (ASD) (Web, free access)   This database provides access and search capability for NIST critically evaluated data on atomic energy levels, wavelengths, and transition probabilities that are reasonably up-to-date. The NIST Atomic Spectroscopy Data Center has carried out these critical compilations.

  10. World Database of Happiness

    NARCIS (Netherlands)

    R. Veenhoven (Ruut)

    1995-01-01

    textabstractABSTRACT The World Database of Happiness is an ongoing register of research on subjective appreciation of life. Its purpose is to make the wealth of scattered findings accessible, and to create a basis for further meta-analytic studies. The database involves four sections:
    1. Bib

  11. World Database of Happiness

    NARCIS (Netherlands)

    R. Veenhoven (Ruut)

    1995-01-01

    textabstractABSTRACT The World Database of Happiness is an ongoing register of research on subjective appreciation of life. Its purpose is to make the wealth of scattered findings accessible, and to create a basis for further meta-analytic studies. The database involves four sections:
    1. Bib

  12. Database Description - Yeast Interacting Proteins Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Yeast Interacting Proteins Database Database Description General information of database Database name Yeast... Interacting Proteins Database Alternative name - Creator Creator Name: Takashi Ito* Creator Affiliation: Di...-4-7136-3989 FAX: +81-4-7136-3979 E-mail : Database classification Metabolic and Signaling Pathways - Protei...n-protein interactions Organism Taxonomy Name: Saccharomyces cerevisiae Taxonomy ID: 4932 Database descripti...ive yeast two-hybrid analysis of budding yeast proteins. Features and manner of utilization of database Prot

  13. The LHCb configuration database

    CERN Document Server

    Abadie, L; Van Herwijnen, Eric; Jacobsson, R; Jost, B; Neufeld, N

    2005-01-01

    The aim of the LHCb configuration database is to store information about all the controllable devices of the detector. The experiment's control system (that uses PVSS ) will configure, start up and monitor the detector from the information in the configuration database. The database will contain devices with their properties, connectivity and hierarchy. The ability to store and rapidly retrieve huge amounts of data, and the navigability between devices are important requirements. We have collected use cases to ensure the completeness of the design. Using the entity relationship modelling technique we describe the use cases as classes with attributes and links. We designed the schema for the tables using relational diagrams. This methodology has been applied to the TFC (switches) and DAQ system. Other parts of the detector will follow later. The database has been implemented using Oracle to benefit from central CERN database support. The project also foresees the creation of tools to populate, maintain, and co...

  14. Cascadia Tsunami Deposit Database

    Science.gov (United States)

    Peters, Robert; Jaffe, Bruce; Gelfenbaum, Guy; Peterson, Curt

    2003-01-01

    The Cascadia Tsunami Deposit Database contains data on the location and sedimentological properties of tsunami deposits found along the Cascadia margin. Data have been compiled from 52 studies, documenting 59 sites from northern California to Vancouver Island, British Columbia that contain known or potential tsunami deposits. Bibliographical references are provided for all sites included in the database. Cascadia tsunami deposits are usually seen as anomalous sand layers in coastal marsh or lake sediments. The studies cited in the database use numerous criteria based on sedimentary characteristics to distinguish tsunami deposits from sand layers deposited by other processes, such as river flooding and storm surges. Several studies cited in the database contain evidence for more than one tsunami at a site. Data categories include age, thickness, layering, grainsize, and other sedimentological characteristics of Cascadia tsunami deposits. The database documents the variability observed in tsunami deposits found along the Cascadia margin.

