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Sample records for acids research database

  1. The 2013 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection

    PubMed Central

    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/). PMID:23203983

  2. The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection.

    PubMed

    Galperin, Michael Y; Fernández-Suárez, Xosé M

    2012-01-01

    The 19th annual Database Issue of Nucleic Acids Research features descriptions of 92 new online databases covering various areas of molecular biology and 100 papers describing recent updates to the databases previously described in NAR and other journals. The highlights of this issue include, among others, a description of neXtProt, a knowledgebase on human proteins; a detailed explanation of the principles behind the NCBI Taxonomy Database; NCBI and EBI papers on the recently launched BioSample databases that store sample information for a variety of database resources; descriptions of the recent developments in the Gene Ontology and UniProt Gene Ontology Annotation projects; updates on Pfam, SMART and InterPro domain databases; update papers on KEGG and TAIR, two universally acclaimed databases that face an uncertain future; and a separate section with 10 wiki-based databases, introduced in an accompanying editorial. The NAR online Molecular Biology Database Collection, available at http://www.oxfordjournals.org/nar/database/a/, has been updated and now lists 1380 databases. Brief machine-readable descriptions of the databases featured in this issue, according to the BioDBcore standards, will be provided at the http://biosharing.org/biodbcore web site. The full content of the Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/).

  3. The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection

    PubMed Central

    Galperin, Michael Y.; Fernández-Suárez, Xosé M.

    2012-01-01

    The 19th annual Database Issue of Nucleic Acids Research features descriptions of 92 new online databases covering various areas of molecular biology and 100 papers describing recent updates to the databases previously described in NAR and other journals. The highlights of this issue include, among others, a description of neXtProt, a knowledgebase on human proteins; a detailed explanation of the principles behind the NCBI Taxonomy Database; NCBI and EBI papers on the recently launched BioSample databases that store sample information for a variety of database resources; descriptions of the recent developments in the Gene Ontology and UniProt Gene Ontology Annotation projects; updates on Pfam, SMART and InterPro domain databases; update papers on KEGG and TAIR, two universally acclaimed databases that face an uncertain future; and a separate section with 10 wiki-based databases, introduced in an accompanying editorial. The NAR online Molecular Biology Database Collection, available at http://www.oxfordjournals.org/nar/database/a/, has been updated and now lists 1380 databases. Brief machine-readable descriptions of the databases featured in this issue, according to the BioDBcore standards, will be provided at the http://biosharing.org/biodbcore web site. The full content of the Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/). PMID:22144685

  4. The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection.

    PubMed

    Fernández-Suárez, Xosé M; Rigden, Daniel J; Galperin, Michael Y

    2014-01-01

    The 2014 Nucleic Acids Research Database Issue includes descriptions of 58 new molecular biology databases and recent updates to 123 databases previously featured in NAR or other journals. For convenience, the issue is now divided into eight sections that reflect major subject categories. Among the highlights of this issue are six databases of the transcription factor binding sites in various organisms and updates on such popular databases as CAZy, Database of Genomic Variants (DGV), dbGaP, DrugBank, KEGG, miRBase, Pfam, Reactome, SEED, TCDB and UniProt. There is a strong block of structural databases, which includes, among others, the new RNA Bricks database, updates on PDBe, PDBsum, ArchDB, Gene3D, ModBase, Nucleic Acid Database and the recently revived iPfam database. An update on the NCBI's MMDB describes VAST+, an improved tool for protein structure comparison. Two articles highlight the development of the Structural Classification of Proteins (SCOP) database: one describes SCOPe, which automates assignment of new structures to the existing SCOP hierarchy; the other one describes the first version of SCOP2, with its more flexible approach to classifying protein structures. This issue also includes a collection of articles on bacterial taxonomy and metagenomics, which includes updates on the List of Prokaryotic Names with Standing in Nomenclature (LPSN), Ribosomal Database Project (RDP), the Silva/LTP project and several new metagenomics resources. The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been expanded to 1552 databases. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/).

  5. The 2015 Nucleic Acids Research Database Issue and molecular biology database collection.

    PubMed

    Galperin, Michael Y; Rigden, Daniel J; Fernández-Suárez, Xosé M

    2015-01-01

    The 2015 Nucleic Acids Research Database Issue contains 172 papers that include descriptions of 56 new molecular biology databases, and updates on 115 databases whose descriptions have been previously published in NAR or other journals. Following the classification that has been introduced last year in order to simplify navigation of the entire issue, these articles are divided into eight subject categories. This year's highlights include RNAcentral, an international community portal to various databases on noncoding RNA; ValidatorDB, a validation database for protein structures and their ligands; SASBDB, a primary repository for small-angle scattering data of various macromolecular complexes; MoonProt, a database of 'moonlighting' proteins, and two new databases of protein-protein and other macromolecular complexes, ComPPI and the Complex Portal. This issue also includes an unusually high number of cancer-related databases and other databases dedicated to genomic basics of disease and potential drugs and drug targets. The size of NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/a/, remained approximately the same, following the addition of 74 new resources and removal of 77 obsolete web sites. The entire Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/).

  6. The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection.

    PubMed

    Rigden, Daniel J; Fernández-Suárez, Xosé M; Galperin, Michael Y

    2016-01-04

    The 2016 Database Issue of Nucleic Acids Research starts with overviews of the resources provided by three major bioinformatics centers, the U.S. National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EMBL-EBI) and Swiss Institute for Bioinformatics (SIB). Also included are descriptions of 62 new databases and updates on 95 databases that have been previously featured in NAR plus 17 previously described elsewhere. A number of papers in this issue deal with resources on nucleic acids, including various kinds of non-coding RNAs and their interactions, molecular dynamics simulations of nucleic acid structure, and two databases of super-enhancers. The protein database section features important updates on the EBI's Pfam, PDBe and PRIDE databases, as well as a variety of resources on pathways, metabolomics and metabolic modeling. This issue also includes updates on popular metagenomics resources, such as MG-RAST, EBI Metagenomics, and probeBASE, as well as a newly compiled Human Pan-Microbe Communities database. A significant fraction of the new and updated databases are dedicated to the genetic basis of disease, primarily cancer, and various aspects of drug research, including resources for patented drugs, their side effects, withdrawn drugs, and potential drug targets. A further six papers present updated databases of various antimicrobial and anticancer peptides. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been updated with the addition of 88 new resources and removal of 23 obsolete websites, which brought the current listing to 1685 databases.

  7. The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection

    PubMed Central

    Rigden, Daniel J.; Fernández-Suárez, Xosé M.; Galperin, Michael Y.

    2016-01-01

    The 2016 Database Issue of Nucleic Acids Research starts with overviews of the resources provided by three major bioinformatics centers, the U.S. National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EMBL-EBI) and Swiss Institute for Bioinformatics (SIB). Also included are descriptions of 62 new databases and updates on 95 databases that have been previously featured in NAR plus 17 previously described elsewhere. A number of papers in this issue deal with resources on nucleic acids, including various kinds of non-coding RNAs and their interactions, molecular dynamics simulations of nucleic acid structure, and two databases of super-enhancers. The protein database section features important updates on the EBI's Pfam, PDBe and PRIDE databases, as well as a variety of resources on pathways, metabolomics and metabolic modeling. This issue also includes updates on popular metagenomics resources, such as MG-RAST, EBI Metagenomics, and probeBASE, as well as a newly compiled Human Pan-Microbe Communities database. A significant fraction of the new and updated databases are dedicated to the genetic basis of disease, primarily cancer, and various aspects of drug research, including resources for patented drugs, their side effects, withdrawn drugs, and potential drug targets. A further six papers present updated databases of various antimicrobial and anticancer peptides. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been updated with the addition of 88 new resources and removal of 23 obsolete websites, which brought the current listing to 1685 databases. PMID:26740669

  8. The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes

    PubMed Central

    Galperin, Michael Y.; Fernández-Suárez, Xosé M.; Rigden, Daniel J.

    2017-01-01

    This year's Database Issue of Nucleic Acids Research contains 152 papers that include descriptions of 54 new databases and update papers on 98 databases, of which 16 have not been previously featured in NAR. As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene expression and its regulation, proteins, protein domains, and protein–protein interactions. Following the recent trend, an increasing number of new and established databases deal with the issues of human health, from cancer-causing mutations to drugs and drug targets. In accordance with this trend, three recently compiled databases that have been selected by NAR reviewers and editors as ‘breakthrough’ contributions, denovo-db, the Monarch Initiative, and Open Targets, cover human de novo gene variants, disease-related phenotypes in model organisms, and a bioinformatics platform for therapeutic target identification and validation, respectively. We expect these databases to attract the attention of numerous researchers working in various areas of genetics and genomics. Looking back at the past 12 years, we present here the ‘golden set’ of databases that have consistently served as authoritative, comprehensive, and convenient data resources widely used by the entire community and offer some lessons on what makes a successful database. The Database Issue is freely available online at the https://academic.oup.com/nar web site. An updated version of the NAR Molecular Biology Database Collection is available at http://www.oxfordjournals.org/nar/database/a/. PMID:28053160

  9. Surgical research using national databases.

    PubMed

    Alluri, Ram K; Leland, Hyuma; Heckmann, Nathanael

    2016-10-01

    Recent changes in healthcare and advances in technology have increased the use of large-volume national databases in surgical research. These databases have been used to develop perioperative risk stratification tools, assess postoperative complications, calculate costs, and investigate numerous other topics across multiple surgical specialties. The results of these studies contain variable information but are subject to unique limitations. The use of large-volume national databases is increasing in popularity, and thorough understanding of these databases will allow for a more sophisticated and better educated interpretation of studies that utilize such databases. This review will highlight the composition, strengths, and weaknesses of commonly used national databases in surgical research.

  10. Surgical research using national databases

    PubMed Central

    Leland, Hyuma; Heckmann, Nathanael

    2016-01-01

    Recent changes in healthcare and advances in technology have increased the use of large-volume national databases in surgical research. These databases have been used to develop perioperative risk stratification tools, assess postoperative complications, calculate costs, and investigate numerous other topics across multiple surgical specialties. The results of these studies contain variable information but are subject to unique limitations. The use of large-volume national databases is increasing in popularity, and thorough understanding of these databases will allow for a more sophisticated and better educated interpretation of studies that utilize such databases. This review will highlight the composition, strengths, and weaknesses of commonly used national databases in surgical research. PMID:27867945

  11. Biological Databases for Human Research

    PubMed Central

    Zou, Dong; Ma, Lina; Yu, Jun; Zhang, Zhang

    2015-01-01

    The completion of the Human Genome Project lays a foundation for systematically studying the human genome from evolutionary history to precision medicine against diseases. With the explosive growth of biological data, there is an increasing number of biological databases that have been developed in aid of human-related research. Here we present a collection of human-related biological databases and provide a mini-review by classifying them into different categories according to their data types. As human-related databases continue to grow not only in count but also in volume, challenges are ahead in big data storage, processing, exchange and curation. PMID:25712261

  12. Use of acid-suppressive drugs in pregnancy and the risk of childhood asthma: bidirectional crossover study using the general practice research database.

    PubMed

    Hak, Eelko; Mulder, Bianca; Schuiling-Veninga, Catharina C M; de Vries, Tjalling W; Jick, Susan S

    2013-11-01

    Recent studies have reported an association between maternal use of gastric acid-suppressive drugs during pregnancy and asthma in the offspring, but the association could have been confounded by unmeasured risk factors. We assessed the association between the use of acid-suppressive drugs during pregnancy and the risk of developing childhood asthma using a bidirectional crossover design. Mother-infant matched sets in the UK General Practitioners Research Database were used to identify children with a drug-treated asthma diagnosis during the years 2006-2010 who were matched to a sibling without asthma as controls. Primary exposure was use of any anti-suppressive drug during pregnancy, and subgroup analyses were conducted according to drug class (e.g. proton pump inhibitors or histamine 2 receptor antagonists) and trimester. Conditional logistic regression was used to estimate odds ratios (OR) with their corresponding 95 % confidence intervals (CIs). A total of 1,874 children with asthma and 1,874 control siblings were included in the analysis. The exposure rate among case and control pregnancies was 22 and 20 %, respectively. After adjustments for gender, birth order, mother's age and general practice visits, the exposure to any gastric-acid suppressive drug during pregnancy slightly increased the risk for developing asthma (OR 1.23, 95 % CI 1.01-1.51; p = 0.042). A trend towards increased risks was observed for those who used proton pump inhibitors and/or histamine 2 receptor antagonists (adjusted OR 1.72, 95 % CI 1.00-2.98; p = 0.048). These findings lend support to the emerging evidence that exposure to acid-suppressive drugs during pregnancy is associated with childhood asthma. More basic research is now warranted to investigate the mechanisms.

  13. Database on veterinary clinical research in homeopathy.

    PubMed

    Clausen, Jürgen; Albrecht, Henning

    2010-07-01

    The aim of the present report is to provide an overview of the first database on clinical research in veterinary homeopathy. Detailed searches in the database 'Veterinary Clinical Research-Database in Homeopathy' (http://www.carstens-stiftung.de/clinresvet/index.php). The database contains about 200 entries of randomised clinical trials, non-randomised clinical trials, observational studies, drug provings, case reports and case series. Twenty-two clinical fields are covered and eight different groups of species are included. The database is free of charge and open to all interested veterinarians and researchers. The database enables researchers and veterinarians, sceptics and supporters to get a quick overview of the status of veterinary clinical research in homeopathy and alleviates the preparation of systematical reviews or may stimulate reproductions or even new studies. 2010 Elsevier Ltd. All rights reserved.

  14. Correlates of Access to Business Research Databases

    ERIC Educational Resources Information Center

    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.…

  15. Correlates of Access to Business Research Databases

    ERIC Educational Resources Information Center

    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.…

  16. Subject Specific Databases: A Powerful Research Tool

    ERIC Educational Resources Information Center

    Young, Terrence E., Jr.

    2004-01-01

    Subject specific databases, or vortals (vertical portals), are databases that provide highly detailed research information on a particular topic. They are the smallest, most focused search tools on the Internet and, in recent years, they've been on the rise. Currently, more of the so-called "mainstream" search engines, subject directories, and…

  17. Database Support for Research in Public Administration

    ERIC Educational Resources Information Center

    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…

  18. Database Support for Research in Public Administration

    ERIC Educational Resources Information Center

    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…

  19. Using Large Diabetes Databases for Research.

    PubMed

    Wild, Sarah; Fischbacher, Colin; McKnight, John

    2016-09-01

    There are an increasing number of clinical, administrative and trial databases that can be used for research. These are particularly valuable if there are opportunities for linkage to other databases. This paper describes examples of the use of large diabetes databases for research. It reviews the advantages and disadvantages of using large diabetes databases for research and suggests solutions for some challenges. Large, high-quality databases offer potential sources of information for research at relatively low cost. Fundamental issues for using databases for research are the completeness of capture of cases within the population and time period of interest and accuracy of the diagnosis of diabetes and outcomes of interest. The extent to which people included in the database are representative should be considered if the database is not population based and there is the intention to extrapolate findings to the wider diabetes population. Information on key variables such as date of diagnosis or duration of diabetes may not be available at all, may be inaccurate or may contain a large amount of missing data. Information on key confounding factors is rarely available for the nondiabetic or general population limiting comparisons with the population of people with diabetes. However comparisons that allow for differences in distribution of important demographic factors may be feasible using data for the whole population or a matched cohort study design. In summary, diabetes databases can be used to address important research questions. Understanding the strengths and limitations of this approach is crucial to interpret the findings appropriately. © 2016 Diabetes Technology Society.

  20. Nationwide Databases in Orthopaedic Surgery Research.

    PubMed

    Bohl, Daniel D; Singh, Kern; Grauer, Jonathan N

    2016-10-01

    The use of nationwide databases to conduct orthopaedic research has expanded markedly in recent years. Nationwide databases offer large sample sizes, sampling of patients who are representative of the country as a whole, and data that enable investigation of trends over time. The most common use of nationwide databases is to study the occurrence of postoperative adverse events. Other uses include the analysis of costs and the investigation of critical hospital metrics, such as length of stay and readmission rates. Although nationwide databases are powerful research tools, readers should be aware of the differences between them and their limitations. These include variations and potential inaccuracies in data collection, imperfections in patient sampling, insufficient postoperative follow-up, and lack of orthopaedic-specific outcomes.

  1. Research on computer virus database management system

    NASA Astrophysics Data System (ADS)

    Qi, Guoquan

    2011-12-01

    The growing proliferation of computer viruses becomes the lethal threat and research focus of the security of network information. While new virus is emerging, the number of viruses is growing, virus classification increasing complex. Virus naming because of agencies' capture time differences can not be unified. Although each agency has its own virus database, the communication between each other lacks, or virus information is incomplete, or a small number of sample information. This paper introduces the current construction status of the virus database at home and abroad, analyzes how to standardize and complete description of virus characteristics, and then gives the information integrity, storage security and manageable computer virus database design scheme.

  2. NALDB: nucleic acid ligand database for small molecules targeting nucleic acid.

    PubMed

    Kumar Mishra, Subodh; Kumar, Amit

    2016-01-01

    Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their Ki, Kd, IC50 values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php. Database URL: http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php.

  3. NALDB: nucleic acid ligand database for small molecules targeting nucleic acid

    PubMed Central

    Kumar Mishra, Subodh; Kumar, Amit

    2016-01-01

    Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their Ki, Kd, IC50 values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php. Database URL: http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php PMID:26896846

  4. Research Resource: The Endometrium Database Resource (EDR)

    PubMed Central

    Darlington, Yolanda; Jeong, Jae-Wook; Lee, Kevin Y.; Franco, Heather L.; Chen, Edward S.; McOwiti, Apollo; Mistretta, Toni-Ann; Steffen, David; DeMayo, Francesco J.

    2013-01-01

    In order to understand the biology of the endometrium and potentially develop new diagnostic tools and treatments for endometrial diseases, the highly orchestrated gene expression/regulation that occurs within the uterus must first be understood. Even though a wealth of information on endometrial gene expression/regulation is available, this information is scattered across several different resources in formats that can be difficult for the average bench scientist to query, integrate, and utilize. The Endometrium Database Resource (EDR) was created as a single evolving resource for protein- and micro-RNA-encoding genes that have been shown by gene expression microarray, Northern blot, or other experiments in the literature to have their expression regulated in the uterus of humans, mice, rats, cows, domestic pigs, guinea pigs, and sheep. Genes are annotated in EDR with basic gene information (eg, gene symbol and chromosome), gene orthologs, and gene ontologies. Links are also provided to external resources for publication/s, nucleic and amino acid sequence, gene product function, and Gene Expression Omnibus (GEO) phase expression graph information. The resource also allows for direct comparison of relative gene expression in different microarray experiments for genes shown in the literature to be differentially expressed in the uterus. It is available via a user-friendly, web-based interface and is available without charge or restriction to the entire scientific community. The EDR can be accessed at http://edr.research.bcm.edu. PMID:23340253

  5. Research resource: the Endometrium Database Resource (EDR).

    PubMed

    Darlington, Yolanda; Jeong, Jae-Wook; Lee, Kevin Y; Franco, Heather L; Chen, Edward S; McOwiti, Apollo; Mistretta, Toni-Ann; Steffen, David; Becnel, Lauren; DeMayo, Francesco J

    2013-03-01

    In order to understand the biology of the endometrium and potentially develop new diagnostic tools and treatments for endometrial diseases, the highly orchestrated gene expression/regulation that occurs within the uterus must first be understood. Even though a wealth of information on endometrial gene expression/regulation is available, this information is scattered across several different resources in formats that can be difficult for the average bench scientist to query, integrate, and utilize. The Endometrium Database Resource (EDR) was created as a single evolving resource for protein- and micro-RNA-encoding genes that have been shown by gene expression microarray, Northern blot, or other experiments in the literature to have their expression regulated in the uterus of humans, mice, rats, cows, domestic pigs, guinea pigs, and sheep. Genes are annotated in EDR with basic gene information (eg, gene symbol and chromosome), gene orthologs, and gene ontologies. Links are also provided to external resources for publication/s, nucleic and amino acid sequence, gene product function, and Gene Expression Omnibus (GEO) phase expression graph information. The resource also allows for direct comparison of relative gene expression in different microarray experiments for genes shown in the literature to be differentially expressed in the uterus. It is available via a user-friendly, web-based interface and is available without charge or restriction to the entire scientific community. The EDR can be accessed at http://edr.research.bcm.edu.

  6. NAPP: the Nucleic Acid Phylogenetic Profile Database.

    PubMed

    Ott, Alban; Idali, Anouar; Marchais, Antonin; Gautheret, Daniel

    2012-01-01

    Nucleic acid phylogenetic profiling (NAPP) classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes. This procedure efficiently distinguishes clusters of functional non-coding elements in bacteria, particularly small RNAs and cis-regulatory RNAs, from other conserved sequences. In contrast to other non-coding RNA detection pipelines, NAPP does not require the presence of conserved RNA secondary structure and therefore is likely to identify previously undetected RNA genes or elements. Furthermore, as NAPP clusters contain both coding and non-coding sequences with similar occurrence profiles, they can be analyzed under a functional perspective. We recently improved the NAPP pipeline and applied it to a collection of 949 bacterial and 68 archaeal species. The database and web interface available at http://napp.u-psud.fr/ enable detailed analysis of NAPP clusters enriched in non-coding RNAs, graphical display of phylogenetic profiles, visualization of predicted RNAs in their genome context and extraction of predicted RNAs for use with genome browsers or other software.

  7. NAPP: the Nucleic Acid Phylogenetic Profile Database

    PubMed Central

    Ott, Alban; Idali, Anouar; Marchais, Antonin; Gautheret, Daniel

    2012-01-01

    Nucleic acid phylogenetic profiling (NAPP) classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes. This procedure efficiently distinguishes clusters of functional non-coding elements in bacteria, particularly small RNAs and cis-regulatory RNAs, from other conserved sequences. In contrast to other non-coding RNA detection pipelines, NAPP does not require the presence of conserved RNA secondary structure and therefore is likely to identify previously undetected RNA genes or elements. Furthermore, as NAPP clusters contain both coding and non-coding sequences with similar occurrence profiles, they can be analyzed under a functional perspective. We recently improved the NAPP pipeline and applied it to a collection of 949 bacterial and 68 archaeal species. The database and web interface available at http://napp.u-psud.fr/ enable detailed analysis of NAPP clusters enriched in non-coding RNAs, graphical display of phylogenetic profiles, visualization of predicted RNAs in their genome context and extraction of predicted RNAs for use with genome browsers or other software. PMID:21984475

  8. Multicenter neonatal databases: Trends in research uses.

    PubMed

    Creel, Liza M; Gregory, Sean; McNeal, Catherine J; Beeram, Madhava R; Krauss, David R

    2017-01-13

    In the US, approximately 12.7% of all live births are preterm, 8.2% of live births were low birth weight (LBW), and 1.5% are very low birth weight (VLBW). Although technological advances have improved mortality rates among preterm and LBW infants, improving overall rates of prematurity and LBW remains a national priority. Monitoring short- and long-term outcomes is critical for advancing medical treatment and minimizing morbidities associated with prematurity or LBW; however, studying these infants can be challenging. Several large, multi-center neonatal databases have been developed to improve research and quality improvement of treatments for and outcomes of premature and LBW infants. The purpose of this systematic review was to describe three multi-center neonatal databases. We conducted a literature search using PubMed and Google Scholar over the period 1990 to August 2014. Studies were included in our review if one of the databases was used as a primary source of data or comparison. Included studies were categorized by year of publication; study design employed, and research focus. A total of 343 studies published between 1991 and 2014 were included. Studies of premature and LBW infants using these databases have increased over time, and provide evidence for both neonatology and community-based pediatric practice. Research into treatment and outcomes of premature and LBW infants is expanding, partially due to the availability of large, multicenter databases. The consistency of clinical conditions and neonatal outcomes studied since 1990 demonstrates that there are dedicated research agendas and resources that allow for long-term, and potentially replicable, studies within this population.

  9. The Cardiac Safety Research Consortium ECG database.

    PubMed

    Kligfield, Paul; Green, Cynthia L

    2012-01-01

    The Cardiac Safety Research Consortium (CSRC) ECG database was initiated to foster research using anonymized, XML-formatted, digitized ECGs with corresponding descriptive variables from placebo- and positive-control arms of thorough QT studies submitted to the US Food and Drug Administration (FDA) by pharmaceutical sponsors. The database can be expanded to other data that are submitted directly to CSRC from other sources, and currently includes digitized ECGs from patients with genotyped varieties of congenital long-QT syndrome; this congenital long-QT database is also linked to ambulatory electrocardiograms stored in the Telemetric and Holter ECG Warehouse (THEW). Thorough QT data sets are available from CSRC for unblinded development of algorithms for analysis of repolarization and for blinded comparative testing of algorithms developed for the identification of moxifloxacin, as used as a positive control in thorough QT studies. Policies and procedures for access to these data sets are available from CSRC, which has developed tools for statistical analysis of blinded new algorithm performance. A recently approved CSRC project will create a data set for blinded analysis of automated ECG interval measurements, whose initial focus will include comparison of four of the major manufacturers of automated electrocardiographs in the United States. CSRC welcomes application for use of the ECG database for clinical investigation.

  10. Construction of databases: advances and significance in clinical research.

    PubMed

    Long, Erping; Huang, Bingjie; Wang, Liming; Lin, Xiaoyu; Lin, Haotian

    2015-12-01

    Widely used in clinical research, the database is a new type of data management automation technology and the most efficient tool for data management. In this article, we first explain some basic concepts, such as the definition, classification, and establishment of databases. Afterward, the workflow for establishing databases, inputting data, verifying data, and managing databases is presented. Meanwhile, by discussing the application of databases in clinical research, we illuminate the important role of databases in clinical research practice. Lastly, we introduce the reanalysis of randomized controlled trials (RCTs) and cloud computing techniques, showing the most recent advancements of databases in clinical research.

  11. Exhaustive Database Searching for Amino Acid Mutations in Proteomes

    SciTech Connect

    Hyatt, Philip Douglas; Pan, Chongle

    2012-01-01

    Amino acid mutations in proteins can be found by searching tandem mass spectra acquired in shotgun proteomics experiments against protein sequences predicted from genomes. Traditionally, unconstrained searches for amino acid mutations have been accomplished by using a sequence tagging approach that combines de novo sequencing with database searching. However, this approach is limited by the performance of de novo sequencing. The Sipros algorithm v2.0 was developed to perform unconstrained database searching using high-resolution tandem mass spectra by exhaustively enumerating all single non-isobaric mutations for every residue in a protein database. The performance of Sipros for amino acid mutation identification exceeded that of an established sequence tagging algorithm, Inspect, based on benchmarking results from a Rhodopseudomonas palustris proteomics dataset. To demonstrate the viability of the algorithm for meta-proteomics, Sipros was used to identify amino acid mutations in a natural microbial community in acid mine drainage.

  12. Bibliographic databases in support of space processing research

    NASA Technical Reports Server (NTRS)

    Jack, Robert F.

    1987-01-01

    The growth in the number and variety of online bibliographic databases has had two notable impacts on the research community: literature is more readily available to the individual researcher, but the researcher must become more familiar with databases in order to fully exploit them. This presentation provides an overview of online information retrieval; identifies some databases which provide citations to literature relevant to space processing; and offers suggestions regarding how to obtain database search services or additional information.

  13. Emission Database for Global Atmospheric Research (EDGAR).

    ERIC Educational Resources Information Center

    Olivier, J. G. J.; And Others

    1994-01-01

    Presents the objective and methodology chosen for the construction of a global emissions source database called EDGAR and the structural design of the database system. The database estimates on a regional and grid basis, 1990 annual emissions of greenhouse gases, and of ozone depleting compounds from all known sources. (LZ)

  14. Emission Database for Global Atmospheric Research (EDGAR).

    ERIC Educational Resources Information Center

    Olivier, J. G. J.; And Others

    1994-01-01

    Presents the objective and methodology chosen for the construction of a global emissions source database called EDGAR and the structural design of the database system. The database estimates on a regional and grid basis, 1990 annual emissions of greenhouse gases, and of ozone depleting compounds from all known sources. (LZ)

  15. [DICOM data conversion technology research for database].

    PubMed

    Wang, Shiyu; Lin, Hao

    2010-12-01

    A comprehensive medical image platform built for medical images network access, measurements and virtual surgery navigation needs the support of medical image databases. The medical image database we built contains two-dimensional images and three-dimensional models. The common databases based on DICOM storing do not meet the requirements. We use the technology of DICOM conversion to convert DICOM into BMP images and indispensable data elements, and then we use the BMP images and indispensable data elements to reconstruct the three-dimensional model. The reliability of DICOM data conversion is verified, and on this basis, a human hip joint medical image database is built. Experimental results show that this method used in building the medical image database can not only meet the requirements of database application, but also greatly reduce the amount of database storage.

  16. The Microcomputer in Historical Research: Accessing Commercial Databases.

    ERIC Educational Resources Information Center

    Rowney, Don Karl

    1985-01-01

    Online information services (e.g., DIALOG, ORBIT) and computer databases (e.g., Social Sciences Citation Index, Historical Abstracts) that historians can use in their historical research are discussed. The important differences among representative databases are described. (RM)

  17. Aggregated Interdisciplinary Databases and the Needs of Undergraduate Researchers

    ERIC Educational Resources Information Center

    Fister, Barbara; Gilbert, Julie; Fry, Amy Ray

    2008-01-01

    After seeing growing frustration among inexperienced undergraduate researchers searching a popular aggregated interdisciplinary database, the authors questioned whether the leading interdisciplinary databases are serving undergraduates' needs. As a preliminary exploration of this question, the authors queried vendors, analyzed their marketing…

  18. Database tools in genetic diseases research.

    PubMed

    Bianco, Anna Monica; Marcuzzi, Annalisa; Zanin, Valentina; Girardelli, Martina; Vuch, Josef; Crovella, Sergio

    2013-02-01

    The knowledge of the human genome is in continuous progression: a large number of databases have been developed to make meaningful connections among worldwide scientific discoveries. This paper reviews bioinformatics resources and database tools specialized in disseminating information regarding genetic disorders. The databases described are useful for managing sample sequences, gene expression and post-transcriptional regulation. In relation to data sets available from genome-wide association studies, we describe databases that could be the starting point for developing studies in the field of complex diseases, particularly those in which the causal genes are difficult to identify.

  19. RIDE: the Research Infrastructure Database for EPOS

    NASA Astrophysics Data System (ADS)

    Bailo, Daniele; Bartoloni, Alessandro; Jeffery, Keith G.; Clemenceau, Alice; Hoffmann, Thomas L.

    2013-04-01

    The European Plate Observing System (EPOS) is a European initiative which aims to promote and make possible innovative approaches for a better understanding of the physical processes laying behind natural events and geo-science phenomena (earthquakes, volcanic eruptions, unrest episodes and tsunamis etc.) by integrating existing national and trans-national Research Infrastructures (RIs). Such integration will increase access and use of the multidisciplinary data recorded by solid Earth monitoring networks, acquired in laboratory experiments and/or produced by computational simulations. Here we present the Research Infrastructures Database for EPOS (RIDE), a database containing technical information about the different RIs declared by EPOS partners and EPOS associate partners, which will eventually compose the EPOS distributed Research Infrastructure. The main goals of RIDE are (i) to allow the EPOS RI to be organized, with interactive access and information mining available to a broad community of users and stakeholders, (ii) to have a first set of information to be stored in the EPOS catalogue, which will be used as a basis for the development of EPOS Core Services, (iii) to enable EPOS partners to revise and update the current RI information, (iv) to show the contents of the EPOS integration plan to all stakeholders, (v) to facilitate the dissemination of existing data infrastructures to different communities and to promote a discussion within the community to implement the present data infrastructures. RIDE - whose driving technology is Apache CouchDB - contains at the current status detailed information on more than 200 Research Infrastructures. It enables any user to visualize RIs and sensors on a map, to carry out statistics on the stored data and to browse through the details of any RI. Based on the content of RIDE it is now possible to estimate the potential size of the new EPOS distributed RI: EPOS is going to integrate more than 7000 sensors (seismic

  20. Hypertext and Database Tools for Qualitative Research.

    ERIC Educational Resources Information Center

    Horney, Mark A.; Healey, Deborah

    This study compared and contrasted the use of hypertext and relational database knowledge representation techniques in the analysis of qualitative data. A parallel analysis of teacher interview transcripts was conducted with two computer programs: "EntryWay," a hypertext editor, and "FoxBase+/Mac," a relational database with a…

  1. AAindex: amino acid index database, progress report 2008

    PubMed Central

    Kawashima, Shuichi; Pokarowski, Piotr; Pokarowska, Maria; Kolinski, Andrzej; Katayama, Toshiaki; Kanehisa, Minoru

    2008-01-01

    AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. We have added a collection of protein contact potentials to the AAindex as a new section. Accordingly AAindex consists of three sections now: AAindex1 for the amino acid index of 20 numerical values, AAindex2 for the amino acid substitution matrix and AAindex3 for the statistical protein contact potentials. All data are derived from published literature. The database can be accessed through the DBGET/LinkDB system at GenomeNet (http://www.genome.jp/dbget-bin/www_bfind?aaindex) or downloaded by anonymous FTP (ftp://ftp.genome.jp/pub/db/community/aaindex/). PMID:17998252

  2. The Cystic Fibrosis Database: Content and Research Opportunities.

    ERIC Educational Resources Information Center

    Shaw, William M., Jr.; And Others

    1991-01-01

    Describes the files contained in the Cystic Fibrosis (CF) database and discusses educational and research opportunities using this database. Topics discussed include queries, evaluating the relevance of items retrieved, and use of the database in an online searching course in the School of Information and Library Science at the University of North…

  3. The Cystic Fibrosis Database: Content and Research Opportunities.

    ERIC Educational Resources Information Center

    Shaw, William M., Jr.; And Others

    1991-01-01

    Describes the files contained in the Cystic Fibrosis (CF) database and discusses educational and research opportunities using this database. Topics discussed include queries, evaluating the relevance of items retrieved, and use of the database in an online searching course in the School of Information and Library Science at the University of North…

  4. The Human Communication Research Centre dialogue database.

    PubMed

    Anderson, A H; Garrod, S C; Clark, A; Boyle, E; Mullin, J

    1992-10-01

    The HCRC dialogue database consists of over 700 transcribed and coded dialogues from pairs of speakers aged from seven to fourteen. The speakers are recorded while tackling co-operative problem-solving tasks and the same pairs of speakers are recorded over two years tackling 10 different versions of our two tasks. In addition there are over 200 dialogues recorded between pairs of undergraduate speakers engaged on versions of the same tasks. Access to the database, and to its accompanying custom-built search software, is available electronically over the JANET system by contacting liz@psy.glasgow.ac.uk, from whom further information about the database and a user's guide to the database can be obtained.

  5. Research Directions in Database Security IV

    DTIC Science & Technology

    1993-07-01

    second algorithm, which is based on multiversion timestamp ordering, is that high level transactions can be forced to read arbitrarily old data values...system. The first, the single ver- sion model, stores only the latest veision of each data item, while the second, the 88 multiversion model, stores... Multiversion Database Model In the standard database model, where there is only one version of each data item, all transactions compete for the most recent

  6. Databases and registers: useful tools for research, no studies.

    PubMed

    Curbelo, Rafael J; Loza, Estíbaliz; de Yébenes, Maria Jesús García; Carmona, Loreto

    2014-04-01

    There are many misunderstandings about databases. Database is a commonly misused term in reference to any set of data entered into a computer. However, true databases serve a main purpose, organising data. They do so by establishing several layers of relationships; databases are hierarchical. Databases commonly organise data over different levels and over time, where time can be measured as the time between visits, or between treatments, or adverse events, etc. In this sense, medical databases are closely related to longitudinal observational studies, as databases allow the introduction of data on the same patient over time. Basically, we could establish four types of databases in medicine, depending on their purpose: (1) administrative databases, (2) clinical databases, (3) registers, and (4) study-oriented databases. But a database is a useful tool for a large variety of studies, not a type of study itself. Different types of databases serve very different purposes, and a clear understanding of the different research designs mentioned in this paper would prevent many of the databases we launch from being just a lot of work and very little science.

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

    PubMed

    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.

  8. Acid precipitation. (Latest citations from Pollution Abstracts database). Published Search

    SciTech Connect

    Not Available

    1993-09-01

    The bibliography contains citations concerning the research of acid precipitation, and the resultant acidification of land and water. Topics include composition, causes, effects, sources, measurements, and controls of acid precipitation. Worldwide geographical distribution of acid precipitation and acidification are covered. (Contains 250 citations and includes a subject term index and title list.)

  9. Comparison Shopping of Tax Research Databases.

    ERIC Educational Resources Information Center

    Scanlan, Jean M.

    1990-01-01

    Examines and compares online sources for primary and secondary federal and state tax information. The criteria used to evaluate the four systems (CCH ACCESS, LEXIS, PHINet, and WESTLAW) include the contents of each database, search features, hardware requirements, software, pricing, availability of CD-ROM, online billing, and network…

  10. Comparison Shopping of Tax Research Databases.

    ERIC Educational Resources Information Center

    Scanlan, Jean M.

    1990-01-01

    Examines and compares online sources for primary and secondary federal and state tax information. The criteria used to evaluate the four systems (CCH ACCESS, LEXIS, PHINet, and WESTLAW) include the contents of each database, search features, hardware requirements, software, pricing, availability of CD-ROM, online billing, and network…

  11. CKAAPs DB: a conserved key amino acid positions database.

    PubMed

    Li, W W; Reddy, B V; Shindyalov, I N; Bourne, P E

    2001-01-01

    The Conserved Key Amino Acid Positions DataBase (CKAAPs DB) provides access to an analysis of structurally similar proteins with dissimilar sequences where key residues within a common fold are identified. The derivation and significance of CKAAPs starting from pairwise structure alignments is described fully in Reddy et al. [Reddy,B.V.B., Li,W.W., Shindyalov,I.N. and Bourne,P.E. (2000) PROTEINS:, in press]. The CKAAPs identified from this theoretical analysis are provided to experimentalists and theoreticians for potential use in protein engineering and modeling. It has been suggested that CKAAPs may be crucial features for protein folding, structural stability and function. Over 170 substructures, as defined by the Combinatorial Extension (CE) database, which are found in approximately 3000 representative polypeptide chains have been analyzed and are available in the CKAAPs DB. CKAAPs DB also provides CKAAPs of the representative set of proteins derived from the CE and FSSP databases. Thus the database contains over 5000 representative poly-peptide chains, covering all known structures in the PDB. A web interface to a relational database permits fast retrieval of structure-sequence alignments, CKAAPs and associated statistics. Users may query by PDB ID, protein name, function and Enzyme Classification number. Users may also submit protein alignments of their own to obtain CKAAPs. An interface to display CKAAPs on each structure from a web browser is also being implemented. CKAAPs DB is maintained by the San Diego Supercomputer Center and accessible at the URL http://ckaaps.sdsc.edu.

  12. GATMD: γ-Aminobutyric Acid Transporter Mutagenesis Database

    PubMed Central

    Anderson, Cynthia M.; Kidd, Patrick D.; Eskandari, Sepehr

    2010-01-01

    Since the cloning of the first γ-aminobutyric acid (GABA) transporter (GAT1; SLC6A1) from rat brain in 1990, more than 50 published studies have provided structure–function information on investigator-designed rat and mouse GAT1 mutants. To date, more than 200 of 599 GAT1 residues have been subjected to mutagenesis experiments by substitution with different amino acids, and the resulting transporter functional properties have significantly advanced our understanding of the mechanism of Na+- and Cl–-coupled GABA transport by this important member of the neurotransmitter:sodium symporter family. Moreover, many studies have addressed the functional consequences of amino acid deletion or insertion at various positions along the primary sequence. The enormity of this growing body of structure–function information has prompted us to develop GABA Transporter Mutagenesis Database (GATMD), a web-accessible, relational database of manually annotated biochemical, functional and pharmacological data reported on GAT1—the most intensely studied GABA transporter isoform. As of the last update of GATMD, 52 GAT1 mutagenesis papers have yielded 3360 experimental records, which collectively contain a total of ∼100 000 annotated parameters. Database URL: http://physiology.sci.csupomona.edu/GATMD/ PMID:21131297

  13. Implementation of the FAA research and development electromagnetic database

    NASA Technical Reports Server (NTRS)

    Mcdowall, R. L.; Grush, D. J.; Cook, D. M.; Glynn, M. S.

    1991-01-01

    The Idaho National Engineering Laboratory (INEL) has been assisting the FAA in developing a database of information about lightning. The FAA Research and Development Electromagnetic Database (FRED) will ultimately contain data from a variety of airborne and ground-based lightning research projects. An outline of the data currently available in FRED is presented. The data sources which the FAA intends to incorporate into FRED are listed. In addition, it describes how the researchers may access and use the FRED menu system.

  14. Using databases in medical education research: AMEE Guide No. 77.

    PubMed

    Cleland, Jennifer; Scott, Neil; Harrild, Kirsten; Moffat, Mandy

    2013-05-01

    This AMEE Guide offers an introduction to the use of databases in medical education research. It is intended for those who are contemplating conducting research in medical education but are new to the field. The Guide is structured around the process of planning your research so that data collection, management and analysis are appropriate for the research question. Throughout we consider contextual possibilities and constraints to educational research using databases, such as the resources available, and provide concrete examples of medical education research to illustrate many points. The first section of the Guide explains the difference between different types of data and classifying data, and addresses the rationale for research using databases in medical education. We explain the difference between qualitative research and qualitative data, the difference between categorical and quantitative data, and the difference types of data which fall into these categories. The Guide reviews the strengths and weaknesses of qualitative and quantitative research. The next section is structured around how to work with quantitative and qualitative databases and provides guidance on the many practicalities of setting up a database. This includes how to organise your database, including anonymising data and coding, as well as preparing and describing your data so it is ready for analysis. The critical matter of the ethics of using databases in medical educational research, including using routinely collected data versus data collected for research purposes, and issues of confidentiality, is discussed. Core to the Guide is drawing out the similarities and differences in working with different types of data and different types of databases. Future AMEE Guides in the research series will address statistical analysis of data in more detail.

  15. The Vocational Guidance Research Database: A Scientometric Approach

    ERIC Educational Resources Information Center

    Flores-Buils, Raquel; Gil-Beltran, Jose Manuel; Caballer-Miedes, Antonio; Martinez-Martinez, Miguel Angel

    2012-01-01

    The scientometric study of scientific output through publications in specialized journals cannot be undertaken exclusively with the databases available today. For this reason, the objective of this article is to introduce the "Base de Datos de Investigacion en Orientacion Vocacional" [Vocational Guidance Research Database], based on the…

  16. The Vocational Guidance Research Database: A Scientometric Approach

    ERIC Educational Resources Information Center

    Flores-Buils, Raquel; Gil-Beltran, Jose Manuel; Caballer-Miedes, Antonio; Martinez-Martinez, Miguel Angel

    2012-01-01

    The scientometric study of scientific output through publications in specialized journals cannot be undertaken exclusively with the databases available today. For this reason, the objective of this article is to introduce the "Base de Datos de Investigacion en Orientacion Vocacional" [Vocational Guidance Research Database], based on the…

  17. National Databases for Neurosurgical Outcomes Research: Options, Strengths, and Limitations.

    PubMed

    Karhade, Aditya V; Larsen, Alexandra M G; Cote, David J; Dubois, Heloise M; Smith, Timothy R

    2017-08-05

    Quality improvement, value-based care delivery, and personalized patient care depend on robust clinical, financial, and demographic data streams of neurosurgical outcomes. The neurosurgical literature lacks a comprehensive review of large national databases. To assess the strengths and limitations of various resources for outcomes research in neurosurgery. A review of the literature was conducted to identify surgical outcomes studies using national data sets. The databases were assessed for the availability of patient demographics and clinical variables, longitudinal follow-up of patients, strengths, and limitations. The number of unique patients contained within each data set ranged from thousands (Quality Outcomes Database [QOD]) to hundreds of millions (MarketScan). Databases with both clinical and financial data included PearlDiver, Premier Healthcare Database, Vizient Clinical Data Base and Resource Manager, and the National Inpatient Sample. Outcomes collected by databases included patient-reported outcomes (QOD); 30-day morbidity, readmissions, and reoperations (National Surgical Quality Improvement Program); and disease incidence and disease-specific survival (Surveillance, Epidemiology, and End Results-Medicare). The strengths of large databases included large numbers of rare pathologies and multi-institutional nationally representative sampling; the limitations of these databases included variable data veracity, variable data completeness, and missing disease-specific variables. The improvement of existing large national databases and the establishment of new registries will be crucial to the future of neurosurgical outcomes research.

  18. So You Have a Research Idea: A Survey of Databases Available for Plastic Surgery Research.

    PubMed

    Adkinson, Joshua M; Casale, Mia T; Kim, John Y S; Khavanin, Nima; Gutowski, Karol A; Gosain, Arun K

    2016-02-01

    Plastic surgery research using large databases has increased dramatically over the past 20 years. With the magnitude and breadth of information available in these databases, researchers are able to more easily answer a wide variety of research questions. This study sought to provide a comprehensive comparative analysis of the relevant databases for plastic surgery research. Database information, data collection methods, acquisition details, and variable availability were collected for 19 large databases. Examples of potential future research utility were ascribed to each database based on this comprehensive analysis. With a greater understanding of the content, strengths, and limitations of these databases, researchers will be better equipped to select the most appropriate database to answer a specific research question.

  19. 3D geo-database research: Retrospective and future directions

    NASA Astrophysics Data System (ADS)

    Breunig, Martin; Zlatanova, Sisi

    2011-07-01

    3D geo-database research is a promising field to support challenging applications such as 3D urban planning, environmental monitoring, infrastructure management, and early warning or disaster management and response. In these fields, interdisciplinary research in GIScience and related fields is needed to support the modelling, analysis, management, and integration of large geo-referenced data sets, which describe human activities and geophysical phenomena. Geo-databases may serve as platforms to integrate 2D maps, 3D geo-scientific models, and other geo-referenced data. However, current geo-databases do not provide sufficient 3D data modelling and data handling techniques. New 3D geo-databases are needed to handle surface and volume models. This article first presents a 25-year retrospective of geo-database research. Data modelling, standards, and indexing of geo-data are discussed in detail. New directions for the development of 3D geo-databases to open new fields for interdisciplinary research are addressed. Two scenarios in the fields of early warning and emergency response demonstrate the combined management of human and geophysical phenomena. The article concludes with a critical outlook on open research problems.

  20. Generation of Comprehensive Thoracic Oncology Database - Tool for Translational Research

    PubMed Central

    Surati, Mosmi; Robinson, Matthew; Nandi, Suvobroto; Faoro, Leonardo; Demchuk, Carley; Kanteti, Rajani; Ferguson, Benjamin; Gangadhar, Tara; Hensing, Thomas; Hasina, Rifat; Husain, Aliya; Ferguson, Mark; Karrison, Theodore; Salgia, Ravi

    2011-01-01

    The Thoracic Oncology Program Database Project was created to serve as a comprehensive, verified, and accessible repository for well-annotated cancer specimens and clinical data to be available to researchers within the Thoracic Oncology Research Program. This database also captures a large volume of genomic and proteomic data obtained from various tumor tissue studies. A team of clinical and basic science researchers, a biostatistician, and a bioinformatics expert was convened to design the database. Variables of interest were clearly defined and their descriptions were written within a standard operating manual to ensure consistency of data annotation. Using a protocol for prospective tissue banking and another protocol for retrospective banking, tumor and normal tissue samples from patients consented to these protocols were collected. Clinical information such as demographics, cancer characterization, and treatment plans for these patients were abstracted and entered into an Access database. Proteomic and genomic data have been included in the database and have been linked to clinical information for patients described within the database. The data from each table were linked using the relationships function in Microsoft Access to allow the database manager to connect clinical and laboratory information during a query. The queried data can then be exported for statistical analysis and hypothesis generation. PMID:21304468

  1. Databases for multilevel biophysiology research available at Physiome.jp.

    PubMed

    Asai, Yoshiyuki; Abe, Takeshi; Li, Li; Oka, Hideki; Nomura, Taishin; Kitano, Hiroaki

    2015-01-01

    Physiome.jp (http://physiome.jp) is a portal site inaugurated in 2007 to support model-based research in physiome and systems biology. At Physiome.jp, several tools and databases are available to support construction of physiological, multi-hierarchical, large-scale models. There are three databases in Physiome.jp, housing mathematical models, morphological data, and time-series data. In late 2013, the site was fully renovated, and in May 2015, new functions were implemented to provide information infrastructure to support collaborative activities for developing models and performing simulations within the database framework. This article describes updates to the databases implemented since 2013, including cooperation among the three databases, interactive model browsing, user management, version management of models, management of parameter sets, and interoperability with applications.

  2. An image database management system for conducting CAD research

    NASA Astrophysics Data System (ADS)

    Gruszauskas, Nicholas; Drukker, Karen; Giger, Maryellen L.

    2007-03-01

    The development of image databases for CAD research is not a trivial task. The collection and management of images and their related metadata from multiple sources is a time-consuming but necessary process. By standardizing and centralizing the methods in which these data are maintained, one can generate subsets of a larger database that match the specific criteria needed for a particular research project in a quick and efficient manner. A research-oriented management system of this type is highly desirable in a multi-modality CAD research environment. An online, webbased database system for the storage and management of research-specific medical image metadata was designed for use with four modalities of breast imaging: screen-film mammography, full-field digital mammography, breast ultrasound and breast MRI. The system was designed to consolidate data from multiple clinical sources and provide the user with the ability to anonymize the data. Input concerning the type of data to be stored as well as desired searchable parameters was solicited from researchers in each modality. The backbone of the database was created using MySQL. A robust and easy-to-use interface for entering, removing, modifying and searching information in the database was created using HTML and PHP. This standardized system can be accessed using any modern web-browsing software and is fundamental for our various research projects on computer-aided detection, diagnosis, cancer risk assessment, multimodality lesion assessment, and prognosis. Our CAD database system stores large amounts of research-related metadata and successfully generates subsets of cases that match the user's desired search criteria.

  3. Heterogeneous biomedical database integration using a hybrid strategy: a p53 cancer research database.

    PubMed

    Bichutskiy, Vadim Y; Colman, Richard; Brachmann, Rainer K; Lathrop, Richard H

    2007-02-20

    Complex problems in life science research give rise to multidisciplinary collaboration, and hence, to the need for heterogeneous database integration. The tumor suppressor p53 is mutated in close to 50% of human cancers, and a small drug-like molecule with the ability to restore native function to cancerous p53 mutants is a long-held medical goal of cancer treatment. The Cancer Research DataBase (CRDB) was designed in support of a project to find such small molecules. As a cancer informatics project, the CRDB involved small molecule data, computational docking results, functional assays, and protein structure data. As an example of the hybrid strategy for data integration, it combined the mediation and data warehousing approaches. This paper uses the CRDB to illustrate the hybrid strategy as a viable approach to heterogeneous data integration in biomedicine, and provides a design method for those considering similar systems. More efficient data sharing implies increased productivity, and, hopefully, improved chances of success in cancer research. (Code and database schemas are freely downloadable, http://www.igb.uci.edu/research/research.html.).

  4. Nucleic Acid Database: a Repository of Three-Dimensional Information about Nucleic Acids

    DOE Data Explorer

    Berman, H. M.; Olson, W. K.; Beveridge, D. L.; Westbrook, J.; Gelbin, A.; Demeny, T.; Hsieh, S. H.; Srinivasan, A. R.; Schneider, B.

    The Nucleic Acid Database (NDB) provides 3-D structural information about nucleic acids.  It is a relational database designed to facilitate the easy search for nucleic acid structures using any of the stored primary or derived structural features. Reports can then be created describing any properties of the selected structures and structures may be viewed in several different formats, including the mmCIF format, the NDB Atlas format, the NDB coordinate format, or the PDB coordinate format. Browsing structure images created directly from coordinates in the repository can also be done. More than 7000 structures have been released as of May 2014. This website also includes a number of specialized tools and interfaces. The NDB Project is funded by the National Institutes of Health and has been funded by the National Science Foundation and the Department of Energy in the past.

  5. NIST Gas Hydrate Research Database and Web Dissemination Channel

    PubMed Central

    Kroenlein, K.; Muzny, C. D.; Kazakov, A.; Diky, V. V.; Chirico, R. D.; Frenkel, M.; Sloan, E. D.

    2010-01-01

    To facilitate advances in application of technologies pertaining to gas hydrates, a freely available data resource containing experimentally derived information about those materials was developed. This work was performed by the Thermodynamic Research Center (TRC) paralleling a highly successful database of thermodynamic and transport properties of molecular pure compounds and their mixtures. Population of the gas-hydrates database required development of guided data capture (GDC) software designed to convert experimental data and metadata into a well organized electronic format, as well as a relational database schema to accommodate all types of numerical and metadata within the scope of the project. To guarantee utility for the broad gas hydrate research community, TRC worked closely with the Committee on Data for Science and Technology (CODATA) task group for Data on Natural Gas Hydrates, an international data sharing effort, in developing a gas hydrate markup language (GHML). The fruits of these efforts are disseminated through the NIST Sandard Reference Data Program [1] as the Clathrate Hydrate Physical Property Database (SRD #156). A web-based interface for this database, as well as scientific results from the Mallik 2002 Gas Hydrate Production Research Well Program [2], is deployed at http://gashydrates.nist.gov. PMID:27134781

  6. NIST Gas Hydrate Research Database and Web Dissemination Channel.

    PubMed

    Kroenlein, K; Muzny, C D; Kazakov, A; Diky, V V; Chirico, R D; Frenkel, M; Sloan, E D

    2010-01-01

    To facilitate advances in application of technologies pertaining to gas hydrates, a freely available data resource containing experimentally derived information about those materials was developed. This work was performed by the Thermodynamic Research Center (TRC) paralleling a highly successful database of thermodynamic and transport properties of molecular pure compounds and their mixtures. Population of the gas-hydrates database required development of guided data capture (GDC) software designed to convert experimental data and metadata into a well organized electronic format, as well as a relational database schema to accommodate all types of numerical and metadata within the scope of the project. To guarantee utility for the broad gas hydrate research community, TRC worked closely with the Committee on Data for Science and Technology (CODATA) task group for Data on Natural Gas Hydrates, an international data sharing effort, in developing a gas hydrate markup language (GHML). The fruits of these efforts are disseminated through the NIST Sandard Reference Data Program [1] as the Clathrate Hydrate Physical Property Database (SRD #156). A web-based interface for this database, as well as scientific results from the Mallik 2002 Gas Hydrate Production Research Well Program [2], is deployed at http://gashydrates.nist.gov.

  7. Norwegian words: A lexical database for clinicians and researchers.

    PubMed

    Lind, Marianne; Simonsen, Hanne Gram; Hansen, Pernille; Holm, Elisabeth; Mevik, Bjørn-Helge

    2015-04-01

    All words have properties linked to form, meaning and usage patterns which influence how easily they are accessed from the mental lexicon in language production, perception and comprehension. Examples of such properties are imageability, phonological and morphological complexity, word class, argument structure, frequency of use and age of acquisition. Due to linguistic and cultural variation the properties and the values associated with them differ across languages. Hence, for research as well as clinical purposes, language specific information on lexical properties is needed. To meet this need, an electronically searchable lexical database with more than 1600 Norwegian words coded for more than 12 different properties has been established. This article presents the content and structure of the database as well as the search options available in the interface. Finally, it briefly describes some of the ways in which the database can be used in research, clinical practice and teaching.

  8. Guidelines for good database selection and use in pharmacoepidemiology research.

    PubMed

    Hall, Gillian C; Sauer, Brian; Bourke, Alison; Brown, Jeffrey S; Reynolds, Matthew W; LoCasale, Robert; Casale, Robert Lo

    2012-01-01

    The use of healthcare databases in research provides advantages such as increased speed, lower costs and limitation of some biases. However, database research has its own challenges as studies must be performed within the limitations of resources, which often are the product of complex healthcare systems. The primary purpose of this document is to assist in the selection and use of data resources in pharmacoepidemiology, highlighting potential limitations and recommending tested procedures. This guidance is presented as a detailed text with a checklist for quick reference and covers six areas: selection of a database, use of multiple data resources, extraction and analysis of the study population, privacy and security, quality and validation procedures and documentation.

  9. Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis

    PubMed Central

    Peng, Zhi-yu; Zhou, Xin; Li, Linchuan; Yu, Xiangchun; Li, Hongjiang; Jiang, Zhiqiang; Cao, Guangyu; Bai, Mingyi; Wang, Xingchun; Jiang, Caifu; Lu, Haibin; Hou, Xianhui; Qu, Lijia; Wang, Zhiyong; Zuo, Jianru; Fu, Xiangdong; Su, Zhen; Li, Songgang; Guo, Hongwei

    2009-01-01

    Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including auxin, gibberellin, cytokinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. Here, we develop an Arabidopsis hormone database, which aims to provide a systematic and comprehensive view of genes participating in plant hormonal regulation, as well as morphological phenotypes controlled by plant hormones. Based on data from mutant studies, transgenic analysis and gene ontology (GO) annotation, we have identified a total of 1026 genes in the Arabidopsis genome that participate in plant hormone functions. Meanwhile, a phenotype ontology is developed to precisely describe myriad hormone-regulated morphological processes with standardized vocabularies. A web interface (http://ahd.cbi.pku.edu.cn) would allow users to quickly get access to information about these hormone-related genes, including sequences, functional category, mutant information, phenotypic description, microarray data and linked publications. Several applications of this database in studying plant hormonal regulation and hormone cross-talk will be presented and discussed. PMID:19015126

  10. Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis.

    PubMed

    Peng, Zhi-yu; Zhou, Xin; Li, Linchuan; Yu, Xiangchun; Li, Hongjiang; Jiang, Zhiqiang; Cao, Guangyu; Bai, Mingyi; Wang, Xingchun; Jiang, Caifu; Lu, Haibin; Hou, Xianhui; Qu, Lijia; Wang, Zhiyong; Zuo, Jianru; Fu, Xiangdong; Su, Zhen; Li, Songgang; Guo, Hongwei

    2009-01-01

    Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including auxin, gibberellin, cytokinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. Here, we develop an Arabidopsis hormone database, which aims to provide a systematic and comprehensive view of genes participating in plant hormonal regulation, as well as morphological phenotypes controlled by plant hormones. Based on data from mutant studies, transgenic analysis and gene ontology (GO) annotation, we have identified a total of 1026 genes in the Arabidopsis genome that participate in plant hormone functions. Meanwhile, a phenotype ontology is developed to precisely describe myriad hormone-regulated morphological processes with standardized vocabularies. A web interface (http://ahd.cbi.pku.edu.cn) would allow users to quickly get access to information about these hormone-related genes, including sequences, functional category, mutant information, phenotypic description, microarray data and linked publications. Several applications of this database in studying plant hormonal regulation and hormone cross-talk will be presented and discussed.

  11. Gas Hydrate Research Database and Web Dissemination Channel

    SciTech Connect

    Micheal Frenkel; Kenneth Kroenlein; V Diky; R.D. Chirico; A. Kazakow; C.D. Muzny; M. Frenkel

    2009-09-30

    To facilitate advances in application of technologies pertaining to gas hydrates, a United States database containing experimentally-derived information about those materials was developed. The Clathrate Hydrate Physical Property Database (NIST Standard Reference Database {number_sign} 156) was developed by the TRC Group at NIST in Boulder, Colorado paralleling a highly-successful database of thermodynamic properties of molecular pure compounds and their mixtures and in association with an international effort on the part of CODATA to aid in international data sharing. Development and population of this database relied on the development of three components of information-processing infrastructure: (1) guided data capture (GDC) software designed to convert data and metadata into a well-organized, electronic format, (2) a relational data storage facility to accommodate all types of numerical and metadata within the scope of the project, and (3) a gas hydrate markup language (GHML) developed to standardize data communications between 'data producers' and 'data users'. Having developed the appropriate data storage and communication technologies, a web-based interface for both the new Clathrate Hydrate Physical Property Database, as well as Scientific Results from the Mallik 2002 Gas Hydrate Production Research Well Program was developed and deployed at http://gashydrates.nist.gov.

  12. A relational database application in support of integrated neuroscience research.

    PubMed

    Rudowsky, Ira; Kulyba, Olga; Kunin, Mikhail; Ogarodnikov, Dmitri; Raphan, Theodore

    2004-12-01

    The development of relational databases has significantly improved the performance of storage, search, and retrieval functions and has made it possible for applications that perform real-time data acquisition and analysis to interact with these types of databases. The purpose of this research was to develop a user interface for interaction between a data acquisition and analysis application and a relational database using the Oracle9i system. The overall system was designed to have an indexing capability that threads into the data acquisition and analysis programs. Tables were designed and relations within the database for indexing the files and information contained within the files were established. The system provides retrieval capabilities over a broad range of media, including analog, event, and video data types. The system's ability to interact with a data capturing program at the time of the experiment to create both multimedia files as well as the meta-data entries in the relational database avoids manual entries in the database and ensures data integrity and completeness for further interaction with the data by analysis applications.

  13. GiSAO.db: a database for ageing research.

    PubMed

    Hofer, Edith; Laschober, Gerhard T; Hackl, Matthias; Thallinger, Gerhard G; Lepperdinger, Günter; Grillari, Johannes; Jansen-Dürr, Pidder; Trajanoski, Zlatko

    2011-05-24

    Age-related gene expression patterns of Homo sapiens as well as of model organisms such as Mus musculus, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster are a basis for understanding the genetic mechanisms of ageing. For an effective analysis and interpretation of expression profiles it is necessary to store and manage huge amounts of data in an organized way, so that these data can be accessed and processed easily. GiSAO.db (Genes involved in senescence, apoptosis and oxidative stress database) is a web-based database system for storing and retrieving ageing-related experimental data. Expression data of genes and miRNAs, annotation data like gene identifiers and GO terms, orthologs data and data of follow-up experiments are stored in the database. A user-friendly web application provides access to the stored data. KEGG pathways were incorporated and links to external databases augment the information in GiSAO.db. Search functions facilitate retrieval of data which can also be exported for further processing. We have developed a centralized database that is very well suited for the management of data for ageing research. The database can be accessed at https://gisao.genome.tugraz.at and all the stored data can be viewed with a guest account.

  14. Key-linked on-line databases for clinical research.

    PubMed

    Müller, Thomas H

    2012-01-01

    Separating patient identification data from clinical data and/or information about biomaterial samples is an effective data protection measure, especially in clinical research employing "on-line", i.e., web-based, data capture. In this paper, we show that this specialised technique can be generalised into a network architecture of interconnected on-line databases potentially serving a variety of purposes. The basic idea of this approach consists of maintaining logical links, i.e., common record keys, between corresponding data structures in pairs of databases while keeping the actual key values hidden from clients. For client systems, simultaneous access to corresponding records is mediated by temporary access tokens. At the relational level, these links are represented by arbitrary unique record keys common to both databases. This architecture allows for integration of related data in different databases without replicating or permanently sharing this data in one place. Each participating on-line database can determine the degree of integration by specifying linkage keys only for those data structures that may be logically connected to other data. Logical links can de designed for specific use cases. In addition, each database controls user access by enforcing its own authorisation scheme. Another advantage is that individual database owners retain considerable leeway in adapting to changing local requirements without compromising the integration into the network. Beyond protecting individual subject identification data, this architecture permits splitting a cooperatively used data pool to achieve many kinds of objectives. Application examples could be clinical registries needing subject contact information for follow-up, biomaterial banks with or without genetic information, and automatic or assisted integration of data from electronic medical records into research data.

  15. THE NATIONAL EXPOSURE RESEARCH LABORATORY'S CONSOLIDATED HUMAN ACTIVITY DATABASE

    EPA Science Inventory

    EPA's National Exposure Research Laboratory (NERL) has combined data from 12 U.S. studies related to human activities into one comprehensive data system that can be accessed via the Internet. The data system is called the Consolidated Human Activity Database (CHAD), and it is ...

  16. Systematically Retrieving Research: A Case Study Evaluating Seven Databases

    ERIC Educational Resources Information Center

    Taylor, Brian; Wylie, Emma; Dempster, Martin; Donnelly, Michael

    2007-01-01

    Objective: Developing the scientific underpinnings of social welfare requires effective and efficient methods of retrieving relevant items from the increasing volume of research. Method: We compared seven databases by running the nearest equivalent search on each. The search topic was chosen for relevance to social work practice with older people.…

  17. Systematically Retrieving Research: A Case Study Evaluating Seven Databases

    ERIC Educational Resources Information Center

    Taylor, Brian; Wylie, Emma; Dempster, Martin; Donnelly, Michael

    2007-01-01

    Objective: Developing the scientific underpinnings of social welfare requires effective and efficient methods of retrieving relevant items from the increasing volume of research. Method: We compared seven databases by running the nearest equivalent search on each. The search topic was chosen for relevance to social work practice with older people.…

  18. THE NATIONAL EXPOSURE RESEARCH LABORATORY'S COMPREHENSIVE HUMAN ACTIVITY DATABASE

    EPA Science Inventory

    EPA's National Exposure Research Laboratory (NERL) has combined data from nine U.S. studies related to human activities into one comprehensive data system that can be accessed via the world-wide web. The data system is called CHAD-Consolidated Human Activity Database-and it is ...

  19. THE NATIONAL EXPOSURE RESEARCH LABORATORY'S CONSOLIDATED HUMAN ACTIVITY DATABASE

    EPA Science Inventory

    EPA's National Exposure Research Laboratory (NERL) has combined data from 12 U.S. studies related to human activities into one comprehensive data system that can be accessed via the Internet. The data system is called the Consolidated Human Activity Database (CHAD), and it is ...

  20. THE NATIONAL EXPOSURE RESEARCH LABORATORY'S COMPREHENSIVE HUMAN ACTIVITY DATABASE

    EPA Science Inventory

    EPA's National Exposure Research Laboratory (NERL) has combined data from nine U.S. studies related to human activities into one comprehensive data system that can be accessed via the world-wide web. The data system is called CHAD-Consolidated Human Activity Database-and it is ...

  1. Geoscience research databases for coastal Alabama ecosystem management

    USGS Publications Warehouse

    Hummell, Richard L.

    1995-01-01

    Effective management of complex coastal ecosystems necessitates access to scientific knowledge that can be acquired through a multidisciplinary approach involving Federal and State scientists that take advantage of agency expertise and resources for the benefit of all participants working toward a set of common research and management goals. Cooperative geostatic investigations have led toward building databases of fundamental scientific knowledge that can be utilized to manage coastal Alabama's natural and future development. These databases have been used to assess the occurrence and economic potential of hard mineral resources in the Alabama EFZ, and to support oil spill contingency planning and environmental analysis for coastal Alabama.

  2. The porcine translational research database: A manually curated, genomics and proteomics-based research resource

    USDA-ARS?s Scientific Manuscript database

    The use of swine in biomedical research has increased dramatically in the last decade. Diverse genomic- and proteomic databases have been developed to facilitate research using human and rodent models. Current porcine gene databases, however, lack the robust annotation to study pig models that are...

  3. Concierge: Personal Database Software for Managing Digital Research Resources

    PubMed Central

    Sakai, Hiroyuki; Aoyama, Toshihiro; Yamaji, Kazutsuna; Usui, Shiro

    2007-01-01

    This article introduces a desktop application, named Concierge, for managing personal digital research resources. Using simple operations, it enables storage of various types of files and indexes them based on content descriptions. A key feature of the software is a high level of extensibility. By installing optional plug-ins, users can customize and extend the usability of the software based on their needs. In this paper, we also introduce a few optional plug-ins: literature management, electronic laboratory notebook, and XooNlps client plug-ins. XooNIps is a content management system developed to share digital research resources among neuroscience communities. It has been adopted as the standard database system in Japanese neuroinformatics projects. Concierge, therefore, offers comprehensive support from management of personal digital research resources to their sharing in open-access neuroinformatics databases such as XooNIps. This interaction between personal and open-access neuroinformatics databases is expected to enhance the dissemination of digital research resources. Concierge is developed as an open source project; Mac OS X and Windows XP versions have been released at the official site (http://concierge.sourceforge.jp). PMID:18974800

  4. Concierge: personal database software for managing digital research resources.

    PubMed

    Sakai, Hiroyuki; Aoyama, Toshihiro; Yamaji, Kazutsuna; Usui, Shiro

    2007-01-01

    This article introduces a desktop application, named Concierge, for managing personal digital research resources. Using simple operations, it enables storage of various types of files and indexes them based on content descriptions. A key feature of the software is a high level of extensibility. By installing optional plug-ins, users can customize and extend the usability of the software based on their needs. In this paper, we also introduce a few optional plug-ins: literature management, electronic laboratory notebook, and XooNlps client plug-ins. XooNIps is a content management system developed to share digital research resources among neuroscience communities. It has been adopted as the standard database system in Japanese neuroinformatics projects. Concierge, therefore, offers comprehensive support from management of personal digital research resources to their sharing in open-access neuroinformatics databases such as XooNIps. This interaction between personal and open-access neuroinformatics databases is expected to enhance the dissemination of digital research resources. Concierge is developed as an open source project; Mac OS X and Windows XP versions have been released at the official site (http://concierge.sourceforge.jp).

  5. Veterinary clinical research database for homeopathy: placebo-controlled trials.

    PubMed

    Clausen, J; Albrecht, H; Mathie, R T

    2013-04-01

    Veterinary homeopathy has led a somewhat shadowy existence since its first introduction. Only in the last three decades has the number of clinical trials increased considerably. This literature is generally not well perceived, which may be partly a consequence of the diffuse and somewhat inaccessible nature of some of the relevant research publications. The Veterinary Clinical Research Database for Homeopathy (VetCR) was launched in 2006 to provide information on existing clinical research in veterinary homeopathy and to facilitate the preparation of systematic reviews. The aim of the present report is to provide an overview of this first database on clinical research in veterinary homeopathy, with a special focus on its content of placebo controlled clinical trials and summarising what is known about placebo effects in animals. In April 2012, the VetCR database contained 302 data records. Among these, 203 controlled trials were identified: 146 randomised and 57 non-randomised. In 97 of those 203 trials, the homeopathic medical intervention was compared to placebo. A program of formal systematic reviews of peer-reviewed randomised controlled trials in veterinary homeopathy is now underway; detailed findings from the program's data extraction and appraisal approach, including the assessment of trial quality (risk of bias), will be reported in due course. Copyright © 2012 Elsevier Ltd. All rights reserved.

  6. A neuroinformatics database system for disease-oriented neuroimaging research.

    PubMed

    Wong, Stephen T C; Hoo, Kent Soo; Cao, Xinhua; Tjandra, Donny; Fu, J C; Dillon, William P

    2004-03-01

    Clinical databases are continually growing and accruing more patient information. One of the challenges for managing this wealth of data is efficient retrieval and analysis of a broad range of image and non-image patient data from diverse data sources. This article describes the design and implementation of a new class of research data warehouse, neuroinformatics database system (NIDS), which will alleviate these problems for clinicians and researchers studying and treating patients with intractable temporal lobe epilepsy. The NIDS is a secured, multi-tier system that enables the user to gather, proofread, analyze, and store data from multiple underlying sources. In addition to data management, the NIDS provides several key functions including image analysis and processing, free text search of patient reports, construction of general queries, and on-line statistical analysis. The establishment of this integrated research database will serve as a foundation for future hypothesis-driven experiments, which could uncover previously unsuspected correlations and perhaps help to identify new and accurate predictors for image diagnosis.

  7. BAO Plate Archive Project: Digitization, Electronic Database and Research Programmes

    NASA Astrophysics Data System (ADS)

    Mickaelian, A. M.; Abrahamyan, H. V.; Andreasyan, H. R.; Azatyan, N. M.; Farmanyan, S. V.; Gigoyan, K. S.; Gyulzadyan, M. V.; Khachatryan, K. G.; Knyazyan, A. V.; Kostandyan, G. R.; Mikayelyan, G. A.; Nikoghosyan, E. H.; Paronyan, G. M.; Vardanyan, A. V.

    2016-06-01

    The most important part of the astronomical observational heritage are astronomical plate archives created on the basis of numerous observations at many observatories. Byurakan Astrophysical Observatory (BAO) plate archive consists of 37,000 photographic plates and films, obtained at 2.6m telescope, 1m and 0.5m Schmidt type and other smaller telescopes during 1947-1991. In 2002-2005, the famous Markarian Survey (also called First Byurakan Survey, FBS) 1874 plates were digitized and the Digitized FBS (DFBS) was created. New science projects have been conducted based on these low-dispersion spectroscopic material. A large project on the whole BAO Plate Archive digitization, creation of electronic database and its scientific usage was started in 2015. A Science Program Board is created to evaluate the observing material, to investigate new possibilities and to propose new projects based on the combined usage of these observations together with other world databases. The Executing Team consists of 11 astronomers and 2 computer scientists and will use 2 EPSON Perfection V750 Pro scanners for the digitization, as well as Armenian Virtual Observatory (ArVO) database will be used to accommodate all new data. The project will run during 3 years in 2015-2017 and the final result will be an electronic database and online interactive sky map to be used for further research projects, mainly including high proper motion stars, variable objects and Solar System bodies.

  8. Advanced Satellite Research Project: SCAR Research Database. Bibliographic analysis

    NASA Technical Reports Server (NTRS)

    Pelton, Joseph N.

    1991-01-01

    The literature search was provided to locate and analyze the most recent literature that was relevant to the research. This was done by cross-relating books, articles, monographs, and journals that relate to the following topics: (1) Experimental Systems - Advanced Communications Technology Satellite (ACTS), and (2) Integrated System Digital Network (ISDN) and Advance Communication Techniques (ISDN and satellites, ISDN standards, broadband ISDN, flame relay and switching, computer networks and satellites, satellite orbits and technology, satellite transmission quality, and network configuration). Bibliographic essay on literature citations and articles reviewed during the literature search task is provided.

  9. U.S. Army Research Laboratory (ARL) multimodal signatures database

    NASA Astrophysics Data System (ADS)

    Bennett, Kelly

    2008-04-01

    The U.S. Army Research Laboratory (ARL) Multimodal Signatures Database (MMSDB) is a centralized collection of sensor data of various modalities that are co-located and co-registered. The signatures include ground and air vehicles, personnel, mortar, artillery, small arms gunfire from potential sniper weapons, explosives, and many other high value targets. This data is made available to Department of Defense (DoD) and DoD contractors, Intel agencies, other government agencies (OGA), and academia for use in developing target detection, tracking, and classification algorithms and systems to protect our Soldiers. A platform independent Web interface disseminates the signatures to researchers and engineers within the scientific community. Hierarchical Data Format 5 (HDF5) signature models provide an excellent solution for the sharing of complex multimodal signature data for algorithmic development and database requirements. Many open source tools for viewing and plotting HDF5 signatures are available over the Web. Seamless integration of HDF5 signatures is possible in both proprietary computational environments, such as MATLAB, and Free and Open Source Software (FOSS) computational environments, such as Octave and Python, for performing signal processing, analysis, and algorithm development. Future developments include extending the Web interface into a portal system for accessing ARL algorithms and signatures, High Performance Computing (HPC) resources, and integrating existing database and signature architectures into sensor networking environments.

  10. Plant database resources at The Institute for Genomic Research.

    PubMed

    Chan, Agnes P; Rabinowicz, Pablo D; Quackenbush, John; Buell, C Robin; Town, Chris D

    2007-01-01

    With the completion of the genome sequences of the model plants Arabidopsis and rice, and the continuing sequencing efforts of other economically important crop plants, an unprecedented amount of genome sequence data is now available for large-scale genomics studies and analyses, such as the identification and discovery of novel genes, comparative genomics, and functional genomics. Efficient utilization of these large data sets is critically dependent on the ease of access and organization of the data. The plant databases at The Institute for Genomic Research (TIGR) have been set up to maintain various data types including genomic sequence, annotation and analyses, expressed transcript assemblies and analyses, and gene expression profiles from microarray studies. We present here an overview of the TIGR database resources for plant genomics and describe methods to access the data.

  11. Scientist, researchers, and acid rain

    SciTech Connect

    Alm, L.R. )

    1989-01-01

    The role of the hidden participants in agenda-setting for environmental issues is discussed. These personnel involve academics, researchers, career bureaucrats, congressional staffers, consultants, and administration appointees below the top level. Scientists have been publicly involved in the acid rain issue from the beginning, using the media to dramatize the possible catastrophic consequences of acid rain. Presently, the scientific community is not in consensus about the solutions to the problem. Since the initial enactment of the National Acid Precipitation Act in 1980, not a single acid rain law has been passed, although many bills have been proposed. Spokesman for the coal and utility industries and Reagan administration personnel have used the scientific disagreements to delay abatement actions and refute claims that acid rain is a severe problem. Another result of the confusion is a distrust and even disdain for academic work. One possible solution to the stalemate is an accurate form for resolving scientific disputes that have a strong political component and that the forum should have a mechanism for converging on accurate science. 19 refs.

  12. Considerations of Online Numeric Databases for Social Science Research,

    DTIC Science & Technology

    1983-09-01

    ROLE OF THE INFORMATION SPECIALIST WITHIN IT DATABASE EVOLUTION Online databases have grown substantially in the last decade. The current edition of...Cuadra Associates Directory of Online Databases , an important industry source, abstracts 1,000 commercially available databases--a figure 25% higher...librarians search bibliographic files online comfortably, they are frequently leery of using numeric online databases . These two online database types 0 differ

  13. Toward an Ontology-Based Framework for Clinical Research Databases

    PubMed Central

    Kong, Y. Megan; Dahlke, Carl; Xiang, Qun; Qian, Yu; Karp, David; Scheuermann, Richard H.

    2010-01-01

    Clinical research includes a wide range of study designs from focused observational studies to complex interventional studies with multiple study arms, treatment and assessment events, and specimen procurement procedures. Participant characteristics from case report forms need to be integrated with molecular characteristics from mechanistic experiments on procured specimens. In order to capture and manage this diverse array of data, we have developed the Ontology-Based eXtensible conceptual model (OBX) to serve as a framework for clinical research data in the Immunology Database and Analysis Portal (ImmPort). By designing OBX around the logical structure of the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI), we have found that a relatively simple conceptual model can represent the relatively complex domain of clinical research. In addition, the common framework provided by BFO makes it straightforward to develop data dictionaries based on reference and application ontologies from the OBO Foundry. PMID:20460173

  14. Acid precipitation. (Latest citations from the Compendex database). Published Search

    SciTech Connect

    Not Available

    1993-06-01

    The bibliography contains citations concerning the causes, effects, sources, and controls of acid precipitation and acidification. Techniques and technology for measurement and analysis of acid precipitation are considered. (Contains 250 citations and includes a subject term index and title list.)

  15. Secondary analysis of large databases for hepatology research.

    PubMed

    Okafor, Philip N; Chiejina, Maria; de Pretis, Nicolo; Talwalkar, Jayant A

    2016-04-01

    Secondary analysis of large datasets involves the utilization of existing data that has typically been collected for other purposes to advance scientific knowledge. This is an established methodology applied in health services research with the unique advantage of efficiently identifying relationships between predictor and outcome variables but which has been underutilized for hepatology research. Our review of 1431 abstracts published in the 2013 European Association for the Study of Liver (EASL) abstract book showed that less than 0.5% of published abstracts utilized secondary analysis of large database methodologies. This review paper describes existing large datasets that can be exploited for secondary analyses in liver disease research. It also suggests potential questions that could be addressed using these data warehouses and highlights the strengths and limitations of each dataset as described by authors that have previously used them. The overall goal is to bring these datasets to the attention of readers and ultimately encourage the consideration of secondary analysis of large database methodologies for the advancement of hepatology.

  16. STEMdex: A Searchable Database of Education Research for Our Community

    NASA Astrophysics Data System (ADS)

    Brinkworth, Carolyn; Nichols-Yehling, M.; Bartolone, L.; Llamas, J.; Crane, M.; Martin, A.; Wenger, M.; Squires, G. K.; Hurt, R. L.

    2014-01-01

    STEMdex is a new resource for the astronomy Education and Outreach community, designed to improve our community’s knowledge of the published literature pertinent to our work. While we all understand that it is important to base our practice on sound research, there are currently 801 peer-reviewed education journals in existence, and members of our community are hard pressed to cover all the published literature. STEMdex consolidates the research relevant to EPO work into a single searchable database, with summaries written by astronomy educators and posted for the entire community to use. The database will ultimately include research across the spectrum of astronomy education, including formal and informal education, outreach, grades K-16, pedagogy, evaluation and many other topics. The site is currently under development, but we have had significant interest from the community, and have a team of 19 EPO professionals and community volunteers from 14 different institutions signed up to contribute to the project. The STEMdex site can be found at stemdex.ipac.caltech.edu.

  17. [Bibliometric analysis of current glaucoma research based on Pubmed database].

    PubMed

    Huang, Wen-bin; Wang, Wei; Zhou, Min-wen; Chen, Shi-da; Zhang, Xiu-lan

    2013-11-01

    To survey the distribution pattern and subject domain knowledge of worldwide glaucoma research based on literatures in Pubmed database. Literatures on glaucoma published in 2007 to 2011 were identified in Pubmed database. The analytic items of an article include published year, country, language author, and journal. After core mesh terms had been characterized by BICOMS, the co-occurrence matrix was built. Cluster analysis was finished by SPSS 20.0. Then visualized network was drawn using ucinet 6.0. Totally 6427 literatures were included, the number of annual articles changed slightly between 2007 and 2011. The United States, England, Germany, Australia, and France together accounted for 77.63% of articles. There were 52 high-frequency subjects and hot topics were clustered into the following 10 categories: (1) Pathology of optic disc and nerve fibers and OCT application, (2) METHODS: of visual field (VF) and visual function examination, (3) Glaucoma drug medications, (4) Pathology and physiology of primary open angle glaucoma (POAG) including VF and intraocular pressure (IOP), (5) Glaucoma surgery, (6) Gene research related to POAG, (7) Glaucoma disease pathology and animal models, (8) Ocular hypertension (OHT) induced complications and corneal changes, (9) Etiology of congenital glaucoma and complications, (10) Etiology and epidemiology of glaucoma. The visualized domain knowledge mapping was successfully built. The pathology of optic disc and nerve fibers, medications, and surgery were well developed. Study on IOP and visual field was in the core domain, which have an important link to etiology, diagnosis, and therapy. The researches on glaucomatous gene, disease pathology model, congenital glaucoma, etiology and epidemiology were not developed well, which are of great promotion space. The distribution pattern and subject domain knowledge of worldwide glaucoma research in the recent five years were shown by using bibliometric analysis.Western developed

  18. Research issues in view-based multimedia database systems

    SciTech Connect

    Gruenwald, L.; Speegle, G.

    1996-12-31

    Audio, video, graphics, and text can be combined into stunning multimedia presentations which enable people to learn, buy, and have fun in ways never before possible. However multimedia is often unorganized and required tremendous storage space. Typical images are measured in tens or hundreds of kilobytes. To control the amount of space needed in this new environment, this paper proposes a multimedia database management system that uses logical representations instead of physical representations, to store edited objects. Research issues associated with such a system are discussed.

  19. Influenza research database: an integrated bioinformatics resource for influenza virus research

    USDA-ARS?s Scientific Manuscript database

    The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research and development of vaccines, diagnostics, an...

  20. The FoodCast research image database (FRIDa).

    PubMed

    Foroni, Francesco; Pergola, Giulio; Argiris, Georgette; Rumiati, Raffaella I

    2013-01-01

    In recent years we have witnessed an increasing interest in food processing and eating behaviors. This is probably due to several reasons. The biological relevance of food choices, the complexity of the food-rich environment in which we presently live (making food-intake regulation difficult), and the increasing health care cost due to illness associated with food (food hazards, food contamination, and aberrant food-intake). Despite the importance of the issues and the relevance of this research, comprehensive and validated databases of stimuli are rather limited, outdated, or not available for non-commercial purposes to independent researchers who aim at developing their own research program. The FoodCast Research Image Database (FRIDa) we present here includes 877 images belonging to eight different categories: natural-food (e.g., strawberry), transformed-food (e.g., french fries), rotten-food (e.g., moldy banana), natural-non-food items (e.g., pinecone), artificial food-related objects (e.g., teacup), artificial objects (e.g., guitar), animals (e.g., camel), and scenes (e.g., airport). FRIDa has been validated on a sample of healthy participants (N = 73) on standard variables (e.g., valence, familiarity, etc.) as well as on other variables specifically related to food items (e.g., perceived calorie content); it also includes data on the visual features of the stimuli (e.g., brightness, high frequency power, etc.). FRIDa is a well-controlled, flexible, validated, and freely available (http://foodcast.sissa.it/neuroscience/) tool for researchers in a wide range of academic fields and industry.

  1. The FoodCast research image database (FRIDa)

    PubMed Central

    Foroni, Francesco; Pergola, Giulio; Argiris, Georgette; Rumiati, Raffaella I.

    2013-01-01

    In recent years we have witnessed an increasing interest in food processing and eating behaviors. This is probably due to several reasons. The biological relevance of food choices, the complexity of the food-rich environment in which we presently live (making food-intake regulation difficult), and the increasing health care cost due to illness associated with food (food hazards, food contamination, and aberrant food-intake). Despite the importance of the issues and the relevance of this research, comprehensive and validated databases of stimuli are rather limited, outdated, or not available for non-commercial purposes to independent researchers who aim at developing their own research program. The FoodCast Research Image Database (FRIDa) we present here includes 877 images belonging to eight different categories: natural-food (e.g., strawberry), transformed-food (e.g., french fries), rotten-food (e.g., moldy banana), natural-non-food items (e.g., pinecone), artificial food-related objects (e.g., teacup), artificial objects (e.g., guitar), animals (e.g., camel), and scenes (e.g., airport). FRIDa has been validated on a sample of healthy participants (N = 73) on standard variables (e.g., valence, familiarity, etc.) as well as on other variables specifically related to food items (e.g., perceived calorie content); it also includes data on the visual features of the stimuli (e.g., brightness, high frequency power, etc.). FRIDa is a well-controlled, flexible, validated, and freely available (http://foodcast.sissa.it/neuroscience/) tool for researchers in a wide range of academic fields and industry. PMID:23459781

  2. Knowledge map of artemisinin research in SCI and Medline database.

    PubMed

    Yao, Qiang; Chen, Jing; Lyu, Peng-Hui; Zhang, Shi-Jing; Ma, Fei-Cheng; Fang, Jian-Guo

    2012-12-01

    Artemisinin was first extracted from the herb Artemisia annua which has been used for many centuries in Chinese traditional medicine as a treatment for fever and malaria. It has been given the 2011 Lasker-DeBakey clinical medical research award. In this paper, knowledge map of artemisinin research was drawn to provide some information for global researchers interested in artemisinin and its relevant references. In this work, bibliometric analysis and knowledge visualization technology were applied to evaluate global scientific production and developing trend of artemisinin research through Science Citation Index (SCI) papers and Medline papers with online version published as following aspects: publication outputs, subject categories, journals, countries, international collaboration, citations, authorship and co-authorship, author key words and co-words analysis. The Thomson Data Analyzer (TDA), Netdraw and Aureka software were employed to analyze the SCI as well as Medline papers data for knowledge mapping. Global literature of artemisinin research has increased rapidly over the past 30 years and has boosted in recent years. Seen from the statistical study in many aspects, Pharmacology & Pharmacy, and Chemistry are still the main subjects of artemisinin research with parasitology and tropical medicine increasing quickly. Malaria Journal and American Journal of Tropical Medicine are top productive journals both in SCI and Medline databases. Quantity and quality of papers in US are in a leading position, although papers quantity and active degree in developing countries such as P.R. China, Thailand and India are relatively high, the quality of papers from these countries needs to be improved. New emerging key words and co-words remind us that mechanism of action, pharmacokinetics, artemisinin-based alternatives, etc. are the future trends of artemisinin research. Through bibliometric analysis the development trends of artemisinin research are predicted. With further

  3. Acid precipitation. (Latest citations from the Aerospace database). Published Search

    SciTech Connect

    Not Available

    1993-12-01

    The bibliography contains citations concerning the measurement and analysis of acid rain and acidification of areas by precipitation. Both global and regionalized areas of acid rain effects are examined. Control techniques applicable to the sources and causes are discussed. (Contains a minimum of 187 citations and includes a subject term index and title list.)

  4. Middle East, North Africa and Western Eurasia Seismic Research Database

    SciTech Connect

    O'Boyle, J L; Ruppert, S D; Hauk, T F; Dodge, D A; Ganzberger, M D; Ryall, F

    2003-07-14

    The National Nuclear Security Administration (NNSA) Ground-Based Nuclear Explosion Monitoring Research and Engineering (GNEM R&E) Program at Lawrence Livermore National Laboratory (LLNL) has made significant progress populating a comprehensive Seismic Research Database (SRDB) used for deriving seismic calibration parameters for the Middle East, North Africa and Western Eurasia (ME/NA/WE) regions. In addition to an overview of select individual information products, we present an overview of our visualization, integration, validation, and organizational processes. Development of these processes and the LLNL SRDB was necessitated by both the very large amount of data and information involved (over 15 terabytes) and the varied data and research result formats utilized. The LLNL SRDB allows for the collection of raw and contextual seismic data used in research, provides an interface for researchers to access data, provides a framework to store research results and integrate datasets, and supports assembly, integration and dissemination of datasets to the NNSA Knowledge Base (KB). The LLNL SRDB is a flexible and extensible framework consisting of a relational database (RDB), Geographical Information System (GIS), and associated product/data visualization and data management tools. This framework is designed to accommodate large volumes of data in diverse formats from many sources (both in-house-derived research and integrated contractor products), in addition to maintaining detailed quality control and metadata. In order to efficiently organize information within the LLNL SRDB, it was necessary to automate procedures needed to create and update database tables, but a large effort is still required by technicians and scientists to load special datasets, review results of automated processing and resolve quality issues. The LLNL SRDB currently has 3 million reconciled event origins and arrivals from several global, regional and local seismic bulletins and 30 million

  5. What Can We Do with Historical Databases?: Applications in Teaching and Research.

    ERIC Educational Resources Information Center

    Lloyd-Jones, R.; Lewis, M. J.

    1994-01-01

    Contends that, in the past few years, historians have shown increasing interest in the utilization of databases and database software for both teaching and research. Focuses on the value of historical databases and illustrates the approach with examples drawn from financial and industrial databases. (CFR)

  6. What Can We Do with Historical Databases?: Applications in Teaching and Research.

    ERIC Educational Resources Information Center

    Lloyd-Jones, R.; Lewis, M. J.

    1994-01-01

    Contends that, in the past few years, historians have shown increasing interest in the utilization of databases and database software for both teaching and research. Focuses on the value of historical databases and illustrates the approach with examples drawn from financial and industrial databases. (CFR)

  7. LLNL Middle East and North Africa research database

    SciTech Connect

    Ruppert, S.D.; Hauk, T.F.; Leach, R.

    1997-07-15

    The Lawrence Livermore National Laboratory (LLNL) CTBT R{ampersand}D program has made significant progress assembling a comprehensive seismic database (DB) for events and derived parameters in the Middle East and North Africa (ME/NA). The LLNL research DB provides not only a coherent framework in which store and organize large volumes of collected seismic waveforms and associated event parameter information but also provides an efficient data processing/research environment. The DB is designed to be flexible and extensible in order to accommodate the large volumes of data in diverse formats from many sources in addition to maintaining detailed quality control and metadata. Researchers can make use of the relational nature of the DB and interactive analysis tools to quickly and efficiently process large volumes of data. Seismic waveforms have been systematically collected form a wide range of local and regional networks using numerous earthquake bulletins and converted a common format based on CSS3.O while undergoing quality control and corrections of errors. By combining traveltime observations, event characterization studies, and regional wave-propagation studies of the LLNL CTBT team, we are assembling a library of ground truth information and event location correction surfaces required to support the ME/NA regionalization program. Corrections and parameters distilled from the LLNL research DB will provide needed contributions to the DOE knowledge base for the ME/NA region and enable the USNDC and IDC to effectively verify CTBT compliance.

  8. The GUDMAP database--an online resource for genitourinary research.

    PubMed

    Harding, Simon D; Armit, Chris; Armstrong, Jane; Brennan, Jane; Cheng, Ying; Haggarty, Bernard; Houghton, Derek; Lloyd-MacGilp, Sue; Pi, Xingjun; Roochun, Yogmatee; Sharghi, Mehran; Tindal, Christopher; McMahon, Andrew P; Gottesman, Brian; Little, Melissa H; Georgas, Kylie; Aronow, Bruce J; Potter, S Steven; Brunskill, Eric W; Southard-Smith, E Michelle; Mendelsohn, Cathy; Baldock, Richard A; Davies, Jamie A; Davidson, Duncan

    2011-07-01

    The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is an international consortium working to generate gene expression data and transgenic mice. GUDMAP includes data from large-scale in situ hybridisation screens (wholemount and section) and microarray gene expression data of microdissected, laser-captured and FACS-sorted components of the developing mouse genitourinary (GU) system. These expression data are annotated using a high-resolution anatomy ontology specific to the developing murine GU system. GUDMAP data are freely accessible at www.gudmap.org via easy-to-use interfaces. This curated, high-resolution dataset serves as a powerful resource for biologists, clinicians and bioinformaticians interested in the developing urogenital system. This paper gives examples of how the data have been used to address problems in developmental biology and provides a primer for those wishing to use the database in their own research.

  9. The GUDMAP database – an online resource for genitourinary research

    PubMed Central

    Harding, Simon D.; Armit, Chris; Armstrong, Jane; Brennan, Jane; Cheng, Ying; Haggarty, Bernard; Houghton, Derek; Lloyd-MacGilp, Sue; Pi, Xingjun; Roochun, Yogmatee; Sharghi, Mehran; Tindal, Christopher; McMahon, Andrew P.; Gottesman, Brian; Little, Melissa H.; Georgas, Kylie; Aronow, Bruce J.; Potter, S. Steven; Brunskill, Eric W.; Southard-Smith, E. Michelle; Mendelsohn, Cathy; Baldock, Richard A.; Davies, Jamie A.; Davidson, Duncan

    2011-01-01

    The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is an international consortium working to generate gene expression data and transgenic mice. GUDMAP includes data from large-scale in situ hybridisation screens (wholemount and section) and microarray gene expression data of microdissected, laser-captured and FACS-sorted components of the developing mouse genitourinary (GU) system. These expression data are annotated using a high-resolution anatomy ontology specific to the developing murine GU system. GUDMAP data are freely accessible at www.gudmap.org via easy-to-use interfaces. This curated, high-resolution dataset serves as a powerful resource for biologists, clinicians and bioinformaticians interested in the developing urogenital system. This paper gives examples of how the data have been used to address problems in developmental biology and provides a primer for those wishing to use the database in their own research. PMID:21652655

  10. MIPS PlantsDB: a database framework for comparative plant genome research.

    PubMed

    Nussbaumer, Thomas; Martis, Mihaela M; Roessner, Stephan K; Pfeifer, Matthias; Bader, Kai C; Sharma, Sapna; Gundlach, Heidrun; Spannagl, Manuel

    2013-01-01

    The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/genomes.jsp) was initially described in NAR in 2007 [Spannagl,M., Noubibou,O., Haase,D., Yang,L., Gundlach,H., Hindemitt, T., Klee,K., Haberer,G., Schoof,H. and Mayer,K.F. (2007) MIPSPlantsDB-plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834-D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB.