  15. Database Description - DGBY | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us DGBY Database... Description General information of database Database name DGBY Alternative name Database for G...-12 Kannondai, Tsukuba, Ibaraki 305-8642 Japan Akira Ando TEL: +81-29-838-8066 E-mail: Database classificati...on Microarray Data and other Gene Expression Databases Organism Taxonomy Name: Sa...ccharomyces cerevisiae Taxonomy ID: 4932 Database description Baker's yeast Saccharomyces cerevisiae is an e

  16. Database Description - RPSD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us RPSD Database... Description General information of database Database name RPSD Alternative name Summary inform...n National Institute of Agrobiological Sciences Toshimasa Yamazaki E-mail : Database classification Structure Database...idopsis thaliana Taxonomy ID: 3702 Taxonomy Name: Glycine max Taxonomy ID: 3847 Database description We have...nts such as rice, and have put together the result and related informations. This database contains the basi

  17. Use of molecular variation in the NCBI dbSNP database.

    Science.gov (United States)

    Sherry, S T; Ward, M; Sirotkin, K

    2000-01-01

    While high quality information regarding variation in genes is currently available in locus-specific or specialized mutation databases, the need remains for a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping, and evolutionary biology. In response to this need, the National Center for Biotechnology Information (NCBI) has established the dbSNP database http://ncbi. nlm.nih.gov/SNP/ to serve as a generalized, central variation database. Submissions to dbSNP will be integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink, and the Human Genome Project data, and the complete contents of dbSNP are available to the public via anonymous FTP. Hum Mutat 15:68-75, 2000. Published 2000 Wiley-Liss, Inc.

  18. The Database Dilemma: Online Search Strategies in Nursing.

    Science.gov (United States)

    Fried, Ava K.; And Others

    1989-01-01

    Describes a study that compared the coverage of the nursing profession, subject heading specificity, and ease of retrieval of the MEDLINE and Nursing & Allied Health (CINAHL) online databases. The strengths and weaknesses of each database are discussed and hints for searching on both databases are provided. (four references) (CLB)

  19. The Danish Bladder Cancer Database

    DEFF Research Database (Denmark)

    Hansen, Erik; Larsson, Heidi Jeanet; Nørgaard, Mette

    2016-01-01

    AIM OF DATABASE: The aim of the Danish Bladder Cancer Database (DaBlaCa-data) is to monitor the treatment of all patients diagnosed with invasive bladder cancer (BC) in Denmark. STUDY POPULATION: All patients diagnosed with BC in Denmark from 2012 onward were included in the study. Results......-intended radiation therapy. DESCRIPTIVE DATA: One-year mortality was 28% (95% confidence interval [CI]: 15-21). One-year cancer-specific mortality was 25% (95% CI: 22-27%). One-year mortality after cystectomy was 14% (95% CI: 10-18). Ninety-day mortality after cystectomy was 3% (95% CI: 1-5) in 2013. One......-year mortality following curative-intended radiation therapy was 32% (95% CI: 24-39) and 1-year cancer-specific mortality was 23% (95% CI: 16-31) in 2013. CONCLUSION: This preliminary DaBlaCa-data report showed that the treatment of MIBC in Denmark overall meet high international academic standards. The database...

  20. Plant databases and data analysis tools

    Science.gov (United States)

    It is anticipated that the coming years will see the generation of large datasets including diagnostic markers in several plant species with emphasis on crop plants. To use these datasets effectively in any plant breeding program, it is essential to have the information available via public database...

  1. Modification Semantics in Now-Relative Databases

    DEFF Research Database (Denmark)

    Torp, Kristian; Jensen, Christian Søndergaard; Snodgrass, R. T.

    2004-01-01

    Most real-world databases record time-varying information. In such databases, the notion of ??the current time,?? or NOW, occurs naturally and prominently. For example, when capturing the past states of a relation using begin and end time columns, tuples that are part of the current state have some...... past time as their begin time and NOW as their end time. While the semantics of such variable databases has been described in detail and is well understood, the modification of variable databases remains unexplored. This paper defines the semantics of modifications involving the variable NOW. More...... specifically,  the problems with modifications in the presence of NOW are explored, illustrating that the main problems are with modifications of tuples that reach into the future. The paper defines the semantics of modifications?including insertions, deletions, and updates?of databases without NOW, with NOW...

  2. [Total quality management of clinical database].

    Science.gov (United States)

    Okubo, Suguru; Miyata, Hiroaki; Tomotaki, Ai; Motomura, Noboru; Murakami, Arata; Ono, Minoru; Iwanaka, Tadashi

    2013-06-01

    Data entry system should be constructed considering utility, accuracy, propriety, and feasibility. The methods for developing useful and accurate clinical databases are 1)system development based on the concept of "error proofing", 2)system test by real users, 3)guidances for participants, and 4)incentive for accurate data entry. In terms of propriety, to gain patient's consent on data collection and to publicly announce objectives and methods of clinical database are necessary. Confidentiality and anonymization of data are also important. Balancing efficacy and propriety for maximization of patients' and societal benefit is one of the important responsibilities of database management organizations. In addition, assessment of data quality such as audit and feedback is useful for enhancing accuracy and reliability of clinical databases.

  3. SENTRA, a database of signal transduction proteins.

    Energy Technology Data Exchange (ETDEWEB)

    D' Souza, M.; Romine, M. F.; Maltsev, N.; Mathematics and Computer Science; PNNL

    2000-01-01

    SENTRA, available via URL http://wit.mcs.anl.gov/WIT2/Sentra/, is a database of proteins associated with microbial signal transduction. The database currently includes the classical two-component signal transduction pathway proteins and methyl-accepting chemotaxis proteins, but will be expanded to also include other classes of signal transduction systems that are modulated by phosphorylation or methylation reactions. Although the majority of database entries are from prokaryotic systems, eukaroytic proteins with bacterial-like signal transduction domains are also included. Currently SENTRA contains signal transduction proteins in 34 complete and almost completely sequenced prokaryotic genomes, as well as sequences from 243 organisms available in public databases (SWISS-PROT and EMBL). The analysis was carried out within the framework of the WIT2 system, which is designed and implemented to support genetic sequence analysis and comparative analysis of sequenced genomes.

  4. The Danish Nonmelanoma Skin Cancer Dermatology Database

    DEFF Research Database (Denmark)

    Lamberg, Anna Lei; Sølvsten, Henrik; Lei, Ulrikke

    2016-01-01

    AIM OF DATABASE: The Danish Nonmelanoma Skin Cancer Dermatology Database was established in 2008. The aim of this database was to collect data on nonmelanoma skin cancer (NMSC) treatment and improve its treatment in Denmark. NMSC is the most common malignancy in the western countries and represents...... a significant challenge in terms of public health management and health care costs. However, high-quality epidemiological and treatment data on NMSC are sparse. STUDY POPULATION: The NMSC database includes patients with the following skin tumors: basal cell carcinoma (BCC), squamous cell carcinoma, Bowen......'s disease, and keratoacanthoma diagnosed by the participating office-based dermatologists in Denmark. MAIN VARIABLES: Clinical and histological diagnoses, BCC subtype, localization, size, skin cancer history, skin phototype, and evidence of metastases and treatment modality are the main variables...

  5. GOVERNING GENETIC DATABASES: COLLECTION, STORAGE AND USE

    Science.gov (United States)

    Gibbons, Susan M.C.; Kaye, Jane

    2008-01-01

    This paper provides an introduction to a collection of five papers, published as a special symposium journal issue, under the title: “Governing Genetic Databases: Collection, Storage and Use”. It begins by setting the scene, to provide a backdrop and context for the papers. It describes the evolving scientific landscape around genetic databases and genomic research, particularly within the biomedical and criminal forensic investigation fields. It notes the lack of any clear, coherent or coordinated legal governance regime, either at the national or international level. It then identifies and reflects on key cross-cutting issues and themes that emerge from the five papers, in particular: terminology and definitions; consent; special concerns around population genetic databases (biobanks) and forensic databases; international harmonisation; data protection; data access; boundary-setting; governance; and issues around balancing individual interests against public good values. PMID:18841252

  6. TCM Database@Taiwan: the world's largest traditional Chinese medicine database for drug screening in silico.

    Science.gov (United States)