  11. University Real Estate Development Database: A Database-Driven Internet Research Tool

    ERIC Educational Resources Information Center

    Wiewel, Wim; Kunst, Kara

    2008-01-01

    The University Real Estate Development Database is an Internet resource developed by the University of Baltimore for the Lincoln Institute of Land Policy, containing over six hundred cases of university expansion outside of traditional campus boundaries. The University Real Estate Development database is a searchable collection of real estate…

  12. University Real Estate Development Database: A Database-Driven Internet Research Tool

    ERIC Educational Resources Information Center

    Wiewel, Wim; Kunst, Kara

    2008-01-01

    The University Real Estate Development Database is an Internet resource developed by the University of Baltimore for the Lincoln Institute of Land Policy, containing over six hundred cases of university expansion outside of traditional campus boundaries. The University Real Estate Development database is a searchable collection of real estate…

  13. Constructing a publically available distracted driving database and research tool.

    PubMed

    Atchley, Paul; Tran, Ashleigh V; Salehinejad, Mohammad Ali

    2017-02-01

    The goal of the current work was to create a publicly available visualization tool of distracted driving research, the purpose of which is to allow the public and other stakeholders to empirically inform questions of their choice that may bear on policy discussions. Fifty years of distracted driving research was used to design a comprehensive database of studies that evaluated the effects of distraction on driving performance. Distraction sources (e.g., texting, talking, visual distraction) and performance measures were defined, and the sample of studies were evaluated and categorized by their measures. The final product yielded 342 studies using various methodologies. Across all measures, 1297 found distractions degraded driving performance, 54 found distraction improved driving performance, and 257 found distraction had no effect on driving performance. An analysis of the most common phone distractions (texting and talking) showed that texting almost always results in degraded performance. Aggregate data reveal no difference in performance decrements for hand-held or hands-free phones even though single studies of those variables vary in their outcomes. This project illustrates how scientific research can be made publically available for use by a diverse audience of stakeholders. An important result of this project is that data aggregated along a simple set of characteristics such as whether or not performance is decreased, improved or not affected, can reveal trends in the data that are less clear from any individual study. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. The potential of UK clinical databases in enhancing paediatric medication research

    PubMed Central

    Wong, Ian C K; Murray, Macey L

    2005-01-01

    The research potential of many UK clinical databases is not being realized. A recent report published by the Royal College of Paediatrics & Child Health stated that there is a need to build research capacity and support in the area of paediatric pharmacology, with specific emphasis on the use of clinical databases. This article presents the databases available in the UK for medication research and gives some examples of paediatric studies conducted. The databases discussed include the Prescription Pricing Authority database, the General Practice Research Database, IMS Health databases (Medical Data Index, MIDAS Prescribing Insights, Disease-Analyser-Mediplus) and the Yellow Card Scheme. Other databases such as the Medicines Monitoring Unit (MEMO) and the Scottish Primary Care Computer System also have research potential in paediatric pharmacoepidemiology, but their population sizes are relatively small. PMID:15948943

  15. 77 FR 66622 - Submission for OMB Review; Comment Request: National Database for Autism Research (NDAR) Data...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-06

    ... Database for Autism Research (NDAR) Data Access Request SUMMARY: Under the provisions of Section 3507(a)(1... control number. Proposed Collection: Title: National Database for Autism Research (NDAR) Data Access... interested recipients of updates, corrections or other changes to the database. Frequency of Response:...

  16. APD3: the antimicrobial peptide database as a tool for research and education

    PubMed Central

    Wang, Guangshun; Li, Xia; Wang, Zhe

    2016-01-01

    The antimicrobial peptide database (APD, http://aps.unmc.edu/AP/) is an original database initially online in 2003. The APD2 (2009 version) has been regularly updated and further expanded into the APD3. This database currently focuses on natural antimicrobial peptides (AMPs) with defined sequence and activity. It includes a total of 2619 AMPs with 261 bacteriocins from bacteria, 4 AMPs from archaea, 7 from protists, 13 from fungi, 321 from plants and 1972 animal host defense peptides. The APD3 contains 2169 antibacterial, 172 antiviral, 105 anti-HIV, 959 antifungal, 80 antiparasitic and 185 anticancer peptides. Newly annotated are AMPs with antibiofilm, antimalarial, anti-protist, insecticidal, spermicidal, chemotactic, wound healing, antioxidant and protease inhibiting properties. We also describe other searchable annotations, including target pathogens, molecule-binding partners, post-translational modifications and animal models. Amino acid profiles or signatures of natural AMPs are important for peptide classification, prediction and design. Finally, we summarize various database applications in research and education. PMID:26602694

  17. Conjugated linoleic acid pork research.

    PubMed

    Dugan, Michael E R; Aalhus, Jennifer L; Kramer, John K G

    2004-06-01

    The driving force behind most conjugated linoleic acid (CLA) research in swine has been related to potential improvements in animal production. Early work that used rodent models indicated that feeding CLA could potentially reduce body fat, increase lean content, increase growth rate, and improve feed conversion efficiency. Producer-backed funding organizations were, therefore, receptive to proposals to extend this research to pigs, and many studies have been completed worldwide. In general, improvements in body composition were found, but evidence indicating that CLA improves growth rate or feed conversion was limited. Inclusion of CLA into pig diets was, however, shown to increase muscle marbling fat and fat hardness, and both of these characteristics have the potential to increase carcass value. Currently, Badische Anilin- & Soda-Fabrik AG (BASF) has the international marketing license to include synthetic CLA in animal feeds, but to date this practice is not approved in Canada or the United States. If and when approval is granted, the next step in realizing CLA's economic potential would be to seek approval for claiming CLA enrichment in pork and pork products. Given the ability of swine to accumulate relatively high amounts of CLA in their tissues, pork and pork products could become an important vehicle for delivery of physiologically significant amounts of CLA to consumers.

  18. A Relational Database for the Discovery of Genes Encoding Amino Acid Biosynthetic Enzymes in Pathogenic Fungi

    PubMed Central

    Giles, Peter F.; Soanes, Darren M.

    2003-01-01

    Fungal phytopathogens continue to cause major economic impact, either directly, through crop losses, or due to the costs of fungicide application. Attempts to understand these organisms are hampered by a lack of fungal genome sequence data. A need exists, however, to develop specific bioinformatics tools to collate and analyse the sequence data that currently is available. A web-accessible gene discovery database (http://cogeme.ex.ac.uk/biosynthesis.html) was developed as a demonstration tool for the analysis of metabolic and signal transduction pathways in pathogenic fungi using incomplete gene inventories. Using Bayesian probability to analyse the currently available gene information from pathogenic fungi, we provide evidence that the obligate pathogen Blumeria graminis possesses all amino acid biosynthetic pathways found in free-living fungi, such as Saccharomyces cerevisiae. Phylogenetic analysis was also used to deduce a gene history of succinate-semialdehyde dehydrogenase, an enzyme in the glutamate and lysine biosynthesis pathways. The database provides a tool and methodology to researchers to direct experimentation towards predicting pathway conservation in pathogenic microorganisms. PMID:18629094

  19. Functional ceramic materials database: an online resource for materials research.

    PubMed

    Scott, D J; Manos, S; Coveney, P V; Rossiny, J C H; Fearn, S; Kilner, J A; Pullar, R C; Alford, N Mc N; Axelsson, A-K; Zhang, Y; Chen, L; Yang, S; Evans, J R G; Sebastian, M T

    2008-02-01

    We present work on the creation of a ceramic materials database which contains data gleaned from literature data sets as well as new data obtained from combinatorial experiments on the London University Search Instrument. At the time of this writing, the database contains data related to two main groups of materials, mainly in the perovskite family. Permittivity measurements of electroceramic materials are the first area of interest, while ion diffusion measurements of oxygen ion conductors are the second. The nature of the database design does not restrict the type of measurements which can be stored; as the available data increase, the database may become a generic, publicly available ceramic materials resource.

  20. Computer access to research on dietary supplements: a database of federally funded dietary supplement research.

    PubMed

    Haggans, Carol J; Regan, Karen S; Brown, Lynda M; Wang, Chunling; Krebs-Smith, Jim; Coates, Paul M; Swanson, Christine A

    2005-07-01

    Dietary supplement use is prevalent in the United States, but support for supplement research has been relatively modest and only recently emphasized at the NIH. The Dietary Supplement Health and Education Act of 1994 led to the creation of the Office of Dietary Supplements (ODS) at the NIH to promote research on dietary supplements. In order to track federally funded dietary supplement research, the ODS developed a database known as Computer Access to Research on Dietary Supplements (CARDS). This article provides an overview of the development and potential uses of the CARDS database. In addition, we report that NIH-funded dietary supplement research steadily increased from fiscal year (FY) 1999 through 2002. The majority of NIH institutes or centers (ICs) funded research relevant to dietary supplements during this time, led by the National Cancer Institute and one of the newest NIH ICs, the National Center for Complementary and Alternative Medicine. CARDS data indicate that NIH-funded dietary supplement research from FY 1999 through 2002 involved primarily vitamins, minerals, botanicals and phytochemicals. Cancer and cardiovascular disease, two of the leading causes of morbidity and mortality in the United States, collectively accounted for almost 45% of the research related to dietary supplements. A variety of types of research studies were funded, with the majority consisting of human intervention studies. This information is useful to evaluate trends in federally funded dietary supplement research, identify research gaps, and help research scientists identify potential sources of NIH funding.

  1. HOWDY: an integrated database system for human genome research

    PubMed Central

    Hirakawa, Mika

    2002-01-01

    HOWDY is an integrated database system for accessing and analyzing human genomic information (http://www-alis.tokyo.jst.go.jp/HOWDY/). HOWDY stores information about relationships between genetic objects and the data extracted from a number of databases. HOWDY consists of an Internet accessible user interface that allows thorough searching of the human genomic databases using the gene symbols and their aliases. It also permits flexible editing of the sequence data. The database can be searched using simple words and the search can be restricted to a specific cytogenetic location. Linear maps displaying markers and genes on contig sequences are available, from which an object can be chosen. Any search starting point identifies all the information matching the query. HOWDY provides a convenient search environment of human genomic data for scientists unsure which database is most appropriate for their search. PMID:11752279

  2. Mining fatty acid databases for detection of novel compounds in aerobic bacteria.

    PubMed

    Dawyndt, Peter; Vancanneyt, Marc; Snauwaert, Cindy; De Baets, Bernard; De Meyer, Hans; Swings, Jean

    2006-09-01

    This study examines how the discriminatory power of an automated bacterial whole-cell fatty acid identification system can be significantly enhanced by exploring the vast amounts of information accumulated during 15 years of routine gas chromatographic analysis of the fatty acid content of aerobic bacteria. Construction of a global peak occurrence histogram based upon a large fatty acid database is shown to serve as a highly informative tool for assessing the delineation of the naming windows used during the automatic recognition of fatty acid compounds. Along the lines of this data mining application, it is suggested that several naming windows of the Sherlock MIS TSBA50 peak naming method may need to be re-evaluated in order to fit more closely with the bulk of observed fatty acid profiles. At the same time, the global peak occurrence histogram has put forward the delineation of 32 new peak naming windows, accounting for a 26% increase in the total number of fatty acid features taken into account for bacterial identification. By scrutinizing the relationships between the newly delineated naming windows and the many taxonomic units covered within a proprietary fatty acid database, all new naming windows were proven to correspond with stable features of some specific groups of microorganisms. This latter analysis clearly underscores the impact of incorporating the new fatty acid compounds for improving the resolution of the bacterial identification system and endorses the applicability of knowledge discovery in databases within the field of microbiology.

  3. LLNL Middle East and North Africa research database

    SciTech Connect

    Dodge, D; Hauk, T; Moore, R M; O'Boyle, J; Ruppert, S

    1999-07-23

    The Lawrence Livermore National Laboratory (LLNL) Comprehensive Nuclear-Test-Ban Treaty Research and Development (CTBT R and D) program has made significant progress populating a comprehensive seismic research database (RDB) for seismic events and derived research products in the Middle East and North Africa (MENA). Our original ME/NA study region has enlarged and is now defined as an area including the Middle East, Africa, Europe, Southwest Asia, the Former Soviet Union and the Scandinavian/Arctic region. The LLNL RDB will facilitate calibration of all International Monitoring System (IMS) stations (primary and auxiliary) or their surrogates (if not yet installed) as well as a variety of gamma stations. The RDB provides not only a coherent framework in which to store and organize large volumes of collected seismic waveforms and associated event parameter information, but also provides an efficient data processing/research environment for deriving location and discrimination correction sur faces and capabilities. In order to accommodate large volumes of data from many sources with diverse formats the RDB is designed to be flexible and extensible in addition to maintaining detailed quality control information and associated metadata. Station parameters, instrument responses, phase pick information, and event bulletins were compiled and made available through the RDB. For seismic events in the MENA region occurring between 1976 and 1999, we have systematically assembled, quality checked and organized event waveforms; continuous seismic data from 1990 to present are archived for many stations. Currently, over 11,400 seismic events and 1.2 million waveforms are maintained in the RDB and made readily available to researchers. In addition to open sources of seismic data, we have established collaborative relationships with several ME/NA countries that have yielded additional ground truth and broadband waveform data essential for regional calibration and capability

  4. Database security and encryption technology research and application

    NASA Astrophysics Data System (ADS)

    Zhu, Li-juan

    2013-03-01

    The main purpose of this paper is to discuss the current database information leakage problem, and discuss the important role played by the message encryption techniques in database security, As well as MD5 encryption technology principle and the use in the field of website or application. This article is divided into introduction, the overview of the MD5 encryption technology, the use of MD5 encryption technology and the final summary. In the field of requirements and application, this paper makes readers more detailed and clearly understood the principle, the importance in database security, and the use of MD5 encryption technology.

  5. Acid Rain Students Do Original Research.

    ERIC Educational Resources Information Center

    Outdoor Communicator, 1984

    1984-01-01

    At Park Senior High School (Cottage Grove, Minnesota), 46 juniors and seniors planted 384 red pine seedlings in connection with their original research on acid rain, with advice from Dr. Harriet Stubbs, director of the Acid Precipitation Awareness Program (West Saint Paul), which has been developing acid rain teaching materials. (MH)

  6. Acid Rain Students Do Original Research.

    ERIC Educational Resources Information Center

    Outdoor Communicator, 1984

    1984-01-01

    At Park Senior High School (Cottage Grove, Minnesota), 46 juniors and seniors planted 384 red pine seedlings in connection with their original research on acid rain, with advice from Dr. Harriet Stubbs, director of the Acid Precipitation Awareness Program (West Saint Paul), which has been developing acid rain teaching materials. (MH)

  7. Brassica ASTRA: an integrated database for Brassica genomic research.

    PubMed

    Love, Christopher G; Robinson, Andrew J; Lim, Geraldine A C; Hopkins, Clare J; Batley, Jacqueline; Barker, Gary; Spangenberg, German C; Edwards, David

    2005-01-01

    Brassica ASTRA is a public database for genomic information on Brassica species. The database incorporates expressed sequences with Swiss-Prot and GenBank comparative sequence annotation as well as secondary Gene Ontology (GO) annotation derived from the comparison with Arabidopsis TAIR GO annotations. Simple sequence repeat molecular markers are identified within resident sequences and mapped onto the closely related Arabidopsis genome sequence. Bacterial artificial chromosome (BAC) end sequences derived from the Multinational Brassica Genome Project are also mapped onto the Arabidopsis genome sequence enabling users to identify candidate Brassica BACs corresponding to syntenic regions of Arabidopsis. This information is maintained in a MySQL database with a web interface providing the primary means of interrogation. The database is accessible at http://hornbill.cspp.latrobe.edu.au.

  8. COPASAAR – A database for proteomic analysis of single amino acid repeats

    PubMed Central

    Depledge, Daniel P; Dalby, Andrew R

    2005-01-01

    Background Single amino acid repeats make up a significant proportion in all of the proteomes that have currently been determined. They have been shown to be functionally and medically significant, and are associated with cancers and neuro-degenerative diseases such as Huntington's Chorea, where a poly-glutamine repeat is responsible for causing the disease. The COPASAAR database is a new tool to facilitate the rapid analysis of single amino acid repeats at a proteome level. The database aims to simplify the comparison of repeat distributions between proteomes in order to provide a better understanding of their function and evolution. Results A comparative analysis of all proteomes in the database (currently 244) shows that single amino acid repeats account for about 12–14% of the proteome of any given species. They are more common in eukaryotes (14%) than in either archaea or bacteria (both 13%). Individual analyses of proteomes show that long single amino acid repeats (6+ residues) are much more common in the Eukaryotes and that longer repeats are usually made up of hydrophilic amino acids such as glutamine, glutamic acid, asparagine, aspartic acid and serine. Conclusion COPASAAR is a useful tool for comparative proteomics that provides rapid access to amino acid repeat data that can be readily data-mined. The COPASAAR database can be queried at the kingdom, proteome or individual protein level. As the amount of available proteome data increases this will be increasingly important in order to automate proteome comparison. The insights gained from these studies will give a better insight into the evolution of protein sequence and function. PMID:16078990

  9. Economic evaluation databases as an aid to healthcare decision makers and researchers.

    PubMed

    Aguiar-Ibáñez, Raquel; Nixon, John; Glanville, Julie; Craig, Dawn; Rice, Stephen; Christie, James; Drummond, Michael F

    2005-12-01

    Economic evaluation databases have been developed to assist in setting priorities and facilitating research within the healthcare sector. This paper presents an overview of the major databases of economic evaluations currently available (HEED, NHS EED, the CEA Registry, CODECS, PEDE, EURONHEED and JEED). It describes the key features of each database and the main user groups. It also presents evidence of the value of access to economic evaluation databases, particularly for the researchers and decision makers who form their main target audience. The research available shows that both decision makers and researchers find economic evaluation databases helpful as a source of information. However, database producers may also need to better understand the requirements of their users and consider adaptations to their products.

  10. An integrated database to support research on Escherichia coli

    SciTech Connect

    Baehr, A.; Dunham, G.; Matsuda, Hideo; Michaels, G.; Taylor, R.; Overbeek, R.; Rudd, K.E.; Ginsburg, A.; Joerg, D.; Kazic, T.; Hagstrom, R.; Zawada, D.; Smith, C.; Yoshida, Kaoru

    1992-01-01

    We have used logic programming to design and implement a prototype database of genomic information for the model bacterial organism Escherichia coli. This report presents the fundamental database primitives that can be used to access and manipulate data relating to the E. coli genome. The present system, combined with a tutorial manual, provides immediate access to the integrated knowledge base for E. coli chromosome data. It also serves as the foundation for development of more user-friendly interfaces that have the same retrieval power and high-level tools to analyze complex chromosome organization.

  11. National Databases with Information on College Students with Disabilities. NCCSD Research Brief. Volume 1, Issue 1

    ERIC Educational Resources Information Center

    Avellone, Lauren; Scott, Sally

    2017-01-01

    The purpose of this research brief was to identify and provide an overview of national databases containing information about college students with disabilities. Eleven instruments from federal and university-based sources were described. Databases reflect a variety of survey methods, respondents, definitions of disability, and research questions.…

  12. The Technology Education Graduate Research Database, 1892-2000. CTTE Monograph.

    ERIC Educational Resources Information Center

    Reed, Philip A., Ed.

    The Technology Education Graduate Research Database (TEGRD) was designed in two parts. The first part was a 384 page bibliography of theses and dissertations from 1892-2000. The second part was an online, searchable database of graduate research completed within technology education from 1892 to the present. The primary goals of the project were:…

  13. Dental Health Services Research Utilizing Comprehensive Clinical Databases and Information Technology.

    ERIC Educational Resources Information Center

    Hayden, William J.

    1997-01-01

    Argues that dental schools are the logical location for development of valid, reliable, and acceptable health services research methods and databases, and describes development of an insurance claims database to demonstrate the types of research possible, as well as weaknesses and shortcomings of pure administrative data. Considers implications…

  14. Comprehensiveness of "Social Work Abstracts" as a Database for Researchers and Practitioners

    ERIC Educational Resources Information Center

    Shek, Daniel T. L.

    2008-01-01

    Objective: The comprehensiveness of "Social Work Abstracts (SWA)" as a database was examined. Method: The coverage of articles of "Research on Social Work Practice" and "Social Work Research" in "SWA" from 1995 to 2005 was examined. "SWA" was compared with other databases on several dimensions. A case study based on the author's publications was…

  15. The Technology Education Graduate Research Database, 1892-2000. CTTE Monograph.

    ERIC Educational Resources Information Center

    Reed, Philip A., Ed.

    The Technology Education Graduate Research Database (TEGRD) was designed in two parts. The first part was a 384 page bibliography of theses and dissertations from 1892-2000. The second part was an online, searchable database of graduate research completed within technology education from 1892 to the present. The primary goals of the project were:…

  16. USDA food and nutrient databases provide the infrastructure for food and nutrition research, policy, and practice.

    PubMed

    Ahuja, Jaspreet K C; Moshfegh, Alanna J; Holden, Joanne M; Harris, Ellen

    2013-02-01

    The USDA food and nutrient databases provide the basic infrastructure for food and nutrition research, nutrition monitoring, policy, and dietary practice. They have had a long history that goes back to 1892 and are unique, as they are the only databases available in the public domain that perform these functions. There are 4 major food and nutrient databases released by the Beltsville Human Nutrition Research Center (BHNRC), part of the USDA's Agricultural Research Service. These include the USDA National Nutrient Database for Standard Reference, the Dietary Supplement Ingredient Database, the Food and Nutrient Database for Dietary Studies, and the USDA Food Patterns Equivalents Database. The users of the databases are diverse and include federal agencies, the food industry, health professionals, restaurants, software application developers, academia and research organizations, international organizations, and foreign governments, among others. Many of these users have partnered with BHNRC to leverage funds and/or scientific expertise to work toward common goals. The use of the databases has increased tremendously in the past few years, especially the breadth of uses. These new uses of the data are bound to increase with the increased availability of technology and public health emphasis on diet-related measures such as sodium and energy reduction. Hence, continued improvement of the databases is important, so that they can better address these challenges and provide reliable and accurate data.

  17. ProtNA-ASA: Protein-nucleic acid structural database with information on accessible surface area

    NASA Astrophysics Data System (ADS)

    Tkachenko, M. Y.; Boryskina, O. P.; Shestopalova, A. V.; Tolstorukov, M. Y.

    The article describes a new database (ProtNA-ASA), which combines the data on conformational parameters of nucleic acids and calculations of the accessible surface area (ASA) of nucleic acid atoms in protein-DNA/RNA complexes. As for October 2008, the database contains 214 DNA-protein and 28 RNA-protein non-homologous complexes. The database provides structural parameters that describe local geometry of base pairs and base-pair steps as well as backbone torsion angles. Additionally, total ASA of DNA/RNA atoms and the accessible area of atoms in the minor and major grooves are calculated. ProtNA-ASA database facilitates studying the relationship between the DNA/RNA conformation and availability of atoms for contact with proteins either in major or in minor groove for different nucleotides. Such an analysis is important for understanding the principles of molecular recognition including indirect sequence readout. The database is publicly available for use at http://www.protna.bio-page.org.

  18. G4IPDB: A database for G-quadruplex structure forming nucleic acid interacting proteins

    PubMed Central

    Mishra, Subodh Kumar; Tawani, Arpita; Mishra, Amit; Kumar, Amit

    2016-01-01

    Nucleic acid G-quadruplex structure (G4) Interacting Proteins DataBase (G4IPDB) is an important database that contains detailed information about proteins interacting with nucleic acids that forms G-quadruplex structures. G4IPDB is the first database that provides comprehensive information about this interaction at a single platform. This database contains more than 200 entries with details of interaction such as interacting protein name and their synonyms, their UniProt-ID, source organism, target name and its sequences, ∆Tm, binding/dissociation constants, protein gene name, protein FASTA sequence, interacting residue in protein, related PDB entries, interaction ID, graphical view, PMID, author’s name and techniques that were used to detect their interactions. G4IPDB also provides an efficient web-based “G-quadruplex predictor tool” that searches putative G-quadruplex forming sequences simultaneously in both sense and anti-sense strands of the query nucleotide sequence and provides the predicted G score. Studying the interaction between proteins and nucleic acids forming G-quadruplex structures could be of therapeutic significance for various diseases including cancer and neurological disease, therefore, having detail information about their interactions on a single platform would be helpful for the discovery and development of novel therapeutics. G4IPDB can be routinely updated (twice in year) and freely available on http://bsbe.iiti.ac.in/bsbe/ipdb/index.php. PMID:27905517

  19. PubDNA Finder: a web database linking full-text articles to sequences of nucleic acids.

    PubMed

    García-Remesal, Miguel; Cuevas, Alejandro; Pérez-Rey, David; Martín, Luis; Anguita, Alberto; de la Iglesia, Diana; de la Calle, Guillermo; Crespo, José; Maojo, Víctor

    2010-11-01

    PubDNA Finder is an online repository that we have created to link PubMed Central manuscripts to the sequences of nucleic acids appearing in them. It extends the search capabilities provided by PubMed Central by enabling researchers to perform advanced searches involving sequences of nucleic acids. This includes, among other features (i) searching for papers mentioning one or more specific sequences of nucleic acids and (ii) retrieving the genetic sequences appearing in different articles. These additional query capabilities are provided by a searchable index that we created by using the full text of the 176 672 papers available at PubMed Central at the time of writing and the sequences of nucleic acids appearing in them. To automatically extract the genetic sequences occurring in each paper, we used an original method we have developed. The database is updated monthly by automatically connecting to the PubMed Central FTP site to retrieve and index new manuscripts. Users can query the database via the web interface provided. PubDNA Finder can be freely accessed at http://servet.dia.fi.upm.es:8080/pubdnafinder

  20. Data recycling: using existing databases to increase research capacity in speech-language development and disorders.

    PubMed

    Justice, Laura M; Breit-Smith, Allison; Rogers, Margaret

    2010-01-01

    This clinical forum was organized to provide a means for informing the research and clinical communities of one mechanism through which research capacity might be enhanced within the field of speech-language pathology. Specifically, forum authors describe the process of conducting secondary analyses of extant databases to answer questions of relevance to speech and language development and disorders. This prologue defines the concept of secondary analysis of databases and provides an overview of each of the articles that make up the forum. Researchers invested in addressing basic and applied problems of relevance to speech and language services in schools can make use of a variety of extant databases to increase research capacity.

  1. Temporal perspective on acid deposition research

    SciTech Connect

    Hendrey, G R

    1980-02-20

    This statement presented to the Subcommittee on Natural Resources of the US House of Representatives gives a definition of acid rain, presents new data on the regional and temporal nature of the problem, and discusses research needs. (ACR)

  2. NCAD, a database integrating the intrinsic conformational preferences of non-coded amino acids

    PubMed Central

    Revilla-López, Guillem; Torras, Juan; Curcó, David; Casanovas, Jordi; Calaza, M. Isabel; Zanuy, David; Jiménez, Ana I.; Cativiela, Carlos; Nussinov, Ruth; Grodzinski, Piotr; Alemán, Carlos

    2010-01-01

    Peptides and proteins find an ever-increasing number of applications in the biomedical and materials engineering fields. The use of non-proteinogenic amino acids endowed with diverse physicochemical and structural features opens the possibility to design proteins and peptides with novel properties and functions. Moreover, non-proteinogenic residues are particularly useful to control the three-dimensional arrangement of peptidic chains, which is a crucial issue for most applications. However, information regarding such amino acids –also called non-coded, non-canonical or non-standard– is usually scattered among publications specialized in quite diverse fields as well as in patents. Making all these data useful to the scientific community requires new tools and a framework for their assembly and coherent organization. We have successfully compiled, organized and built a database (NCAD, Non-Coded Amino acids Database) containing information about the intrinsic conformational preferences of non-proteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, conformational propensities established experimentally, and applications. The architecture of the database is presented in this work together with the first family of non-coded residues included, namely, α-tetrasubstituted α-amino acids. Furthermore, the NCAD usefulness is demonstrated through a test-case application example. PMID:20455555

  3. A Multilateral Use and Processing of A Large Bibliographic Database for Research Information

    NASA Astrophysics Data System (ADS)

    Konishi, Osamu; Obayashi, Haruo

    In order to explain the multilateral use of bibliographic database in research activities, nuclear fusion research field as the comprehensive science was selected. The processing method of the above mentioned database is mainly described. Considering advantages of the bibliographic and indexed information of such database, its use is classified into three types: 1. To use for reference information, 2. To obtain facts and knowledge from information, and 3. To process and analyse information. Each sample corresponding to the above is introduced as follows, and the usefulness of a large scale database is made clear. 1) Use of online search in research activities, 2) Construction of scientific terms list utilizing keywords and their frequency in the database, and 3) To analyse bibliographic information metrically and evaluate research. This is an application of scientometrics.

  4. Healthcare Databases in Thailand and Japan: Potential Sources for Health Technology Assessment Research.

    PubMed

    Saokaew, Surasak; Sugimoto, Takashi; Kamae, Isao; Pratoomsoot, Chayanin; Chaiyakunapruk, Nathorn

    2015-01-01

    Health technology assessment (HTA) has been continuously used for value-based healthcare decisions over the last decade. Healthcare databases represent an important source of information for HTA, which has seen a surge in use in Western countries. Although HTA agencies have been established in Asia-Pacific region, application and understanding of healthcare databases for HTA is rather limited. Thus, we reviewed existing databases to assess their potential for HTA in Thailand where HTA has been used officially and Japan where HTA is going to be officially introduced. Existing healthcare databases in Thailand and Japan were compiled and reviewed. Databases' characteristics e.g. name of database, host, scope/objective, time/sample size, design, data collection method, population/sample, and variables were described. Databases were assessed for its potential HTA use in terms of safety/efficacy/effectiveness, social/ethical, organization/professional, economic, and epidemiological domains. Request route for each database was also provided. Forty databases- 20 from Thailand and 20 from Japan-were included. These comprised of national censuses, surveys, registries, administrative data, and claimed databases. All databases were potentially used for epidemiological studies. In addition, data on mortality, morbidity, disability, adverse events, quality of life, service/technology utilization, length of stay, and economics were also found in some databases. However, access to patient-level data was limited since information about the databases was not available on public sources. Our findings have shown that existing databases provided valuable information for HTA research with limitation on accessibility. Mutual dialogue on healthcare database development and usage for HTA among Asia-Pacific region is needed.

  5. A comprehensive clinical research database based on CDISC ODM and i2b2.

    PubMed

    Meineke, Frank A; Stäubert, Sebastian; Löbe, Matthias; Winter, Alfred

    2014-01-01

    We present a working approach for a clinical research database as part of an archival information system. The CDISC ODM standard is target for clinical study and research relevant routine data, thus decoupling the data ingest process from the access layer. The presented research database is comprehensive as it covers annotating, mapping and curation of poorly annotated source data. Besides a conventional relational database the medical data warehouse i2b2 serves as main frontend for end-users. The system we developed is suitable to support patient recruitment, cohort identification and quality assurance in daily routine.

  6. USDA food and nutrient databases provide the infrastructure for food and nutrition research, policy and practice

    USDA-ARS?s Scientific Manuscript database

    The USDA food and nutrient databases provide the basic infrastructure for food and nutrition research, nutrition monitoring, and dietary practice. They have had a long history that goes back to 1892, and are unique, as they are the only databases available in the public domain that perform these fu...

  7. Open-Access Metabolomics Databases for Natural Product Research: Present Capabilities and Future Potential

    PubMed Central

    Johnson, Sean R.; Lange, Bernd Markus

    2015-01-01

    Various databases have been developed to aid in assigning structures to spectral peaks observed in metabolomics experiments. In this review article, we discuss the utility of currently available open-access spectral and chemical databases for natural products discovery. We also provide recommendations on how the research community can contribute to further improvements. PMID:25789275

  8. The ECLS-K Study and Database: A Resource for School Social Work Practitioners and Researchers

    ERIC Educational Resources Information Center

    Williams, Sheara A.

    2008-01-01

    The purpose of this article is to introduce the Early Childhood Longitudinal Study-Kindergarten (ECLS-K) database to school social work practitioners and researchers. This database not only serves as a viable source for evidence-based practice pertaining to the influences of families and schools on the academic achievement of children beginning at…

  9. Design of a decentralized reusable research database architecture to support data acquisition in large research projects.

    PubMed

    Iavindrasana, Jimison; Depeursinge, Adrien; Ruch, Patrick; Spahni, Stéphane; Geissbuhler, Antoine; Müller, Henning

    2007-01-01

    The diagnostic and therapeutic processes, as well as the development of new treatments, are hindered by the fragmentation of information which underlies them. In a multi-institutional research study database, the clinical information system (CIS) contains the primary data input. An important part of the money of large scale clinical studies is often paid for data creation and maintenance. The objective of this work is to design a decentralized, scalable, reusable database architecture with lower maintenance costs for managing and integrating distributed heterogeneous data required as basis for a large-scale research project. Technical and legal aspects are taken into account based on various use case scenarios. The architecture contains 4 layers: data storage and access are decentralized at their production source, a connector as a proxy between the CIS and the external world, an information mediator as a data access point and the client side. The proposed design will be implemented inside six clinical centers participating in the @neurIST project as part of a larger system on data integration and reuse for aneurism treatment.

  10. A proposed key escrow system for secure patient information disclosure in biomedical research databases.

    PubMed

    Ferris, Todd A; Garrison, Gregory M; Lowe, Henry J

    2002-01-01

    Access to clinical data is of increasing importance to biomedical research. The pending HIPAA privacy regulations provide specific requirements for the release of protected health information. Under the regulations, biomedical researchers may utilize anonymized data, or adhere to HIPAA requirements regarding protected health information. In order to provide researchers with anonymized data from a clinical research database, we reviewed several published strategies for de-identification of protected health information. Critical analysis with respect to this project suggests that de-identification alone is problematic when applied to clinical research databases. We propose a hybrid system; utilizing secure key escrow, de-identification, and role-based access for IRB approved researchers.

  11. Landslide databases for applied landslide impact research: the example of the landslide database for the Federal Republic of Germany

    NASA Astrophysics Data System (ADS)

    Damm, Bodo; Klose, Martin

    2014-05-01

    This contribution presents an initiative to develop a national landslide database for the Federal Republic of Germany. It highlights structure and contents of the landslide database and outlines its major data sources and the strategy of information retrieval. Furthermore, the contribution exemplifies the database potentials in applied landslide impact research, including statistics of landslide damage, repair, and mitigation. The landslide database offers due to systematic regional data compilation a differentiated data pool of more than 5,000 data sets and over 13,000 single data files. It dates back to 1137 AD and covers landslide sites throughout Germany. In seven main data blocks, the landslide database stores besides information on landslide types, dimensions, and processes, additional data on soil and bedrock properties, geomorphometry, and climatic or other major triggering events. A peculiarity of this landslide database is its storage of data sets on land use effects, damage impacts, hazard mitigation, and landslide costs. Compilation of landslide data is based on a two-tier strategy of data collection. The first step of information retrieval includes systematic web content mining and exploration of online archives of emergency agencies, fire and police departments, and news organizations. Using web and RSS feeds and soon also a focused web crawler, this enables effective nationwide data collection for recent landslides. On the basis of this information, in-depth data mining is performed to deepen and diversify the data pool in key landslide areas. This enables to gather detailed landslide information from, amongst others, agency records, geotechnical reports, climate statistics, maps, and satellite imagery. Landslide data is extracted from these information sources using a mix of methods, including statistical techniques, imagery analysis, and qualitative text interpretation. The landslide database is currently migrated to a spatial database system

  12. Nigeria Anopheles Vector Database: An Overview of 100 Years' Research

    PubMed Central

    Okorie, Patricia Nkem; McKenzie, F. Ellis; Ademowo, Olusegun George; Bockarie, Moses; Kelly-Hope, Louise

    2011-01-01

    Anopheles mosquitoes are important vectors of malaria and lymphatic filariasis (LF), which are major public health diseases in Nigeria. Malaria is caused by infection with a protozoan parasite of the genus Plasmodium and LF by the parasitic worm Wuchereria bancrofti. Updating our knowledge of the Anopheles species is vital in planning and implementing evidence based vector control programs. To present a comprehensive report on the spatial distribution and composition of these vectors, all published data available were collated into a database. Details recorded for each source were the locality, latitude/longitude, time/period of study, species, abundance, sampling/collection methods, morphological and molecular species identification methods, insecticide resistance status, including evidence of the kdr allele, and P. falciparum sporozoite rate and W. bancrofti microfilaria prevalence. This collation resulted in a total of 110 publications, encompassing 484,747 Anopheles mosquitoes in 632 spatially unique descriptions at 142 georeferenced locations being identified across Nigeria from 1900 to 2010. Overall, the highest number of vector species reported included An. gambiae complex (65.2%), An. funestus complex (17.3%), An. gambiae s.s. (6.5%). An. arabiensis (5.0%) and An. funestus s.s. (2.5%), with the molecular forms An. gambiae M and S identified at 120 locations. A variety of sampling/collection and species identification methods were used with an increase in molecular techniques in recent decades. Insecticide resistance to pyrethroids and organochlorines was found in the main Anopheles species across 45 locations. Presence of P. falciparum and W. bancrofti varied between species with the highest sporozoite rates found in An. gambiae s.s, An. funestus s.s. and An. moucheti, and the highest microfilaria prevalence in An. gambiae s.l., An. arabiensis, and An. gambiae s.s. This comprehensive geo-referenced database provides an essential baseline on Anopheles

  13. Impact of IPAD on CAD/CAM database university research

    NASA Technical Reports Server (NTRS)

    Leach, L. M.; Wozny, M. J.

    1984-01-01

    IPAD program has provided direction, focus and software products which impacted on CAD/CAM data base research and follow-on research. The relationship of IPAD to the research projects which involve the storage of geometric data in common data ase facilities such as data base machines, the exchange of data between heterogeneous data bases, the development of IGES processors, the migration of lrge CAD/CAM data base management systems to noncompatible hosts, and the value of RIM as a research tool is described.

  14. Impact of IPAD on CAD/CAM database university research

    NASA Technical Reports Server (NTRS)

    Leach, L. M.; Wozny, M. J.

    1984-01-01

    IPAD program has provided direction, focus and software products which impacted on CAD/CAM data base research and follow-on research. The relationship of IPAD to the research projects which involve the storage of geometric data in common data ase facilities such as data base machines, the exchange of data between heterogeneous data bases, the development of IGES processors, the migration of lrge CAD/CAM data base management systems to noncompatible hosts, and the value of RIM as a research tool is described.

  15. Development and testing of a database of NIH research funding of AAPM members: A report from the AAPM Working Group for the Development of a Research Database (WGDRD).

    PubMed

    Whelan, Brendan; Moros, Eduardo G; Fahrig, Rebecca; Deye, James; Yi, Thomas; Woodward, Michael; Keall, Paul; Siewerdsen, Jeff H

    2017-04-01

    To produce and maintain a database of National Institutes of Health (NIH) funding of the American Association of Physicists in Medicine (AAPM) members, to perform a top-level analysis of these data, and to make these data (hereafter referred to as the AAPM research database) available for the use of the AAPM and its members. NIH-funded research dating back to 1985 is available for public download through the NIH exporter website, and AAPM membership information dating back to 2002 was supplied by the AAPM. To link these two sources of data, a data mining algorithm was developed in Matlab. The false-positive rate was manually estimated based on a random sample of 100 records, and the false-negative rate was assessed by comparing against 99 member-supplied PI_ID numbers. The AAPM research database was queried to produce an analysis of trends and demographics in research funding dating from 2002 to 2015. A total of 566 PI_ID numbers were matched to AAPM members. False-positive and -negative rates were respectively 4% (95% CI: 1-10%, N = 100) and 10% (95% CI: 5-18%, N = 99). Based on analysis of the AAPM research database, in 2015 the NIH awarded $USD 110M to members of the AAPM. The four NIH institutes which historically awarded the most funding to AAPM members were the National Cancer Institute, National Institute of Biomedical Imaging and Bioengineering, National Heart Lung and Blood Institute, and National Institute of Neurological Disorders and Stroke. In 2015, over 85% of the total NIH research funding awarded to AAPM members was via these institutes, representing 1.1% of their combined budget. In the same year, 2.0% of AAPM members received NIH funding for a total of $116M, which is lower than the historic mean of $120M (in 2015 USD). A database of NIH-funded research awarded to AAPM members has been developed and tested using a data mining approach, and a top-level analysis of funding trends has been performed. Current funding of AAPM members is lower than

  16. Design and deployment of a large brain-image database for clinical and nonclinical research

    NASA Astrophysics Data System (ADS)

    Yang, Guo Liang; Lim, Choie Cheio Tchoyoson; Banukumar, Narayanaswami; Aziz, Aamer; Hui, Francis; Nowinski, Wieslaw L.

    2004-04-01

    An efficient database is an essential component of organizing diverse information on image metadata and patient information for research in medical imaging. This paper describes the design, development and deployment of a large database system serving as a brain image repository that can be used across different platforms in various medical researches. It forms the infrastructure that links hospitals and institutions together and shares data among them. The database contains patient-, pathology-, image-, research- and management-specific data. The functionalities of the database system include image uploading, storage, indexing, downloading and sharing as well as database querying and management with security and data anonymization concerns well taken care of. The structure of database is multi-tier client-server architecture with Relational Database Management System, Security Layer, Application Layer and User Interface. Image source adapter has been developed to handle most of the popular image formats. The database has a user interface based on web browsers and is easy to handle. We have used Java programming language for its platform independency and vast function libraries. The brain image database can sort data according to clinically relevant information. This can be effectively used in research from the clinicians" points of view. The database is suitable for validation of algorithms on large population of cases. Medical images for processing could be identified and organized based on information in image metadata. Clinical research in various pathologies can thus be performed with greater efficiency and large image repositories can be managed more effectively. The prototype of the system has been installed in a few hospitals and is working to the satisfaction of the clinicians.

  17. Patient Confidentiality in the Research Use of Clinical Medical Databases

    PubMed Central

    Krishna, Rajeev; Kelleher, Kelly; Stahlberg, Eric

    2007-01-01

    Electronic medical record keeping has led to increased interest in analyzing historical patient data to improve care delivery. Such research use of patient data, however, raises concerns about confidentiality and institutional liability. Institutional review boards must balance patient data security with a researcher’s ability to explore potentially important clinical relationships. We considered the issues involved when patient records from health care institutions are used in medical research. We also explored current regulations on patient confidentiality, the need for identifying information in research, and the effectiveness of deidentification and data security. We will present an algorithm for researchers to use to think about the data security needs of their research, and we will introduce a vocabulary for documenting these techniques in proposals and publications. PMID:17329644

  18. A Temporal Abstraction-based Extract, Transform and Load Process for Creating Registry Databases for Research.

    PubMed

    Post, Andrew; Kurc, Tahsin; Overcash, Marc; Cantrell, Dedra; Morris, Tim; Eckerson, Kristi; Tsui, Circe; Willey, Terry; Quyyumi, Arshed; Eapen, Danny; Umpierrez, Guillermo; Ziemer, David; Saltz, Joel

    2011-01-01

    In the CTSA era there is great interest in aggregating and comparing populations across institutions. These sites likely represent data differently in their clinical data warehouses and other databases. Clinical data warehouses frequently are structured in a generalized way that supports many constituencies. For research, there is a need to transform these heterogeneous data into a shared representation, and to perform categorization and interpretation to optimize the data representation for investigators. We are addressing this need by extending an existing temporal abstraction-based clinical database query system, PROTEMPA. The extended system allows specifying data types of interest in federated databases, extracting the data into a shared representation, transforming it through categorization and interpretation, and loading it into a registry database that can be refreshed. Such a registry's access control, data representation and query tools can be tailored to the needs of research while keeping local databases as the source of truth.

  19. Healthcare Databases in Thailand and Japan: Potential Sources for Health Technology Assessment Research

    PubMed Central

    Saokaew, Surasak; Sugimoto, Takashi; Kamae, Isao; Pratoomsoot, Chayanin; Chaiyakunapruk, Nathorn

    2015-01-01

    Background Health technology assessment (HTA) has been continuously used for value-based healthcare decisions over the last decade. Healthcare databases represent an important source of information for HTA, which has seen a surge in use in Western countries. Although HTA agencies have been established in Asia-Pacific region, application and understanding of healthcare databases for HTA is rather limited. Thus, we reviewed existing databases to assess their potential for HTA in Thailand where HTA has been used officially and Japan where HTA is going to be officially introduced. Method Existing healthcare databases in Thailand and Japan were compiled and reviewed. Databases’ characteristics e.g. name of database, host, scope/objective, time/sample size, design, data collection method, population/sample, and variables were described. Databases were assessed for its potential HTA use in terms of safety/efficacy/effectiveness, social/ethical, organization/professional, economic, and epidemiological domains. Request route for each database was also provided. Results Forty databases– 20 from Thailand and 20 from Japan—were included. These comprised of national censuses, surveys, registries, administrative data, and claimed databases. All databases were potentially used for epidemiological studies. In addition, data on mortality, morbidity, disability, adverse events, quality of life, service/technology utilization, length of stay, and economics were also found in some databases. However, access to patient-level data was limited since information about the databases was not available on public sources. Conclusion Our findings have shown that existing databases provided valuable information for HTA research with limitation on accessibility. Mutual dialogue on healthcare database development and usage for HTA among Asia-Pacific region is needed. PMID:26560127

  20. NaKnowBaseTM: The EPA Nanomaterials Research Database

    EPA Science Inventory

    The ability to predict the environmental and health implications of engineered nanomaterials is an important research priority due to the exponential rate at which nanotechnology is being incorporated into consumer, industrial and biomedical applications. To address this need and...

  1. Emerging acid deposition research and monitoring issues

    SciTech Connect

    Birnbaum, R.

    1997-12-31

    The research baselines established for acid rain in the 1980s position scientists and policy makers to evaluate the environmental effectiveness of the acid rain control program and to test the variety of scientific hypotheses made regarding the chemical, transport and biological processes involved in acidic deposition. Several new research questions have evolved. How effective are the emissions reductions? What is the residual risk? How have ecological recovery rates been affected and what other environmental factors influence recovery? What are the critical requirements to measure ecological change including the extent and rate while also capturing the extent and severity of emerging ecological stressors (such as watershed nitrogen saturation)? These and other questions are currently being synthesized within and outside of EPA to develop a long-term strategy to provide guidance to emerging research and monitoring issues.

  2. Standardizing Terminology and Definitions of Medication Adherence and Persistence in Research employing Electronic Databases

    PubMed Central

    Raebel, Marsha A.; Schmittdiel, Julie; Karter, Andrew J.; Konieczny, Jennifer L.; Steiner, John F.

    2013-01-01

    Objective To propose a unifying set of definitions for prescription adherence research utilizing electronic health record prescribing databases, prescription dispensing databases, and pharmacy claims databases and to provide a conceptual framework to operationalize these definitions consistently across studies. Methods We reviewed recent literature to identify definitions in electronic database studies of prescription-filling patterns for chronic oral medications. We then develop a conceptual model and propose standardized terminology and definitions to describe prescription-filling behavior from electronic databases. Results The conceptual model we propose defines two separate constructs: medication adherence and persistence. We define primary and secondary adherence as distinct sub-types of adherence. Metrics for estimating secondary adherence are discussed and critiqued, including a newer metric (New Prescription Medication Gap measure) that enables estimation of both primary and secondary adherence. Discussion Terminology currently used in prescription adherence research employing electronic databases lacks consistency. We propose a clear, consistent, broadly applicable conceptual model and terminology for such studies. The model and definitions facilitate research utilizing electronic medication prescribing, dispensing, and/or claims databases and encompasses the entire continuum of prescription-filling behavior. Conclusion Employing conceptually clear and consistent terminology to define medication adherence and persistence will facilitate future comparative effectiveness research and meta-analytic studies that utilize electronic prescription and dispensing records. PMID:23774515

  3. Acid mine drainage. (Latest citations from the NTIS bibliographic database). Published Search

    SciTech Connect

    1995-01-01

    The bibliography contains citations concerning laboratory and field analyses of acid mine drainage. Topics include site investigations and characterization, remediation and monitoring programs, contaminant treatment research, and control and abatement studies. Chemical analyses of affected areas, and evaluation of terrestrial and aquatic ecosystem responses to acid drainage are also discussed. (Contains 250 citations and includes a subject term index and title list.)