    Chen, Calvin Yu-Chian

    2011-01-06

    Rapid advancing computational technologies have greatly speeded up the development of computer-aided drug design (CADD). Recently, pharmaceutical companies have increasingly shifted their attentions toward traditional Chinese medicine (TCM) for novel lead compounds. Despite the growing number of studies on TCM, there is no free 3D small molecular structure database of TCM available for virtual screening or molecular simulation. To address this shortcoming, we have constructed TCM Database@Taiwan (http://tcm.cmu.edu.tw/) based on information collected from Chinese medical texts and scientific publications. TCM Database@Taiwan is currently the world's largest non-commercial TCM database. This web-based database contains more than 20,000 pure compounds isolated from 453 TCM ingredients. Both cdx (2D) and Tripos mol2 (3D) formats of each pure compound in the database are available for download and virtual screening. The TCM database includes both simple and advanced web-based query options that can specify search clauses, such as molecular properties, substructures, TCM ingredients, and TCM classification, based on intended drug actions. The TCM database can be easily accessed by all researchers conducting CADD. Over the last eight years, numerous volunteers have devoted their time to analyze TCM ingredients from Chinese medical texts as well as to construct structure files for each isolated compound. We believe that TCM Database@Taiwan will be a milestone on the path towards modernizing traditional Chinese medicine.

  7. FORMIDABEL: The Belgian Ants Database.

    Science.gov (United States)

    Brosens, Dimitri; Vankerkhoven, François; Ignace, David; Wegnez, Philippe; Noé, Nicolas; Heughebaert, André; Bortels, Jeannine; Dekoninck, Wouter

    2013-01-01

    FORMIDABEL is a database of Belgian Ants containing more than 27.000 occurrence records. These records originate from collections, field sampling and literature. The database gives information on 76 native and 9 introduced ant species found in Belgium. The collection records originated mainly from the ants collection in Royal Belgian Institute of Natural Sciences (RBINS), the 'Gaspar' Ants collection in Gembloux and the zoological collection of the University of Liège (ULG). The oldest occurrences date back from May 1866, the most recent refer to August 2012. FORMIDABEL is a work in progress and the database is updated twice a year. THE LATEST VERSION OF THE DATASET IS PUBLICLY AND FREELY ACCESSIBLE THROUGH THIS URL: http://ipt.biodiversity.be/resource.do?r=formidabel. The dataset is also retrievable via the GBIF data portal through this link: http://data.gbif.org/datasets/resource/14697 A dedicated geo-portal, developed by the Belgian Biodiversity Platform is accessible at: http://www.formicidae-atlas.be FORMIDABEL is a joint cooperation of the Flemish ants working group "Polyergus" (http://formicidae.be) and the Wallonian ants working group "FourmisWalBru" (http://fourmiswalbru.be). The original database was created in 2002 in the context of the preliminary red data book of Flemish Ants (Dekoninck et al. 2003). Later, in 2005, data from the Southern part of Belgium; Wallonia and Brussels were added. In 2012 this dataset was again updated for the creation of the first Belgian Ants Atlas (Figure 1) (Dekoninck et al. 2012). The main purpose of this atlas was to generate maps for all outdoor-living ant species in Belgium using an overlay of the standard Belgian ecoregions. By using this overlay for most species, we can discern a clear and often restricted distribution pattern in Belgium, mainly based on vegetation and soil types.

  8. Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature.

    Science.gov (United States)

    Ravikumar, Komandur Elayavilli; Wagholikar, Kavishwar B; Li, Dingcheng; Kocher, Jean-Pierre; Liu, Hongfang