  4. BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data.

    PubMed

    Hospital, Adam; Andrio, Pau; Cugnasco, Cesare; Codo, Laia; Becerra, Yolanda; Dans, Pablo D; Battistini, Federica; Torres, Jordi; Goñi, Ramón; Orozco, Modesto; Gelpí, Josep Ll

    2016-01-04

    Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories are obtained after months of calculations, analysed in situ, and in practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists in the nucleic acids world. We present here a novel database system to store MD trajectories and analyses of nucleic acids. The initial data set available consists mainly of the benchmark of the new molecular dynamics force-field, parmBSC1. It contains 156 simulations, with over 120 μs of total simulation time. A deposition protocol is available to accept the submission of new trajectory data. The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. The analyses available include backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses. Individual trajectories and combined meta-trajectories can be downloaded from the portal. The system is accessible through http://mmb.irbbarcelona.org/BIGNASim/. Supplementary Material is also available on-line at http://mmb.irbbarcelona.org/BIGNASim/SuppMaterial/.

  5. How can the research potential of the clinical quality databases be maximized? The Danish experience.

    PubMed

    Nørgaard, M; Johnsen, S P

    2016-02-01

    In Denmark, the need for monitoring of clinical quality and patient safety with feedback to the clinical, administrative and political systems has resulted in the establishment of a network of more than 60 publicly financed nationwide clinical quality databases. Although primarily devoted to monitoring and improving quality of care, the potential of these databases as data sources in clinical research is increasingly being recognized. In this review, we describe these databases focusing on their use as data sources for clinical research, including their strengths and weaknesses as well as future concerns and opportunities. The research potential of the clinical quality databases is substantial but has so far only been explored to a limited extent. Efforts related to technical, legal and financial challenges are needed in order to take full advantage of this potential. © 2016 The Association for the Publication of the Journal of Internal Medicine.

  6. Importance of databases of nucleic acids for bioinformatic analysis focused to genomics

    NASA Astrophysics Data System (ADS)

    Jimenez-Gutierrez, L. R.; Barrios-Hernández, C. J.; Pedraza-Ferreira, G. R.; Vera-Cala, L.; Martinez-Perez, F.

    2016-08-01

    Recently, bioinformatics has become a new field of science, indispensable in the analysis of millions of nucleic acids sequences, which are currently deposited in international databases (public or private); these databases contain information of genes, RNA, ORF, proteins, intergenic regions, including entire genomes from some species. The analysis of this information requires computer programs; which were renewed in the use of new mathematical methods, and the introduction of the use of artificial intelligence. In addition to the constant creation of supercomputing units trained to withstand the heavy workload of sequence analysis. However, it is still necessary the innovation on platforms that allow genomic analyses, faster and more effectively, with a technological understanding of all biological processes.

  7. Generation of comprehensive thoracic oncology database--tool for translational research.

    PubMed

    Surati, Mosmi; Robinson, Matthew; Nandi, Suvobroto; Faoro, Leonardo; Demchuk, Carley; Kanteti, Rajani; Ferguson, Benjamin; Gangadhar, Tara; Hensing, Thomas; Hasina, Rifat; Husain, Aliya; Ferguson, Mark; Karrison, Theodore; Salgia, Ravi

    2011-01-22

    The Thoracic Oncology Program Database Project was created to serve as a comprehensive, verified, and accessible repository for well-annotated cancer specimens and clinical data to be available to researchers within the Thoracic Oncology Research Program. This database also captures a large volume of genomic and proteomic data obtained from various tumor tissue studies. A team of clinical and basic science researchers, a biostatistician, and a bioinformatics expert was convened to design the database. Variables of interest were clearly defined and their descriptions were written within a standard operating manual to ensure consistency of data annotation. Using a protocol for prospective tissue banking and another protocol for retrospective banking, tumor and normal tissue samples from patients consented to these protocols were collected. Clinical information such as demographics, cancer characterization, and treatment plans for these patients were abstracted and entered into an Access database. Proteomic and genomic data have been included in the database and have been linked to clinical information for patients described within the database. The data from each table were linked using the relationships function in Microsoft Access to allow the database manager to connect clinical and laboratory information during a query. The queried data can then be exported for statistical analysis and hypothesis generation.

  8. Influenza Research Database: An integrated bioinformatics resource for influenza virus research

    PubMed Central

    Zhang, Yun; Aevermann, Brian D.; Anderson, Tavis K.; Burke, David F.; Dauphin, Gwenaelle; Gu, Zhiping; He, Sherry; Kumar, Sanjeev; Larsen, Christopher N.; Lee, Alexandra J.; Li, Xiaomei; Macken, Catherine; Mahaffey, Colin; Pickett, Brett E.; Reardon, Brian; Smith, Thomas; Stewart, Lucy; Suloway, Christian; Sun, Guangyu; Tong, Lei; Vincent, Amy L.; Walters, Bryan; Zaremba, Sam; Zhao, Hongtao; Zhou, Liwei; Zmasek, Christian; Klem, Edward B.; Scheuermann, Richard H.

    2017-01-01

    The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research and development of vaccines, diagnostics and therapeutics against influenza virus by providing a comprehensive collection of influenza-related data integrated from various sources, a growing suite of analysis and visualization tools for data mining and hypothesis generation, personal workbench spaces for data storage and sharing, and active user community support. Here, we describe the recent improvements in IRD including the use of cloud and high performance computing resources, analysis and visualization of user-provided sequence data with associated metadata, predictions of novel variant proteins, annotations of phenotype-associated sequence markers and their predicted phenotypic effects, hemagglutinin (HA) clade classifications, an automated tool for HA subtype numbering conversion, linkouts to disease event data and the addition of host factor and antiviral drug components. All data and tools are freely available without restriction from the IRD website at https://www.fludb.org. PMID:27679478

  9. [Research on the performance comparing and building of affective computing database based on physiological parameters].

    PubMed

    Li, Xin; Du, Xiaojuan; Zhang, Yunpeng; Ying, Lijuan; Li, Changwuz

    2014-08-01

    The validity and reasonableness of emotional data are the key issues in the cognitive affective computing research. Effects of the emotion recognition are decided by the quality of selected data directly. Therefore, it is an important part of affective computing research to build affective computing database with good performance, so that it is the hot spot of research in this field. In this paper, the performance of two classical cognitive affective computing databases, the Massachusetts Institute of Technology (MIT) cognitive affective computing database and Germany Augsburg University emotion recognition database were compared, their data structure and data types were compared respectively, and emotional recognition effect based on the data were studied comparatively. The results indicated that the analysis based on the physical parameters could get the effective emotional recognition, and would be a feasible method of pressure emotional evaluation. Because of the lack of stress emotional evaluation data based on the physiological parameters domestically, there is not a public stress emotional database. We hereby built a dataset for the stress evaluation towards the high stress group in colleges, candidates of postgraduates of Ph. D and master as the subjects. We then acquired their physiological parameters, and performed the pressure analysis based on this database. The results indicated that this dataset had a certain reference value for the stress evaluation, and we hope this research can provide a reference and support for emotion evaluation and analysis.

  10. Large-scale spatial population databases in infectious disease research

    PubMed Central

    2012-01-01

    Modelling studies on the spatial distribution and spread of infectious diseases are becoming increasingly detailed and sophisticated, with global risk mapping and epidemic modelling studies now popular. Yet, in deriving populations at risk of disease estimates, these spatial models must rely on existing global and regional datasets on population distribution, which are often based on outdated and coarse resolution data. Moreover, a variety of different methods have been used to model population distribution at large spatial scales. In this review we describe the main global gridded population datasets that are freely available for health researchers and compare their construction methods, and highlight the uncertainties inherent in these population datasets. We review their application in past studies on disease risk and dynamics, and discuss how the choice of dataset can affect results. Moreover, we highlight how the lack of contemporary, detailed and reliable data on human population distribution in low income countries is proving a barrier to obtaining accurate large-scale estimates of population at risk and constructing reliable models of disease spread, and suggest research directions required to further reduce these barriers. PMID:22433126

  11. Databases and coordinated research projects at the IAEA on atomic processes in plasmas

    NASA Astrophysics Data System (ADS)

    Braams, Bastiaan J.; Chung, Hyun-Kyung

    2012-05-01

    The Atomic and Molecular Data Unit at the IAEA works with a network of national data centres to encourage and coordinate production and dissemination of fundamental data for atomic, molecular and plasma-material interaction (A+M/PMI) processes that are relevant to the realization of fusion energy. The Unit maintains numerical and bibliographical databases and has started a Wiki-style knowledge base. The Unit also contributes to A+M database interface standards and provides a search engine that offers a common interface to multiple numerical A+M/PMI databases. Coordinated Research Projects (CRPs) bring together fusion energy researchers and atomic, molecular and surface physicists for joint work towards the development of new data and new methods. The databases and current CRPs on A+M/PMI processes are briefly described here.

  12. Databases and coordinated research projects at the IAEA on atomic processes in plasmas

    SciTech Connect

    Braams, Bastiaan J.; Chung, Hyun-Kyung

    2012-05-25

    The Atomic and Molecular Data Unit at the IAEA works with a network of national data centres to encourage and coordinate production and dissemination of fundamental data for atomic, molecular and plasma-material interaction (A+M/PMI) processes that are relevant to the realization of fusion energy. The Unit maintains numerical and bibliographical databases and has started a Wiki-style knowledge base. The Unit also contributes to A+M database interface standards and provides a search engine that offers a common interface to multiple numerical A+M/PMI databases. Coordinated Research Projects (CRPs) bring together fusion energy researchers and atomic, molecular and surface physicists for joint work towards the development of new data and new methods. The databases and current CRPs on A+M/PMI processes are briefly described here.

  13. Real-time magnetic resonance imaging and electromagnetic articulography database for speech production research (TC)

    PubMed Central

    Narayanan, Shrikanth; Toutios, Asterios; Ramanarayanan, Vikram; Lammert, Adam; Kim, Jangwon; Lee, Sungbok; Nayak, Krishna; Kim, Yoon-Chul; Zhu, Yinghua; Goldstein, Louis; Byrd, Dani; Bresch, Erik; Ghosh, Prasanta; Katsamanis, Athanasios; Proctor, Michael

    2014-01-01

    USC-TIMIT is an extensive database of multimodal speech production data, developed to complement existing resources available to the speech research community and with the intention of being continuously refined and augmented. The database currently includes real-time magnetic resonance imaging data from five male and five female speakers of American English. Electromagnetic articulography data have also been presently collected from four of these speakers. The two modalities were recorded in two independent sessions while the subjects produced the same 460 sentence corpus used previously in the MOCHA-TIMIT database. In both cases the audio signal was recorded and synchronized with the articulatory data. The database and companion software are freely available to the research community. PMID:25190403

  14. Oral contraceptives and venous thromboembolic disease. Analyses of the UK General Practice Research Database and the UK Mediplus database.

    PubMed

    Farmer, R D; Lawrenson, R A; Todd, J C; Williams, T J; MacRae, K

    1999-01-01

    The results of three independent studies of venous thromboembolic disease (VTE) and oral contraceptives are reviewed together with two further cohort/case-control studies which we conducted using the MediPlus and General Practice Research Database (GPRD) databases. These latter studies jointly involved 395 cases and uniquely examined the association between VTE and individual combined oral contraceptive (COC) formulations. The two studies yielded very similar results. Crude incidence rates for idiopathic VTE of 4.6 and 3.8 were found per 10,000 exposed woman-years (EWY), in the MediPlus and GPRD studies respectively. Incidence rates increased markedly with age, and in both databases the rates amongst users of levonorgestrel products were lower than those amongst users of desogestrel and gestodene products. A case fatality rate of 3% and a mortality rate of 10 per million EWY were estimated. Odds ratios (OR) were calculated for confounding variables and different COC formulations. Both database studies indicated an excess of current smokers and women with high body mass indices amongst cases. There were significantly more cases with asthma in the GPRD study and cases who had been using their COC for less than a year. No statistically significant differences between COC formulations were found in the analyses where controls were matched to cases by practice and year of birth in both the MediPlus and GPRD studies. In the GPRD study we also ran a study where controls were matched by practice and within 5 year age bands. In this study the OR were consistently higher for the newer or 'third generation' products than when controls were matched by year of birth. However only the acne formulation/OC containing cyproterone acetate and 35 microg ethinyloestradiol yielded a significant OR of 2.3. It may be concluded that improvements in prescribing are paramount as the results strongly indicate that overweight women and those who smoke are at a greater risk of VTE. Further

  15. Data Recycling: Using Existing Databases to Increase Research Capacity in Speech-Language Development and Disorders

    ERIC Educational Resources Information Center

    Justice, Laura M.; Breit-Smith, Allison; Rogers, Margaret

    2010-01-01

    Purpose: This clinical forum was organized to provide a means for informing the research and clinical communities of one mechanism through which research capacity might be enhanced within the field of speech-language pathology. Specifically, forum authors describe the process of conducting secondary analyses of extant databases to answer questions…

  16. University Management of Research: A Data-Based Policy and Planning. AIR 1989 Annual Forum Paper.

    ERIC Educational Resources Information Center

    Strubbe, J.

    The development of an appropriate research policy for a university as well as for the national and international levels can be accomplished only if quantitative data and qualitative evaluations (scientific contribution, results, goal-achievement) are made available to illustrate research activities. A database is described that would enable…

  17. Data Recycling: Using Existing Databases to Increase Research Capacity in Speech-Language Development and Disorders

    ERIC Educational Resources Information Center

    Justice, Laura M.; Breit-Smith, Allison; Rogers, Margaret

    2010-01-01

    Purpose: This clinical forum was organized to provide a means for informing the research and clinical communities of one mechanism through which research capacity might be enhanced within the field of speech-language pathology. Specifically, forum authors describe the process of conducting secondary analyses of extant databases to answer questions…

  18. The Pitfalls of Cyberspace and Electronic Database Research--Who Sells What to Whom for Which Audience?

    ERIC Educational Resources Information Center

    Willey, Susan

    2000-01-01

    Raises questions about the validity and reliability of doing research online via the proliferation of academic databases. Finds different versions of the Lexis-Nexis database have differing search capabilities. Argues that dependence on database research findings means dependence on decisions made by a few people who design search engines and…

  19. Acid mine drainage. (Latest citations from the NTIS bibliographic database). Published Search

    SciTech Connect

    1997-06-01

    The bibliography contains citations concerning laboratory and field analyses of acid mine drainage. Topics include site investigations and characterization, remediation and monitoring programs, contaminant treatment research, and control and abatement studies. Chemical analyses of affected areas, and evaluation of terrestrial and aquatic ecosystem responses to acid drainage are also discussed. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  20. Acid mine drainage. (Latest citations from the NTIS bibliographic database). Published Search

    SciTech Connect

    1996-04-01

    The bibliography contains citations concerning laboratory and field analyses of acid mine drainage. Topics include site investigations and characterization, remediation and monitoring programs, contaminant treatment research, and control and abatement studies. Chemical analyses of affected areas, and evaluation of terrestrial and aquatic ecosystem responses to acid drainage are also discussed. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  1. Facilitating Research in Physician Assistant Programs: Creating a Student-Level Longitudinal Database.

    PubMed

    Morgan, Perri; Humeniuk, Katherine M; Everett, Christine M

    2015-09-01

    As physician assistant (PA) roles expand and diversify in the United States and around the world, there is a pressing need for research that illuminates how PAs may best be selected, educated, and used in health systems to maximize their potential contributions to health. Physician assistant education programs are well positioned to advance this research by collecting and organizing data on applicants, students, and graduates. Our PA program is creating a permanent longitudinal education database for research that contains extensive student-level data. This database will allow us to conduct research on all phases of PA education, from admission processes through the professional practice of our graduates. In this article, we describe our approach to constructing a longitudinal student-level research database and discuss the strengths and limitations of longitudinal databases for research on education and the practice of PAs. We hope to encourage other PA programs to initiate similar projects so that, in the future, data can be combined for use in multi-institutional research that can contribute to improved education for PA students across programs.

  2. A Review of Databases Used in Orthopaedic Surgery Research and an Analysis of Database Use in Arthroscopy: The Journal of Arthroscopic and Related Surgery.

    PubMed

    Weinreb, Jeffrey H; Yoshida, Ryu; Cote, Mark P; O'Sullivan, Michael B; Mazzocca, Augustus D

    2017-01-01

    The purpose of this study was to evaluate how database use has changed over time in Arthroscopy: The Journal of Arthroscopic and Related Surgery and to inform readers about available databases used in orthopaedic literature. An extensive literature search was conducted to identify databases used in Arthroscopy and other orthopaedic literature. All articles published in Arthroscopy between January 1, 2006, and December 31, 2015, were reviewed. A database was defined as a national, widely available set of individual patient encounters, applicable to multiple patient populations, used in orthopaedic research in a peer-reviewed journal, not restricted by encounter setting or visit duration, and with information available in English. Databases used in Arthroscopy included PearlDiver, the American College of Surgeons National Surgical Quality Improvement Program, the Danish Common Orthopaedic Database, the Swedish National Knee Ligament Register, the Hospital Episodes Statistics database, and the National Inpatient Sample. Database use increased significantly from 4 articles in 2013 to 11 articles in 2015 (P = .012), with no database use between January 1, 2006, and December 31, 2012. Database use increased significantly between January 1, 2006, and December 31, 2015, in Arthroscopy. Level IV, systematic review of Level II through IV studies. Copyright © 2016 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

  3. A proposed key escrow system for secure patient information disclosure in biomedical research databases.

    PubMed Central

    Ferris, Todd A.; Garrison, Gregory M.; Lowe, Henry J.

    2002-01-01

    Access to clinical data is of increasing importance to biomedical research. The pending HIPAA privacy regulations provide specific requirements for the release of protected health information. Under the regulations, biomedical researchers may utilize anonymized data, or adhere to HIPAA requirements regarding protected health information. In order to provide researchers with anonymized data from a clinical research database, we reviewed several published strategies for de-identification of protected health information. Critical analysis with respect to this project suggests that de-identification alone is problematic when applied to clinical research databases. We propose a hybrid system; utilizing secure key escrow, de-identification, and role-based access for IRB approved researchers. PMID:12463824

  4. Acid deposition research in the private sector

    SciTech Connect

    Kinsman, J.D.; Wisniewski, J.; Nelson, J.

    1984-02-01

    Acid deposition research funded by the private sector since 1980 is reviewed. Types of studies (e.g., atmospheric processes, emissions and monitoring, environmental effects) supported by the private sector during this period are overviewed. The specific industries/organizations (e.g., electric utility industry, environmental interest groups) funding reserach during 1980-1982 are discussed, with relation to the number of studies supported and funds (by year) provided by each. Finally, 13 research projects supported by the private sector and initiated by December 1983, each at greater than $1 million, are described.

  5. Privacy protection and public goods: building a genetic database for health research in Newfoundland and Labrador

    PubMed Central

    Pullman, Daryl; Perrot-Daley, Astrid; Hodgkinson, Kathy; Street, Catherine; Rahman, Proton

    2013-01-01

    Objective To provide a legal and ethical analysis of some of the implementation challenges faced by the Population Therapeutics Research Group (PTRG) at Memorial University (Canada), in using genealogical information offered by individuals for its genetics research database. Materials and methods This paper describes the unique historical and genetic characteristics of the Newfoundland and Labrador founder population, which gave rise to the opportunity for PTRG to build the Newfoundland Genealogy Database containing digitized records of all pre-confederation (1949) census records of the Newfoundland founder population. In addition to building the database, PTRG has developed the Heritability Analytics Infrastructure, a data management structure that stores genotype, phenotype, and pedigree information in a single database, and custom linkage software (KINNECT) to perform pedigree linkages on the genealogy database. Discussion A newly adopted legal regimen in Newfoundland and Labrador is discussed. It incorporates health privacy legislation with a unique research ethics statute governing the composition and activities of research ethics boards and, for the first time in Canada, elevating the status of national research ethics guidelines into law. The discussion looks at this integration of legal and ethical principles which provides a flexible and seamless framework for balancing the privacy rights and welfare interests of individuals, families, and larger societies in the creation and use of research data infrastructures as public goods. Conclusion The complementary legal and ethical frameworks that now coexist in Newfoundland and Labrador provide the legislative authority, ethical legitimacy, and practical flexibility needed to find a workable balance between privacy interests and public goods. Such an approach may also be instructive for other jurisdictions as they seek to construct and use biobanks and related research platforms for genetic research. PMID

  6. Appropriateness of the food-pics image database for experimental eating and appetite research with adolescents.

    PubMed

    Jensen, Chad D; Duraccio, Kara M; Barnett, Kimberly A; Stevens, Kimberly S

    2016-12-01

    Research examining effects of visual food cues on appetite-related brain processes and eating behavior has proliferated. Recently investigators have developed food image databases for use across experimental studies examining appetite and eating behavior. The food-pics image database represents a standardized, freely available image library originally validated in a large sample primarily comprised of adults. The suitability of the images for use with adolescents has not been investigated. The aim of the present study was to evaluate the appropriateness of the food-pics image library for appetite and eating research with adolescents. Three hundred and seven adolescents (ages 12-17) provided ratings of recognizability, palatability, and desire to eat, for images from the food-pics database. Moreover, participants rated the caloric content (high vs. low) and healthiness (healthy vs. unhealthy) of each image. Adolescents rated approximately 75% of the food images as recognizable. Approximately 65% of recognizable images were correctly categorized as high vs. low calorie and 63% were correctly classified as healthy vs. unhealthy in 80% or more of image ratings. These results suggest that a smaller subset of the food-pics image database is appropriate for use with adolescents. With some modifications to included images, the food-pics image database appears to be appropriate for use in experimental appetite and eating-related research conducted with adolescents. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Moving to Google Cloud: Renovation of Global Borehole Temperature Database for Climate Research

    NASA Astrophysics Data System (ADS)

    Xiong, Y.; Huang, S.

    2013-12-01

    Borehole temperature comprises an independent archive of information on climate change which is complementary to the instrumental and other proxy climate records. With support from the international geothermal community, a global database of borehole temperatures has been constructed for the specific purpose of the study on climate change. Although this database has become an important data source in climate research, there are certain limitations partially because the framework of the existing borehole temperature database was hand-coded some twenty years ago. A database renovation work is now underway to take the advantages of the contemporary online database technologies. The major intended improvements include 1) dynamically linking a borehole site to Google Earth to allow for inspection of site specific geographical information; 2) dynamically linking an original key reference of a given borehole site to Google Scholar to allow for a complete list of related publications; and 3) enabling site selection and data download based on country, coordinate range, and contributor. There appears to be a good match between the enhancement requirements for this database and the functionalities of the newly released Google Fusion Tables application. Google Fusion Tables is a cloud-based service for data management, integration, and visualization. This experimental application can consolidate related online resources such as Google Earth, Google Scholar, and Google Drive for sharing and enriching an online database. It is user friendly, allowing users to apply filters and to further explore the internet for additional information regarding the selected data. The users also have ways to map, to chart, and to calculate on the selected data, and to download just the subset needed. The figure below is a snapshot of the database currently under Google Fusion Tables renovation. We invite contribution and feedback from the geothermal and climate research community to make the

  8. Towards a database for genotype-phenotype association research: mining data from encyclopaedia.

    PubMed

    Pajić, Vesna S; Pavloviç-Lazetić, Gordana M; Beljanski, Milos V; Brandt, Bernd W; Pajić, Milos B

    2013-01-01

    To associate phenotypic characteristics of an organism to molecules encoded by its genome, there is a need for well-structured genotype and phenotype data. We use a novel method for extracting data on phenotype and genotype characteristics of microorganisms from text. As a resource, we use an encyclopedia of microorganisms, which holds phenotypic and genotypic data and create a structured, flexible data resource, which can be exported to a range of database formats, containing genotype and phenotype data for 2412 species and 873 genera of microbes. This data source has great potential as a resource for future biological research on genotype-phenotype associations. In this paper, we focus on describing the structure and content of the resulting database and on evaluating the method used for extracting the data. We conclude that the resulting database can be used as a reliable complementary resource for research into genotype-phenotype association.

  9. Progress in lactic acid bacterial phage research

    PubMed Central

    2014-01-01

    Research on lactic acid bacteria (LAB) has advanced significantly over the past number of decades and these developments have been driven by the parallel advances in technologies such as genomics, bioinformatics, protein expression systems and structural biology, combined with the ever increasing commercial relevance of this group of microorganisms. Some of the more significant and impressive outputs have been in the domain of bacteriophage-host interactions which provides a prime example of the cutting-edge model systems represented by LAB research. Here, we present a retrospective overview of the key advances in LAB phage research including phage-host interactions and co-evolution. We describe how in many instances this knowledge can be pivotal in creating real improvements in the application of LAB cultures in commercial practice. PMID:25185514

  10. Adopting a corporate perspective on databases. Improving support for research and decision making.

    PubMed

    Meistrell, M; Schlehuber, C

    1996-03-01

    The Veterans Health Administration (VHA) is at the forefront of designing and managing health care information systems that accommodate the needs of clinicians, researchers, and administrators at all levels. Rather than using one single-site, centralized corporate database VHA has constructed several large databases with different configurations to meet the needs of users with different perspectives. The largest VHA database is the Decentralized Hospital Computer Program (DHCP), a multisite, distributed data system that uses decoupled hospital databases. The centralization of DHCP policy has promoted data coherence, whereas the decentralization of DHCP management has permitted system development to be done with maximum relevance to the users'local practices. A more recently developed VHA data system, the Event Driven Reporting system (EDR), uses multiple, highly coupled databases to provide workload data at facility, regional, and national levels. The EDR automatically posts a subset of DHCP data to local and national VHA management. The development of the EDR illustrates how adoption of a corporate perspective can offer significant database improvements at reasonable cost and with modest impact on the legacy system.

  11. BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types.

    PubMed

    Howe, E A; de Souza, A; Lahr, D L; Chatwin, S; Montgomery, P; Alexander, B R; Nguyen, D-T; Cruz, Y; Stonich, D A; Walzer, G; Rose, J T; Picard, S C; Liu, Z; Rose, J N; Xiang, X; Asiedu, J; Durkin, D; Levine, J; Yang, J J; Schürer, S C; Braisted, J C; Southall, N; Southern, M R; Chung, T D Y; Brudz, S; Tanega, C; Schreiber, S L; Bittker, J A; Guha, R; Clemons, P A

    2015-01-01

    BARD, the BioAssay Research Database (https://bard.nih.gov/) is a public database and suite of tools developed to provide access to bioassay data produced by the NIH Molecular Libraries Program (MLP). Data from 631 MLP projects were migrated to a new structured vocabulary designed to capture bioassay data in a formalized manner, with particular emphasis placed on the description of assay protocols. New data can be submitted to BARD with a user-friendly set of tools that assist in the creation of appropriately formatted datasets and assay definitions. Data published through the BARD application program interface (API) can be accessed by researchers using web-based query tools or a desktop client. Third-party developers wishing to create new tools can use the API to produce stand-alone tools or new plug-ins that can be integrated into BARD. The entire BARD suite of tools therefore supports three classes of researcher: those who wish to publish data, those who wish to mine data for testable hypotheses, and those in the developer community who wish to build tools that leverage this carefully curated chemical biology resource. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by US Government employees and is in the public domain in the US.

  12. Pharmacophore-based database mining for probing fragmental drug-likeness of diketo acid analogues.

    PubMed

    Bak, A; Magdziarz, T; Polanski, J

    2012-01-01

    A number of the structurally diverse chemical compounds with functional diketo acid (DKA) subunit(s) have been revealed by combined online and MoStBiodat 3D pharmacophore-guided ZINC and PubChem database screening. We used the structural data available from such screening to analyse the similarities of the compounds containing the DKA fragment. Generally, the analysis by principal component analysis and self-organizing neural network approaches reveals four families of compounds complying with the chemical constitution (aromatic, aliphatic) of the compounds. From a practical point of view, similar studies may reveal potential bioisosteres of known drugs, e.g. raltegravir/elvitegravir. In this context, it seems that mono-halogenated aryl substructures with para group show the closest similarity to these compounds, in contrast to structures where the aromatic ring is halogenated in both ortho- and para-locations.

  13. Voluntary fortification with folic acid in Spain: An updated food composition database.

    PubMed

    Samaniego-Vaesken, M L; Alonso-Aperte, E; Varela-Moreiras, G

    2016-02-15

    Folic acid (FA) is a key vitamin in the prevention of many diseases including neural tube defects. In Spain, only voluntary FA food fortification is allowed and there is a lack of compositional data to assess the contribution of these products to population's dietary folate intakes. Since 2007, our group has been compiling and updating a FA fortified food composition database. FA levels were obtained from retailers in Madrid and information provided by manufacturers. FA was also quantified by an affinity chromatography-HPLC method. In the present study we recorded 375 products. Our results show a high variability in the declared FA levels amongst different products, and food groups, which is also dependant on the commercial brand. FA overages are commonly added by manufacturers to some fortified products. FA content label claims are missing in 64% of products. This database is a useful tool to manage FA fortified foods data but it is necessary to continuously update it for the sound evaluation and monitoring of population's FA dietary intakes. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. The Chinchilla Research Resource Database: resource for an otolaryngology disease model

    PubMed Central

    Shimoyama, Mary; Smith, Jennifer R.; De Pons, Jeff; Tutaj, Marek; Khampang, Pawjai; Hong, Wenzhou; Erbe, Christy B.; Ehrlich, Garth D.; Bakaletz, Lauren O.; Kerschner, Joseph E.

    2016-01-01

    The long-tailed chinchilla (Chinchilla lanigera) is an established animal model for diseases of the inner and middle ear, among others. In particular, chinchilla is commonly used to study diseases involving viral and bacterial pathogens and polymicrobial infections of the upper respiratory tract and the ear, such as otitis media. The value of the chinchilla as a model for human diseases prompted the sequencing of its genome in 2012 and the more recent development of the Chinchilla Research Resource Database (http://crrd.mcw.edu) to provide investigators with easy access to relevant datasets and software tools to enhance their research. The Chinchilla Research Resource Database contains a complete catalog of genes for chinchilla and, for comparative purposes, human. Chinchilla genes can be viewed in the context of their genomic scaffold positions using the JBrowse genome browser. In contrast to the corresponding records at NCBI, individual gene reports at CRRD include functional annotations for Disease, Gene Ontology (GO) Biological Process, GO Molecular Function, GO Cellular Component and Pathway assigned to chinchilla genes based on annotations from the corresponding human orthologs. Data can be retrieved via keyword and gene-specific searches. Lists of genes with similar functional attributes can be assembled by leveraging the hierarchical structure of the Disease, GO and Pathway vocabularies through the Ontology Search and Browser tool. Such lists can then be further analyzed for commonalities using the Gene Annotator (GA) Tool. All data in the Chinchilla Research Resource Database is freely accessible and downloadable via the CRRD FTP site or using the download functions available in the search and analysis tools. The Chinchilla Research Resource Database is a rich resource for researchers using, or considering the use of, chinchilla as a model for human disease. Database URL: http://crrd.mcw.edu PMID:27173523

  15. The Chinchilla Research Resource Database: resource for an otolaryngology disease model.

    PubMed

    Shimoyama, Mary; Smith, Jennifer R; De Pons, Jeff; Tutaj, Marek; Khampang, Pawjai; Hong, Wenzhou; Erbe, Christy B; Ehrlich, Garth D; Bakaletz, Lauren O; Kerschner, Joseph E

    2016-01-01

    The long-tailed chinchilla (Chinchilla lanigera) is an established animal model for diseases of the inner and middle ear, among others. In particular, chinchilla is commonly used to study diseases involving viral and bacterial pathogens and polymicrobial infections of the upper respiratory tract and the ear, such as otitis media. The value of the chinchilla as a model for human diseases prompted the sequencing of its genome in 2012 and the more recent development of the Chinchilla Research Resource Database (http://crrd.mcw.edu) to provide investigators with easy access to relevant datasets and software tools to enhance their research. The Chinchilla Research Resource Database contains a complete catalog of genes for chinchilla and, for comparative purposes, human. Chinchilla genes can be viewed in the context of their genomic scaffold positions using the JBrowse genome browser. In contrast to the corresponding records at NCBI, individual gene reports at CRRD include functional annotations for Disease, Gene Ontology (GO) Biological Process, GO Molecular Function, GO Cellular Component and Pathway assigned to chinchilla genes based on annotations from the corresponding human orthologs. Data can be retrieved via keyword and gene-specific searches. Lists of genes with similar functional attributes can be assembled by leveraging the hierarchical structure of the Disease, GO and Pathway vocabularies through the Ontology Search and Browser tool. Such lists can then be further analyzed for commonalities using the Gene Annotator (GA) Tool. All data in the Chinchilla Research Resource Database is freely accessible and downloadable via the CRRD FTP site or using the download functions available in the search and analysis tools. The Chinchilla Research Resource Database is a rich resource for researchers using, or considering the use of, chinchilla as a model for human disease.Database URL: http://crrd.mcw.edu.

  16. Heavy Oil Database from the National Institute for Petroleum and Energy Research (NIPER)

    DOE Data Explorer

    The Heavy Oil Database resulted from work funded by DOE and performed at the National Institute for Petroleum and Energy Research (NIPER). It contains information on more than 500 resevoirs in a Microsoft Excel spreadsheet. The information was collected in 1992 and updated periodically through 2003. Save the zipped file to your PC, then open to access the data.

  17. Database as a Tool for Promoting Research Activities in the Classroom: An Example in Teaching Humanities.

    ERIC Educational Resources Information Center

    Degl'Innocenti, Riccardo; Ferraris, Maria

    1988-01-01

    Describes Datamondo, an instructional package that introduces the use of a newspaper database in humanities teaching at the secondary level in Italy. The effectiveness of the package in developing basic linguistic skills and as a research tool is evaluated. (8 references) (Author/CLB)

  18. Analysis of Institutionally Specific Retention Research: A Comparison between Survey and Institutional Database Methods

    ERIC Educational Resources Information Center

    Caison, Amy L.

    2007-01-01

    This study empirically explores the comparability of traditional survey-based retention research methodology with an alternative approach that relies on data commonly available in institutional student databases. Drawing on Tinto's [Tinto, V. (1993). "Leaving College: Rethinking the Causes and Cures of Student Attrition" (2nd Ed.), The University…

  19. Research Goes to School II: How to Go On-Line to the Information Database.

    ERIC Educational Resources Information Center

    Newman, Joan; Motomatsu, Nancy

    Designed to help educators locate the most up-to-date research and information available for decision making, this handbook summarizes a vast collection of current educational, technical, and sociological information in computer databases. As online information systems multiply and become more consumer-oriented, and as microcomputers and modems…

  20. Analysis of Institutionally Specific Retention Research: A Comparison between Survey and Institutional Database Methods

    ERIC Educational Resources Information Center

    Caison, Amy L.

    2007-01-01

    This study empirically explores the comparability of traditional survey-based retention research methodology with an alternative approach that relies on data commonly available in institutional student databases. Drawing on Tinto's [Tinto, V. (1993). "Leaving College: Rethinking the Causes and Cures of Student Attrition" (2nd Ed.), The University…

  1. Accessing the public MIMIC-II intensive care relational database for clinical research

    PubMed Central

    2013-01-01

    Background The Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II) database is a free, public resource for intensive care research. The database was officially released in 2006, and has attracted a growing number of researchers in academia and industry. We present the two major software tools that facilitate accessing the relational database: the web-based QueryBuilder and a downloadable virtual machine (VM) image. Results QueryBuilder and the MIMIC-II VM have been developed successfully and are freely available to MIMIC-II users. Simple example SQL queries and the resulting data are presented. Clinical studies pertaining to acute kidney injury and prediction of fluid requirements in the intensive care unit are shown as typical examples of research performed with MIMIC-II. In addition, MIMIC-II has also provided data for annual PhysioNet/Computing in Cardiology Challenges, including the 2012 Challenge “Predicting mortality of ICU Patients”. Conclusions QueryBuilder is a web-based tool that provides easy access to MIMIC-II. For more computationally intensive queries, one can locally install a complete copy of MIMIC-II in a VM. Both publicly available tools provide the MIMIC-II research community with convenient querying interfaces and complement the value of the MIMIC-II relational database. PMID:23302652

  2. Quality standards for real-world research. Focus on observational database studies of comparative effectiveness.

    PubMed

    Roche, Nicolas; Reddel, Helen; Martin, Richard; Brusselle, Guy; Papi, Alberto; Thomas, Mike; Postma, Dirjke; Thomas, Vicky; Rand, Cynthia; Chisholm, Alison; Price, David

    2014-02-01

    Real-world research can use observational or clinical trial designs, in both cases putting emphasis on high external validity, to complement the classical efficacy randomized controlled trials (RCTs) with high internal validity. Real-world research is made necessary by the variety of factors that can play an important a role in modulating effectiveness in real life but are often tightly controlled in RCTs, such as comorbidities and concomitant treatments, adherence, inhalation technique, access to care, strength of doctor-caregiver communication, and socio-economic and other organizational factors. Real-world studies belong to two main categories: pragmatic trials and observational studies, which can be prospective or retrospective. Focusing on comparative database observational studies, the process aimed at ensuring high-quality research can be divided into three parts: preparation of research, analyses and reporting, and discussion of results. Key points include a priori planning of data collection and analyses, identification of appropriate database(s), proper outcomes definition, study registration with commitment to publish, bias minimization through matching and adjustment processes accounting for potential confounders, and sensitivity analyses testing the robustness of results. When these conditions are met, observational database studies can reach a sufficient level of evidence to help create guidelines (i.e., clinical and regulatory decision-making).

  3. AN OVERVIEW OF COMPUTATIONAL LIFE SCIENCE DATABASES & EXCHANGE FORMATS OF RELEVANCE TO CHEMICAL BIOLOGY RESEARCH

    PubMed Central

    Hall, Aaron Smalter; Shan, Yunfeng; Lushington, Gerald; Visvanathan, Mahesh

    2016-01-01

    Databases and exchange formats describing biological entities such as chemicals and proteins, along with their relationships, are a critical component of research in life sciences disciplines, including chemical biology wherein small information about small molecule properties converges with cellular and molecular biology. Databases for storing biological entities are growing not only in size, but also in type, with many similarities between them and often subtle differences. The data formats available to describe and exchange these entities are numerous as well. In general, each format is optimized for a particular purpose or database, and hence some understanding of these formats is required when choosing one for research purposes. This paper reviews a selection of different databases and data formats with the goal of summarizing their purposes, features, and limitations. Databases are reviewed under the categories of 1) protein interactions, 2) metabolic pathways, 3) chemical interactions, and 4) drug discovery. Representation formats will be discussed according to those describing chemical structures, and those describing genomic/proteomic entities. PMID:22934944

  4. Data-based research in therapeutic recreation: state of the art.

    PubMed

    Schleien, S J; Yermakoff, N

    1983-01-01

    During difficult financial times, it is critical not only to evaluate therapeutic recreation programs and document client progress but also to disseminate objective program data to therapeutic recreation and other practitioners. The purpose of this state-of-the-art research inquiry was to provide the therapeutic recreation discipline and other related helping professions with an accurate and current assessment of empirically based research concerning the provision of recreation for special populations. Eight professional journals in recreation, special education, and psychology from 1977 (the year of PL 94-142) through the current literature were reviewed. Articles using a data-based research methodology in the area of recreation/leisure for special populations were identified. Articles were analyzed according to target population, subject age, purpose of study, and research design. Of the 83 data-based research reports found, 40 studies addressed the mentally retarded population, 26 involved children (birth to 13 years), and the case study (23) and survey (23) research designs were most prevalent. A plea for future data-based research by therapeutic recreation professionals to improve services is made.

  5. The plant organelles database (PODB): a collection of visualized plant organelles and protocols for plant organelle research.

    PubMed

    Mano, Shoji; Miwa, Tomoki; Nishikawa, Shuh-ichi; Mimura, Tetsuro; Nishimura, Mikio

    2008-01-01

    The plant organelles database (PODB; http://podb.nibb.ac.jp/Organellome) was built to promote a comprehensive understanding of organelle dynamics, including organelle function, biogenesis, differentiation, movement and interactions with other organelles. This database consists of three individual parts, the organellome database, the functional analysis database and external links to other databases and homepages. The organellome database provides images of various plant organelles that were visualized with fluorescent and nonfluorescent probes in various tissues of several plant species at different developmental stages. The functional analysis database is a collection of protocols for plant organelle research. External links give access primarily to other databases and Web pages with information on transcriptomes and proteomes. All the data and protocols in the organellome database and the functional analysis database are populated by direct submission of experimentally determined data from plant researchers and can be freely downloaded. Our database promotes the exchange of information between plant organelle researchers for the comprehensive study of the organelle dynamics that support integrated functions in higher plants. We would also appreciate contributions of data and protocols from all plant researchers to maximize the usefulness of the database.

  6. Current Trends and New Challenges of Databases and Web Applications for Systems Driven Biological Research

    PubMed Central

    Sreenivasaiah, Pradeep Kumar; Kim, Do Han

    2010-01-01

    Dynamic and rapidly evolving nature of systems driven research imposes special requirements on the technology, approach, design and architecture of computational infrastructure including database and Web application. Several solutions have been proposed to meet the expectations and novel methods have been developed to address the persisting problems of data integration. It is important for researchers to understand different technologies and approaches. Having familiarized with the pros and cons of the existing technologies, researchers can exploit its capabilities to the maximum potential for integrating data. In this review we discuss the architecture, design and key technologies underlying some of the prominent databases and Web applications. We will mention their roles in integration of biological data and investigate some of the emerging design concepts and computational technologies that are likely to have a key role in the future of systems driven biomedical research. PMID:21423387

  7. Current trends and new challenges of databases and web applications for systems driven biological research.

    PubMed

    Sreenivasaiah, Pradeep Kumar; Kim, Do Han

    2010-01-01

    Dynamic and rapidly evolving nature of systems driven research imposes special requirements on the technology, approach, design and architecture of computational infrastructure including database and Web application. Several solutions have been proposed to meet the expectations and novel methods have been developed to address the persisting problems of data integration. It is important for researchers to understand different technologies and approaches. Having familiarized with the pros and cons of the existing technologies, researchers can exploit its capabilities to the maximum potential for integrating data. In this review we discuss the architecture, design and key technologies underlying some of the prominent databases and Web applications. We will mention their roles in integration of biological data and investigate some of the emerging design concepts and computational technologies that are likely to have a key role in the future of systems driven biomedical research.

  8. [Effective data collection in cancer research: an all-in-one database solution].

    PubMed

    Huszka, C; Dahl, E; Knüchel, R; Donner, A

    2006-01-01

    Tissue banks containing human malignant and benign tissue have become highly important for modem cancer research. They provide an excellent source of information with respect to pathological states and processes. Nowadays tissue samples can be examined using a broad variety of molecular biology methods, at the levels of DNA, RNA and protein. However, these new possibilities impose great expectations from the user side towards tissue banks and their associated databases. Nowadays a database that only manages tissue samples is not timely anymore. In fact a modern database should be capable of registering arbitraty amounts of tissue relevant information in an easily searchable way. In order to simplify the often complicated and time consuming process of data collection, we have developed a software solution that centralizes various aspects of tumor tissue banking. The main task of this software is not only to administer tissue samples but also to provide a centralized data platform for scientists which support their research. To achieve our goals we have constructed a tissue database which is supported by an Oracle System. The access to this database has been made possible with a light-weight, self-developed Java Client Program. The system possesses high levels of security and the access to information in the database is strictly controlled by preset permissions. A flexible search mechanism is also readily available for speedy data extraction according to various criteria. This solution provides us with an "All-in-one" tool for the purpose of flexible and efficient data collection and management in cancer research.

  9. [Relevance of design and structure of data-bases in research].

    PubMed

    Sevillano García, M D

    2004-09-01

    Research studies require a methodological frame providing concepts and approach procedures. The so-called scientific method encompasses systematic data collection and problem solving notions. Epidemiology and statistics are essential disciplines in this process. The goal of this course is to provide knowledge for design of databases, with special attention to the definition of variables and to measurement scales. A small database on headache is made using fictitious information. A questionnaire designed for this purpose is used as a foundation. Finally, we present a graphic design on the percentage distribution of the variable gender, as an example of the summary statistics.

  10. Immediate dissemination of student discoveries to a model organism database enhances classroom-based research experiences.

    PubMed

    Wiley, Emily A; Stover, Nicholas A

    2014-01-01

    Use of inquiry-based research modules in the classroom has soared over recent years, largely in response to national calls for teaching that provides experience with scientific processes and methodologies. To increase the visibility of in-class studies among interested researchers and to strengthen their impact on student learning, we have extended the typical model of inquiry-based labs to include a means for targeted dissemination of student-generated discoveries. This initiative required: 1) creating a set of research-based lab activities with the potential to yield results that a particular scientific community would find useful and 2) developing a means for immediate sharing of student-generated results. Working toward these goals, we designed guides for course-based research aimed to fulfill the need for functional annotation of the Tetrahymena thermophila genome, and developed an interactive Web database that links directly to the official Tetrahymena Genome Database for immediate, targeted dissemination of student discoveries. This combination of research via the course modules and the opportunity for students to immediately "publish" their novel results on a Web database actively used by outside scientists culminated in a motivational tool that enhanced students' efforts to engage the scientific process and pursue additional research opportunities beyond the course.

  11. Immediate Dissemination of Student Discoveries to a Model Organism Database Enhances Classroom-Based Research Experiences

    PubMed Central

    Wiley, Emily A.; Stover, Nicholas A.

    2014-01-01

    Use of inquiry-based research modules in the classroom has soared over recent years, largely in response to national calls for teaching that provides experience with scientific processes and methodologies. To increase the visibility of in-class studies among interested researchers and to strengthen their impact on student learning, we have extended the typical model of inquiry-based labs to include a means for targeted dissemination of student-generated discoveries. This initiative required: 1) creating a set of research-based lab activities with the potential to yield results that a particular scientific community would find useful and 2) developing a means for immediate sharing of student-generated results. Working toward these goals, we designed guides for course-based research aimed to fulfill the need for functional annotation of the Tetrahymena thermophila genome, and developed an interactive Web database that links directly to the official Tetrahymena Genome Database for immediate, targeted dissemination of student discoveries. This combination of research via the course modules and the opportunity for students to immediately “publish” their novel results on a Web database actively used by outside scientists culminated in a motivational tool that enhanced students’ efforts to engage the scientific process and pursue additional research opportunities beyond the course. PMID:24591511

  12. Perfluoroalkyl acids: recent research highlights | Science ...

    EPA Pesticide Factsheets

    Perfluorinated compounds are organic chemicals in which all hydrogen molecules of the carbon-chain are substituted by fluorine molecules. Generally, there are two types of perfluorinated compounds, the perfluoroalkanes that are primarily used clinically for oxygenation and respiratory ventilation, and the perfluoroalkyl acids (PFAAs). Environmentally relevant PFAAs are a family of about 30 chemicals that consist of a carbon backbone typically 4-14 molecules in length and a charged functional group composed of either sulfonates, carboxylates or phosphonates (and to a lesser extent, phosphinates). While many (>100) derivatives ofPFAAs (such as alcohols, amides, esters and acids) are used for industrial and consumer applications, they can be degraded or metabolized to PFAAs as end-stage products. Thus, PFAAs, rather than their intermediates or derivatives, have drawn the most public attention and research interest. The most widely known PFAAs are the eight-carbon (C8) sulfonate (perfluorooctane sulfonate, PFOS) and carboxylate (perfluorooctanoic acid, PFOA), although the C4 (perfluorobutane) and C6 (perfluorohexane) sulfonates, as well as the C4, C6 and C9 (perfluorononanoic) carboxylates have also been used in commerce. The perfluoroalkyl phosphonates (PFPAs) are fairly new entities for this class ofchemicals. They are typically used as leveling and wetting agents, and defoaming additives in the production of pesticides. They were considered biologically inert by

  13. Registry of Experimental Cancers of the National Cancer Institute. A database resource for cancer research.

    PubMed Central

    Berman, J. J.; Moore, G. W.; O'Neill, T. P.; Liebelt, A. G.; Saffiotti, U.

    1993-01-01

    The National Cancer Institute established the Registry of Experimental Cancers in March 1970. This registry consists of a permanent collection of pathological materials on spontaneous and induced lesions in laboratory animals that includes histological slides, paraffin blocks, autopsy findings, pathological diagnoses, photographs, and experimental records. The material presently is composed of approximately 60,000 consecutive records and is a valuable resource for researchers interested in tumors and other lesions arising spontaneously or from specific induction protocols in experimental animals. The entire registry database was transferred to an object-oriented database that permits registry staff to write programs for the different data field objects, thus customizing searches and other database functions. Twenty-seven animal species are represented and a total of 6,496 diagnostic entities and 1,106 treatment and control protocols are listed. Archival material may be retrieved for analysis of molecular markers. PMID:8434635

  14. GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research

    PubMed Central

    Jung, Sook; Jesudurai, Christopher; Staton, Margaret; Du, Zhidian; Ficklin, Stephen; Cho, Ilhyung; Abbott, Albert; Tomkins, Jeffrey; Main, Dorrie

    2004-01-01

    Background Peach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose. The genomics and genetics data of peach can play a significant role in the gene discovery and the genetic understanding of related species. The effective utilization of these peach resources, however, requires the development of an integrated and centralized database with associated analysis tools. Description The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, an annotated peach EST database, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm. To demonstrate the utility of the integrated and fully annotated database and analysis tools, we describe a case study where we anchored Rosaceae sequences to the peach physical and genetic map by sequence similarity. Conclusions The GDR has been initiated to meet the major deficiency in Rosaceae genomics and genetics research, namely a centralized web database and bioinformatics tools for data storage, analysis and exchange. GDR can be accessed at . PMID:15357877

  15. The FP4026 Research Database on the fundamental period of RC infilled frame structures.

    PubMed

    Asteris, Panagiotis G

    2016-12-01

    The fundamental period of vibration appears to be one of the most critical parameters for the seismic design of buildings because it strongly affects the destructive impact of the seismic forces. In this article, important research data (entitled FP4026 Research Database (Fundamental Period-4026 cases of infilled frames) based on a detailed and in-depth analytical research on the fundamental period of reinforced concrete structures is presented. In particular, the values of the fundamental period which have been analytically determined are presented, taking into account the majority of the involved parameters. This database can be extremely valuable for the development of new code proposals for the estimation of the fundamental period of reinforced concrete structures fully or partially infilled with masonry walls.

  16. The Society of Thoracic Surgeons Adult Cardiac Surgery Database: 2017 Update on Research.

    PubMed

    Thourani, Vinod H; Badhwar, Vinay; Shahian, David M; Edwards, Fred H; O'Brien, Sean; Habib, Robert H; Kelly, John J; Rankin, J Scott; Prager, Richard; Jacobs, Jeffrey P

    2017-07-01

    Containing more than 6 million cumulative operative records and accounting for 90% to 95% of adult cardiac surgery performed in the United States, The Society of Thoracic Surgeons Adult Cardiac Surgery Database is an invaluable resource for performance assessment, quality improvement, and clinical research. This article reviews the seven major research efforts published in 2016 that utilized the Adult Cardiac Surgery Database. Two studies evaluated national trends in clinical practice, three assessed the effect of several risk factors on postoperative morbidity and mortality, and two developed new models to evaluate quality of care. The findings of these studies have enhanced clinical practice and delineated areas for future quality improvement research. Copyright © 2017 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

  17. Astronomy Education Research Observations from the iSTAR international Study of Astronomical Reasoning Database

    NASA Astrophysics Data System (ADS)

    Tatge, C. B.; Slater, S. J.; Slater, T. F.; Schleigh, S.; McKinnon, D.

    2016-12-01

    Historically, an important part of the scientific research cycle is to situate any research project within the landscape of the existing scientific literature. In the field of discipline-based astronomy education research, grappling with the existing literature base has proven difficult because of the difficulty in obtaining research reports from around the world, particularly early ones. In order to better survey and efficiently utilize the wide and fractured range and domain of astronomy education research methods and results, the iSTAR international Study of Astronomical Reasoning database project was initiated. The project aims to host a living, online repository of dissertations, theses, journal articles, and grey literature resources to serve the world's discipline-based astronomy education research community. The first domain of research artifacts ingested into the iSTAR database were doctoral dissertations. To the authors' great surprise, nearly 300 astronomy education research dissertations were found from the last 100-years. Few, if any, of the literature reviews from recent astronomy education dissertations surveyed even come close to summarizing this many dissertations, most of which have not been published in traditional journals, as re-publishing one's dissertation research as a journal article was not a widespread custom in the education research community until recently. A survey of the iSTAR database dissertations reveals that the vast majority of work has been largely quantitative in nature until the last decade. We also observe that modern-era astronomy education research writings reaches as far back as 1923 and that the majority of dissertations come from the same eight institutions. Moreover, most of the astronomy education research work has been done covering learners' grasp of broad knowledge of astronomy rather than delving into specific learning targets, which has been more in vogue during the last two decades. The surprisingly wide breadth

  18. DriverDBv2: a database for human cancer driver gene research.

    PubMed

    Chung, I-Fang; Chen, Chen-Yang; Su, Shih-Chieh; Li, Chia-Yang; Wu, Kou-Juey; Wang, Hsei-Wei; Cheng, Wei-Chung

    2016-01-04

    We previously presented DriverDB, a database that incorporates ∼ 6000 cases of exome-seq data, in addition to annotation databases and published bioinformatics algorithms dedicated to driver gene/mutation identification. The database provides two points of view, 'Cancer' and 'Gene', to help researchers visualize the relationships between cancers and driver genes/mutations. In the updated DriverDBv2 database (http://ngs.ym.edu.tw/driverdb) presented herein, we incorporated >9500 cancer-related RNA-seq datasets and >7000 more exome-seq datasets from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and published papers. Seven additional computational algorithms (meaning that the updated database contains 15 in total), which were developed for driver gene identification, are incorporated into our analysis pipeline, and the results are provided in the 'Cancer' section. Furthermore, there are two main new features, 'Expression' and 'Hotspot', in the 'Gene' section. 'Expression' displays two expression profiles of a gene in terms of sample types and mutation types, respectively. 'Hotspot' indicates the hotspot mutation regions of a gene according to the results provided by four bioinformatics tools. A new function, 'Gene Set', allows users to investigate the relationships among mutations, expression levels and clinical data for a set of genes, a specific dataset and clinical features.

  19. RESPIRATORY INFECTIONS RESEARCH IN AFGHANISTAN: BIBLIOMETRIC ANALYSIS WITH THE DATABASE PUBMED.

    PubMed

    Pilsczek, Florian H

    2015-01-01

    Infectious diseases research in a low-income country like Afghanistan is important. In this study an internet-based database Pubmed was used for bibliometric analysis of infectious diseases research activity. Research publications entries in PubMed were analysed according to number of publications, topic, publication type, and country of investigators. Between 2002-2011, 226 (77.7%) publications with the following research topics were identified: respiratory infections 3 (1.3%); parasites 8 (3.5%); diarrhoea 10 (4.4%); tuberculosis 10 (4.4%); human immunodeficiency virus (HIV) 11 (4.9%); multi-drug resistant bacteria (MDR) 18 (8.0%); polio 31 (13.7%); leishmania 31 (13.7%); malaria 46 (20.4%). From 2002-2011, 11 (4.9%) publications were basic science laboratory-based research studies. Between 2002-2011, 8 (3.5%) publications from Afghan institutions were identified. In conclusion, the internet-based database Pubmed can be consulted to collect data for guidance of infectious diseases research activity of low-income countries. The presented data suggest that infectious diseases research in Afghanistan is limited for respiratory infections research, has few studies conducted by Afghan institutions, and limited laboratory-based research contributions.

  20. Sys-BodyFluid: a systematical database for human body fluid proteome research.

    PubMed

    Li, Su-Jun; Peng, Mao; Li, Hong; Liu, Bo-Shu; Wang, Chuan; Wu, Jia-Rui; Li, Yi-Xue; Zeng, Rong

    2009-01-01

    Recently, body fluids have widely become an important target for proteomic research and proteomic study has produced more and more body fluid related protein data. A database is needed to collect and analyze these proteome data. Thus, we developed this web-based body fluid proteome database Sys-BodyFluid. It contains eleven kinds of body fluid proteomes, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk and amniotic fluid. Over 10,000 proteins are presented in the Sys-BodyFluid. Sys-BodyFluid provides the detailed protein annotations, including protein description, Gene Ontology, domain information, protein sequence and involved pathways. These proteome data can be retrieved by using protein name, protein accession number and sequence similarity. In addition, users can query between these different body fluids to get the different proteins identification information. Sys-BodyFluid database can facilitate the body fluid proteomics and disease proteomics research as a reference database. It is available at http://www.biosino.org/bodyfluid/.

  1. Insight: An ontology-based integrated database and analysis platform for epilepsy self-management research.

    PubMed

    Sahoo, Satya S; Ramesh, Priya; Welter, Elisabeth; Bukach, Ashley; Valdez, Joshua; Tatsuoka, Curtis; Bamps, Yvan; Stoll, Shelley; Jobst, Barbara C; Sajatovic, Martha

    2016-10-01

    We present Insight as an integrated database and analysis platform for epilepsy self-management research as part of the national Managing Epilepsy Well Network. Insight is the only available informatics platform for accessing and analyzing integrated data from multiple epilepsy self-management research studies with several new data management features and user-friendly functionalities. The features of Insight include, (1) use of Common Data Elements defined by members of the research community and an epilepsy domain ontology for data integration and querying, (2) visualization tools to support real time exploration of data distribution across research studies, and (3) an interactive visual query interface for provenance-enabled research cohort identification. The Insight platform contains data from five completed epilepsy self-management research studies covering various categories of data, including depression, quality of life, seizure frequency, and socioeconomic information. The data represents over 400 participants with 7552 data points. The Insight data exploration and cohort identification query interface has been developed using Ruby on Rails Web technology and open source Web Ontology Language Application Programming Interface to support ontology-based reasoning. We have developed an efficient ontology management module that automatically updates the ontology mappings each time a new version of the Epilepsy and Seizure Ontology is released. The Insight platform features a Role-based Access Control module to authenticate and effectively manage user access to different research studies. User access to Insight is managed by the Managing Epilepsy Well Network database steering committee consisting of representatives of all current collaborating centers of the Managing Epilepsy Well Network. New research studies are being continuously added to the Insight database and the size as well as the unique coverage of the dataset allows investigators to conduct

  2. Creating a sampling frame for population-based veteran research: representativeness and overlap of VA and Department of Defense databases.

    PubMed

    Washington, Donna L; Sun, Su; Canning, Mark

    2010-01-01

    Most veteran research is conducted in Department of Veterans Affairs (VA) healthcare settings, although most veterans obtain healthcare outside the VA. Our objective was to determine the adequacy and relative contributions of Veterans Health Administration (VHA), Veterans Benefits Administration (VBA), and Department of Defense (DOD) administrative databases for representing the U.S. veteran population, using as an example the creation of a sampling frame for the National Survey of Women Veterans. In 2008, we merged the VHA, VBA, and DOD databases. We identified the number of unique records both overall and from each database. The combined databases yielded 925,946 unique records, representing 51% of the 1,802,000 U.S. women veteran population. The DOD database included 30% of the population (with 8% overlap with other databases). The VHA enrollment database contributed an additional 20% unique women veterans (with 6% overlap with VBA databases). VBA databases contributed an additional 2% unique women veterans (beyond 10% overlap with other databases). Use of VBA and DOD databases substantially expands access to the population of veterans beyond those in VHA databases, regardless of VA use. Adoption of these additional databases would enhance the value and generalizability of a wide range of studies of both male and female veterans.

  3. Research information needs on terrestrial vertebrate species of the interior Columbia basin and northern portions of the Klamath and Great Basins: a research, development, and application database.

    Treesearch

    Bruce G. Marcot

    1997-01-01

    Research information needs on selected invertebrates and all vertebrates of the interior Columbia River basin and adjacent areas in the United States were collected into a research, development, and application database as part of the Interior Columbia Basin Ecosystem Management Project. The database includes 482 potential research study topics on 232 individual...

  4. The research infrastructure of Chinese foundations, a database for Chinese civil society studies.

    PubMed

    Ma, Ji; Wang, Qun; Dong, Chao; Li, Huafang

    2017-07-25

    This paper provides technical details and user guidance on the Research Infrastructure of Chinese Foundations (RICF), a database of Chinese foundations, civil society, and social development in general. The structure of the RICF is deliberately designed and normalized according to the Three Normal Forms. The database schema consists of three major themes: foundations' basic organizational profile (i.e., basic profile, board member, supervisor, staff, and related party tables), program information (i.e., program information, major program, program relationship, and major recipient tables), and financial information (i.e., financial position, financial activities, cash flow, activity overview, and large donation tables). The RICF's data quality can be measured by four criteria: data source reputation and credibility, completeness, accuracy, and timeliness. Data records are properly versioned, allowing verification and replication for research purposes.

  5. Building a recruitment database for asthma trials: a conceptual framework for the creation of the UK Database of Asthma Research Volunteers.

    PubMed

    Nwaru, Bright I; Soyiri, Ireneous N; Simpson, Colin R; Griffiths, Chris; Sheikh, Aziz

    2016-05-26

    Randomised clinical trials are the 'gold standard' for evaluating the effectiveness of healthcare interventions. However, successful recruitment of participants remains a key challenge for many trialists. In this paper, we present a conceptual framework for creating a digital, population-based database for the recruitment of asthma patients into future asthma trials in the UK. Having set up the database, the goal is to then make it available to support investigators planning asthma clinical trials. The UK Database of Asthma Research Volunteers will comprise a web-based front-end that interactively allows participant registration, and a back-end that houses the database containing participants' key relevant data. The database will be hosted and maintained at a secure server at the Asthma UK Centre for Applied Research based at The University of Edinburgh. Using a range of invitation strategies, key demographic and clinical data will be collected from those pre-consenting to consider participation in clinical trials. These data will, with consent, in due course, be linkable to other healthcare, social, economic, and genetic datasets. To use the database, asthma investigators will send their eligibility criteria for participant recruitment; eligible participants will then be informed about the new trial and asked if they wish to participate. A steering committee will oversee the running of the database, including approval of usage access. Novel communication strategies will be utilised to engage participants who are recruited into the database in order to avoid attrition as a result of waiting time to participation in a suitable trial, and to minimise the risk of their being approached when already enrolled in a trial. The value of this database will be whether it proves useful and usable to researchers in facilitating recruitment into clinical trials on asthma and whether patient privacy and data security are protected in meeting this aim. Successful recruitment is

  6. How to conduct clinical research studies using high quality-clinical databases in the critical care.

    PubMed

    Francais, Adrien; Vesin, Aurélien; Timsit, Jean-François

    2008-09-01

    The sources of intensive care-related information and the means of communication increase rapidly. We presented here an overview of what should be done to collect high quality database. In a second part, the principle of the choice of the research question, the outcome, the explanatory variables and the statistical methods to address the question are overviewed, emphasizing major and frequent pitfalls which should be avoided.

  7. Second Research Coordination Meeting on Reference Database for Neutron Activation Analysis -- Summary Report

    SciTech Connect

    Firestone, Richard B.; Kellett, Mark A.

    2008-03-19

    The second meeting of the Co-ordinated Research Project on"Reference Database for Neutron Activation Analysis" was held at the IAEA, Vienna from 7-9 May, 2007. A summary of the presentations made by participants is given, along with reports on specifically assigned tasks and subsequent discussions. In order to meet the overall objectives of this CRP, the outputs have been reiterated and new task assignments made.

  8. Advances in Parallel Computing and Databases for Digital Pathology in Cancer Research

    DTIC Science & Technology

    2016-11-13

    Through a number of efforts such as the National Strategic Computing Initiative (NSCI), there has been a push to merge these “ Big Data ” and...potential for applications in cancer research. II. PARALLEL COMPUTING AND BIG DATA Parallel computing is the ability to take a given program and split it...Recently, we have been developing a “Polystore” database system called BigDAWG (short for the Big Data Working Group) that brings together disparate DBMSs

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

    PubMed Central

    Cousineau, J; Girard, N; Monardes, C; Leroux, T; Jean, M Stanton

    2012-01-01

    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. PMID:23113174

  10. A European Flood Database: facilitating comprehensive flood research beyond administrative boundaries

    NASA Astrophysics Data System (ADS)

    Hall, J.; Arheimer, B.; Aronica, G. T.; Bilibashi, A.; Boháč, M.; Bonacci, O.; Borga, M.; Burlando, P.; Castellarin, A.; Chirico, G. B.; Claps, P.; Fiala, K.; Gaál, L.; Gorbachova, L.; Gül, A.; Hannaford, J.; Kiss, A.; Kjeldsen, T.; Kohnová, S.; Koskela, J. J.; Macdonald, N.; Mavrova-Guirguinova, M.; Ledvinka, O.; Mediero, L.; Merz, B.; Merz, R.; Molnar, P.; Montanari, A.; Osuch, M.; Parajka, J.; Perdigão, R. A. P.; Radevski, I.; Renard, B.; Rogger, M.; Salinas, J. L.; Sauquet, E.; Šraj, M.; Szolgay, J.; Viglione, A.; Volpi, E.; Wilson, D.; Zaimi, K.; Blöschl, G.

    2015-06-01

    The current work addresses one of the key building blocks towards an improved understanding of flood processes and associated changes in flood characteristics and regimes in Europe: the development of a comprehensive, extensive European flood database. The presented work results from ongoing cross-border research collaborations initiated with data collection and joint interpretation in mind. A detailed account of the current state, characteristics and spatial and temporal coverage of the European Flood Database, is presented. At this stage, the hydrological data collection is still growing and consists at this time of annual maximum and daily mean discharge series, from over 7000 hydrometric stations of various data series lengths. Moreover, the database currently comprises data from over 50 different data sources. The time series have been obtained from different national and regional data sources in a collaborative effort of a joint European flood research agreement based on the exchange of data, models and expertise, and from existing international data collections and open source websites. These ongoing efforts are contributing to advancing the understanding of regional flood processes beyond individual country boundaries and to a more coherent flood research in Europe.

  11. The Society of Thoracic Surgeons Congenital Heart Surgery Database: 2016 Update on Research.

    PubMed

    Jacobs, Marshall L; Jacobs, Jeffrey P; Pasquali, Sara K; Hill, Kevin D; Hornik, Christoph; O'Brien, Sean M; Shahian, David M; Habib, Robert H; Edwards, Fred H

    2016-09-01

    The Society of Thoracic Surgeons Congenital Heart Surgery Database (STS CHSD) is the largest congenital and pediatric cardiac surgical clinical data registry in the world. With more than 400,000 total operations from nearly all centers performing pediatric and congenital heart operations in North America, the STS CHSD is an unparalleled platform for clinical investigation, outcomes research, and quality improvement activities in this subspecialty. In 2015, several major original publications reported analyses of data in the CHSD pertaining to specific diagnostic and procedural groups, age-defined cohorts, or the entire population of patients in the database. Additional publications reported the most recent development, evaluation, and application of metrics for quality measurement and reporting of pediatric and congenital heart operation outcomes. This use of the STS CHSD for outcomes research and for quality measurement continues to expand as database participation and the available wealth of data in it continue to grow. This article reviews outcomes research and quality improvement articles published in 2015 based on STS CHSD data.

  12. CmMDb: A Versatile Database for Cucumis melo Microsatellite Markers and Other Horticulture Crop Research

    PubMed Central

    Bhawna; Chaduvula, Pavan K.; Bonthala, Venkata S.; Manjusha, Verma; Siddiq, Ebrahimali A.; Polumetla, Ananda K.; Prasad, Gajula M. N. V.

    2015-01-01

    Cucumis melo L. that belongs to Cucurbitaceae family ranks among one of the highest valued horticulture crops being cultivated across the globe. Besides its economical and medicinal importance, Cucumis melo L. is a valuable resource and model system for the evolutionary studies of cucurbit family. However, very limited numbers of molecular markers were reported for Cucumis melo L. so far that limits the pace of functional genomic research in melon and other similar horticulture crops. We developed the first whole genome based microsatellite DNA marker database of Cucumis melo L. and comprehensive web resource that aids in variety identification and physical mapping of Cucurbitaceae family. The Cucumis melo L. microsatellite database (CmMDb: http://65.181.125.102/cmmdb2/index.html) encompasses 39,072 SSR markers along with its motif repeat, motif length, motif sequence, marker ID, motif type and chromosomal locations. The database is featured with novel automated primer designing facility to meet the needs of wet lab researchers. CmMDb is a freely available web resource that facilitates the researchers to select the most appropriate markers for marker-assisted selection in melons and to improve breeding strategies. PMID:25885062

  13. CmMDb: a versatile database for Cucumis melo microsatellite markers and other horticulture crop research.

    PubMed

    Bhawna; Chaduvula, Pavan K; Bonthala, Venkata S; Manjusha, Verma; Siddiq, Ebrahimali A; Polumetla, Ananda K; Prasad, Gajula M N V

    2015-01-01

    Cucumis melo L. that belongs to Cucurbitaceae family ranks among one of the highest valued horticulture crops being cultivated across the globe. Besides its economical and medicinal importance, Cucumis melo L. is a valuable resource and model system for the evolutionary studies of cucurbit family. However, very limited numbers of molecular markers were reported for Cucumis melo L. so far that limits the pace of functional genomic research in melon and other similar horticulture crops. We developed the first whole genome based microsatellite DNA marker database of Cucumis melo L. and comprehensive web resource that aids in variety identification and physical mapping of Cucurbitaceae family. The Cucumis melo L. microsatellite database (CmMDb: http://65.181.125.102/cmmdb2/index.html) encompasses 39,072 SSR markers along with its motif repeat, motif length, motif sequence, marker ID, motif type and chromosomal locations. The database is featured with novel automated primer designing facility to meet the needs of wet lab researchers. CmMDb is a freely available web resource that facilitates the researchers to select the most appropriate markers for marker-assisted selection in melons and to improve breeding strategies.

  14. Towards efficient use of research resources: a nationwide database of ongoing primary care research projects in the Netherlands.

    PubMed

    Kortekaas, Marlous F; van de Pol, Alma C; van der Horst, Henriëtte E; Burgers, Jako S; Slort, Willemjan; de Wit, Niek J

    2014-04-01

    PURPOSE. Although in the last decades primary care research has evolved with great success, there is a growing need to prioritize the topics given the limited resources available. Therefore, we constructed a nationwide database of ongoing primary care research projects in the Netherlands, and we assessed if the distribution of research topics matched with primary care practice. We conducted a survey among the main primary care research centres in the Netherlands and gathered details of all ongoing primary care research projects. We classified the projects according to research topic, relation to professional guidelines and knowledge deficits, collaborative partners and funding source. Subsequently, we compared the frequency distribution of clinical topics of research projects to the prevalence of problems in primary care practice. We identified 296 ongoing primary care research projects from 11 research centres. Most projects were designed as randomized controlled trial (35%) or observational cohort (34%), and government funded mostly (60%). Thematically, most research projects addressed chronic diseases, mainly cardiovascular risk management (8%), depressive disorders (8%) and diabetes mellitus (7%). One-fifth of the projects was related to defined knowledge deficits in primary care guidelines. From a clinical primary care perspective, research projects on dermatological problems were significantly underrepresented (P = 0.01). This survey of ongoing projects demonstrates that primary care research has a firm basis in the Netherlands, with a strong focus on chronic disease. The fit with primary care practice can improve, and future research should address knowledge deficits in professional guidelines more.

  15. The Subviral RNA Database: a toolbox for viroids, the hepatitis delta virus and satellite RNAs research

    PubMed Central

    Rocheleau, Lynda; Pelchat, Martin

    2006-01-01

    Background Viroids, satellite RNAs, satellites viruses and the human hepatitis delta virus form the 'brotherhood' of the smallest known infectious RNA agents, known as the subviral RNAs. For most of these species, it is generally accepted that characteristics such as cell movement, replication, host specificity and pathogenicity are encoded in their RNA sequences and their resulting RNA structures. Although many sequences are indexed in publicly available databases, these sequence annotation databases do not provide the advanced searches and data manipulation capability for identifying and characterizing subviral RNA motifs. Description The Subviral RNA database is a web-based environment that facilitates the research and analysis of viroids, satellite RNAs, satellites viruses, the human hepatitis delta virus, and related RNA sequences. It integrates a large number of Subviral RNA sequences, their respective RNA motifs, analysis tools, related publication links and additional pertinent information (ex. links, conferences, announcements), allowing users to efficiently retrieve and analyze relevant information about these small RNA agents. Conclusion With its design, the Subviral RNA Database could be considered as a fundamental building block for the study of these related RNAs. It is freely available via a web browser at the URL: . PMID:16519798

  16. MIMIC II: a massive temporal ICU patient database to support research in intelligent patient monitoring

    NASA Technical Reports Server (NTRS)

    Saeed, M.; Lieu, C.; Raber, G.; Mark, R. G.

    2002-01-01

    Development and evaluation of Intensive Care Unit (ICU) decision-support systems would be greatly facilitated by the availability of a large-scale ICU patient database. Following our previous efforts with the MIMIC (Multi-parameter Intelligent Monitoring for Intensive Care) Database, we have leveraged advances in networking and storage technologies to develop a far more massive temporal database, MIMIC II. MIMIC II is an ongoing effort: data is continuously and prospectively archived from all ICU patients in our hospital. MIMIC II now consists of over 800 ICU patient records including over 120 gigabytes of data and is growing. A customized archiving system was used to store continuously up to four waveforms and 30 different parameters from ICU patient monitors. An integrated user-friendly relational database was developed for browsing of patients' clinical information (lab results, fluid balance, medications, nurses' progress notes). Based upon its unprecedented size and scope, MIMIC II will prove to be an important resource for intelligent patient monitoring research, and will support efforts in medical data mining and knowledge-discovery.

  17. A DICOM based radiotherapy plan database for research collaboration and reporting

    NASA Astrophysics Data System (ADS)

    Westberg, J.; Krogh, S.; Brink, C.; Vogelius, I. R.

    2014-03-01

    Purpose: To create a central radiotherapy (RT) plan database for dose analysis and reporting, capable of calculating and presenting statistics on user defined patient groups. The goal is to facilitate multi-center research studies with easy and secure access to RT plans and statistics on protocol compliance. Methods: RT institutions are able to send data to the central database using DICOM communications on a secure computer network. The central system is composed of a number of DICOM servers, an SQL database and in-house developed software services to process the incoming data. A web site within the secure network allows the user to manage their submitted data. Results: The RT plan database has been developed in Microsoft .NET and users are able to send DICOM data between RT centers in Denmark. Dose-volume histogram (DVH) calculations performed by the system are comparable to those of conventional RT software. A permission system was implemented to ensure access control and easy, yet secure, data sharing across centers. The reports contain DVH statistics for structures in user defined patient groups. The system currently contains over 2200 patients in 14 collaborations. Conclusions: A central RT plan repository for use in multi-center trials and quality assurance was created. The system provides an attractive alternative to dummy runs by enabling continuous monitoring of protocol conformity and plan metrics in a trial.

  18. The Subviral RNA Database: a toolbox for viroids, the hepatitis delta virus and satellite RNAs research.

    PubMed

    Rocheleau, Lynda; Pelchat, Martin

    2006-03-06

    Viroids, satellite RNAs, satellites viruses and the human hepatitis delta virus form the 'brotherhood' of the smallest known infectious RNA agents, known as the subviral RNAs. For most of these species, it is generally accepted that characteristics such as cell movement, replication, host specificity and pathogenicity are encoded in their RNA sequences and their resulting RNA structures. Although many sequences are indexed in publicly available databases, these sequence annotation databases do not provide the advanced searches and data manipulation capability for identifying and characterizing subviral RNA motifs. The Subviral RNA database is a web-based environment that facilitates the research and analysis of viroids, satellite RNAs, satellites viruses, the human hepatitis delta virus, and related RNA sequences. It integrates a large number of Subviral RNA sequences, their respective RNA motifs, analysis tools, related publication links and additional pertinent information (ex. links, conferences, announcements), allowing users to efficiently retrieve and analyze relevant information about these small RNA agents. With its design, the Subviral RNA Database could be considered as a fundamental building block for the study of these related RNAs. It is freely available via a web browser at the URL: http://subviral.med.uottawa.ca.

  19. Longitudinal research databases in medical education: facilitating the study of educational outcomes over time and across institutions.

    PubMed

    Cook, David A; Andriole, Dorothy A; Durning, Steven J; Roberts, Nicole K; Triola, Marc M

    2010-08-01

    Many education research questions cannot be answered using participants from one institution or short periods of follow-up. In response to societal demands for accountability and evidence of effectiveness, new models of research must be developed to study the outcomes of educational activities. Following the 2007 Millennium Conference on Medical Education Research, organizers assigned a task force to explore the use of longitudinal databases in education research. This article summarizes the task force's findings. Similar to the Framingham studies in clinical medicine, longitudinal databases assemble prospectively collected information to retrospectively answer questions of interest. Many studies using such databases have been published. The task force identified three general approaches to database-type research. First, institutions can obtain identified information from existing sources, link it with school-specific information and other identified information, deidentify it, and merge it with similar information from other collaborating schools. Second, researchers can obtain from existing sources deidentified information on large samples and explore associations within this dataset. Third, investigators can design and implement databases to prospectively collect trainee information over time and across multiple institutions for the purpose of education research. Although costly, such comprehensive, purpose-built databases would ensure the availability of information needed to answer a variety of medical education research questions. Millennium Conference participants believed that stakeholders should explore the funding and development of such prospective databases. In the meantime, education researchers should use existing sources of individualized learner data to better understand how to develop competent, compassionate clinicians.

  20. Adjusting for COPD severity in database research: developing and validating an algorithm

    PubMed Central

    Goossens, Lucas MA; Baker, Christine L; Monz, Brigitta U; Zou, Kelly H; Mölken, Maureen PMH Rutten-van

    2011-01-01

    Purpose When comparing chronic obstructive lung disease (COPD) interventions in database research, it is important to adjust for severity. Global Initiative for Chronic Obstructive Lung Disease (GOLD) guidelines grade severity according to lung function. Most databases lack data on lung function. Previous database research has approximated COPD severity using demographics and healthcare utilization. This study aims to derive an algorithm for COPD severity using baseline data from a large respiratory trial (UPLIFT). Methods Partial proportional odds logit models were developed for probabilities of being in GOLD stages II, III and IV. Concordance between predicted and observed stage was assessed using kappa-statistics. Models were estimated in a random selection of 2/3 of patients and validated in the remainder. The analysis was repeated in a subsample with a balanced distribution across severity stages. Univariate associations of COPD severity with the covariates were tested as well. Results More severe COPD was associated with being male and younger, having quit smoking, lower BMI, osteoporosis, hospitalizations, using certain medications, and oxygen. After adjusting for these variables, co-morbidities, previous healthcare resource use (eg, emergency room, hospitalizations) and inhaled corticosteroids, xanthines, or mucolytics were no longer independently associated with COPD severity, although they were in univariate tests. The concordance was poor (kappa = 0.151) and only slightly better in the balanced sample (kappa = 0.215). Conclusion COPD severity cannot be reliably predicted from demographics and healthcare use. This limitation should be considered when interpreting findings from database studies, and additional research should explore other methods to account for COPD severity. PMID:22259243

  1. Limitations of administrative databases in spine research: a study in obesity.

    PubMed

    Golinvaux, Nicholas S; Bohl, Daniel D; Basques, Bryce A; Fu, Michael C; Gardner, Elizabeth C; Grauer, Jonathan N

    2014-12-01

    The use of national inpatient databases for spine surgery research has been increasing. Unfortunately, without firsthand knowledge of each specific database, it can be difficult to judge the validity of such studies. Large databases that rely on administrative data, such as International Classification of Diseases, Ninth Revision (ICD-9) codes, may misrepresent patient information and could thus affect the results of studies that use these data. The present study uses obesity, an easily quantified and objective variable, as an example comorbidity to assess the accuracy of ICD-9 codes in the setting of their continued use in spine database studies. A cross-sectional study at a large academic medical center. All patients spending at least one night in the hospital as an inpatient between April 1, 2013 and April 16, 2013. Obstetrics and gynecology, psychiatry, and pediatric patients were excluded. Proportion of patients for whom ICD-9 obesity diagnosis codes assigned at hospital discharge match chart-documented body mass index (BMI). The medical record was reviewed for each patient, and obesity ICD-9 codes were directly compared with documented BMI. The study included 2,075 patients. Of 573 "obese" patients (calculated BMI 30-39.9), only 109 received the correct code (278.00), giving this ICD-9 code a sensitivity of 0.19. Of 174 "morbidly obese" patients (calculated BMI >40), only 84 received the correct code (278.01), giving this ICD-9 code a sensitivity of 0.48. Using obesity as an example, this study highlights the potential errors inherent to using ICD-9-coded databases for spine surgery research. Should a study based on such data use "obesity" as a variable in any analyses, the reader should interpret these results with caution. We further suggest that obesity is likely not the only comorbidity to which these results apply. As database research continues to represent an increasing proportion of publications in the field of spine surgery, it is important to

  2. Human health risk assessment database, "the NHSRC toxicity value database": supporting the risk assessment process at US EPA's National Homeland Security Research Center.

    PubMed

    Moudgal, Chandrika J; Garrahan, Kevin; Brady-Roberts, Eletha; Gavrelis, Naida; Arbogast, Michelle; Dun, Sarah

    2008-11-15

    The toxicity value database of the United States Environmental Protection Agency's (EPA) National Homeland Security Research Center has been in development since 2004. The toxicity value database includes a compilation of agent property, toxicity, dose-response, and health effects data for 96 agents: 84 chemical and radiological agents and 12 biotoxins. The database is populated with multiple toxicity benchmark values and agent property information from secondary sources, with web links to the secondary sources, where available. A selected set of primary literature citations and associated dose-response data are also included. The toxicity value database offers a powerful means to quickly and efficiently gather pertinent toxicity and dose-response data for a number of agents that are of concern to the nation's security. This database, in conjunction with other tools, will play an important role in understanding human health risks, and will provide a means for risk assessors and managers to make quick and informed decisions on the potential health risks and determine appropriate responses (e.g., cleanup) to agent release. A final, stand alone MS ACESSS working version of the toxicity value database was completed in November, 2007.

  3. Human health risk assessment database, 'the NHSRC toxicity value database': Supporting the risk assessment process at US EPA's National Homeland Security Research Center

    SciTech Connect

    Moudgal, Chandrika J.

    2008-11-15

    The toxicity value database of the United States Environmental Protection Agency's (EPA) National Homeland Security Research Center has been in development since 2004. The toxicity value database includes a compilation of agent property, toxicity, dose-response, and health effects data for 96 agents: 84 chemical and radiological agents and 12 biotoxins. The database is populated with multiple toxicity benchmark values and agent property information from secondary sources, with web links to the secondary sources, where available. A selected set of primary literature citations and associated dose-response data are also included. The toxicity value database offers a powerful means to quickly and efficiently gather pertinent toxicity and dose-response data for a number of agents that are of concern to the nation's security. This database, in conjunction with other tools, will play an important role in understanding human health risks, and will provide a means for risk assessors and managers to make quick and informed decisions on the potential health risks and determine appropriate responses (e.g., cleanup) to agent release. A final, stand alone MS ACESSS working version of the toxicity value database was completed in November, 2007.

  4. Down syndrome: issues to consider in a national registry, research database and biobank.

    PubMed

    McCabe, Linda L; McCabe, Edward R B

    2011-01-01

    As the quality of life for individuals with Down syndrome continues to improve due to anticipatory healthcare, early intervention, mainstreaming in schools, and increased expectations, the lack of basic information regarding individuals with Down syndrome is being recognized, and the need to facilitate research through a national registry, research database and biobank is being discussed. We believe that there should not be ownership of the samples and information, but instead prefer stewardship of the samples and information to benefit the participants who provided them. We endorse a model with data and sample managers and a research review board to interface between the investigators and participants. Information and samples would be coded, and only a few data managers would know the relationship between the codes and identifying information. Research results once published should be included in an online newsletter. If appropriate, individual results should be shared with participants. A Down syndrome registry, research database and biobank should be accountable to participants, families, medical care providers, government, and funding sources.

  5. Chess databases as a research vehicle in psychology: Modeling large data.

    PubMed

    Vaci, Nemanja; Bilalić, Merim

    2016-09-01

    The game of chess has often been used for psychological investigations, particularly in cognitive science. The clear-cut rules and well-defined environment of chess provide a model for investigations of basic cognitive processes, such as perception, memory, and problem solving, while the precise rating system for the measurement of skill has enabled investigations of individual differences and expertise-related effects. In the present study, we focus on another appealing feature of chess-namely, the large archive databases associated with the game. The German national chess database presented in this study represents a fruitful ground for the investigation of multiple longitudinal research questions, since it collects the data of over 130,000 players and spans over 25 years. The German chess database collects the data of all players, including hobby players, and all tournaments played. This results in a rich and complete collection of the skill, age, and activity of the whole population of chess players in Germany. The database therefore complements the commonly used expertise approach in cognitive science by opening up new possibilities for the investigation of multiple factors that underlie expertise and skill acquisition. Since large datasets are not common in psychology, their introduction also raises the question of optimal and efficient statistical analysis. We offer the database for download and illustrate how it can be used by providing concrete examples and a step-by-step tutorial using different statistical analyses on a range of topics, including skill development over the lifetime, birth cohort effects, effects of activity and inactivity on skill, and gender differences.

  6. Fine-grained policy control in U.S. Army Research Laboratory (ARL) multimodal signatures database

    NASA Astrophysics Data System (ADS)

    Bennett, Kelly; Grueneberg, Keith; Wood, David; Calo, Seraphin

    2014-06-01

    The U.S. Army Research Laboratory (ARL) Multimodal Signatures Database (MMSDB) consists of a number of colocated relational databases representing a collection of data from various sensors. Role-based access to this data is granted to external organizations such as DoD contractors and other government agencies through a client Web portal. In the current MMSDB system, access control is only at the database and firewall level. In order to offer finer grained security, changes to existing user profile schemas and authentication mechanisms are usually needed. In this paper, we describe a software middleware architecture and implementation that allows fine-grained access control to the MMSDB at a dataset, table, and row level. Result sets from MMSDB queries issued in the client portal are filtered with the use of a policy enforcement proxy, with minimal changes to the existing client software and database. Before resulting data is returned to the client, policies are evaluated to determine if the user or role is authorized to access the data. Policies can be authored to filter data at the row, table or column level of a result set. The system uses various technologies developed in the International Technology Alliance in Network and Information Science (ITA) for policy-controlled information sharing and dissemination1. Use of the Policy Management Library provides a mechanism for the management and evaluation of policies to support finer grained access to the data in the MMSDB system. The GaianDB is a policy-enabled, federated database that acts as a proxy between the client application and the MMSDB system.

  7. Computer-Aided Systems Engineering for Flight Research Projects Using a Workgroup Database

    NASA Technical Reports Server (NTRS)

    Mizukami, Masahi

    2004-01-01

    An online systems engineering tool for flight research projects has been developed through the use of a workgroup database. Capabilities are implemented for typical flight research systems engineering needs in document library, configuration control, hazard analysis, hardware database, requirements management, action item tracking, project team information, and technical performance metrics. Repetitive tasks are automated to reduce workload and errors. Current data and documents are instantly available online and can be worked on collaboratively. Existing forms and conventional processes are used, rather than inventing or changing processes to fit the tool. An integrated tool set offers advantages by automatically cross-referencing data, minimizing redundant data entry, and reducing the number of programs that must be learned. With a simplified approach, significant improvements are attained over existing capabilities for minimal cost. By using a workgroup-level database platform, personnel most directly involved in the project can develop, modify, and maintain the system, thereby saving time and money. As a pilot project, the system has been used to support an in-house flight experiment. Options are proposed for developing and deploying this type of tool on a more extensive basis.

  8. USDA-ARS Riesel Watersheds, Riesel, Texas, USA: Water quality research database

    NASA Astrophysics Data System (ADS)

    Harmel, R. Daren; Haney, Richard L.; Smith, Douglas R.; White, Michael; King, Kevin W.

    2014-10-01

    The 75 year legacy database including discharge, sediment loss, land management, and meteorological data for the USDA-ARS Riesel Watersheds, Riesel, TX, USA has been available on the web for more than a decade (www.ars.usda.gov/spa/hydro-data) and used in numerous studies and publications; however, only recently have these data been added to the Sustaining the Earth's Watersheds, Agricultural Research Data System (STEWARDS) database (www.nrrig.mwa.ars.usda.gov/stewards/stewards.html). In addition, water quality data including dissolved inorganic N and P compounds measured from more than 1000 storm runoff events, 1300 base flow sampling events (lateral subsurface return flow or seepage flow), and 157 precipitation events through 2012 were added. The objectives of this manuscript are to present relevant background information on these data, summarize the data collection and analysis methodology, present the measured data along with cursory analyses, and convey the commitment of the USDA-ARS Riesel Watersheds to long-term data accessibility and database enhancement for water quality data and research.

  9. Modeling the High Speed Research Cycle 2B Longitudinal Aerodynamic Database Using Multivariate Orthogonal Functions

    NASA Technical Reports Server (NTRS)

    Morelli, E. A.; Proffitt, M. S.

    1999-01-01

    The data for longitudinal non-dimensional, aerodynamic coefficients in the High Speed Research Cycle 2B aerodynamic database were modeled using polynomial expressions identified with an orthogonal function modeling technique. The discrepancy between the tabular aerodynamic data and the polynomial models was tested and shown to be less than 15 percent for drag, lift, and pitching moment coefficients over the entire flight envelope. Most of this discrepancy was traced to smoothing local measurement noise and to the omission of mass case 5 data in the modeling process. A simulation check case showed that the polynomial models provided a compact and accurate representation of the nonlinear aerodynamic dependencies contained in the HSR Cycle 2B tabular aerodynamic database.

  10. High Tech High School Interns Develop a Mid-Ocean Ridge Database for Research and Education

    NASA Astrophysics Data System (ADS)

    Staudigel, D.; Delaney, R.; Staudigel, H.; Koppers, A. A.; Miller, S. P.

    2004-12-01

    Mid-ocean ridges (MOR) represent one of the most important geographical and geological features on planet Earth. MORs are the locations where plates spread apart, they are the locations of the majority of the Earths' volcanoes that harbor some of the most extreme life forms. These concepts attract much research, but mid-ocean ridges are still effectively underrepresented in the Earth science class rooms. As two High Tech High School students, we began an internship at Scripps to develop a database for mid-ocean ridges as a resource for science and education. This Ridge Catalog will be accessible via http://earthref.org/databases/RC/ and applies a similar structure, design and data archival principle as the Seamount Catalog under EarthRef.org. Major research goals of this project include the development of (1) an archival structure for multibeam and sidescan data, standard bathymetric maps (including ODP-DSDP drill site and dredge locations) or any other arbitrary digital objects relating to MORs, and (2) to compile a global data set for some of the most defining characteristics of every ridge segment including ridge segment length, depth and azimuth and half spreading rates. One of the challenges included the need of making MOR data useful to the scientist as well as the teacher in the class room. Since the basic structure follows the design of the Seamount Catalog closely, we could move our attention to the basic data population of the database. We have pulled together multibeam data for the MOR segments from various public archives (SIOExplorer, SIO-GDC, NGDC, Lamont), and pre-processed it for public use. In particular, we have created individual bathymetric maps for each ridge segment, while merging the multibeam data with global satellite bathymetry data from Smith & Sandwell (1997). The global scale of this database will give it the ability to be used for any number of applications, from cruise planning to data

  11. Evolution of primary care databases in UK: a scientometric analysis of research output

    PubMed Central

    Vezyridis, Paraskevas; Timmons, Stephen

    2016-01-01

    Objective To identify publication and citation trends, most productive institutions and countries, top journals, most cited articles and authorship networks from articles that used and analysed data from primary care databases (CPRD, THIN, QResearch) of pseudonymised electronic health records (EHRs) in UK. Methods Descriptive statistics and scientometric tools were used to analyse a SCOPUS data set of 1891 articles. Open access software was used to extract networks from the data set (Table2Net), visualise and analyse coauthorship networks of scholars and countries (Gephi) and density maps (VOSviewer) of research topics co-occurrence and journal cocitation. Results Research output increased overall at a yearly rate of 18.65%. While medicine is the main field of research, studies in more specialised areas include biochemistry and pharmacology. Researchers from UK, USA and Spanish institutions have published the most papers. Most of the journals that publish this type of research and most cited papers come from UK and USA. Authorship varied between 3 and 6 authors. Keyword analyses show that smoking, diabetes, cardiovascular diseases and mental illnesses, as well as medication that can treat such medical conditions, such as non-steroid anti-inflammatory agents, insulin and antidepressants constitute the main topics of research. Coauthorship network analyses show that lead scientists, directors or founders of these databases are, to various degrees, at the centre of clusters in this scientific community. Conclusions There is a considerable increase of publications in primary care research from EHRs. The UK has been well placed at the centre of an expanding global scientific community, facilitating international collaborations and bringing together international expertise in medicine, biochemical and pharmaceutical research. PMID:27729352

  12. Do we really know our patient population in database research? A comparison of the femoral shaft fracture patient populations in three commonly used national databases.

    PubMed

    Samuel, A M; Lukasiewicz, A M; Webb, M L; Bohl, D D; Basques, B A; Varthi, A G; Leslie, M P; Grauer, J N

    2016-03-01

    While use of large national clinical databases for orthopaedic trauma research has increased dramatically, there has been little study of the differences in populations contained therein. In this study we aimed to compare populations of patients with femoral shaft fractures across three commonly used national databases, specifically with regard to age and comorbidities. Patients were identified in the Nationwide Inpatient Sample (NIS), National Surgical Quality Improvement Program (NSQIP) and National Trauma Data Bank (NTDB). The distributions of age and Charleston comorbidity index (CCI) reflected a predominantly older population with more comorbidities in NSQIP (mean age 71.5; sd 15.6), mean CCI 4.9; sd 1.9) than in the NTDB (mean age 45.2; sd 21.4), mean CCI = 2.1; sd 2.0). Bimodal distributions in the NIS population showed a more mixed population (mean age 56.9; sd 24.9), mean CCI 3.2; sd 2.3). Differences in age and CCI were all statistically significant (p < 0.001). While these databases have been commonly used for orthopaedic trauma research, differences in the populations they represent are not always readily apparent. Care must be taken to understand fully these differences before performing or evaluating database research, as the outcomes they detail can only be analysed in context. Researchers and those evaluating research should be aware that orthopaedic trauma populations contained in commonly studied national databases may differ substantially based on sampling methods and inclusion criteria. ©2016 The British Editorial Society of Bone & Joint Surgery.

  13. A public image database to support research in computer aided diagnosis.

    PubMed

    Reeves, A P; Biancardi, A M; Yankelevitz, D; Fotin, S; Keller, B M; Jirapatnakul, A; Lee, J

    2009-01-01

    The Public Lung Database to address drug response (PLD) has been developed to support research in computer aided diagnosis (CAD). Originally established for applications involving the characterization of pulmonary nodules, the PLD has been augmented to provide initial datasets for CAD research of other diseases. In general, the best performance for a CAD system is achieved when it is trained with a large amount of well documented data. Such training databases are very expensive to create and their lack of general availability limits the targets that can be considered for CAD applications and hampers development of the CAD field. The approach taken with the PLD has been to make available small datasets together with both manual and automated documentation. Furthermore, datasets with special properties are provided either to span the range of task complexity or to provide small change repeat images for direct calibration and evaluation of CAD systems. This resource offers a starting point for other research groups wishing to pursue CAD research in new directions. It also provides an on-line reference for better defining the issues relating to specific CAD tasks.