    2015-06-06

    Advances in the next generation sequencing technology has accelerated the pace of individualized medicine (IM), which aims to incorporate genetic/genomic information into medicine. One immediate need in interpreting sequencing data is the assembly of information about genetic variants and their corresponding associations with other entities (e.g., diseases or medications). Even with dedicated effort to capture such information in biological databases, much of this information remains 'locked' in the unstructured text of biomedical publications. There is a substantial lag between the publication and the subsequent abstraction of such information into databases. Multiple text mining systems have been developed, but most of them focus on the sentence level association extraction with performance evaluation based on gold standard text annotations specifically prepared for text mining systems. We developed and evaluated a text mining system, MutD, which extracts protein mutation-disease associations from MEDLINE abstracts by incorporating discourse level analysis, using a benchmark data set extracted from curated database records. MutD achieves an F-measure of 64.3% for reconstructing protein mutation disease associations in curated database records. Discourse level analysis component of MutD contributed to a gain of more than 10% in F-measure when compared against the sentence level association extraction. Our error analysis indicates that 23 of the 64 precision errors are true associations that were not captured by database curators and 68 of the 113 recall errors are caused by the absence of associated disease entities in the abstract. After adjusting for the defects in the curated database, the revised F-measure of MutD in association detection reaches 81.5%. Our quantitative analysis reveals that MutD can effectively extract protein mutation disease associations when benchmarking based on curated database records. The analysis also demonstrates that incorporating

  9. QSAR Modeling Using Large-Scale Databases: Case Study for HIV-1 Reverse Transcriptase Inhibitors.

    Science.gov (United States)

    Tarasova, Olga A; Urusova, Aleksandra F; Filimonov, Dmitry A; Nicklaus, Marc C; Zakharov, Alexey V; Poroikov, Vladimir V

    2015-07-27

    Large-scale databases are important sources of training sets for various QSAR modeling approaches. Generally, these databases contain information extracted from different sources. This variety of sources can produce inconsistency in the data, defined as sometimes widely diverging activity results for the same compound against the same target. Because such inconsistency can reduce the accuracy of predictive models built from these data, we are addressing the question of how best to use data from publicly and commercially accessible databases to create accurate and predictive QSAR models. We investigate the suitability of commercially and publicly available databases to QSAR modeling of antiviral activity (HIV-1 reverse transcriptase (RT) inhibition). We present several methods for the creation of modeling (i.e., training and test) sets from two, either commercially or freely available, databases: Thomson Reuters Integrity and ChEMBL. We found that the typical predictivities of QSAR models obtained using these different modeling set compilation methods differ significantly from each other. The best results were obtained using training sets compiled for compounds tested using only one method and material (i.e., a specific type of biological assay). Compound sets aggregated by target only typically yielded poorly predictive models. We discuss the possibility of "mix-and-matching" assay data across aggregating databases such as ChEMBL and Integrity and their current severe limitations for this purpose. One of them is the general lack of complete and semantic/computer-parsable descriptions of assay methodology carried by these databases that would allow one to determine mix-and-matchability of result sets at the assay level.

  10. Evaluation of unique identifiers used as keys to match identical publications in Pure and SciVal

    DEFF Research Database (Denmark)

    Madsen, Heidi Holst; Madsen, Dicte; Gauffriau, Marianne

    2016-01-01

    , and erroneous optical or special character recognition. The case study explores the use of UIDs in the integration between the databases Pure and SciVal. Specifically journal publications in English are matched between the two databases. We find all error types except erroneous optical or special character...... recognition in our publication sets. In particular the duplicate DOIs constitute a problem for the calculation of bibliometric indicators as both keeping the duplicates to improve the reliability of citation counts and deleting them to improve the reliability of publication counts will distort the calculation...

  11. The Development and Usage of the Overseas Sinology Database

    Directory of Open Access Journals (Sweden)

    Ling Bao

    2007-12-01

    Full Text Available The Overseas Sinology Database is composed of three databases: scholar, organization, and journal. The thesis database is regard as separate and is attached to the scholar database. The database information comes from major areas of the world, especially the countries adjacent to China, and updates are done continuously. The Sinology Database is in several different languages and should satisfy the differing needs of data collection and database application. The data quality is strictly controlled during the whole data life cycle, which includes data collection, processing, storage, and accessing. In addition, according to the standards and specifications of the metadata, metadata are created to accompany the data, which satisfies the cooperation among different databases. Finally, besides the function of searching, statistical calculation, and sorting, the database is also used for data mining and knowledge discovery. Through these methods, conclusions about changes in Sinology can be drawn, which will aid us in understanding the world and China in particular.