  14. Overcoming barriers to a research-ready national commercial claims database.

    PubMed

    Newman, David; Herrera, Carolina-Nicole; Parente, Stephen T

    2014-11-01

    Billions of dollars have been spent on the goal of making healthcare data available to clinicians and researchers in the hopes of improving healthcare and lowering costs. However, the problems of data governance, distribution, and accessibility remain challenges for the healthcare system to overcome. In this study, we discuss some of the issues around holding, reporting, and distributing data, including the newest "big data" challenge: making the data accessible to researchers and policy makers. This article presents a case study in "big healthcare data" involving the Health Care Cost Institute (HCCI). HCCI is a nonprofit, nonpartisan, independent research institute that serves as a voluntary repository of national commercial healthcare claims data. Governance of large healthcare databases is complicated by the data-holding model and further complicated by issues related to distribution to research teams. For multi-payer healthcare claims databases, the 2 most common models of data holding (mandatory and voluntary) have different data security requirements. Furthermore, data transport and accessibility may require technological investment. HCCI's efforts offer insights from which other data managers and healthcare leaders may benefit when contemplating a data collaborative.

  15. Conference Proceedings: “Down Syndrome: National Conference on Patient Registries, Research Databases, and Biobanks”

    PubMed Central

    Oster-Granite, Mary Lou; Parisi, Melissa A.; Abbeduto, Leonard; Berlin, Dorit S.; Bodine, Cathy; Bynum, Dana; Capone, George; Collier, Elaine; Hall, Dan; Kaeser, Lisa; Kaufmann, Petra; Krischer, Jeffrey; Livingston, Michelle; McCabe, Linda L.; Pace, Jill; Pfenninger, Karl; Rasmussen, Sonja A.; Reeves, Roger H.; Rubinstein, Yaffa; Sherman, Stephanie; Terry, Sharon F.; Whitten, Michelle Sie; Williams, Stephen; McCabe, Edward R.B.; Maddox, Yvonne T.

    2011-01-01

    A December 2010 meeting, “Down Syndrome: National Conference on Patient Registries, Research Databases, and Biobanks,” was jointly sponsored by the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) at the National Institutes of Health (NIH) in Bethesda, MD, and the Global Down Syndrome Foundation (GDSF)/Linda Crnic Institute for Down Syndrome based in Denver, CO. Approximately 70 attendees and organizers from various advocacy groups, federal agencies (Centers for Disease Control and Prevention, and various NIH Institutes, Centers, and Offices), members of industry, clinicians, and researchers from various academic institutions were greeted by Drs. Yvonne Maddox, Deputy Director of NICHD, and Edward McCabe, Executive Director of the Linda Crnic Institute for Down Syndrome. They charged the participants to focus on the separate issues of contact registries, research databases, and biobanks through both podium presentations and breakout session discussions. Among the breakout groups for each of the major sessions, participants were asked to generate responses to questions posed by the organizers concerning these three research resources as they related to Down syndrome and then to report back to the group at large with a summary of their discussions. This report represents a synthesis of the discussions and suggested approaches formulated by the group as a whole. PMID:21835664

  16. The Cancer Epidemiology Descriptive Cohort Database: A Tool to Support Population-Based Interdisciplinary Research.

    PubMed

    Kennedy, Amy E; Khoury, Muin J; Ioannidis, John P A; Brotzman, Michelle; Miller, Amy; Lane, Crystal; Lai, Gabriel Y; Rogers, Scott D; Harvey, Chinonye; Elena, Joanne W; Seminara, Daniela

    2016-10-01

    We report on the establishment of a web-based Cancer Epidemiology Descriptive Cohort Database (CEDCD). The CEDCD's goals are to enhance awareness of resources, facilitate interdisciplinary research collaborations, and support existing cohorts for the study of cancer-related outcomes. Comprehensive descriptive data were collected from large cohorts established to study cancer as primary outcome using a newly developed questionnaire. These included an inventory of baseline and follow-up data, biospecimens, genomics, policies, and protocols. Additional descriptive data extracted from publicly available sources were also collected. This information was entered in a searchable and publicly accessible database. We summarized the descriptive data across cohorts and reported the characteristics of this resource. As of December 2015, the CEDCD includes data from 46 cohorts representing more than 6.5 million individuals (29% ethnic/racial minorities). Overall, 78% of the cohorts have collected blood at least once, 57% at multiple time points, and 46% collected tissue samples. Genotyping has been performed by 67% of the cohorts, while 46% have performed whole-genome or exome sequencing in subsets of enrolled individuals. Information on medical conditions other than cancer has been collected in more than 50% of the cohorts. More than 600,000 incident cancer cases and more than 40,000 prevalent cases are reported, with 24 cancer sites represented. The CEDCD assembles detailed descriptive information on a large number of cancer cohorts in a searchable database. Information from the CEDCD may assist the interdisciplinary research community by facilitating identification of well-established population resources and large-scale collaborative and integrative research. Cancer Epidemiol Biomarkers Prev; 25(10); 1392-401. ©2016 AACR. ©2016 American Association for Cancer Research.

  17. Consumer attitudes towards the establishment of a national Australian familial cancer research database by the Inherited Cancer Connect (ICCon) Partnership.

    PubMed

    Forrest, Laura; Mitchell, Gillian; Thrupp, Letitia; Petelin, Lara; Richardson, Kate; Mascarenhas, Lyon; Young, Mary-Anne

    2017-08-18

    Clinical genetics units hold large amounts of information which could be utilised to benefit patients and their families. In Australia, a national research database, the Inherited Cancer Connect (ICCon) database, is being established that comprises clinical genetic data held for all carriers of mutations in cancer predisposition genes. Consumer input was sought to establish the acceptability of the inclusion of clinical genetic data into a research database. A qualitative approach using a modified nominal group technique was used to collect data through consumer forums conducted in three Australian states. Individuals who had previously received care from Familial Cancer Centres were invited to participate. Twenty-four consumers participated in three forums. Participants expressed positive attitudes about the establishment of the ICCon database, which were informed by the perceived benefits of the database including improved health outcomes for individuals with inherited cancer syndromes. Most participants were comfortable to waive consent for their clinical information to be included in the research database in a de-identified format. As major stakeholders, consumers have an integral role in contributing to the development and conduct of the ICCon database. As an initial step in the development of the ICCon database, the forums demonstrated consumers' acceptance of important aspects of the database including waiver of consent.

  18. Aspergillus flavus Blast2GO gene ontology database: elevated growth temperature alters amino acid metabolism

    USDA-ARS?s Scientific Manuscript database

    The availability of a representative gene ontology (GO) database is a prerequisite for a successful functional genomics study. Using online Blast2GO resources we constructed a GO database of Aspergillus flavus. Of the predicted total 13,485 A. flavus genes 8,987 were annotated with GO terms. The mea...

  19. Research for amino acids in lunar samples.

    NASA Technical Reports Server (NTRS)

    Gehrke, C. W.; Zumwalt, R. W.; Kuo, K.; Rash, J. J.; Aue , W. A.; Stalling, D. L.; Kvenvolden, K. A.; Ponnamperuma, C.

    1972-01-01

    The study was primarily directed toward the examination of Apollo 14 lunar fines for indigenous amino acids or materials which could be converted to amino acids on hydrolysis with 6 N hydrochloric acid. Initial experiments were conducted to confirm the integrity of the derivatization reactions and reagents, and to optimize the gas-liquid chromatographic (GLC) instrumental and chromatographic system for the separation and flame ionization detection of the amino acid derivatives. In studies on the recovery of amino acids added to lunar fines, low recoveries were obtained when 10 ng of each amino acid were added to 50 mg of virgin fines, but the subsequent addition of 50 ng of each to the previously extracted sample resulted in much higher recoveries.

  20. Research for amino acids in lunar samples.

    NASA Technical Reports Server (NTRS)

    Gehrke, C. W.; Zumwalt, R. W.; Kuo, K.; Rash, J. J.; Aue , W. A.; Stalling, D. L.; Kvenvolden, K. A.; Ponnamperuma, C.

    1972-01-01

    The study was primarily directed toward the examination of Apollo 14 lunar fines for indigenous amino acids or materials which could be converted to amino acids on hydrolysis with 6 N hydrochloric acid. Initial experiments were conducted to confirm the integrity of the derivatization reactions and reagents, and to optimize the gas-liquid chromatographic (GLC) instrumental and chromatographic system for the separation and flame ionization detection of the amino acid derivatives. In studies on the recovery of amino acids added to lunar fines, low recoveries were obtained when 10 ng of each amino acid were added to 50 mg of virgin fines, but the subsequent addition of 50 ng of each to the previously extracted sample resulted in much higher recoveries.

  1. YM500v3: a database for small RNA sequencing in human cancer research

    PubMed Central

    Chung, I-Fang; Chang, Shing-Jyh; Chen, Chen-Yang; Liu, Shu-Hsuan; Li, Chia-Yang; Chan, Chia-Hao; Shih, Chuan-Chi; Cheng, Wei-Chung

    2017-01-01

    We previously presented the YM500 database, which contains >8000 small RNA sequencing (smRNA-seq) data sets and integrated analysis results for various cancer miRNome studies. In the updated YM500v3 database (http://ngs.ym.edu.tw/ym500/) presented herein, we not only focus on miRNAs but also on other functional small non-coding RNAs (sncRNAs), such as PIWI-interacting RNAs (piRNAs), tRNA-derived fragments (tRFs), small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). There is growing knowledge of the role of sncRNAs in gene regulation and tumorigenesis. We have also incorporated >10 000 cancer-related RNA-seq and >3000 more smRNA-seq data sets into the YM500v3 database. Furthermore, there are two main new sections, ‘Survival' and ‘Cancer', in this updated version. The ‘Survival’ section provides the survival analysis results in all cancer types or in a user-defined group of samples for a specific sncRNA. The ‘Cancer’ section provides the results of differential expression analyses, miRNA–gene interactions and cancer miRNA-related pathways. In the ‘Expression’ section, sncRNA expression profiles across cancer and sample types are newly provided. Cancer-related sncRNAs hold potential for both biotech applications and basic research. PMID:27899625

  2. Massive Scale Cyber Traffic Analysis: A Driver for Graph Database Research

    SciTech Connect

    Joslyn, Cliff A.; Choudhury, S.; Haglin, David J.; Howe, Bill; Nickless, William K.; Olsen, Bryan K.

    2013-06-19

    We describe the significance and prominence of network traffic analysis (TA) as a graph- and network-theoretical domain for advancing research in graph database systems. TA involves observing and analyzing the connections between clients, servers, hosts, and actors within IP networks, both at particular times and as extended over times. Towards that end, NetFlow (or more generically, IPFLOW) data are available from routers and servers which summarize coherent groups of IP packets flowing through the network. IPFLOW databases are routinely interrogated statistically and visualized for suspicious patterns. But the ability to cast IPFLOW data as a massive graph and query it interactively, in order to e.g.\\ identify connectivity patterns, is less well advanced, due to a number of factors including scaling, and their hybrid nature combining graph connectivity and quantitative attributes. In this paper, we outline requirements and opportunities for graph-structured IPFLOW analytics based on our experience with real IPFLOW databases. Specifically, we describe real use cases from the security domain, cast them as graph patterns, show how to express them in two graph-oriented query languages SPARQL and Datalog, and use these examples to motivate a new class of "hybrid" graph-relational systems.

  3. FmMDb: A Versatile Database of Foxtail Millet Markers for Millets and Bioenergy Grasses Research

    PubMed Central

    Misra, Gopal; Prasad, Manoj

    2013-01-01

    The prominent attributes of foxtail millet (Setaria italica L.) including its small genome size, short life cycle, inbreeding nature, and phylogenetic proximity to various biofuel crops have made this crop an excellent model system to investigate various aspects of architectural, evolutionary and physiological significances in Panicoid bioenergy grasses. After release of its whole genome sequence, large-scale genomic resources in terms of molecular markers were generated for the improvement of both foxtail millet and its related species. Hence it is now essential to congregate, curate and make available these genomic resources for the benefit of researchers and breeders working towards crop improvement. In view of this, we have constructed the Foxtail millet Marker Database (FmMDb; http://www.nipgr.res.in/foxtail.html), a comprehensive online database for information retrieval, visualization and management of large-scale marker datasets with unrestricted public access. FmMDb is the first database which provides complete marker information to the plant science community attempting to produce elite cultivars of millet and bioenergy grass species, thus addressing global food insecurity. PMID:23951158

  4. Administrative Databases in Orthopaedic Research: Pearls and Pitfalls of Big Data.

    PubMed

    Patel, Alpesh A; Singh, Kern; Nunley, Ryan M; Minhas, Shobhit V

    2016-03-01

    The drive for evidence-based decision-making has highlighted the shortcomings of traditional orthopaedic literature. Although high-quality, prospective, randomized studies in surgery are the benchmark in orthopaedic literature, they are often limited by size, scope, cost, time, and ethical concerns and may not be generalizable to larger populations. Given these restrictions, there is a growing trend toward the use of large administrative databases to investigate orthopaedic outcomes. These datasets afford the opportunity to identify a large numbers of patients across a broad spectrum of comorbidities, providing information regarding disparities in care and outcomes, preoperative risk stratification parameters for perioperative morbidity and mortality, and national epidemiologic rates and trends. Although there is power in these databases in terms of their impact, potential problems include administrative data that are at risk of clerical inaccuracies, recording bias secondary to financial incentives, temporal changes in billing codes, a lack of numerous clinically relevant variables and orthopaedic-specific outcomes, and the absolute requirement of an experienced epidemiologist and/or statistician when evaluating results and controlling for confounders. Despite these drawbacks, administrative database studies are fundamental and powerful tools in assessing outcomes on a national scale and will likely be of substantial assistance in the future of orthopaedic research.

  5. The Cancer Epidemiology Descriptive Cohort Database: A Tool to Support Population-Based Interdisciplinary Research

    PubMed Central

    Kennedy, Amy E.; Khoury, Muin J.; Ioannidis, John P.A.; Brotzman, Michelle; Miller, Amy; Lane, Crystal; Lai, Gabriel Y.; Rogers, Scott D.; Harvey, Chinonye; Elena, Joanne W.; Seminara, Daniela

    2017-01-01

    Background We report on the establishment of a web-based Cancer Epidemiology Descriptive Cohort Database (CEDCD). The CEDCD’s goals are to enhance awareness of resources, facilitate interdisciplinary research collaborations, and support existing cohorts for the study of cancer-related outcomes. Methods Comprehensive descriptive data were collected from large cohorts established to study cancer as primary outcome using a newly developed questionnaire. These included an inventory of baseline and follow-up data, biospecimens, genomics, policies, and protocols. Additional descriptive data extracted from publicly available sources were also collected. This information was entered in a searchable and publicly accessible database. We summarized the descriptive data across cohorts and reported the characteristics of this resource. Results As of December 2015, the CEDCD includes data from 46 cohorts representing more than 6.5 million individuals (29% ethnic/racial minorities). Overall, 78% of the cohorts have collected blood at least once, 57% at multiple time points, and 46% collected tissue samples. Genotyping has been performed by 67% of the cohorts, while 46% have performed whole-genome or exome sequencing in subsets of enrolled individuals. Information on medical conditions other than cancer has been collected in more than 50% of the cohorts. More than 600,000 incident cancer cases and more than 40,000 prevalent cases are reported, with 24 cancer sites represented. Conclusions The CEDCD assembles detailed descriptive information on a large number of cancer cohorts in a searchable database. Impact Information from the CEDCD may assist the interdisciplinary research community by facilitating identification of well-established population resources and large-scale collaborative and integrative research. PMID:27439404

  6. The Society of Thoracic Surgeons Congenital Heart Surgery Database: 2017 Update on Research.

    PubMed

    Jacobs, Marshall L; Jacobs, Jeffrey P; Hill, Kevin D; Hornik, Christoph; O'Brien, Sean M; Pasquali, Sara K; Vener, David; Kumar, S Ram; Habib, Robert H; Shahian, David M; Edwards, Fred H; Fernandez, Felix G

    2017-09-01

    The Society of Thoracic Surgeons Congenital Heart Surgery Database (STS CHSD) is the largest congenital and pediatric cardiac surgical clinical data registry in the world. It contains data pertaining to more than 435,000 total operations. The most recent biannual feedback report to participants (Spring 2017, Report of the Twenty-Sixth Harvest) included analysis of data submitted from 127 hospitals in North America. That represents nearly all centers performing pediatric and congenital heart operations in the United States and Canada. As an unparalleled platform for assessment of outcomes and for quality improvement activities in the subspecialty of surgery for pediatric and congenital heart disease, the STS CHSD continues to be a primary data source for clinical investigations and for research and innovations related to quality measurement. In 2016, several major original publications reported analyses of data in the CHSD pertaining to various processes of care, including assessment of variation across centers and associations between specific practices, patient characteristics, and outcomes. Additional publications reported the most recent development, evaluation, and application of metrics for quality measurement and reporting of pediatric and congenital heart operation outcomes and center level performance. Use of the STS CHSD for outcomes research and for quality measurement continues to expand as database participation has grown to include nearly all centers in North America, and the available wealth of data in the database continues to grow. This article reviews outcomes research and quality improvement articles published in 2016 that are based on STS CHSD data. Copyright © 2017 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

  7. SeqHound: biological sequence and structure database as a platform for bioinformatics research

    PubMed Central

    2002-01-01

    Background SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment. Results SeqHound is based on the National Center for Biotechnology Information data model and programming tools. It offers daily updated contents of all Entrez sequence databases in addition to 3-D structural data and information about sequence redundancies, sequence neighbours, taxonomy, complete genomes, functional annotation including Gene Ontology terms and literature links to PubMed. SeqHound is accessible via a web server through a Perl, C or C++ remote API or an optimized local API. It provides functionality necessary to retrieve specialized subsets of sequences, structures and structural domains. Sequences may be retrieved in FASTA, GenBank, ASN.1 and XML formats. Structures are available in ASN.1, XML and PDB formats. Emphasis has been placed on complete genomes, taxonomy, domain and functional annotation as well as 3-D structural functionality in the API, while fielded text indexing functionality remains under development. SeqHound also offers a streamlined WWW interface for simple web-user queries. Conclusions The system has proven useful in several published bioinformatics projects such as the BIND database and offers a cost-effective infrastructure for research. SeqHound will continue to develop and be provided as a service of the Blueprint Initiative at the Samuel Lunenfeld Research Institute. The source code and examples are available under the terms of the GNU public license at the Sourceforge site http://sourceforge.net/projects/slritools/ in the SLRI Toolkit. PMID:12401134

  8. Databases for LDEF results

    NASA Technical Reports Server (NTRS)

    Bohnhoff-Hlavacek, Gail

    1992-01-01

    One of the objectives of the team supporting the LDEF Systems and Materials Special Investigative Groups is to develop databases of experimental findings. These databases identify the hardware flown, summarize results and conclusions, and provide a system for acknowledging investigators, tracing sources of data, and future design suggestions. To date, databases covering the optical experiments, and thermal control materials (chromic acid anodized aluminum, silverized Teflon blankets, and paints) have been developed at Boeing. We used the Filemaker Pro software, the database manager for the Macintosh computer produced by the Claris Corporation. It is a flat, text-retrievable database that provides access to the data via an intuitive user interface, without tedious programming. Though this software is available only for the Macintosh computer at this time, copies of the databases can be saved to a format that is readable on a personal computer as well. Further, the data can be exported to more powerful relational databases, capabilities, and use of the LDEF databases and describe how to get copies of the database for your own research.

  9. Interacting with the National Database for Autism Research (NDAR) via the LONI Pipeline Workflow Environment

    PubMed Central

    Torgerson, Carinna M.; Quinn, Catherine; Dinov, Ivo; Liu, Zhizhong; Petrosyan, Petros; Pelphrey, Kevin; Haselgrove, Christian; Kennedy, David N.; Toga, Arthur W.; Van Horn, John Darrell

    2015-01-01

    The National Database for Autism Research (NDAR) seeks to gather, curate, and make openly available neuroimaging data from NIH-funded studies of autism spectrum disorder (ASD). NDAR has recently made its database accessible through the LONI Pipeline processing environment to enable large-scale analyses of cortical architecture and function via local, cluster, or “cloud”-based computing resources. This presents a unique opportunity to overcome many of the customary limitations to fostering biomedical neuroimaging as a science of discovery. Providing open access to primary neuroimaging data, workflow methods, and high-performance computing will increase uniformity in data collection protocols, encourage greater reliability of published data, results replication, and broaden the range of researchers now able to perform larger studies than ever before. To illustrate the use of NDAR and LONI Pipeline for performing several commonly performed neuroimaging processing steps and analyses, this paper presents example workflows useful for ASD neuroimaging researchers seeking to begin using this valuable combination of online data and computational resources. PMID:25666423

  10. The Corvids Literature Database--500 years of ornithological research from a crow's perspective.

    PubMed

    Droege, Gabriele; Töpfer, Till

    2016-01-01

    Corvids (Corvidae) play a major role in ornithological research. Because of their worldwide distribution, diversity and adaptiveness, they have been studied extensively. The aim of the Corvids Literature Database (CLD, http://www.corvids.de/cld) is to record all publications (citation format) on all extant and extinct Crows, Ravens, Jays and Magpies worldwide and tag them with specific keywords making them available for researchers worldwide. The self-maintained project started in 2006 and today comprises 8000 articles, spanning almost 500 years. The CLD covers publications from 164 countries, written in 36 languages and published by 8026 authors in 1503 journals (plus books, theses and other publications). Forty-nine percent of all records are available online as full-text documents or deposited in the physical CLD archive. The CLD contains 442 original corvid descriptions. Here, we present a metadata assessment of articles recorded in the CLD including a gap analysis and prospects for future research. Database URL: http://www.corvids.de/cld. © The Author(s) 2016. Published by Oxford University Press.

  11. Turning text into research networks: information retrieval and computational ontologies in the creation of scientific databases.

    PubMed

    Ceci, Flávio; Pietrobon, Ricardo; Gonçalves, Alexandre Leopoldo

    2012-01-01

    Web-based, free-text documents on science and technology have been increasing growing on the web. However, most of these documents are not immediately processable by computers slowing down the acquisition of useful information. Computational ontologies might represent a possible solution by enabling semantically machine readable data sets. But, the process of ontology creation, instantiation and maintenance is still based on manual methodologies and thus time and cost intensive. We focused on a large corpus containing information on researchers, research fields, and institutions. We based our strategy on traditional entity recognition, social computing and correlation. We devised a semi automatic approach for the recognition, correlation and extraction of named entities and relations from textual documents which are then used to create, instantiate, and maintain an ontology. We present a prototype demonstrating the applicability of the proposed strategy, along with a case study describing how direct and indirect relations can be extracted from academic and professional activities registered in a database of curriculum vitae in free-text format. We present evidence that this system can identify entities to assist in the process of knowledge extraction and representation to support ontology maintenance. We also demonstrate the extraction of relationships among ontology classes and their instances. We have demonstrated that our system can be used for the conversion of research information in free text format into database with a semantic structure. Future studies should test this system using the growing number of free-text information available at the institutional and national levels.

  12. Adaptive clustering of image database (ACID) as an efficient tool for improving retrieval in a CBIR system.

    PubMed

    Reljin, Branimir; Zajić, Goran; Reljin, Nikola; Reljin, Irini

    2012-01-01

    The paper describes a content-based image retrieval (CBIR) system with relevance feedback (RF). Instead of standard relevance feedback procedure, an adaptive clustering of image database (ACID) according to particular subjective needs is introduced in our system. Images labeled by the user as relevant are collected in clusters, and their representative members are used in further searching procedure instead of all images contained in the database. By this way, some history of previous retrieving is embedded into a searching process enabling faster and more subjective retrieval. Moreover, clusters are adaptively updated after each retrieving session, following actual user's needs. The efficiency of the proposed ACID system is tested with images from Corel and MIT datasets.

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

    PubMed Central

    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. PMID:26107821

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

    PubMed

    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.

  15. Research Update: The materials genome initiative: Data sharing and the impact of collaborative ab initio databases

    NASA Astrophysics Data System (ADS)

    Jain, Anubhav; Persson, Kristin A.; Ceder, Gerbrand

    2016-05-01

    Materials innovations enable new technological capabilities and drive major societal advancements but have historically required long and costly development cycles. The Materials Genome Initiative (MGI) aims to greatly reduce this time and cost. In this paper, we focus on data reuse in the MGI and, in particular, discuss the impact of three different computational databases based on density functional theory methods to the research community. We also discuss and provide recommendations on technical aspects of data reuse, outline remaining fundamental challenges, and present an outlook on the future of MGI's vision of data sharing.

  16. A review of polycyclic aromatic hydrocarbons (PAHs) research progress in China based on CNKI database

    NASA Astrophysics Data System (ADS)

    Zhang, Zhao

    2017-03-01

    This article using the retroactive content analysis method summarizes the research progress of air polycyclic aromatic hydrocarbons during 1983 to 2016, and is based on the 72 search results about "Air Polycyclic Aromatic Hydrocarbons" in CNKI database. This article directly points out the study achievements and improvements about air polycyclic aromatic hydrocarbons from 4 aspects, the reviews of the studies of PAHs in a special stage, the studies on PAHs determination and analysis method, the studies on PAHs concentration in different places and the studies on the relationship between PAHs concentration in air and human health, respectively.

  17. Scientific Research Database of the 2008 Ms8.0 Wenchuan Earthquake

    NASA Astrophysics Data System (ADS)

    Liang, C.; Yang, Y.; Yu, Y.

    2013-12-01

    Nearly 5 years after the 2008 Ms8.0 Wenchuan Earthquake, the Ms7.0 Lushan earthquake stroke 70km away along the same fault system. Given the tremendous life loss and property damages as well as the short time and distance intervals between the two large magnitude events, the scientific probing into their causing factors and future seismic activities in the nearby region will continue to be in the center of earthquake research in China and even the world for years to come. In the past five years, scientists have made significant efforts to study the Wenchuan earthquake from various aspects using different datasets and methods. Their studies cover a variety of topics including seismogenic environment, earthquake precursors, rupture process, co-seismic phenomenon, hazard relief, reservoir induced seismicity and more. These studies have been published in numerous journals in Chinese, English and many other languages. In addition, 54 books regarding to this earthquake have been published. The extremely diversified nature of all publications makes it very difficult and time-consuming, if not impossible, to sort out information needed by individual researcher in an efficient way. An information platform that collects relevant scientific information and makes them accessible in various ways can be very handy. With this mission in mind, the Earthquake Research Group in the Chengdu University of Technology has developed a website www.wceq.org to attack this target: (1) articles published by major journals and books are recorded into a database. Researchers will be able to find articles by topics, journals, publication dates, authors and keywords e.t.c by a few clicks; (2) to fast track the latest developments, researchers can also follow upon updates in the current month, last 90days, 180 days and 365 days by clicking on corresponding links; (3) the modern communication tools such as Facebook, Twitter and their Chinese counterparts are accommodated in this site to share

  18. Assessing urology and nephrology research activity in Arab countries using ISI web of science bibliometric database.

    PubMed

    Sweileh, Waleed M; Zyoud, Sa'ed H; Al-Jabi, Samah W; Sawalha, Ansam F

    2014-04-23

    Bibliometric analysis is increasingly being used for research assessment. The main objective of this study was to assess research output in Urology and Nephrology subject from the Arab countries. Original scientific articles or reviews published from the 21 Arab countries in "Urology and Nephrology" subject were screened using the ISI Web of Science database. Research productivity was evaluated based on a methodology developed and used in other bibliometric studies by analyzing the annual productivity, names of journals, citations; top 10 active institution and authors as well as country contribution to Urology and Nephrology research. Three thousand and seventy six documents in "urology and nephrology" subject category were retrieved from 104 journals. This represents 1.4% of the global research output in "urology and nephrology". Four hundred and two documents (12.66%) were published in Annales D Urologie Journal. The h-index of the retrieved documents was 57. The total number of citations, at the time of data analysis, was 30401 with an average citation of 9.57 per document. Egypt, with a total publication of 1284 (40.43%) ranked first among the Arab countries in "urology and nephrology" subject category. Mansoura University in Egypt was the most productive institution with a total of 561 (15.33%) documents. Arab researchers collaborated most with researchers from the United States of America (226; 7.12%) in urology and nephrology research. The present data reveals a good contribution of some Arab countries to the field of "urology and nephrology". More efforts are needed by some other Arab countries to bridge the gap in urology and nephrology research. Overall, the quality of urology/nephrology research is considered relatively high as measured by h-index. Cooperation in urology/nephrology research should be encouraged in the Arab world to bridge the gap with that from developed countries.

  19. Assessing urology and nephrology research activity in Arab countries using ISI web of science bibliometric database

    PubMed Central

    2014-01-01

    Background Bibliometric analysis is increasingly being used for research assessment. The main objective of this study was to assess research output in Urology and Nephrology subject from the Arab countries. Original scientific articles or reviews published from the 21 Arab countries in “Urology and Nephrology” subject were screened using the ISI Web of Science database. Research productivity was evaluated based on a methodology developed and used in other bibliometric studies by analyzing the annual productivity, names of journals, citations; top 10 active institution and authors as well as country contribution to Urology and Nephrology research. Results Three thousand and seventy six documents in “urology and nephrology” subject category were retrieved from 104 journals. This represents 1.4% of the global research output in “urology and nephrology”. Four hundred and two documents (12.66%) were published in Annales D Urologie Journal. The h-index of the retrieved documents was 57. The total number of citations, at the time of data analysis, was 30401 with an average citation of 9.57 per document. Egypt, with a total publication of 1284 (40.43%) ranked first among the Arab countries in “urology and nephrology” subject category. Mansoura University in Egypt was the most productive institution with a total of 561 (15.33%) documents. Arab researchers collaborated most with researchers from the United States of America (226; 7.12%) in urology and nephrology research. Conclusion The present data reveals a good contribution of some Arab countries to the field of “urology and nephrology”. More efforts are needed by some other Arab countries to bridge the gap in urology and nephrology research. Overall, the quality of urology/nephrology research is considered relatively high as measured by h-index. Cooperation in urology/nephrology research should be encouraged in the Arab world to bridge the gap with that from developed countries. PMID:24758477

  20. A database of chromatographic properties and mass spectra of fatty acid methyl esters from omega-3 products.

    PubMed

    Wasta, Ziar; Mjøs, Svein A

    2013-07-19

    Fatty acids in products claimed to contain oils with the omega-3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) were analyzed as fatty acid methyl esters by gas chromatography-mass spectrometry using electron impact ionization. To cover the variation in products on the market, the 20 products that were studied in detail were selected from a larger sample set by statistical methodology. The samples were analyzed on two different stationary phases (polyethylene glycol and cyanopropyl) and the fatty acid methyl esters were identified by methodology that combines the mass spectra and retention indices into a single score value. More that 100 fatty acids had a chromatographic area above 0.1% of the total, in at least one product. Retention indices are reported as equivalent chain lengths, and overlap patterns on the two columns are discussed. Both columns were found suitable for analysis of major and nutritionally important fatty acids, but the large number of minor compounds that may act as interferents will be problematic if low limits of quantification are required in analyses of similar sample types. A database of mass spectral libraries and equivalent chain lengths of the detected compounds has been compiled and is available online. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. Monitoring of equine health in Denmark: the importance, purpose, research areas and content of a future database.

    PubMed

    Hartig, Wendy; Houe, Hans; Andersen, Pia Haubro

    2013-04-01

    The plentiful data on Danish horses are currently neither organized nor easily accessible, impeding register-based epidemiological studies on Danish horses. A common database could be beneficial. In principle, databases can contain a wealth of information, but no single database can serve every purpose. Hence the establishment of a Danish equine health database should be preceded by careful consideration of its purpose and content, and stakeholder attitudes should be investigated. The objectives of the present study were to identify stakeholder attitudes to the importance, purpose, research areas and content of a health database for horses in Denmark. A cross-sectional study was conducted with 13 horse-related stakeholder groups in Denmark. The groups surveyed included equine veterinarians, researchers, veterinary students, representatives from animal welfare organizations, horse owners, trainers, farriers, authority representatives, ordinary citizens, and representatives from laboratories, insurance companies, medical equipment companies and pharmaceutical companies. Supplementary attitudes were inferred from qualitative responses. The overall response rate for all stakeholder groups was 45%. Stakeholder group-specific response rates were 27-80%. Sixty-eight percent of questionnaire respondents thought a national equine health database was important. Most respondents wanted the database to contribute to improved horse health and welfare, to be used for research into durability and disease heritability, and to serve as a basis for health declarations for individual horses. The generally preferred purpose of the database was thus that it should focus on horse health and welfare rather than on performance or food safety, and that it should be able to function both at a population and an individual horse level. In conclusion, there is a positive attitude to the establishment of a health database for Danish horses. These results could enrich further reflection on the

  2. National Database for Autism Research (NDAR): Big Data Opportunities for Health Services Research and Health Technology Assessment

    PubMed Central

    Payakachat, Nalin; Tilford, J. Mick; Ungar, Wendy J.

    2015-01-01

    The National Database for Autism Research (NDAR) is a US National Institutes of Health (NIH)-funded research data repository created by integrating heterogeneous datasets through data sharing agreements between autism researchers and the NIH. To date, NDAR is considered the largest neuroscience and genomic data repository for autism research. In addition to biomedical data, NDAR contains a large collection of clinical and behavioral assessments and health outcomes from novel interventions. Importantly, NDAR has a global unique patient identifier that can be linked to aggregated individual-level data for hypothesis generation and testing, and for replicating research findings. As such, NDAR promotes collaboration and maximizes public investment in the original data collection. As screening and diagnostic technologies as well as interventions for children with autism are expensive, health services research (HSR) and health technology assessment (HTA) are needed to generate more evidence to facilitate implementation when warranted. This article describes NDAR and explains its value to health services researchers and decision scientists interested in autism and other mental health conditions. We provide a description of the scope and structure of NDAR and illustrate how data are likely to grow over time and become available for HSR and HTA. PMID:26446859

  3. National Database for Autism Research (NDAR): Big Data Opportunities for Health Services Research and Health Technology Assessment.

    PubMed

    Payakachat, Nalin; Tilford, J Mick; Ungar, Wendy J

    2016-02-01

    The National Database for Autism Research (NDAR) is a US National Institutes of Health (NIH)-funded research data repository created by integrating heterogeneous datasets through data sharing agreements between autism researchers and the NIH. To date, NDAR is considered the largest neuroscience and genomic data repository for autism research. In addition to biomedical data, NDAR contains a large collection of clinical and behavioral assessments and health outcomes from novel interventions. Importantly, NDAR has a global unique patient identifier that can be linked to aggregated individual-level data for hypothesis generation and testing, and for replicating research findings. As such, NDAR promotes collaboration and maximizes public investment in the original data collection. As screening and diagnostic technologies as well as interventions for children with autism are expensive, health services research (HSR) and health technology assessment (HTA) are needed to generate more evidence to facilitate implementation when warranted. This article describes NDAR and explains its value to health services researchers and decision scientists interested in autism and other mental health conditions. We provide a description of the scope and structure of NDAR and illustrate how data are likely to grow over time and become available for HSR and HTA.

  4. Overview of ESSL's severe convective storms research using the European Severe Weather Database ESWD

    NASA Astrophysics Data System (ADS)

    Dotzek, Nikolai; Groenemeijer, Pieter; Feuerstein, Bernold; Holzer, Alois M.

    Severe thunderstorms constitute a major weather hazard in Europe, with an estimated total damage of 5-8 billion euros each year nowadays. Even though there is an upward trend in damage due to increases in vulnerability and possibly also due to climate change impacts, a pan-European database of severe thunderstorm reports in a homogeneous data format did not exist until a few years ago. The development of this European Severe Weather Database (ESWD) provided the final impetus for the establishment of the European Severe Storms Laboratory (ESSL) as a non-profit research organisation in 2006, after having started as an informal network in 2002. Our paper provides an overview of the first research results that have been achieved by ESSL. We start by outlining the reporting practice and quality-control procedure for the database, which has been enhanced by a major software upgrade in the fall of 2008. It becomes apparent that the state of reporting converges to a realistic description of the severe storms climatology, corroborating, for instance, earlier estimates of tornado occurrence in Europe. Nevertheless, a further rise in the number of reported events must be expected, even without the presence of any physical trends. The European tornado and damaging wind intensity distributions as a function of the Fujita scale are quantitatively similar to long-term distributions from the USA, except for a strong underreporting of weak events (F0) that still persists in Europe. In addition, the ESSL has recently proposed a new wind speed scale, the Energy- or " E-scale" which is linked to physical quantities and can be calibrated. Finally, we demonstrate the large potential of ESWD data use for forecast or nowcasting/warning verification purposes.

  5. Food-pics: an image database for experimental research on eating and appetite

    PubMed Central

    Blechert, Jens; Meule, Adrian; Busch, Niko A.; Ohla, Kathrin

    2014-01-01

    Our current environment is characterized by the omnipresence of food cues. The sight and smell of real foods, but also graphically depictions of appetizing foods, can guide our eating behavior, for example, by eliciting food craving and influencing food choice. The relevance of visual food cues on human information processing has been demonstrated by a growing body of studies employing food images across the disciplines of psychology, medicine, and neuroscience. However, currently used food image sets vary considerably across laboratories and image characteristics (contrast, brightness, etc.) and food composition (calories, macronutrients, etc.) are often unspecified. These factors might have contributed to some of the inconsistencies of this research. To remedy this, we developed food-pics, a picture database comprising 568 food images and 315 non-food images along with detailed meta-data. A total of N = 1988 individuals with large variance in age and weight from German speaking countries and North America provided normative ratings of valence, arousal, palatability, desire to eat, recognizability and visual complexity. Furthermore, data on macronutrients (g), energy density (kcal), and physical image characteristics (color composition, contrast, brightness, size, complexity) are provided. The food-pics image database is freely available under the creative commons license with the hope that the set will facilitate standardization and comparability across studies and advance experimental research on the determinants of eating behavior. PMID:25009514

  6. Food-pics: an image database for experimental research on eating and appetite.

    PubMed

    Blechert, Jens; Meule, Adrian; Busch, Niko A; Ohla, Kathrin

    2014-01-01

    Our current environment is characterized by the omnipresence of food cues. The sight and smell of real foods, but also graphically depictions of appetizing foods, can guide our eating behavior, for example, by eliciting food craving and influencing food choice. The relevance of visual food cues on human information processing has been demonstrated by a growing body of studies employing food images across the disciplines of psychology, medicine, and neuroscience. However, currently used food image sets vary considerably across laboratories and image characteristics (contrast, brightness, etc.) and food composition (calories, macronutrients, etc.) are often unspecified. These factors might have contributed to some of the inconsistencies of this research. To remedy this, we developed food-pics, a picture database comprising 568 food images and 315 non-food images along with detailed meta-data. A total of N = 1988 individuals with large variance in age and weight from German speaking countries and North America provided normative ratings of valence, arousal, palatability, desire to eat, recognizability and visual complexity. Furthermore, data on macronutrients (g), energy density (kcal), and physical image characteristics (color composition, contrast, brightness, size, complexity) are provided. The food-pics image database is freely available under the creative commons license with the hope that the set will facilitate standardization and comparability across studies and advance experimental research on the determinants of eating behavior.

  7. The role of patent and non-patent databases in patent research in universities

    NASA Astrophysics Data System (ADS)

    Tolstaya, A. M.; Suslina, I. V.; Tolstaya, P. M.

    2017-01-01

    This studies deal with the description and systematization of the popular patent retrieval resources. The importance of the non-patent information when conducting patent research for the intellectual property created in educational and scientific activity of the university is highlighted. The differences in the patent and non-patent information are found out. Based on the databases` analysis the authors conducted the patent research on "Wireless endoscopic capsules" (development of the NRNU MEPhI). This study can be used to facilitate the university work on the new product development in order to improve the efficiency of the process of the commercialization of the intellectual activity results, including the entering the international market.

  8. Red herring in acid rain research

    SciTech Connect

    Havas, M.; Hutchinson, T.C.; Likens, G.E.

    1984-06-01

    Five common misconceptions, red herrings, regarding the effects of acid deposition on aquatic ecosystems are described in an attempt to clarify some of the confusion they have created. These misconceptions are the following: Bog lakes have been acidic for thousands of years; thus the acidification of lakes is not a recent phenomenon. The early methods for measuring pH are in error; therfore, no statements can be made regarding historical trends. Acidification of lakes and streams results from changed land use practices (forestry, agriculture, animal husbandry) and not acid deposition. The decrease in fish populations is caused by overfishing, disease, and water pollution, not acidification. Because lakes that receive identical rainfall can have considerable different pHs, regional lake acidification cannot be due to acid precipitation. It is easy to suggest a whole series of alternative, and often unlikely, explanations of the causes and consequences of acid deposition. These keep scientists busy for years assembling and examining data only to conclude that the explanation is not valid. These tactics cause, and perhaps are designed to cause, continuous delay in remedial action. They fail to take into account the large body of information that deals with the sources of the acid deposition and the seriousness of its effects.

  9. U.S. Department of Agriculture Agricultural Research Service Mahantango Creek Watershed, Pennsylvania, United States: long-term precipitation database

    USDA-ARS?s Scientific Manuscript database

    A long-term precipitation database has been developed by the U.S. Department of Agriculture, Agricultural Research Service, Pasture Systems and Watershed Management Research Unit (PSWMRU) to support intensive hydrologic and water quality research within WE-38, a 7.3 km**2 experimental watershed loca...

  10. The development and implementation of a computerized database for clinical research in minimal access surgery. An international pilot study.

    PubMed

    Birch, D W; Park, A; Bailey, M; Witzke, W; Witzke, D; Hoskins, J

    2001-09-01

    The measurement of outcomes after minimal access surgery (MAS) relies on the maintenance of an accurate, prospective clinical database. The development of a system for data management often proves to be challenging, expensive, and extremely time-consuming. We developed a computerized relational database for MAS using Microsoft Access 97 to reside on a hospital server, taking advantage of existing network connections, security, and backup systems. The design of the database includes a point-and-click approach with dropdown boxes for diagnoses, procedures, and complications (limited free-text entry). A fundamental feature of this database allows surgeons and surgical trainees to record clinical information at the point and time of data acquisition. A "beta version" or fully functional draft of the database was presented to a group of surgeons from a variety of specialties (n = 8), and a structured interview based on a questionnaire was used to elicit the surgeon's evaluations of the database. Using the information from the interviews, the database was extensively revised and restructured. We have developed a relational database that reflects the needs of surgeons interested in clinical research. This database may serve as a template for other centers. It can be expanded to adopt new procedures or modified for other surgical specialties.

  11. Human genetic research databases and biobanks: towards uniform terminology and Australian best practice.

    PubMed

    Chalmers, Don; Nicol, Dianne

    2008-02-01

    This article examines international best practice for the establishment, maintenance and use of human genetic research databases (HGRDs), particularly focusing on large-scale population biobanks, and considers the measures that should be taken in Australia to comply with this best practice. These HGRDs play a pivotal role in basic research aimed at understanding the basis of human disease at the genetic level, and applied research aimed at putting that basic knowledge into practical application. In particular, the large-scale biobanks are vital research tools in the drive to uncover the causes and consequences of human health and disease. Biobanks are being established at regional, national and international levels throughout the world. Although their governance structures are uniformly complex, some best practices are emerging with regard to consent (particularly consent to future research and withdrawal of consent), privacy and data protection and intellectual property ownership and access. Best practices with regard to benefit-sharing are emerging much more slowly. This article reviews these international best practices with the aim of providing guidance for the development of appropriate regulatory structures in Australia.

  12. MaizeGDB: The Maize Model Organism Database for Basic, Translational, and Applied Research

    PubMed Central

    Lawrence, Carolyn J.; Harper, Lisa C.; Schaeffer, Mary L.; Sen, Taner Z.; Seigfried, Trent E.; Campbell, Darwin A.

    2008-01-01

    In 2001 maize became the number one production crop in the world with the Food and Agriculture Organization of the United Nations reporting over 614 million tonnes produced. Its success is due to the high productivity per acre in tandem with a wide variety of commercial uses. Not only is maize an excellent source of food, feed, and fuel, but also its by-products are used in the production of various commercial products. Maize's unparalleled success in agriculture stems from basic research, the outcomes of which drive breeding and product development. In order for basic, translational, and applied researchers to benefit from others' investigations, newly generated data must be made freely and easily accessible. MaizeGDB is the maize research community's central repository for genetics and genomics information. The overall goals of MaizeGDB are to facilitate access to the outcomes of maize research by integrating new maize data into the database and to support the maize research community by coordinating group activities. PMID:18769488

  13. How I do it: a practical database management system to assist clinical research teams with data collection, organization, and reporting.

    PubMed

    Lee, Howard; Chapiro, Julius; Schernthaner, Rüdiger; Duran, Rafael; Wang, Zhijun; Gorodetski, Boris; Geschwind, Jean-François; Lin, MingDe

    2015-04-01

    The objective of this study was to demonstrate that an intra-arterial liver therapy clinical research database system is a more workflow efficient and robust tool for clinical research than a spreadsheet storage system. The database system could be used to generate clinical research study populations easily with custom search and retrieval criteria. A questionnaire was designed and distributed to 21 board-certified radiologists to assess current data storage problems and clinician reception to a database management system. Based on the questionnaire findings, a customized database and user interface system were created to perform automatic calculations of clinical scores including staging systems such as the Child-Pugh and Barcelona Clinic Liver Cancer, and facilitates data input and output. Questionnaire participants were favorable to a database system. The interface retrieved study-relevant data accurately and effectively. The database effectively produced easy-to-read study-specific patient populations with custom-defined inclusion/exclusion criteria. The database management system is workflow efficient and robust in retrieving, storing, and analyzing data. Copyright © 2015 AUR. Published by Elsevier Inc. All rights reserved.

  14. NASA's Astromaterials Database: Enabling Research Through Increased Access to Sample Data, Metadata and Imagery

    NASA Technical Reports Server (NTRS)

    Evans, Cindy; Todd, Nancy

    2014-01-01

    The Astromaterials Acquisition & Curation Office at NASA's Johnson Space Center (JSC) is the designated facility for curating all of NASA's extraterrestrial samples. Today, the suite of collections includes the lunar samples from the Apollo missions, cosmic dust particles falling into the Earth's atmosphere, meteorites collected in Antarctica, comet and interstellar dust particles from the Stardust mission, asteroid particles from Japan's Hayabusa mission, solar wind atoms collected during the Genesis mission, and space-exposed hardware from several missions. To support planetary science research on these samples, JSC's Astromaterials Curation Office hosts NASA's Astromaterials Curation digital repository and data access portal [http://curator.jsc.nasa.gov/], providing descriptions of the missions and collections, and critical information about each individual sample. Our office is designing and implementing several informatics initiatives to better serve the planetary research community. First, we are re-hosting the basic database framework by consolidating legacy databases for individual collections and providing a uniform access point for information (descriptions, imagery, classification) on all of our samples. Second, we continue to upgrade and host digital compendia that summarize and highlight published findings on the samples (e.g., lunar samples, meteorites from Mars). We host high resolution imagery of samples as it becomes available, including newly scanned images of historical prints from the Apollo missions. Finally we are creating plans to collect and provide new data, including 3D imagery, point cloud data, micro CT data, and external links to other data sets on selected samples. Together, these individual efforts will provide unprecedented digital access to NASA's Astromaterials, enabling preservation of the samples through more specific and targeted requests, and supporting new planetary science research and collaborations on the samples.

  15. Turning Text into Research Networks: Information Retrieval and Computational Ontologies in the Creation of Scientific Databases

    PubMed Central

    Ceci, Flávio; Pietrobon, Ricardo; Gonçalves, Alexandre Leopoldo

    2012-01-01

    Background Web-based, free-text documents on science and technology have been increasing growing on the web. However, most of these documents are not immediately processable by computers slowing down the acquisition of useful information. Computational ontologies might represent a possible solution by enabling semantically machine readable data sets. But, the process of ontology creation, instantiation and maintenance is still based on manual methodologies and thus time and cost intensive. Method We focused on a large corpus containing information on researchers, research fields, and institutions. We based our strategy on traditional entity recognition, social computing and correlation. We devised a semi automatic approach for the recognition, correlation and extraction of named entities and relations from textual documents which are then used to create, instantiate, and maintain an ontology. Results We present a prototype demonstrating the applicability of the proposed strategy, along with a case study describing how direct and indirect relations can be extracted from academic and professional activities registered in a database of curriculum vitae in free-text format. We present evidence that this system can identify entities to assist in the process of knowledge extraction and representation to support ontology maintenance. We also demonstrate the extraction of relationships among ontology classes and their instances. Conclusion We have demonstrated that our system can be used for the conversion of research information in free text format into database with a semantic structure. Future studies should test this system using the growing number of free-text information available at the institutional and national levels. PMID:22235242

  16. TarNet: An Evidence-Based Database for Natural Medicine Research

    PubMed Central

    Ren, Guomin; Sun, Guibo; Sun, Xiaobo

    2016-01-01

    Background Complex diseases seriously threaten human health. Drug discovery approaches based on “single genes, single drugs, and single targets” are limited in targeting complex diseases. The development of new multicomponent drugs for complex diseases is imperative, and the establishment of a suitable solution for drug group-target protein network analysis is a key scientific problem that must be addressed. Herbal medicines have formed the basis of sophisticated systems of traditional medicine and have given rise to some key drugs that remain in use today. The search for new molecules is currently taking a different route, whereby scientific principles of ethnobotany and ethnopharmacognosy are being used by chemists in the discovery of different sources and classes of compounds. Results In this study, we developed TarNet, a manually curated database and platform of traditional medicinal plants with natural compounds that includes potential bio-target information. We gathered information on proteins that are related to or affected by medicinal plant ingredients and data on protein–protein interactions (PPIs). TarNet includes in-depth information on both plant–compound–protein relationships and PPIs. Additionally, TarNet can provide researchers with network construction analyses of biological pathways and protein–protein interactions (PPIs) associated with specific diseases. Researchers can upload a gene or protein list mapped to our PPI database that has been manually curated to generate relevant networks. Multiple functions are accessible for network topological calculations, subnetwork analyses, pathway analyses, and compound–protein relationships. Conclusions TarNet will serve as a useful analytical tool that will provide information on medicinal plant compound-affected proteins (potential targets) and system-level analyses for systems biology and network pharmacology researchers. TarNet is freely available at http://www.herbbol.org:8001/tarnet

  17. Using SDSS & GalaxyZoo Databases to Ask Research-able Questions in Learning Astronomy

    NASA Astrophysics Data System (ADS)

    Slater, Timothy F.

    2010-01-01

    Using Galaxy Zoo1 at: http://zoo1.galaxyzoo.org/ accessing SDSS and a multi-phase backwards faded scaffolding approach, we first ask students to classify 30 galaxies and consider proposed conclusion: "most galaxies are elliptical” based on the evidence collected. Here, student attention is isolated from generating a question or even a data collection protocol, but focused on the issue of "does the evidence match the conclusion?” The next phase focuses on generating conclusions from evidence, whereas the previous phase was focused on evaluating conclusions. Students explain their reasoning provide evidence in response to "What conclusions and generalizations can you make from the following data collected by a student in terms of do spiral galaxies generally spin clockwise or anticlockwise given that one observes 36 spirals spinning clockwise, 21 spirals spinning anticlockwise, and 16 appearing to be edge-on or unclear.” Next, students are asked to consider what evidence needs to be collected in order to complete a scientific inquiry related to a given question. Students propose what evidence is needed in order to pursue, "What fraction of galaxies observed appear to be in the process of merging with other galaxies?” Note students are explicitly asked not to actually gather data as it detracts from developing an understanding of how data collection needs to be tightly aligned with the question. And, in practice, students can intellectually engage with a data collection plan that is simply too ominous to actually collect. By this point, students have extended experience with inquiry in this domain. Students are now ready to wrestle with creating a fruitful question. Students are tasked to design an answerable research question, propose a plan to pursue evidence, collect data using the present astronomical data base and create an evidence-based conclusion about the nature and or frequency of galaxies.

  18. A Green's function database platform for seismological research and education: applications and examples

    NASA Astrophysics Data System (ADS)

    Heimann, Sebastian; Kriegerowski, Marius; Dahm, Torsten; Simone, Cesca; Wang, Rongjiang

    2016-04-01

    The study of seismic sources from measured waveforms requires synthetic elementary seismograms (Green's functions, GF) calculated for specific earth models and source receiver geometries. Since the calculation of GFs is computationally expensive and requires careful parameter testing and quality control, pre-calculated GF databases, which can be re-used for different types of applications, can be of advantage. We developed a GF database web platform for the seismological community (http://kinherd.org/), where a researcher can share Green's function stores and retrieve synthetic seismograms on the fly for various point and extended earthquake source models for many different earth models at local, regional and global scale. This web service is part of a rich new toolset for the creation and handling of Green's functions and synthetic seismograms (http://emolch.github.com/pyrocko/gf). It can be used off-line or in client mode. We demonstrate core features of the GF platform with different applications on global, regional and local scales. These include the automatic inversion of kinematic source parameter from teleseismic body waves, the improved depth estimate of shallow induced earthquakes from regional seismological arrays, or the relative moment tensor inversion of local earthquakes from volcanic induced seismicity.

  19. Using the Turning Research Into Practice (TRIP) database: how do clinicians really search?*

    PubMed Central

    Meats, Emma; Brassey, Jon; Heneghan, Carl; Glasziou, Paul

    2007-01-01

    Objectives: Clinicians and patients are increasingly accessing information through Internet searches. This study aimed to examine clinicians' current search behavior when using the Turning Research Into Practice (TRIP) database to examine search engine use and the ways it might be improved. Methods: A Web log analysis was undertaken of the TRIP database—a meta-search engine covering 150 health resources including MEDLINE, The Cochrane Library, and a variety of guidelines. The connectors for terms used in searches were studied, and observations were made of 9 users' search behavior when working with the TRIP database. Results: Of 620,735 searches, most used a single term, and 12% (n = 75,947) used a Boolean operator: 11% (n = 69,006) used “AND” and 0.8% (n = 4,941) used “OR.” Of the elements of a well-structured clinical question (population, intervention, comparator, and outcome), the population was most commonly used, while fewer searches included the intervention. Comparator and outcome were rarely used. Participants in the observational study were interested in learning how to formulate better searches. Conclusions: Web log analysis showed most searches used a single term and no Boolean operators. Observational study revealed users were interested in conducting efficient searches but did not always know how. Therefore, either better training or better search interfaces are required to assist users and enable more effective searching. PMID:17443248

  20. CottonGen: a genomics, genetics and breeding database for cotton research

    PubMed Central

    Yu, Jing; Jung, Sook; Cheng, Chun-Huai; Ficklin, Stephen P.; Lee, Taein; Zheng, Ping; Jones, Don; Percy, Richard G.; Main, Dorrie

    2014-01-01

    CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, visualization and data retrieval of cotton research data. CottonGen contains annotated whole genome sequences, unigenes from expressed sequence tags (ESTs), markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. Annotated whole genome sequences of Gossypium raimondii are available with aligned genetic markers and transcripts. These whole genome data can be accessed through genome pages, search tools and GBrowse, a popular genome browser. Most of the published cotton genetic maps can be viewed and compared using CMap, a comparative map viewer, and are searchable via map search tools. Search tools also exist for markers, quantitative trait loci (QTLs), germplasm, publications and trait evaluation data. CottonGen also provides online analysis tools such as NCBI BLAST and Batch BLAST. PMID:24203703

  1. Identifying clinical/translational research cohorts: ascertainment via querying an integrated multi-source database

    PubMed Central

    Hurdle, John F; Haroldsen, Stephen C; Hammer, Andrew; Spigle, Cindy; Fraser, Alison M; Mineau, Geraldine P; Courdy, Samir J

    2013-01-01

    Background Ascertainment of potential subjects has been a longstanding problem in clinical research. Various methods have been proposed, including using data in electronic health records. However, these methods typically suffer from scaling effects—some methods work well for large cohorts; others work for small cohorts only. Objective We propose a method that provides a simple identification of pre-research cohorts and relies on data available in most states in the USA: merged public health data sources. Materials and methods The Utah Population Database Limited query tool allows users to build complex queries that may span several types of health records, such as cancer registries, inpatient hospital discharges, and death certificates; in addition, these can be combined with family history information. The architectural approach incorporates several coding systems for medical information. It provides a front-end graphical user interface and enables researchers to build and run queries and view aggregate results. Multiple strategies have been incorporated to maintain confidentiality. Results This tool was rapidly adopted; since its release, 241 users representing a wide range of disciplines from 17 institutions have signed the user agreement and used the query tool. Three examples are discussed: pregnancy complications co-occurring with cardiovascular disease; spondyloarthritis; and breast cancer. Discussion and conclusions This query tool was designed to provide results as pre-research so that institutional review board approval would not be required. This architecture uses well-described technologies that should be within the reach of most institutions. PMID:23059733

  2. Identifying clinical/translational research cohorts: ascertainment via querying an integrated multi-source database.

    PubMed

    Hurdle, John F; Haroldsen, Stephen C; Hammer, Andrew; Spigle, Cindy; Fraser, Alison M; Mineau, Geraldine P; Courdy, Samir J

    2013-01-01

    Ascertainment of potential subjects has been a longstanding problem in clinical research. Various methods have been proposed, including using data in electronic health records. However, these methods typically suffer from scaling effects-some methods work well for large cohorts; others work for small cohorts only. We propose a method that provides a simple identification of pre-research cohorts and relies on data available in most states in the USA: merged public health data sources. The Utah Population Database Limited query tool allows users to build complex queries that may span several types of health records, such as cancer registries, inpatient hospital discharges, and death certificates; in addition, these can be combined with family history information. The architectural approach incorporates several coding systems for medical information. It provides a front-end graphical user interface and enables researchers to build and run queries and view aggregate results. Multiple strategies have been incorporated to maintain confidentiality. This tool was rapidly adopted; since its release, 241 users representing a wide range of disciplines from 17 institutions have signed the user agreement and used the query tool. Three examples are discussed: pregnancy complications co-occurring with cardiovascular disease; spondyloarthritis; and breast cancer. This query tool was designed to provide results as pre-research so that institutional review board approval would not be required. This architecture uses well-described technologies that should be within the reach of most institutions.

  3. Research on food and nutrition characteristics of conjugated fatty acids.

    PubMed

    Tsuduki, Tsuyoshi

    2015-01-01

    In this study, the physiological effects of fatty acids with conjugated double bonds were widely examined in vitro and in vivo. Initially, a method for determination of conjugated fatty acids in food and biological samples was established. I then clarified that the oxidative stability of conjugated fatty acids was improved by the form of triacylglycerol and addition of an antioxidant, and the influence of this effect on the metabolism and pharmacokinetics of conjugated fatty acids was clarified in vivo. In addition, antitumor, anti-angiogenesis, and antiobesity effects of conjugated fatty acids were found for the first time, thus demonstrating the usefulness of conjugated fatty acids. This communication mainly outlines the data obtained for conjugated linolenic acid. In addition, this review summarizes my research on conjugated fatty acid.

  4. [Spanish contribution to the creation of a European analytical database of trans-fatty acids].

    PubMed

    Cuadrado, C; Carbajal, A; Núñez, C; Ruiz-Roso, B; Moreiras, O

    1998-01-01

    Within the AAIR Program of the EU titled Evaluation of the Ingestion of Trans Fatty Acids (FA) and its association with cardiovascular risk factors in European countries (TRANSFAIR), which is being carried out in 16 countries with different alimentary habits, among which is our country, we have developed the following study. Based on the information derived from the last National Nutrition and Feeding Study (ENNA-3), we have made up a list of foods which make up 95% of the total ingestion of lipids, and it also includes those which although they are not included within this percentage, may have an especially high trans isomer content as a result of their processing. The foods selected for the analysis belong to different food groups: cereals, milk products, oils and fats, meats, various, and pre-cooked foods, until making up a total of 100 foods for each country. The central analysis laboratory is that of the Department of Human Nutrition, TNO Nutrition and Food Research, Zeist (The Netherlands). In each sample, in addition to the total lipids, one determines the saturated and unsaturated fatty acids, including the cis and trans isomers. The trans FA's measured were: C14:1 T9, C16:1 T9, C18:1 T, C18:2 T, C18:3 T + C20:1 T, C20:2 T11,14, and C22:1 T13. Of the samples analyzed, the highest percentages of trans FA with respect to the total FA corresponded to the following foods: French fries, pre-cooked and frozen croquettes sliced bread, margarine, cakes, and frozen mille feuilles dough of different industrial brands. The lowest percentages of trans FA's were found in refined vegetable oils (sunflower and olive), those used for deep frying, and those discarded in catering, as well as in some commercial brands of cookies and ice creams. Pure chocolate, different brands of sweetened powdered cocoa, and ready to make chocolate, did not contain and trans FA.

  5. Process of formulating USDA's Expanded Flavonoid Database for the Assessment of Dietary intakes: a new tool for epidemiological research.

    PubMed

    Bhagwat, Seema A; Haytowitz, David B; Wasswa-Kintu, Shirley I; Pehrsson, Pamela R

    2015-08-14

    The scientific community continues to be interested in potential links between flavonoid intakes and beneficial health effects associated with certain chronic diseases such as CVD, some cancers and type 2 diabetes. Three separate flavonoid databases (Flavonoids, Isoflavones and Proanthocyanidins) developed by the USDA Agricultural Research Service since 1999 with frequent updates have been used to estimate dietary flavonoid intakes, and investigate their health effects. However, each of these databases contains only a limited number of foods. The USDA has constructed a new Expanded Flavonoids Database for approximately 2900 commonly consumed foods, using analytical values from their existing flavonoid databases (Flavonoid Release 3.1 and Isoflavone Release 2.0) as the foundation to calculate values for all the twenty-nine flavonoid compounds included in these two databases. Thus, the new database provides full flavonoid profiles for twenty-nine predominant dietary flavonoid compounds for every food in the database. Original analytical values in Flavonoid Release 3.1 and Isoflavone Release 2.0 for corresponding foods were retained in the newly constructed database. Proanthocyanidins are not included in the expanded database. The process of formulating the new database includes various calculation techniques. This article describes the process of populating values for the twenty-nine flavonoid compounds for every food in the dataset, along with challenges encountered and resolutions suggested. The new expanded flavonoid database released on the Nutrient Data Laboratory's website would provide uniformity in estimations of flavonoid content in foods and will be a valuable tool for epidemiological studies to assess dietary intakes.

  6. Propellant Mass Gauging: Database of Vehicle Applications and Research and Development Studies

    NASA Technical Reports Server (NTRS)

    Dodge, Franklin T.

    2008-01-01

    Gauging the mass of propellants in a tank in low gravity is not a straightforward task because of the uncertainty of the liquid configuration in the tank and the possibility of there being more than one ullage bubble. Several concepts for such a low-gravity gauging system have been proposed, and breadboard or flight-like versions have been tested in normal gravity or even in low gravity, but at present, a flight-proven reliable gauging system is not available. NASA desired a database of the gauging techniques used in current and past vehicles during ascent or under settled conditions, and during short coasting (unpowered) periods, for both cryogenic and storable propellants. Past and current research and development efforts on gauging systems that are believed to be applicable in low-gravity conditions were also desired. This report documents the results of that survey.

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

    PubMed

    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.

  8. [Bibliometric and thematic analysis of the scientific literature about omega-3 fatty acids indexed in international databases on health sciences].

    PubMed

    Sanz-Valero, J; Gil, Á; Wanden-Berghe, C; Martínez de Victoria, E

    2012-11-01

    To evaluate by bibliometric and thematic analysis the scientific literature on omega-3 fatty acids indexed in international databases on health sciences and to establish a comparative base for future analysis. Searches were conducted with the descriptor (MeSH, as Major Topic) "Fatty Acids, Omega-3" from the first date available until December 31, 2010. Databases consulted: MEDLINE (via PubMed), EMBASE, ISI Web of Knowledge, CINAHL and LILACS. The most common type of document was originals articles. Obsolescence was set at 5 years. The geographical distribution of authors who appear as first author was EEUU and the articles were written predominantly in English. The study population was 90.98% (95% CI 89.25 to 92.71) adult humans. The documents were classified into 59 subject areas and the most studied topic 16.24% (95% CI 14.4 to 18.04) associated with omega-3, was cardiovascular disease. This study indicates that the scientific literature on omega-3 fatty acids is a full force area of knowledge. The Anglo-Saxon institutions dominate the scientific production and it is mainly oriented to the study of cardiovascular disease.

  9. Acid rain and related air-pollution research. A directory of USDA and state projects in CRIS. Final report

    SciTech Connect

    Not Available

    1987-05-01

    The directory is a listing of the ongoing and recently completed research projects from the Current Research Information System (CRIS) database of the U.S. Department of Agriculture (USDA), which deal with acid rain and the related effects of air pollutants on crops and livestock. The projects were identified in March 1986, and include research active as of October 1982. The CRIS database contains projects conducted or sponsored by the USDA, State agricultural experiment stations and land-grant institutions, State forestry schools and other cooperating State institutions. CRIS is operated by the Cooperative State Research Service, USDA. Project abstracts appear in the main entry section, which is organized into chapters based upon plant, animal and natural resource categories used for classifying projects in the CRIS database. Projects assigned more than one category are repeated in each of the applicable chapters. Additional points of access are provided by a keyword/title index, investigator index, and performing institution index.

  10. In search of yoga: Research trends in a western medical database.

    PubMed

    McCall, Marcy C

    2014-01-01

    The promotion of yoga practice as a preventative and treatment therapy for health outcomes in the western hemisphere is increasing rapidly. As the commercial success of yoga burgeons in popular culture, it is important to investigate the trends of yoga as a therapeutic intervention in academic literature. The free-access search engine, PubMed is a preeminent resource to identify health-related research articles published for academics, health practitioners and others. To report the recent yoga-related publications in the western healthcare context with particular interest in the subject and type of yoga titles. A bibliometric analysis to describe the annual trends in publication on PubMed from January 1950 to December 2012. The number of yoga-related titles included in the PubMed database is limited until a marked increase 2000 and steady surge since 2007. Bibliometric analysis indicates that more than 200 new titles are added per annum since 2011. Systematic reviews and yoga trials are increasing exponentially, indicating a potential increase in the quality of evidence. Titles including pain management, stress or anxiety, depression and cancer conditions are highly correlated with yoga and healthcare research. The prevalence of yoga research in western healthcare is increasing. The marked increase in volume indicates the need for more systematic analysis of the literature in terms of quality and results.

  11. Oncoshare: Lessons Learned from Building an Integrated Multi-institutional Database for Comparative Effectiveness Research

    PubMed Central

    Weber, Susan C; Seto, Tina; Olson, Cliff; Kenkare, Pragati; Kurian, Allison W.; Das, Amar K.

    2012-01-01

    Comparative effectiveness research (CER) using observational data requires informatics methods for the extraction, standardization, sharing, and integration of data derived from a variety of electronic sources. In the Oncoshare project, we have developed such methods as part of a collaborative multi-institutional CER study of patterns, predictors, and outcome of breast cancer care. In this paper, we present an evaluation of the approaches we undertook and the lessons we learned in building and validating the Oncoshare data resource. Specifically, we determined that 1) the state or regional cancer registry makes the most efficient starting point for determining inclusion of subjects; 2) the data dictionary should be based on existing registry standards, such as Surveillance, Epidemiology and End Results (SEER), when applicable; 3) the Social Security Administration Death Master File (SSA DMF), rather than clinical resources, provides standardized ascertainment of mortality outcomes; and 4) CER database development efforts, despite the immediate availability of electronic data, may take as long as two years to produce validated, reliable data for research. Through our efforts using these methods, Oncoshare integrates complex, longitudinal data from multiple electronic medical records and registries and provides a rich, validated resource for research on oncology care. PMID:23304372

  12. Acid mine drainage. (Latest citations from the Selected Water Resources Abstracts database). Published Search

    SciTech Connect

    Not Available

    1993-11-01

    The bibliography contains citations concerning the control and treatment of acid mine drainage. Techniques discussed for treating wastes containing heavy metals include precipitation, cementation, ion exchange, charge membrane, ultrafiltration, ozonation, solvent extraction, and electrodialysis. The environmental impacts of acid mine drainage on rivers, streams, and lakes are also discussed. (Contains 250 citations and includes a subject term index and title list.)

  13. Acid mine drainage. (Latest citations from the Selected Water Resources Abstracts database). Published Search

    SciTech Connect

    Not Available

    1993-09-01

    The bibliography contains citations concerning the control and treatment of acid mine drainage. Techniques discussed for treating wastes containing heavy metals include precipitation, cementation, ion exchange, charge membrane, ultrafiltration, ozonation, solvent extraction, and electrodialysis. The environmental impacts of acid mine drainage on rivers, streams, and lakes are also discussed. (Contains 250 citations and includes a subject term index and title list.)

  14. Cancer studies based on secondary data analysis of the Taiwan's National Health Insurance Research Database

    PubMed Central

    Chiang, Jui-Kun; Lin, Chih-Wen; Wang, Chun-Lung; Koo, Malcolm; Kao, Yee-Hsin

    2017-01-01

    Abstract There has been a surge in the academic publication output based on secondary analyses of the data from the Taiwan's National Health Insurance claim records. It has become a challenge to comprehend such a rapid expansion of the literature. Therefore, this study aimed to explore the conceptual content of National Health Insurance Research Database-based cancer research, using the abstract of articles extracted from PubMed between 2002 and 2015. Search terms including “National Health Insurance Research Database (NHIRD) AND Taiwan,” “Taiwan AND population-based,” and “Taiwan AND nationwide” were used to search in PubMed with the publication date limited to between 1997 and 2015. The retrieved articles were manually screened to retain only those that were cancer-related and were based on secondary data analysis of the NHIRD. A total 589 articles were selected for subsequent text mining using the R software. Among the 589 articles, the top 5 most studied cancer types were breast (16.3%), lung (11.4%), colorectal (10.4%), liver (8.3%), and prostate (7.5%). The articles that received the highest number of citations by PubMed Central articles were cited 92 times. The top 3 most frequently occurred keywords in the abstracts of the 589 articles were cancer, patient, and risk, with 3670, 2535, and 1652 times, respectively. Analysis of key conception indicated that the most common conceptions were diabetes, survival, breast cancer, lung cancer, and colorectal cancer. In conclusion, in this study of 589 published articles on secondary data analysis of the NHIRD, indexed by PubMed between 2002 and 2015, we found that while the risk factors of cancer, treatment of cancer, and survival of cancer patients were popular research topics, end-of-life cancer care issues were less studied. Further studies should explore these areas since they are as important as treatment of the disease itself for many patients. PMID:28445277

  15. U.S. Department of Energy Human Subjects Research Database (HSRD) A model for internal oversight and external transparency

    SciTech Connect

    Oak Ridge Institute for Science and Education

    2012-12-12

    This poster introduces the Department of Energy (DOE) Human Subjects Research Database (HSRD), which contains information on all Department of Energy research projects involving human subjects that: are funded by DOE; are conducted in DOE facilities; are performed by DOE personnel; include current or former DOE or contract personnel.

  16. Image Databases.

    ERIC Educational Resources Information Center

    Pettersson, Rune

    Different kinds of pictorial databases are described with respect to aims, user groups, search possibilities, storage, and distribution. Some specific examples are given for databases used for the following purposes: (1) labor markets for artists; (2) document management; (3) telling a story; (4) preservation (archives and museums); (5) research;…

  17. Integrating databases for research on health and performance in small animals and horses in the Nordic countries.

    PubMed

    Egenvall, Agneta; Nødtvedt, Ane; Roepstorff, Lars; Bonnett, Brenda

    2011-01-01

    In a world of limited resources, using existing databases in research is a potentially cost-effective way to increase knowledge, given that correct and meaningful results are gained.Nordic examples of the use of secondary small animal and equine databases include studies based on data from tumour registries, breeding registries, young horse quality contest results, competition data, insurance databases, clinic data, prescription data and hunting ability tests. In spite of this extensive use of secondary databases, integration between databases is less common. The aim of this presentation is to briefly review key papers that exemplify different ways of utilizing data from multiple sources, to highlight the benefits and limitations of the approaches, to discuss key issues/challenges that must be addressed when integrating data and to suggest future directions. Data from pedigree databases have been individually merged with competition data and young horse quality contest data, and true integration has also been done with canine insurance data and with equine clinical data. Data have also been merged on postal code level; i.e. insurance data were merged to a digitized map of Sweden and additional meteorological information added. In addition to all the data quality and validity issues inherent in the use of a single database, additional obstacles arise when combining information from several databases. Loss of individuals due to incorrect or mismatched identifying information can be considerable. If there are any possible biases affecting whether or not individuals can be properly linked, misinformation may result in a further reduction in power. Issues of confidentiality may be more difficult to address across multiple databases. For example, human identity information must be protected, but may be required to ensure valid merging of data. There is a great potential to better address complex issues of health and disease in companion animals and horses by integrating

  18. Strategies for identifying pregnancies in the automated medical records of the General Practice Research Database.

    PubMed

    Hardy, Janet R; Holford, Theodore R; Hall, Gillian C; Bracken, Michael B

    2004-11-01

    To develop a method for identifying the beginning and ending records of pregnancies in the automated medical records of the General Practice Research Database (GPRD). Women's records from 1991 to 1999 were searched for codes from 17 pregnancy marker and 7 pregnancy outcome categories. Using the retrieved records, all possible pregnancy marker-outcome combinations were formed per woman. For each combination, the difference in days between record event dates was calculated. Restrictions were applied to select the combination with the earliest pregnancy marker mapped to the first outcome for each pregnancy. Iterations of the algorithm identified multiple pregnancies per woman when present. The algorithm was evaluated by analyzing time between marker and outcome event dates of mapped pregnancies and by analyzing unmapped pregnancy markers and outcomes. A total of 297,082 pregnancies were identified: 80% by general practitioner (GP) visit codes as the earliest pregnancy marker and 14% by laboratory or procedure codes. Limiting pregnancies to one per woman aged 15-44 years yielded 209,266 pregnancies. Pregnancy mapping success was greater than 80%. Plotting the pregnancies by weeks from earliest pregnancy marker to outcome and by pregnancy marker category showed two peaks in the distribution: 2-3 weeks and 33 weeks. Arranging codes and time into algorithms provides a useful tool for pregnancy identification in databases whose size prohibits the audit of printed records. Evaluation of our algorithm confirmed a high degree of mapping success and a sensible time distribution from pregnancy marker to outcome. Copyright 2004 John Wiley & Sons, Ltd.

  19. Linkage of mother-baby pairs in the German Pharmacoepidemiological Research Database.

    PubMed

    Garbe, Edeltraut; Suling, Marc; Kloss, Sebastian; Lindemann, Christina; Schmid, Ulrike

    2011-03-01

    Administrative healthcare databases are increasingly being used to investigate potential drug risks in pregnancy. Our study aimed to develop an algorithm for linkage of mother-baby pairs (MBPs) in the German Pharmacoepidemiological Research Database (GePaRD) as a prerequisite for such studies. GePaRD contains sociodemographic data, drug dispensations, ambulatory, and hospital information on more than 14 million insurants from four German statutory health insurances (SHIs) covering all regions in Germany. Linkage was based on co-insurance information of the newborn with the potential mother (direct linkage) or of both potential mother and newborn with the potential father (indirect linkage). Linkage is not possible if the baby is co-insured with the father and the mother is self-insured. Further information on birth or childbed was used to validate the potential mother as true mother in MBP. Descriptive comparisons between linked and unlinked mothers were conducted. Of 323,993 newborns identified between 2004 and 2006, 250,355 (77.3%) could be linked in MBP. Of those, 189,702 (75.8%) MBP were based on direct linkage. Mean age was similar in linked (31.1 years, standard deviation (SD = 5.4) and unlinked (31.8 years, SD = 5.5) mothers as was the proportion of caesarean sections in both groups (28.9% vs. 29.3%). The developed algorithm permits linkage of a great number of newborns with their mothers and creates a potential data source for investigation of drug risks in pregnancy. Further validation studies are needed also including information on pregnancies not resulting in live births. Copyright © 2010 John Wiley & Sons, Ltd.

  20. NOAA's Integrated Tsunami Database: Data for improved forecasts, warnings, research, and risk assessments

    NASA Astrophysics Data System (ADS)

    Stroker, Kelly; Dunbar, Paula; Mungov, George; Sweeney, Aaron; McCullough, Heather; Carignan, Kelly

    2015-04-01

    The National Oceanic and Atmospheric Administration (NOAA) has primary responsibility in the United States for tsunami forecast, warning, research, and supports community resiliency. NOAA's National Geophysical Data Center (NGDC) and co-located World Data Service for Geophysics provide a unique collection of data enabling communities to ensure preparedness and resilience to tsunami hazards. Immediately following a damaging or fatal tsunami event there is a need for authoritative data and information. The NGDC Global Historical Tsunami Database (http://www.ngdc.noaa.gov/hazard/) includes all tsunami events, regardless of intensity, as well as earthquakes and volcanic eruptions that caused fatalities, moderate damage, or generated a tsunami. The long-term data from these events, including photographs of damage, provide clues to what might happen in the future. NGDC catalogs the information on global historical tsunamis and uses these data to produce qualitative tsunami hazard assessments at regional levels. In addition to the socioeconomic effects of a tsunami, NGDC also obtains water level data from the coasts and the deep-ocean at stations operated by the NOAA/NOS Center for Operational Oceanographic Products and Services, the NOAA Tsunami Warning Centers, and the National Data Buoy Center (NDBC) and produces research-quality data to isolate seismic waves (in the case of the deep-ocean sites) and the tsunami signal. These water-level data provide evidence of sea-level fluctuation and possible inundation events. NGDC is also building high-resolution digital elevation models (DEMs) to support real-time forecasts, implemented at 75 US coastal communities. After a damaging or fatal event NGDC begins to collect and integrate data and information from many organizations into the hazards databases. Sources of data include our NOAA partners, the U.S. Geological Survey, the UNESCO Intergovernmental Oceanographic Commission (IOC) and International Tsunami Information Center

  1. The Virtual Skeleton Database: An Open Access Repository for Biomedical Research and Collaboration

    PubMed Central

    Bonaretti, Serena; Pfahrer, Marcel; Niklaus, Roman; Büchler, Philippe

    2013-01-01

    Background Statistical shape models are widely used in biomedical research. They are routinely implemented for automatic image segmentation or object identification in medical images. In these fields, however, the acquisition of the large training datasets, required to develop these models, is usually a time-consuming process. Even after this effort, the collections of datasets are often lost or mishandled resulting in replication of work. Objective To solve these problems, the Virtual Skeleton Database (VSD) is proposed as a centralized storage system where the data necessary to build statistical shape models can be stored and shared. Methods The VSD provides an online repository system tailored to the needs of the medical research community. The processing of the most common image file types, a statistical shape model framework, and an ontology-based search provide the generic tools to store, exchange, and retrieve digital medical datasets. The hosted data are accessible to the community, and collaborative research catalyzes their productivity. Results To illustrate the need for an online repository for medical research, three exemplary projects of the VSD are presented: (1) an international collaboration to achieve improvement in cochlear surgery and implant optimization, (2) a population-based analysis of femoral fracture risk between genders, and (3) an online application developed for the evaluation and comparison of the segmentation of brain tumors. Conclusions The VSD is a novel system for scientific collaboration for the medical image community with a data-centric concept and semantically driven search option for anatomical structures. The repository has been proven to be a useful tool for collaborative model building, as a resource for biomechanical population studies, or to enhance segmentation algorithms. PMID:24220210

  2. A synopsis of original research projects published in scientific database in the Russian Federation.

    PubMed

    Smirnova, Daria; Pavlichenko, Alexey; Karpenko, Olga; Schmeleva, Liubov; Morozov, Petr

    2015-06-01

    The article describes the current state of scientific publications in the field of psychiatry in the Russian Federation. Issues of academic dissertations, lack of access to recent Russian language research in foreign databases, and recent reforms in the Ministry of Education and Science for overcoming these limitations are discussed in detail. Four exemplary dissertation studies published in Russian language are summarized. The first research examines the contribution of patient's verbal behavior to the reliable diagnosis of mild depression, identifying objective signs for distinguishing it from normal sadness; the mood component influenced the whole mental status and was represented in both structure and semantics of patients' speech. The second paper describes the course of panic disorder with agoraphobia, with the notable results that debut of panic disorder with full-blown panic attacks, often declines to a second accompanied with agoraphobia, which after several years gives way to limited symptom attacks and decreased agoraphobic avoidance. The third study describes the high prevalence of affective and anxiety disorders in patients with diabetes mellitus type 1 and 2, and the role of personality traits in adherence to treatment in patients with poor glucose control. The fourth project uses functional MRI for probing the features of neuronal resting-state networks in patients with temporal lobe epilepsy; the association with affective symptoms provides a model for investigating the pathophysiology of mood disorder. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Visibility of healthcare research institutes through the Web of Science database.

    PubMed

    González-Albo, B; Moreno-Solano, L; Aparicio, J; Bordons, M

    2017-06-15

    The strategic importance of healthcare research institutes (HRIs) in health sciences research in Spain has motivated this analysis of the feasibility of studing their contribution to the Spanish scientific output through their presence as a signatory institution in the publications. We identified the output of the HRIs in the Web of Science database, comparing their observed output (the institutes are explicitly listed in the authors' workplace) and potential output (estimated based on the linked hospitals). The studies based on scientific publications do not help us reliably identify the contribution of the HRIs because their observed production is much lower than the potential output, although their visibility tends to increase over time. This article highlights the importance of HRI members including the institute among their work addresses to increase the visibility of these organisations and to facilitate studies aimed at assessing their activity in the national and international context. Copyright © 2017 Elsevier España, S.L.U. and Sociedad Española de Medicina Interna (SEMI). All rights reserved.

  4. The Developmental Brain Disorders Database (DBDB): a curated neurogenetics knowledge base with clinical and research applications.

    PubMed

    Mirzaa, Ghayda M; Millen, Kathleen J; Barkovich, A James; Dobyns, William B; Paciorkowski, Alex R

    2014-06-01

    The number of single genes associated with neurodevelopmental disorders has increased dramatically over the past decade. The identification of causative genes for these disorders is important to clinical outcome as it allows for accurate assessment of prognosis, genetic counseling, delineation of natural history, inclusion in clinical trials, and in some cases determines therapy. Clinicians face the challenge of correctly identifying neurodevelopmental phenotypes, recognizing syndromes, and prioritizing the best candidate genes for testing. However, there is no central repository of definitions for many phenotypes, leading to errors of diagnosis. Additionally, there is no system of levels of evidence linking genes to phenotypes, making it difficult for clinicians to know which genes are most strongly associated with a given condition. We have developed the Developmental Brain Disorders Database (DBDB: https://www.dbdb.urmc.rochester.edu/home), a publicly available, online-curated repository of genes, phenotypes, and syndromes associated with neurodevelopmental disorders. DBDB contains the first referenced ontology of developmental brain phenotypes, and uses a novel system of levels of evidence for gene-phenotype associations. It is intended to assist clinicians in arriving at the correct diagnosis, select the most appropriate genetic test for that phenotype, and improve the care of patients with developmental brain disorders. For researchers interested in the discovery of novel genes for developmental brain disorders, DBDB provides a well-curated source of important genes against which research sequencing results can be compared. Finally, DBDB allows novel observations about the landscape of the neurogenetics knowledge base. © 2014 Wiley Periodicals, Inc.

  5. Database and Registry Research in Orthopaedic Surgery: Part 2: Clinical Registry Data.

    PubMed

    Pugely, Andrew J; Martin, Christopher T; Harwood, Jared; Ong, Kevin L; Bozic, Kevin J; Callaghan, John J

    2015-11-04

    The use of large-scale national databases for observational research in orthopaedic surgery has grown substantially in the last decade, and the data sets can be categorized as either administrative claims or clinical registries. Clinical registries contain secondary data on patients with a specific diagnosis or procedure. The data are typically used for patient outcome surveillance to improve patient safety and health-care quality. Registries used in orthopaedic research exist at the regional, national, and international levels, and many were designed to specifically collect outcomes relevant to orthopaedics, such as short-term surgical complications, longer-term outcomes (implant survival or reoperations), and patient-reported outcomes. Although heterogeneous, clinical registries-in contrast to claims data-typically have a more robust list of variables, with relatively precise prospective data input, management infrastructure, and reporting systems. Some weaknesses of clinical registries include a smaller number of patients, inconstant follow-up duration, and use of sampling methods that may limit generalizability. Within the U.S., national joint registry adoption has lagged international joint registries. Given the changing health-care environment, it is likely that clinical registries will provide valuable information that has the potential to influence clinical practice improvement and health-care policy in the future.

  6. The Plant Organelles Database 3 (PODB3) update 2014: integrating electron micrographs and new options for plant organelle research.

    PubMed

    Mano, Shoji; Nakamura, Takanori; Kondo, Maki; Miwa, Tomoki; Nishikawa, Shuh-ichi; Mimura, Tetsuro; Nagatani, Akira; Nishimura, Mikio

    2014-01-01

    The Plant Organelles Database 2 (PODB2), which was first launched in 2006 as PODB, provides static image and movie data of plant organelles, protocols for plant organelle research and external links to relevant websites. PODB2 has facilitated plant organellar research and the understanding of plant organelle dynamics. To provide comprehensive information on plant organelles in more detail, PODB2 was updated to PODB3 (http://podb.nibb.ac.jp/Organellome/). PODB3 contains two additional components: the electron micrograph database and the perceptive organelles database. Through the electron micrograph database, users can examine the subcellular and/or suborganellar structures in various organs of wild-type and mutant plants. The perceptive organelles database provides information on organelle dynamics in response to external stimuli. In addition to the extra components, the user interface for access has been enhanced in PODB3. The data in PODB3 are directly submitted by plant researchers and can be freely downloaded for use in further analysis. PODB3 contains all the information included in PODB2, and the volume of data and protocols deposited in PODB3 continue to grow steadily. We welcome contributions of data from all plant researchers to enhance the utility and comprehensiveness of PODB3.

  7. Governance and oversight of researcher access to electronic health data: the role of the Independent Scientific Advisory Committee for MHRA database research, 2006-2015.

    PubMed

    Waller, P; Cassell, J A; Saunders, M H; Stevens, R

    2017-03-01

    In order to promote understanding of UK governance and assurance relating to electronic health records research, we present and discuss the role of the Independent Scientific Advisory Committee (ISAC) for MHRA database research in evaluating protocols proposing the use of the Clinical Practice Research Datalink. We describe the development of the Committee's activities between 2006 and 2015, alongside growth in data linkage and wider national electronic health records programmes, including the application and assessment processes, and our approach to undertaking this work. Our model can provide independence, challenge and support to data providers such as the Clinical Practice Research Datalink database which has been used for well over 1,000 medical research projects. ISAC's role in scientific oversight ensures feasible and scientifically acceptable plans are in place, while having both lay and professional membership addresses governance issues in order to protect the integrity of the database and ensure that public confidence is maintained.

  8. SyStemCell: A Database Populated with Multiple Levels of Experimental Data from Stem Cell Differentiation Research

    PubMed Central

    Zeng, Lingyao; Sun, Jiehuan; Li, Wei; Sun, Han; He, Ying; Li, Jing; Zhang, Guoqing; Wang, Chuan; Li, Yixue; Xie, Lu

    2012-01-01

    Elucidation of the mechanisms of stem cell differentiation is of great scientific interest. Increasing evidence suggests that stem cell differentiation involves changes at multiple levels of biological regulation, which together orchestrate the complex differentiation process; many related studies have been performed to investigate the various levels of regulation. The resulting valuable data, however, remain scattered. Most of the current stem cell-relevant databases focus on a single level of regulation (mRNA expression) from limited stem cell types; thus, a unifying resource would be of great value to compile the multiple levels of research data available. Here we present a database for this purpose, SyStemCell, deposited with multi-level experimental data from stem cell research. The database currently covers seven levels of stem cell differentiation-associated regulatory mechanisms, including DNA CpG 5-hydroxymethylcytosine/methylation, histone modification, transcript products, microRNA-based regulation, protein products, phosphorylation proteins and transcription factor regulation, all of which have been curated from 285 peer-reviewed publications selected from PubMed. The database contains 43,434 genes, recorded as 942,221 gene entries, for four organisms (Homo sapiens, Mus musculus, Rattus norvegicus, and Macaca mulatta) and various stem cell sources (e.g., embryonic stem cells, neural stem cells and induced pluripotent stem cells). Data in SyStemCell can be queried by Entrez gene ID, symbol, alias, or browsed by specific stem cell type at each level of genetic regulation. An online analysis tool is integrated to assist researchers to mine potential relationships among different regulations, and the potential usage of the database is demonstrated by three case studies. SyStemCell is the first database to bridge multi-level experimental information of stem cell studies, which can become an important reference resource for stem cell researchers. The database

  9. The research of network database security technology based on web service

    NASA Astrophysics Data System (ADS)

    Meng, Fanxing; Wen, Xiumei; Gao, Liting; Pang, Hui; Wang, Qinglin

    2013-03-01

    Database technology is one of the most widely applied computer technologies, its security is becoming more and more important. This paper introduced the database security, network database security level, studies the security technology of the network database, analyzes emphatically sub-key encryption algorithm, applies this algorithm into the campus-one-card system successfully. The realization process of the encryption algorithm is discussed, this method is widely used as reference in many fields, particularly in management information system security and e-commerce.

  10. The Digital Astronaut: An integrated modeling and database system for space biomedical research and operations

    NASA Astrophysics Data System (ADS)

    White, Ronald J.; McPhee, Jancy C.

    2007-02-01

    The Digital Astronaut is an integrated, modular modeling and database system that will support space biomedical research and operations in a variety of fundamental ways. This system will enable the identification and meaningful interpretation of the medical and physiological research required for human space exploration, a determination of the effectiveness of specific individual human countermeasures in reducing risk and meeting health and performance goals on challenging exploration missions and an evaluation of the appropriateness of various medical interventions during mission emergencies, accidents and illnesses. Such a computer-based, decision support system will enable the construction, validation and utilization of important predictive simulations of the responses of the whole human body to the types of stresses experienced during space flight and low-gravity environments. These simulations will be essential for direct, real-time analysis and maintenance of astronaut health and performance capabilities. The Digital Astronaut will collect and integrate past and current human data across many physiological disciplines and simulations into an operationally useful form that will not only summarize knowledge in a convenient and novel way but also reveal gaps that must be filled via new research in order to effectively ameliorate biomedical risks. Initial phases of system development will focus on simulating ground-based analog systems that are just beginning to collect multidisciplinary data in a standardized way (e.g., the International Multidisciplinary Artificial Gravity Project). During later phases, the focus will shift to development and planning for missions and to exploration mission operations. Then, the Digital Astronaut system will enable evaluation of the effectiveness of multiple, simultaneously applied countermeasures (a task made difficult by the many-system physiological effects of individual countermeasures) and allow for the prescription of

  11. Modeling plant-level industrial energy demand with the Manufacturing Energy Consumption Survey (MECS) database and the Longitudinal Research Database (LRD)

    SciTech Connect

    Boyd, G.A.; Neifer, M.J.; Ross, M.H.

    1992-08-01

    This report discusses Phase 1 of a project to help the US Department of Energy determine the applicability of the Manufacturing Energy Consumption Survey (MECS) database and the Longitudinal Research Database (LRD) for industrial modeling and analysis. Research was conducted at the US Bureau of the Census; disclosure of the MECS/LRD data used as a basis for this report was subject to the Bureau`s confidentiality restriction. The project is designed to examine the plant-level energy behavior of energy-intensive industries. In Phase 1, six industries at the four-digit standard industrial classification (SIC) level were studied. The utility of analyzing four-digit SIC samples at the plant level is mixed, but the plant-level structure of the MECS/LRD makes analyzing samples disaggregated below the four-digit level feasible, particularly when the MECS/LRD data are combined with trade association or other external data. When external data are used, the validity of using value of shipments as a measure of output for analyzing energy use can also be examined. Phase 1 results indicate that technical efficiency and the distribution of energy intensities vary significantly at the plant level. They also show that the six industries exhibit monopsony-like behavior; that is, energy prices vary significantly at the plant level, with lower prices being correlated with a higher level of energy consumption. Finally, they show to what degree selected energy-intensive products are manufactured outside their primary industry.

  12. Outcomes research in psoriasis and psoriatic arthritis using large databases and research networks: a report from the GRAPPA 2013 Annual Meeting.

    PubMed

    Armstrong, April W; Gelfand, Joel M; Garg, Amit

    2014-06-01

    Advances in healthcare informatics have increased the ability to address real-world, clinically relevant questions using large databases. When examining data sources, researchers and clinicians need to consider data validity, potential sources of misclassification, whether the source is sufficiently powered to detect clinically relevant differences, ability to obtain longitudinal data, containment of patients within a database, and ability to obtain structured point-of-care data. Population-based databases create opportunities for characterizing natural history of psoriatic diseases, conducting comparative effectiveness research, determining comorbidities, and providing epidemiology-based rational approaches to mechanistic investigations. Herein, we discuss the major data sources for clinical research in psoriasis, including electronic medical records, research networks, disease registries, and others.

  13. The Research Potential of the Electronic OED Database at the University of Waterloo: A Case Study.

    ERIC Educational Resources Information Center

    Berg, Donna Lee

    1991-01-01

    Discusses the history and structure of the online database of the second edition of the Oxford English Dictionary (OED) and the software tools developed at the University of Waterloo to manipulate the unusually complex database. Four sample searches that indicate some types of problems that might be encountered are appended. (DB)

  14. Patterns of Undergraduates' Use of Scholarly Databases in a Large Research University

    ERIC Educational Resources Information Center

    Mbabu, Loyd Gitari; Bertram, Albert; Varnum, Ken

    2013-01-01

    Authentication data was utilized to explore undergraduate usage of subscription electronic databases. These usage patterns were linked to the information literacy curriculum of the library. The data showed that out of the 26,208 enrolled undergraduate students, 42% of them accessed a scholarly database at least once in the course of the entire…

  15. The Research Potential of the Electronic OED Database at the University of Waterloo: A Case Study.

    ERIC Educational Resources Information Center

    Berg, Donna Lee

    1991-01-01

    Discusses the history and structure of the online database of the second edition of the Oxford English Dictionary (OED) and the software tools developed at the University of Waterloo to manipulate the unusually complex database. Four sample searches that indicate some types of problems that might be encountered are appended. (DB)

  16. CottonGen: a genomics, genetics and breeding database for cotton research

    USDA-ARS?s Scientific Manuscript database

    CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, vis...

  17. Patterns of Undergraduates' Use of Scholarly Databases in a Large Research University

    ERIC Educational Resources Information Center

    Mbabu, Loyd Gitari; Bertram, Albert; Varnum, Ken

    2013-01-01

    Authentication data was utilized to explore undergraduate usage of subscription electronic databases. These usage patterns were linked to the information literacy curriculum of the library. The data showed that out of the 26,208 enrolled undergraduate students, 42% of them accessed a scholarly database at least once in the course of the entire…

  18. Development and Feasibility Testing of a Critical Care EEG Monitoring Database for Standardized Clinical Reporting and Multicenter Collaborative Research.