  12. PADB : Published Association Database

    Directory of Open Access Journals (Sweden)

    Lee Jin-Sung

    2007-09-01

    Full Text Available Abstract Background Although molecular pathway information and the International HapMap Project data can help biomedical researchers to investigate the aetiology of complex diseases more effectively, such information is missing or insufficient in current genetic association databases. In addition, only a few of the environmental risk factors are included as gene-environment interactions, and the risk measures of associations are not indexed in any association databases. Description We have developed a published association database (PADB; http://www.medclue.com/padb that includes both the genetic associations and the environmental risk factors available in PubMed database. Each genetic risk factor is linked to a molecular pathway database and the HapMap database through human gene symbols identified in the abstracts. And the risk measures such as odds ratios or hazard ratios are extracted automatically from the abstracts when available. Thus, users can review the association data sorted by the risk measures, and genetic associations can be grouped by human genes or molecular pathways. The search results can also be saved to tab-delimited text files for further sorting or analysis. Currently, PADB indexes more than 1,500,000 PubMed abstracts that include 3442 human genes, 461 molecular pathways and about 190,000 risk measures ranging from 0.00001 to 4878.9. Conclusion PADB is a unique online database of published associations that will serve as a novel and powerful resource for reviewing and interpreting huge association data of complex human diseases.

  13. Database and Expert Systems Applications

    DEFF Research Database (Denmark)

    Viborg Andersen, Kim; Debenham, John; Wagner, Roland

    submissions. The papers are organized in topical sections on workflow automation, database queries, data classification and recommendation systems, information retrieval in multimedia databases, Web applications, implementational aspects of databases, multimedia databases, XML processing, security, XML...... schemata, query evaluation, semantic processing, information retrieval, temporal and spatial databases, querying XML, organisational aspects of databases, natural language processing, ontologies, Web data extraction, semantic Web, data stream management, data extraction, distributed database systems...

  14. NASA scientific and technical publications: A catalog of special publications, reference publications, conference publications, and technical papers, 1991-1992

    Science.gov (United States)

    1993-01-01

    This catalog lists 458 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered into the NASA Scientific and Technical Information database during accession year 1991 through 1992. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

  15. NASA scientific and technical publications: A catalog of special publications, reference publications, conference publications, and technical papers, 1989

    Science.gov (United States)

    1990-01-01

    This catalog lists 190 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered into the NASA scientific and technical information database during accession year 1989. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

  16. NASA scientific and technical publications: A catalog of Special Publications, Reference Publications, Conference Publications, and Technical Papers, 1987

    Science.gov (United States)

    1988-01-01

    This catalog lists 239 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered in the NASA scientific and technical information database during accession year 1987. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

  17. NASA scientific and technical publications: A catalog of special publications, reference publications, conference publications, and technical papers, 1987-1990

    Science.gov (United States)

    1991-01-01

    This catalog lists 783 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered into NASA Scientific and Technical Information Database during the year's 1987 through 1990. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

  18. Publications in psychology: French issues

    Directory of Open Access Journals (Sweden)

    FRANK ARNOULD

    2009-06-01

    Full Text Available This paper discusses the situation of psychology publications in France, in particular, the visibility of French research through journals and bibliographic databases; the role of publications for the evalua-tion of researchers and laboratories, and the contribution of French psychologists to a national publica-tions archiving platform.

  19. IEEE Conference Publications in Libraries.

    Science.gov (United States)

    Johnson, Karl E.

    1984-01-01

    Conclusions of surveys (63 libraries, OCLC database, University of Rhode Island users) assessing handling of Institute of Electrical and Electronics Engineers (IEEE) conference publications indicate that most libraries fully catalog these publications using LC cataloging, and library patrons frequently require series access to publications. Eight…

  20. IEEE Conference Publications in Libraries.

    Science.gov (United States)

    Johnson, Karl E.

    1984-01-01

    Conclusions of surveys (63 libraries, OCLC database, University of Rhode Island users) assessing handling of Institute of Electrical and Electronics Engineers (IEEE) conference publications indicate that most libraries fully catalog these publications using LC cataloging, and library patrons frequently require series access to publications. Eight…