    PubMed

    Lee, Jong Woo; LaRoche, Suzette; Choi, Hyunmi; Rodriguez Ruiz, Andres A; Fertig, Evan; Politsky, Jeffrey M; Herman, Susan T; Loddenkemper, Tobias; Sansevere, Arnold J; Korb, Pearce J; Abend, Nicholas S; Goldstein, Joshua L; Sinha, Saurabh R; Dombrowski, Keith E; Ritzl, Eva K; Westover, Michael B; Gavvala, Jay R; Gerard, Elizabeth E; Schmitt, Sarah E; Szaflarski, Jerzy P; Ding, Kan; Haas, Kevin F; Buchsbaum, Richard; Hirsch, Lawrence J; Wusthoff, Courtney J; Hopp, Jennifer L; Hahn, Cecil D

    2016-04-01

    The rapid expansion of the use of continuous critical care electroencephalogram (cEEG) monitoring and resulting multicenter research studies through the Critical Care EEG Monitoring Research Consortium has created the need for a collaborative data sharing mechanism and repository. The authors describe the development of a research database incorporating the American Clinical Neurophysiology Society standardized terminology for critical care EEG monitoring. The database includes flexible report generation tools that allow for daily clinical use. Key clinical and research variables were incorporated into a Microsoft Access database. To assess its utility for multicenter research data collection, the authors performed a 21-center feasibility study in which each center entered data from 12 consecutive intensive care unit monitoring patients. To assess its utility as a clinical report generating tool, three large volume centers used it to generate daily clinical critical care EEG reports. A total of 280 subjects were enrolled in the multicenter feasibility study. The duration of recording (median, 25.5 hours) varied significantly between the centers. The incidence of seizure (17.6%), periodic/rhythmic discharges (35.7%), and interictal epileptiform discharges (11.8%) was similar to previous studies. The database was used as a clinical reporting tool by 3 centers that entered a total of 3,144 unique patients covering 6,665 recording days. The Critical Care EEG Monitoring Research Consortium database has been successfully developed and implemented with a dual role as a collaborative research platform and a clinical reporting tool. It is now available for public download to be used as a clinical data repository and report generating tool.

  19. Nailfold capillaroscopy in systemic sclerosis: data from the EULAR scleroderma trials and research (EUSTAR) database.

    PubMed

    Ingegnoli, Francesca; Ardoino, Ilaria; Boracchi, Patrizia; Cutolo, Maurizio

    2013-09-01

    The aims of this study were to obtain cross-sectional data on capillaroscopy in an international multi-center cohort of Systemic Sclerosis (SSc) and to investigate the frequency of the capillaroscopic patterns and their disease-phenotype associations. Data collected between June 2004 and October 2011 in the EULAR Scleroderma Trials and Research (EUSTAR) registry were examined. Patients' profiles based on clinical and laboratory data were obtained by cluster analysis and the association between profiles and capillaroscopy was investigated by multinomial logistic regression. 62 of the 110 EUSTAR centers entered data on capillaroscopy in the EUSTAR database. 376 of the 2754 patients (13.65%) were classified as scleroderma pattern absent, but non-specific capillary abnormalities were noted in 55.48% of the cases. Four major patients' profiles were identified characterized by a progressive severity for skin involvement, as well as an increased number of systemic manifestations. The "early" and "active" scleroderma patterns were generally observed in patients with mild/moderate skin involvement and a low number of disease manifestations, while the "late" scleroderma pattern was found more frequently in the more severe forms of the disease. These data indicate the importance of capillaroscopy in SSc management and that capillaroscopic patterns are directly related to the extent of organ involvement. Copyright © 2013 Elsevier Inc. All rights reserved.

  20. Unraveling the Web of Viroinformatics: Computational Tools and Databases in Virus Research

    PubMed Central

    Priyadarshini, Pragya; Vrati, Sudhanshu

    2014-01-01

    The beginning of the second century of research in the field of virology (the first virus was discovered in 1898) was marked by its amalgamation with bioinformatics, resulting in the birth of a new domain—viroinformatics. The availability of more than 100 Web servers and databases embracing all or specific viruses (for example, dengue virus, influenza virus, hepatitis virus, human immunodeficiency virus [HIV], hemorrhagic fever virus [HFV], human papillomavirus [HPV], West Nile virus, etc.) as well as distinct applications (comparative/diversity analysis, viral recombination, small interfering RNA [siRNA]/short hairpin RNA [shRNA]/microRNA [miRNA] studies, RNA folding, protein-protein interaction, structural analysis, and phylotyping and genotyping) will definitely aid the development of effective drugs and vaccines. However, information about their access and utility is not available at any single source or on any single platform. Therefore, a compendium of various computational tools and resources dedicated specifically to virology is presented in this article. PMID:25428870

  1. Juvenile Huntington's disease: a population-based study using the General Practice Research Database

    PubMed Central

    Douglas, Ian; Evans, Stephen; Rawlins, Michael D; Smeeth, Liam; Tabrizi, Sarah J; Wexler, Nancy S

    2013-01-01

    Background The juvenile form of Huntington's disease (HD) is a rare disorder. There are no population-based estimates of either its incidence or prevalence in any population in the world. The present study was undertaken to estimate the frequency of juvenile HD in the UK and to examine the range of pharmacological treatments used in its management. Method The records of individuals under the age of 21 who had recorded diagnoses of HD were retrieved from the General Practice Research Database from 1990 through 2010. From these data estimates of incidence and prevalence were made as well as the specific treatments used in the treatment of its physical and psychological manifestations. Results 12 incident and 21 prevalent patients with juvenile HD were identified. The 21 prevalent cases included the 12 incident cases. The minimum population-based estimate of incidence is 0.70 (95% CI 0.36 to 1.22) per million patient-years. The minimum estimate of prevalence is 6.77/million (95% CI 5.60 to 8.12) per million patient-years. Patients were most frequently prescribed antidepressants, hypnotics, antipsychotics and treatments for motor abnormalities. Conclusions In the UK, juvenile HD is an extremely rare and complex disorder. The prescribing data demonstrate that the clinical management of juvenile HD is undertaken with no formal evidence base for the efficacy or safety of the treatments used. Research into the safety and efficacy of appropriate therapies is urgently required to offset the haphazard nature of prescribing. Multinational collaboration will be necessary to enrol sufficient numbers. Exploratory studies, though, should begin now. PMID:23558730

  2. Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications

    PubMed Central

    Hegedűs, Tamás; Chaubey, Pururawa Mayank; Várady, György; Szabó, Edit; Sarankó, Hajnalka; Hofstetter, Lia; Roschitzki, Bernd; Sarkadi, Balázs

    2015-01-01

    Based on recent results, the determination of the easily accessible red blood cell (RBC) membrane proteins may provide new diagnostic possibilities for assessing mutations, polymorphisms or regulatory alterations in diseases. However, the analysis of the current mass spectrometry-based proteomics datasets and other major databases indicates inconsistencies—the results show large scattering and only a limited overlap for the identified RBC membrane proteins. Here, we applied membrane-specific proteomics studies in human RBC, compared these results with the data in the literature, and generated a comprehensive and expandable database using all available data sources. The integrated web database now refers to proteomic, genetic and medical databases as well, and contains an unexpected large number of validated membrane proteins previously thought to be specific for other tissues and/or related to major human diseases. Since the determination of protein expression in RBC provides a method to indicate pathological alterations, our database should facilitate the development of RBC membrane biomarker platforms and provide a unique resource to aid related further research and diagnostics. Database URL: http://rbcc.hegelab.org PMID:26078478

  3. Integrating the intrinsic conformational preferences of non-coded α-amino acids modified at the peptide bond into the NCAD database

    PubMed Central

    Revilla-López, Guillem; Rodríguez-Ropero, Francisco; Curcó, David; Torras, Juan; Calaza, M. Isabel; Zanuy, David; Jiménez, Ana I.; Cativiela, Carlos; Nussinov, Ruth; Alemán, Carlos

    2011-01-01

    Recently, we reported a database (NCAD, Non-Coded Amino acids Database; http://recerca.upc.edu/imem/index.htm) that was built to compile information about the intrinsic conformational preferences of non-proteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, the experimentally-established conformational propensities, and applications (J. Phys. Chem. B 2010, 114, 7413). The database initially contained the information available for α-tetrasubstituted α-amino acids. In this work, we extend NCAD to three families of compounds, which can be used to engineer peptides and proteins incorporating modifications at the –NHCO– peptide bond. Such families are: N-substituted α-amino acids, thio-α-amino acids, and diamines and diacids used to build retropeptides. The conformational preferences of these compounds have been analyzed and described based on the information captured in the database. In addition, we provide an example of the utility of the database and of the compounds it compiles in protein and peptide engineering. Specifically, the symmetry of a sequence engineered to stabilize the 310-helix with respect to the α-helix has been broken without perturbing significantly the secondary structure through targeted replacements using the information contained in the database. PMID:21491493

  4. Acid precipitation. (Latest citations from the Selected Water Resources Abstracts database). Published Search

    SciTech Connect

    Not Available

    1993-07-01

    The bibliography contains citations concerning the causes, and ecological and economic consequences of acid precipitation and deposition. Emissions of sulfur and nitrogen compounds, loading rates at specific study sites, the role of buffering materials on the acidification of lakes and streams, and the effects on aquatic life are considered. The effects on soil chemistry and vegetation are also discussed. (Contains 250 citations and includes a subject term index and title list.)

  5. The impact of standardizing the definition of visits on the consistency of multi-database observational health research.

    PubMed

    Voss, Erica A; Ma, Qianli; Ryan, Patrick B

    2015-03-08

    Use of administrative claims from multiple sources for research purposes is challenged by the lack of consistency in the structure of the underlying data and definition of data across claims data providers. This paper evaluates the impact of applying a standardized revenue code-based logic for defining inpatient encounters across two different claims databases. We selected members who had complete enrollment in 2012 from the Truven MarketScan Commercial Claims and Encounters (CCAE) and the Optum Clinformatics (Optum) databases. The overall prevalence of inpatient conditions in the raw data was compared to that in the common data model (CDM) with the standardized visit definition applied. In CCAE, 87.18% of claims from 2012 that were classified as part of inpatient visits in the raw data were also classified as part of inpatient visits after the data were standardized to CDM, and this overlap was consistent from 2006 to 2011. In contrast, Optum had 83.18% concordance in classification of 2012 claims from inpatient encounters before and after standardization, but the consistency varied over time. The re-classification of inpatient encounters substantially impacted the observed prevalence of medical conditions occurring in the inpatient setting and the consistency in prevalence estimates between the databases. On average, before standardization, each condition in Optum was 12% more prevalent than that same condition in CCAE; after standardization, the prevalence of conditions had a mean difference of only 1% between databases. Amongst 7,039 conditions reviewed, the difference in the prevalence of 67% of conditions in these two databases was reduced after standardization. In an effort to improve consistency in research results across database one should review sources of database heterogeneity, such as the way data holders process raw claims data. Our study showed that applying the Observational Medical Outcomes Partnership (OMOP) CDM with a standardized approach for

  6. Estimation of Trans Fatty Acid Intake in Japanese Adults Using 16-Day Diet Records Based on a Food Composition Database Developed for the Japanese Population

    PubMed Central

    Yamada, Mai; Sasaki, Satoshi; Murakami, Kentaro; Takahashi, Yoshiko; Okubo, Hitomi; Hirota, Naoko; Notsu, Akiko; Todoriki, Hidemi; Miura, Ayako; Fukui, Mitsuru; Date, Chigusa

    2010-01-01

    Background The Standard Tables of Food Composition in Japan do not include information on trans fatty acids. Previous studies estimating trans fatty acid intake among Japanese have limitations regarding the databases utilized and diet assessment methodologies. We developed a comprehensive database of trans fatty acid food composition, and used this database to estimate intake among a Japanese population. Methods The database was developed using analytic values from the literature and nutrient analysis software encompassing foods in the US, as well as values estimated from recipes or nutrient compositions. We collected 16-day diet records from 225 adults aged 30 to 69 years living in 4 areas of Japan. Trans fatty acid intake was estimated based on the database and the 16-day diet records. Results Mean total fat and trans fatty acid intake was 56.9 g/day (27.7% total energy) and 1.7 g/day (0.8% total energy), respectively, for women and 66.8 g/day (25.5% total energy) and 1.7 g/day (0.7% total energy) for men. Trans fatty acid intake accounted for greater than 1% of total energy intake, which is the maximum recommended according to the World Health Organization, in 24.4% of women and 5.7% of men, and was particularly high among women living in urban areas and those aged 30–49 years. The largest contributors to trans fatty acid intake were confectionaries in women and fats and oils in men. Conclusions Although mean trans fatty acid intake was below the maximum recommended intake of the World Health Organization, intake among subgroups was of concern. Further public health efforts to reduce trans fatty acid intake should be encouraged. PMID:20037259

  7. Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database.

    PubMed Central

    Billoud, B; Kontic, M; Viari, A

    1996-01-01

    At the DNA/RNA level, biological signals are defined by a combination of spatial structures and sequence motifs. Until now, few attempts had been made in writing general purpose search programs that take into account both sequence and structure criteria. Indeed, the most successful structure scanning programs are usually dedicated to particular structures and are written using general purpose programming languages through a complex and time consuming process where the biological problem of defining the structure and the computer engineering problem of looking for it are intimately intertwined. In this paper, we describe a general representation of structures, suitable for database scanning, together with a programming language, Palingol, designed to manipulate it. Palingol has specific data types, corresponding to structural elements-basically helices-that can be arranged in any way to form a complex structure. As a consequence of the declarative approach used in Palingol, the user should only focus on 'what to search for' while the language engine takes care of 'how to look for it'. Therefore, it becomes simpler to write a scanning program and the structural constraints that define the required structure are more clearly identified. PMID:8628670

  8. Development of USDA's expanded flavonoid database: A Tool for Epidemiological Research

    USDA-ARS?s Scientific Manuscript database

    The scientific community continues to be interested in potential links between flavonoid intakes and beneficial health effects associated with certain chronic diseases such as cardiovascular diseases, some cancers and type 2 diabetes. Three separate flavonoid databases (Flavonoids (5 subclasses: fl...

  9. Research and writing in the history of health sciences, 1970-1982: a quantitative analysis of NLM's HISTLINE database.

    PubMed Central

    Kopp, J J

    1985-01-01

    HISTLINE, the MEDLARS file on the history of the health sciences, was analyzed to determine predominant areas of historical research and publication in the years 1970-1982, as reflected in this database produced within the History of Medicine Division at the National Library of Medicine. Subject content, chronologic and geographic breakdowns, and subjects of biographical studies are examined in view of their frequency in the file. Speculation for the predominance of particular descriptors and individuals is presented. An examination is made of the journals publishing the most medical history. Strengths and weaknesses of the database as reflected in this study also are discussed. PMID:3888330

  10. Making sense of congenital cardiac disease with a research database: The Congenital Heart Surgeons' Society Data Center.

    PubMed

    Hickey, Edward J; McCrindle, Brian W; Caldarone, Christopher A; Williams, William G; Blackstone, Eugene H

    2008-12-01

    Challenges inherent in researching rare congenital cardiac lesions led to creation of the Congenital Heart Surgeons' Society Data Center (Data Center) two decades ago. The Data Center pools experiences from up to 60 institutions, and over 4,700 children have been prospectively recruited within nine diagnostic inception cohorts. This report describes the operations of our research database, with particular focus on analytic strategies employed. A procedural log is created of all investigations and interventions, and reports from enrolling institutions are subsequently obtained. Cross-sectional follow-up is undertaken annually by the Data Center. All data are linked to the individual child, and quality control mechanisms ensure that completeness and accuracy are maximised. Specific advantages of Data Center analytic approaches include multi-phase parametric hazard analysis, re-sampling techniques for reliable risk factor identification, competing risks methodology, and propensity-adjusted comparisons. Virtues of applying these techniques to a research database are illustrated by clinically pertinent questions that have been addressed in place of what would be difficult through randomised trials. The Data Center is a cost-effective, versatile tool for researching congenital cardiac surgical outcomes. Research databases are ideally suited to in-depth investigations of survival and functional outcomes. Multi-center propensity-adjusted analyses represent efficient surrogates for randomised trials. Well-designed observational prospective studies should remain a principle mode of researching congenital cardiac disease.

  11. Genome databases

    SciTech Connect

    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.

  12. An MRspec database query and visualization engine with applications as a clinical diagnostic and research tool.

    PubMed

    Miscevic, Filip; Foong, Justin; Schmitt, Benjamin; Blaser, Susan; Brudno, Michael; Schulze, Andreas

    2016-12-01

    Proton magnetic resonance spectroscopy (MRspec), one of the very few techniques for in vivo assessment of neuro-metabolic profiles, is often complicated by lack of standard population norms and paucity of computational tools. 7035 scans and clinical information from 4430 pediatric patients were collected from 2008 to 2014. Scans were conducted using a 1.5T (n=3664) or 3T scanner (n=3371), and with either a long (144ms, n=5559) or short echo time (35ms, n=1476). 3055 of these scans were localized in the basal ganglia (BG), 1211 in parieto-occipital white matter (WM). 34 metabolites were quantified using LCModel. A web application using MySQL, Python and Flask was developed to facilitate the exploration of the data set. Already piloting the application revealed numerous insights. (1), N-acetylaspartate (NAA) increased throughout all ages. During early infancy, total choline was highly varied and myo-inositol demonstrated a downward trend. (2), Total creatine (tCr) and creatine increased throughout childhood and adolescence, though phosphocreatine (PCr) remained constant beyond 200days. (3), tCr was higher in BG than WM. (4), No obvious gender-related differences were observed. (5), Field strength affects quantification using LCModel for some metabolites, most prominently for tCr and total NAA. (6), Outlier analysis identified patients treated with vigabatrin through elevated γ-aminobutyrate, and patients with Klippel-Feil syndrome, Leigh disease and L2-hydroxyglutaric aciduria through low choline in BG. We have established the largest MRSpec database and developed a robust and flexible computational tool for facilitating the exploration of vast metabolite datasets that proved its value for discovering neurochemical trends for clinical diagnosis, treatment monitoring, and research. Open access will lead to its widespread use, improving the diagnostic yield and contributing to better understanding of metabolic processes and conditions in the brain. Copyright © 2016

  13. Comprehensive Research Synopsis and Systematic Meta-Analyses in Parkinson's Disease Genetics: The PDGene Database

    PubMed Central

    Lill, Christina M.; Roehr, Johannes T.; McQueen, Matthew B.; Kavvoura, Fotini K.; Bagade, Sachin; Schjeide, Brit-Maren M.; Schjeide, Leif M.; Meissner, Esther; Zauft, Ute; Allen, Nicole C.; Liu, Tian; Schilling, Marcel; Anderson, Kari J.; Beecham, Gary; Berg, Daniela; Biernacka, Joanna M.; Brice, Alexis; DeStefano, Anita L.; Do, Chuong B.; Eriksson, Nicholas; Factor, Stewart A.; Farrer, Matthew J.; Foroud, Tatiana; Gasser, Thomas; Hamza, Taye; Hardy, John A.; Heutink, Peter; Hill-Burns, Erin M.; Klein, Christine; Latourelle, Jeanne C.; Maraganore, Demetrius M.; Martin, Eden R.; Martinez, Maria; Myers, Richard H.; Nalls, Michael A.; Pankratz, Nathan; Payami, Haydeh; Satake, Wataru; Scott, William K.; Sharma, Manu; Singleton, Andrew B.; Stefansson, Kari; Toda, Tatsushi; Tung, Joyce Y.; Vance, Jeffery; Wood, Nick W.; Zabetian, Cyrus P.; Young, Peter; Tanzi, Rudolph E.; Khoury, Muin J.; Zipp, Frauke; Lehrach, Hans; Ioannidis, John P. A.; Bertram, Lars

    2012-01-01

    More than 800 published genetic association studies have implicated dozens of potential risk loci in Parkinson's disease (PD). To facilitate the interpretation of these findings, we have created a dedicated online resource, PDGene, that comprehensively collects and meta-analyzes all published studies in the field. A systematic literature screen of ∼27,000 articles yielded 828 eligible articles from which relevant data were extracted. In addition, individual-level data from three publicly available genome-wide association studies (GWAS) were obtained and subjected to genotype imputation and analysis. Overall, we performed meta-analyses on more than seven million polymorphisms originating either from GWAS datasets and/or from smaller scale PD association studies. Meta-analyses on 147 SNPs were supplemented by unpublished GWAS data from up to 16,452 PD cases and 48,810 controls. Eleven loci showed genome-wide significant (P<5×10−8) association with disease risk: BST1, CCDC62/HIP1R, DGKQ/GAK, GBA, LRRK2, MAPT, MCCC1/LAMP3, PARK16, SNCA, STK39, and SYT11/RAB25. In addition, we identified novel evidence for genome-wide significant association with a polymorphism in ITGA8 (rs7077361, OR 0.88, P = 1.3×10−8). All meta-analysis results are freely available on a dedicated online database (www.pdgene.org), which is cross-linked with a customized track on the UCSC Genome Browser. Our study provides an exhaustive and up-to-date summary of the status of PD genetics research that can be readily scaled to include the results of future large-scale genetics projects, including next-generation sequencing studies. PMID:22438815

  14. The stabilization effect of dielectric constant and acidic amino acids on arginine-arginine (Arg-Arg) pairings: database survey and computational studies.

    PubMed

    Zhang, Zhengyan; Xu, Zhijian; Yang, Zhuo; Liu, Yingtao; Wang, Jin'an; Shao, Qiang; Li, Shujin; Lu, Yunxiang; Zhu, Weiliang

    2013-05-02

    Database survey in this study revealed that about one-third of the protein structures deposited in the Protein Data Bank (PDB) contain arginine-arginine (Arg-Arg) pairing with a carbon···carbon (CZ···CZ) interaction distance less than 5 Å. All the Arg-Arg pairings were found to bury in a polar environment composed of acidic residues, water molecules, and strong polarizable or negatively charged moieties from binding site or bound ligand. Most of the Arg-Arg pairings are solvent exposed and 68.3% Arg-Arg pairings are stabilized by acidic residues, forming Arg-Arg-Asp/Glu clusters. Density functional theory (DFT) was then employed to study the effect of environment on the pairing structures. It was revealed that Arg-Arg pairings become thermodynamically stable (about -1 kcal/mol) as the dielectric constant increases to 46.8 (DMSO), in good agreement with the results of the PDB survey. DFT calculations also demonstrated that perpendicular Arg-Arg pairing structures are favorable in low dielectric constant environment, while in high dielectric constant environment parallel structures are favorable. Additionally, the acidic residues can stabilize the Arg-Arg pairing structures to a large degree. Energy decomposition analysis of Arg-Arg pairings and Arg-Arg-Asp/Glu clusters showed that both solvation and electrostatic energies contribute significantly to their stability. The results reported herein should be very helpful for understanding Arg-Arg pairing and its application in drug design.

  15. MetaBase—the wiki-database of biological databases

    PubMed Central

    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

  16. Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications.

    PubMed

    Hegedűs, Tamás; Chaubey, Pururawa Mayank; Várady, György; Szabó, Edit; Sarankó, Hajnalka; Hofstetter, Lia; Roschitzki, Bernd; Stieger, Bruno; Sarkadi, Balázs

    2015-01-01

    Based on recent results, the determination of the easily accessible red blood cell (RBC) membrane proteins may provide new diagnostic possibilities for assessing mutations, polymorphisms or regulatory alterations in diseases. However, the analysis of the current mass spectrometry-based proteomics datasets and other major databases indicates inconsistencies-the results show large scattering and only a limited overlap for the identified RBC membrane proteins. Here, we applied membrane-specific proteomics studies in human RBC, compared these results with the data in the literature, and generated a comprehensive and expandable database using all available data sources. The integrated web database now refers to proteomic, genetic and medical databases as well, and contains an unexpected large number of validated membrane proteins previously thought to be specific for other tissues and/or related to major human diseases. Since the determination of protein expression in RBC provides a method to indicate pathological alterations, our database should facilitate the development of RBC membrane biomarker platforms and provide a unique resource to aid related further research and diagnostics.

  17. Swedish scientists take acid-rain research to developing nations

    SciTech Connect

    Abate, T.

    1995-12-01

    In the realm of acid-rain research, Sweden looms large on the world stage. It is the country where scientists first proved more than 30 years ago that airborne chemicals could and did cross international boundaries to acidify lakes and forests far from where the pollution was generated. Now, Swedish scientists are leading an international effort to map acid-rain patterns in the developing countries of Asia, where new industrial activity seems to be recreating problems that European and North American policy makers have already taken steps to solve. Topics covered in this article include acid rain on the rise in Asia; visualizing and validating the data; funding as the key to steady research.

  18. Solubility Database

    National Institute of Standards and Technology Data Gateway

    SRD 106 IUPAC-NIST Solubility Database (Web, free access)   These solubilities are compiled from 18 volumes (Click here for List) of the International Union for Pure and Applied Chemistry(IUPAC)-NIST Solubility Data Series. The database includes liquid-liquid, solid-liquid, and gas-liquid systems. Typical solvents and solutes include water, seawater, heavy water, inorganic compounds, and a variety of organic compounds such as hydrocarbons, halogenated hydrocarbons, alcohols, acids, esters and nitrogen compounds. There are over 67,500 solubility measurements and over 1800 references.

  19. Progress in nucleic acid research and molecular biology

    SciTech Connect

    Cohn, W.E. . Biology Div.); Moldave, K. )

    1989-01-01

    This book contain the proceedings on progress in nucleic acid research and molecular biology. Topics covered include: polynucleotide-protein cross-links induced by ultraviolet light and their use for structural investigation of nucleoproteins; left-handed Z-DNA and genetic recombination, and structure and function of signal recognition particle RNA.

  20. [The use of bibliographic databases by Spanish-speaking Latin American biomedical researchers: a cross-sectional study].

    PubMed

    Ospina, Edgar Guillermo; Reveiz Herault, Ludovic; Cardona, Andrés Felipe

    2005-04-01

    To describe how Spanish-speaking biomedical professionals in Latin America access and utilize bibliographic databases. Based on a MEDLINE search, 2 515 articles published between August 2002 and August 2003 were identified that dealt with and/or had authors from 16 countries: Argentina, Bolivia, Chile, Colombia, Costa Rica, Cuba, Ecuador, Guatemala, Honduras, Mexico, Nicaragua, Panama, Paraguay, Peru, Uruguay, and Venezuela. The search was limited to references to basic science, clinical science, or social medicine. A survey was sent by e-mail to researchers who lived in 15 of the 16 countries (the exception being Nicaragua). The survey asked about the researcher's area of work (basic science, clinical science, or public health), the level of skill in using databases, the frequency and type of access to the databases most utilized, the impact from not having access to the full text of articles when preparing a manuscript, and how the respondent usually obtained the full-text version of articles. A total of 586 e-mail messages with the survey were sent out, and 185 responses were received (32%). The databases most utilized to obtain biomedical information were MEDLINE (34.1%), general search engines (Google, Yahoo!, and AltaVista) (15.9%), on-line journals (9.8%), BIREME-LILACS (6.0%), BioMedNet (5.4%), the databases of the Centers for Disease Control and Prevention of the United States of America (5.2%), and the Cochrane Library (4.9%). Of the respondents, 64% said they had average or advanced abilities in using MEDLINE. However, 71% of the respondents did not use or were not aware of the MEDLINE Medical Subject Headings (MeSH), a controlled vocabulary established by the National Library of Medicine of the United States of America for indexing articles. The frequency of accessing the databases was similar in all the countries studied, without significant differences in terms of the type of access (authorized access to commercial databases, unauthorized access to

  1. ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes

    SciTech Connect

    Novichkov, Pavel S.; Ratnere, Igor; Wolf, Yuri I.; Koonin, Eugene V.; Dubchak, Inna

    2009-07-23

    The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution. Construction of a data set with appropriate characteristics is a major hurdle for this type of studies. With the current rate of genome sequencing, it is difficult to follow the progress of the field and to determine which of the available genome sets meet the requirements of a given research project, in particular, with respect to the minimum and maximum levels of similarity between the included genomes. Additionally, extraction of specific content, such as genomic alignments or families of orthologs, from a selected set of genomes is a complicated and time-consuming process. The database addresses these problems by providing an intuitive and efficient web interface to browse precomputed ATGCs, select appropriate ones and access ATGC-derived data such as multiple alignments of orthologous proteins, matrices of pairwise intergenomic distances based on genome-wide analysis of synonymous and nonsynonymous substitution rates and others. The ATGC database will be regularly updated following new releases of the NCBI RefSeq. The database is hosted by the Genomics Division at Lawrence Berkeley National laboratory and is publicly available at http://atgc.lbl.gov.

  2. When humans are the exception: cross-species databases at the interface of biological and clinical research.

    PubMed

    Leonelli, Sabina

    2012-04-01

    Cross-species comparison has long been regarded as a stepping-stone for medical research, enabling the discovery and testing of prospective treatments before they undergo clinical trial on humans. Post-genomic medicine has made cross-species comparison crucial in another respect: the 'community databases' developed to collect and disseminate data on model organisms are now often used as a template for the dissemination of data on humans and as a tool for comparing results of medical significance across the human-animal boundary. This paper identifies and discusses four key problems encountered by database curators when integrating human and non-human data within the same database: (1) picking criteria for what counts as reliable evidence, (2) selecting metadata, (3) standardising and describing research materials and (4) choosing nomenclature to classify data. An analysis of these hurdles reveals epistemic disagreement and controversies underlying cross-species comparisons, which in turn highlight important differences in the experimental cultures of biologists and clinicians trying to make sense of these data. By considering database development through the eyes of curators, this study casts new light on the complex conjunctions of biological and clinical practice, model organisms and human subjects, and material and virtual sources of evidence--thus emphasizing the fragmented, localized and inherently translational nature of biomedicine.

  3. ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes

    PubMed Central

    Novichkov, Pavel S.; Ratnere, Igor; Wolf, Yuri I.; Koonin, Eugene V.; Dubchak, Inna

    2009-01-01

    The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution. Construction of a data set with appropriate characteristics is a major hurdle for this type of studies. With the current rate of genome sequencing, it is difficult to follow the progress of the field and to determine which of the available genome sets meet the requirements of a given research project, in particular, with respect to the minimum and maximum levels of similarity between the included genomes. Additionally, extraction of specific content, such as genomic alignments or families of orthologs, from a selected set of genomes is a complicated and time-consuming process. The database addresses these problems by providing an intuitive and efficient web interface to browse precomputed ATGCs, select appropriate ones and access ATGC-derived data such as multiple alignments of orthologous proteins, matrices of pairwise intergenomic distances based on genome-wide analysis of synonymous and nonsynonymous substitution rates and others. The ATGC database will be regularly updated following new releases of the NCBI RefSeq. The database is hosted by the Genomics Division at Lawrence Berkeley National laboratory and is publicly available at http://atgc.lbl.gov PMID:18845571

  4. Design and utilization of a Flight Test Engineering Database Management System at the NASA Dryden Flight Research Facility

    NASA Technical Reports Server (NTRS)

    Knighton, Donna L.

    1992-01-01

    A Flight Test Engineering Database Management System (FTE DBMS) was designed and implemented at the NASA Dryden Flight Research Facility. The X-29 Forward Swept Wing Advanced Technology Demonstrator flight research program was chosen for the initial system development and implementation. The FTE DBMS greatly assisted in planning and 'mass production' card preparation for an accelerated X-29 research program. Improved Test Plan tracking and maneuver management for a high flight-rate program were proven, and flight rates of up to three flights per day, two times per week were maintained.

  5. The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community.

    PubMed

    Arnaud, Martha B; Chibucos, Marcus C; Costanzo, Maria C; Crabtree, Jonathan; Inglis, Diane O; Lotia, Adil; Orvis, Joshua; Shah, Prachi; Skrzypek, Marek S; Binkley, Gail; Miyasato, Stuart R; Wortman, Jennifer R; Sherlock, Gavin

    2010-01-01

    The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD combines high-quality manual curation of the experimental scientific literature examining the genetics and molecular biology of Aspergilli, cutting-edge comparative genomics approaches to iteratively refine and improve structural gene annotations across multiple Aspergillus species, and web-based research tools for accessing and exploring the data. All of these data are freely available at http://www.aspgd.org. We welcome feedback from users and the research community at aspergillus-curator@genome.stanford.edu.

  6. Design and utilization of a Flight Test Engineering Database Management System at the NASA Dryden Flight Research Facility

    NASA Technical Reports Server (NTRS)

    Knighton, Donna L.

    1992-01-01

    A Flight Test Engineering Database Management System (FTE DBMS) was designed and implemented at the NASA Dryden Flight Research Facility. The X-29 Forward Swept Wing Advanced Technology Demonstrator flight research program was chosen for the initial system development and implementation. The FTE DBMS greatly assisted in planning and 'mass production' card preparation for an accelerated X-29 research program. Improved Test Plan tracking and maneuver management for a high flight-rate program were proven, and flight rates of up to three flights per day, two times per week were maintained.

  7. Workshop report: Identifying opportunities for global integration of toxicogenomics databases, 26-27 June 2013, Research Triangle Park, NC, USA.

    PubMed

    Hendrickx, Diana M; Boyles, Rebecca R; Kleinjans, Jos C S; Dearry, Allen

    2014-12-01

    A joint US-EU workshop on enhancing data sharing and exchange in toxicogenomics was held at the National Institute for Environmental Health Sciences. Currently, efficient reuse of data is hampered by problems related to public data availability, data quality, database interoperability (the ability to exchange information), standardization and sustainability. At the workshop, experts from universities and research institutes presented databases, studies, organizations and tools that attempt to deal with these problems. Furthermore, a case study showing that combining toxicogenomics data from multiple resources leads to more accurate predictions in risk assessment was presented. All participants agreed that there is a need for a web portal describing the diverse, heterogeneous data resources relevant for toxicogenomics research. Furthermore, there was agreement that linking more data resources would improve toxicogenomics data analysis. To outline a roadmap to enhance interoperability between data resources, the participants recommend collecting user stories from the toxicogenomics research community on barriers in data sharing and exchange currently hampering answering to certain research questions. These user stories may guide the prioritization of steps to be taken for enhancing integration of toxicogenomics databases.

  8. The National Hospital Discharge Survey and Nationwide Inpatient Sample: the databases used affect results in THA research.

    PubMed

    Bekkers, Stijn; Bot, Arjan G J; Makarawung, Dennis; Neuhaus, Valentin; Ring, David

    2014-11-01

    The National Hospital Discharge Survey (NHDS) and the Nationwide Inpatient Sample (NIS) collect sample data and publish annual estimates of inpatient care in the United States, and both are commonly used in orthopaedic research. However, there are important differences between the databases, and because of these differences, asking these two databases the same question may result in different answers. The degree to which this is true for arthroplasty-related research has, to our knowledge, not been characterized. We tested the following null hypotheses: (1) there are no differences between the NHDS and NIS in patient characteristics, comorbidities, and adverse events in patients with hip osteoarthritis treated with THA, and (2) there are no differences between databases in factors associated with inpatient mortality, adverse events, and length of hospital stay after THA. The NHDS and NIS databases use different methods of data collection and weighting to provide data representative of all nonfederal hospital discharges in the United States. In 2006 the NHDS database contained 203,149 patients with hip arthritis treated with hip arthroplasty, and the NIS database included 193,879 patients. Multivariable analyses for factors associated with inpatient mortality, adverse events, and days of care were constructed for each database. We found that 26 of 42 of the factors in demographics, comorbidities, and adverse events after THA in the NIS and NHDS databases differed more than 10%. Age and days of care were associated with inpatient mortality with the NHDS and the NIS although the effect rates differ more than 10%. The NIS identified seven other factors not identified by the NHDS: wound complications, congestive heart failure, new mental disorder, chronic pulmonary disease, dementia, geographic region Northeast, acute postoperative anemia, and sex, that were associated with inpatient mortality even after controlling for potentially confounding variables. For inpatient

  9. SU-E-P-26: Oncospace: A Shared Radiation Oncology Database System Designed for Personalized Medicine, Decision Support, and Research

    SciTech Connect

    Bowers, M; Robertson, S; Moore, J; Wong, J; DeWeese, T; McNutt, T; Phillips, M; Hendrickson, K; Song, W; Kwok, P

    2015-06-15

    Purpose: Advancement in Radiation Oncology (RO) practice develops through evidence based medicine and clinical trial. Knowledge usable for treatment planning, decision support and research is contained in our clinical data, stored in an Oncospace database. This data store and the tools for populating and analyzing it are compatible with standard RO practice and are shared with collaborating institutions. The question is - what protocol for system development and data sharing within an Oncospace Consortium? We focus our example on the technology and data meaning necessary to share across the Consortium. Methods: Oncospace consists of a database schema, planning and outcome data import and web based analysis tools.1) Database: The Consortium implements a federated data store; each member collects and maintains its own data within an Oncospace schema. For privacy, PHI is contained within a single table, accessible to the database owner.2) Import: Spatial dose data from treatment plans (Pinnacle or DICOM) is imported via Oncolink. Treatment outcomes are imported from an OIS (MOSAIQ).3) Analysis: JHU has built a number of webpages to answer analysis questions. Oncospace data can also be analyzed via MATLAB or SAS queries.These materials are available to Consortium members, who contribute enhancements and improvements. Results: 1) The Oncospace Consortium now consists of RO centers at JHU, UVA, UW and the University of Toronto. These members have successfully installed and populated Oncospace databases with over 1000 patients collectively.2) Members contributing code and getting updates via SVN repository. Errors are reported and tracked via Redmine. Teleconferences include strategizing design and code reviews.3) Successfully remotely queried federated databases to combine multiple institutions’ DVH data for dose-toxicity analysis (see below – data combined from JHU and UW Oncospace). Conclusion: RO data sharing can and has been effected according to the Oncospace

  10. The Novel Object and Unusual Name (NOUN) Database: A collection of novel images for use in experimental research.

    PubMed

    Horst, Jessica S; Hout, Michael C

    2016-12-01

    Many experimental research designs require images of novel objects. Here we introduce the Novel Object and Unusual Name (NOUN) Database. This database contains 64 primary novel object images and additional novel exemplars for ten basic- and nine global-level object categories. The objects' novelty was confirmed by both self-report and a lack of consensus on questions that required participants to name and identify the objects. We also found that object novelty correlated with qualifying naming responses pertaining to the objects' colors. The results from a similarity sorting task (and a subsequent multidimensional scaling analysis on the similarity ratings) demonstrated that the objects are complex and distinct entities that vary along several featural dimensions beyond simply shape and color. A final experiment confirmed that additional item exemplars comprised both sub- and superordinate categories. These images may be useful in a variety of settings, particularly for developmental psychology and other research in the language, categorization, perception, visual memory, and related domains.

  11. Hedgehog Signaling Pathway Database: a repository of current annotation efforts and resources for the Hh research community.

    PubMed

    Hervold, Kieran; Martin, Andrew; Kirkpatrick, Roger A; Mc Kenna, Paul F; Ramirez-Weber, F A

    2007-01-01

    The Hedgehog Signaling Pathway Database is a curated repository of information pertaining to the Hedgehog developmental pathway. It was designed to provide centralized access to a wide range of relevant information in an organism-agnostic manner. Data are provided for all genes and gene targets known to be involved in the Hh pathway across various organisms. The data provided include DNA and protein sequences as well as domain structure motifs. All known human diseases associated with the Hh pathway are indexed including experimental data on therapeutic agents and their molecular targets. Hh researchers will find useful information on relevant protocols, tissue cell lines and reagents used in current Hh research projects. Curated content is also provided for publications, grants and patents relating to the Hh pathway. The database can be accessed at http://www.hedgehog.sfsu.edu.

  12. The Pharmacoepidemiologic Prescription Database of North Jutland - a valid tool in pharmacoepidemiological research.

    PubMed

    Nielsen, G L; Sørensen, H T; Zhou, W; Steffensen, F H; Olsen, J

    1997-01-01

    In this paper we describe the options of a pharmacoepidemiologic database comprising data on all reimbursed prescriptions taken up at pharmacies in the County of Northern Jutland since 1991 including precise identification of the individual person for whom the medicin was prescribed. The County comprises 487,000 inhabitants equal to approximately 10% of the total Danish population.

  13. Heart ‘omics’ in AGEing (HOMAGE): design, research objectives and characteristics of the common database

    PubMed Central

    Jacobs, Lotte; Thijs, Lutgarde; Jin, Yu; Zannad, Faiez; Mebazaa, Alexandre; Rouet, Philippe; Pinet, Florence; Bauters, Christophe; Pieske, Burkert; Tomaschitz, Andreas; Mamas, Mamas; Diez, Javier; McDonald, Kenneth; Cleland, John G. F.; Rocca, Hans-Peter Brunner-La; Heymans, Stephane; Latini, Roberto; Masson, Serge; Sever, Peter; Delles, Christian; Pocock, Stuart; Collier, Timothy; Kuznetsova, Tatiana; Staessen, Jan A

    2014-01-01

    Abstract Heart failure is common in older people and its prevalence is increasing. The Heart ‘omics’ in AGEing (HOMAGE) project aims to provide a biomarker approach that will improve the early diagnosis of heart failure. A large clinical database, based on (1) prospective population studies or (2) cross-sectional, prospective studies or randomized controlled trials (RCTs) of patients at risk for or with overt cardiovascular disease will be constructed to determine most promising ‘omics’-based biomarkers to identify the risk of developing heart failure and/or comorbidities. Population studies, patient cohorts and RCTs are eligible for inclusion in the common database, if they received ethical approval to obtain and share data and have baseline information on cardiovascular risk factors. Currently, the HOMAGE database includes 43,065 subjects, from 20 studies in eight European countries, including healthy subjects from three population studies in France, Belgium and Italy (n  =  7,124), patients with heart failure (n  =  4,312) from four cohorts in the UK, Spain and Switzerland and patients at high risk for cardiovascular disease (n  =  31,629) in 13 cohorts. It is anticipated that more partners will join the consortium and enlarge the pooled data. This large merged database will be a useful resource with which to identify candidate biomarkers that play a role in the mechanism underlying the onset and progression of heart failure. PMID:25332706

  14. USDA-ARS Riesel Watersheds, Riesel, Texas, USA: Water quality research database

    USDA-ARS?s Scientific Manuscript database

    The 75 year legacy database including discharge, sediment loss, land management, and meteorological data for the USDA-ARS Riesel Watersheds has been available on the web for more than a decade (www.ars.usda.gov/spa/hydro-data); however, only recently have additional water quality data been added. T...

  15. Successful Keyword Searching: Initiating Research on Popular Topics Using Electronic Databases.

    ERIC Educational Resources Information Center

    MacDonald, Randall M.; MacDonald, Susan Priest

    Students are using electronic resources more than ever before to locate information for assignments. Without the proper search terms, results are incomplete, and students are frustrated. Using the keywords, key people, organizations, and Web sites provided in this book and compiled from the most commonly used databases, students will be able to…

  16. The U.S. Dairy Forage Research Center (USDFRC) condensed tannin NMR database

    USDA-ARS?s Scientific Manuscript database

    This perspective describes a solution-state NMR database for flavan-3-ol monomers and condensed tannin dimers through tetramers obtained from the literature to 2015, containing data searchable by structure, molecular formula, degrees of polymerization, 1H and 13C chemical shifts of the condensed tan...

  17. D Digital Model Database Applied to Conservation and Research of Wooden Construction in China

    NASA Astrophysics Data System (ADS)

    Zheng, Y.

    2013-07-01

    Protected by the Tai-Hang Mountains, Shanxi Province, located in north central China, is a highly prosperous, densely populated valley and considered to be one of the cradles of Chinese civilization. Its continuous habitation and rich culture have given rise to a large number of temple complexes and pavilions. Among these structures, 153 can be dated as early as from the Tang dynasty (618- 907C.E.) to the end of the Yuan dynasty (1279-1368C.E.) in Southern Shanxi area. The buildings are the best-preserved examples of wooden Chinese architecture in existence, exemplifying historic building technology and displaying highly intricate architectural decoration and detailing. They have survived war, earthquakes, and, in the last hundred years, neglect. In 2005, a decade-long conservation project was initiated by the State Administration of Cultural Heritage of China (SACH) to conserve and document these important buildings. The conservation process requires stabilization, conservation of important features, and, where necessary, partial dismantlement in order to replace unsound structural elements. Project team of CHCC have developed a practical recording system that created a record of all building components prior to and during the conservation process. After that we are trying to establish a comprehensive database which include all of the 153 earlier buildings, through which we can easily entering, browse, indexing information of the wooden construction, even deep into component details. The Database can help us to carry out comparative studies of these wooden structures, and, provide important support for the continued conservation of these heritage buildings. For some of the most important wooden structure, we have established three-dimensional models. Connected the Database with 3D Digital Model based on ArcGIS, we have developed 3D Digital Model Database for these cherish buildings. The 3D Digital Model Database helps us set up an integrate information inventory

  18. Improving Care And Research Electronic Data Trust Antwerp (iCAREdata): a research database of linked data on out-of-hours primary care.

    PubMed

    Colliers, Annelies; Bartholomeeusen, Stefaan; Remmen, Roy; Coenen, Samuel; Michiels, Barbara; Bastiaens, Hilde; Van Royen, Paul; Verhoeven, Veronique; Holmgren, Philip; De Ruyck, Bernard; Philips, Hilde

    2016-05-04

    Primary out-of-hours care is developing throughout Europe. High-quality databases with linked data from primary health services can help to improve research and future health services. In 2014, a central clinical research database infrastructure was established (iCAREdata: Improving Care And Research Electronic Data Trust Antwerp, www.icaredata.eu ) for primary and interdisciplinary health care at the University of Antwerp, linking data from General Practice Cooperatives, Emergency Departments and Pharmacies during out-of-hours care. Medical data are pseudonymised using the services of a Trusted Third Party, which encodes private information about patients and physicians before data is sent to iCAREdata. iCAREdata provides many new research opportunities in the fields of clinical epidemiology, health care management and quality of care. A key aspect will be to ensure the quality of data registration by all health care providers. This article describes the establishment of a research database and the possibilities of linking data from different primary out-of-hours care providers, with the potential to help to improve research and the quality of health care services.

  19. Experiment Databases

    NASA Astrophysics Data System (ADS)

    Vanschoren, Joaquin; Blockeel, Hendrik

    Next to running machine learning algorithms based on inductive queries, much can be learned by immediately querying the combined results of many prior studies. Indeed, all around the globe, thousands of machine learning experiments are being executed on a daily basis, generating a constant stream of empirical information on machine learning techniques. While the information contained in these experiments might have many uses beyond their original intent, results are typically described very concisely in papers and discarded afterwards. If we properly store and organize these results in central databases, they can be immediately reused for further analysis, thus boosting future research. In this chapter, we propose the use of experiment databases: databases designed to collect all the necessary details of these experiments, and to intelligently organize them in online repositories to enable fast and thorough analysis of a myriad of collected results. They constitute an additional, queriable source of empirical meta-data based on principled descriptions of algorithm executions, without reimplementing the algorithms in an inductive database. As such, they engender a very dynamic, collaborative approach to experimentation, in which experiments can be freely shared, linked together, and immediately reused by researchers all over the world. They can be set up for personal use, to share results within a lab or to create open, community-wide repositories. Here, we provide a high-level overview of their design, and use an existing experiment database to answer various interesting research questions about machine learning algorithms and to verify a number of recent studies.

  20. A plant resource and experiment management system based on the Golm Plant Database as a basic tool for omics research

    PubMed Central

    Köhl, Karin I; Basler, Georg; Lüdemann, Alexander; Selbig, Joachim; Walther, Dirk

    2008-01-01

    and barcode labels facilitate identification and management of the material. Web pages are provided as user interfaces to facilitate maintaining the system in an environment with many desktop computers and a rapidly changing user community. Web based search tools are the basis for joint use of the material by all researchers of the institute. Conclusion The Golm Plant Database system, which is based on a relational database, collects the genetic and environmental information on plant material during its production or experimental use at the Max-Planck-Institute of Molecular Plant Physiology. It thus provides information according to the MIAME standard for the component 'Sample' in a highly standardised format. The Plant Database system thus facilitates collaborative work and allows efficient queries in data analysis for systems biology research. PMID:18495032

  1. Heavy-atom Database System: a tool for the preparation of heavy-atom derivatives of protein crystals based on amino-acid sequence and crystallization conditions.

    PubMed

    Sugahara, Michihiro; Asada, Yukuhiko; Ayama, Haruhiko; Ukawa, Hisashi; Taka, Hideyuki; Kunishima, Naoki

    2005-09-01

    Heavy-atom Database System (HATODAS) is a WWW-based tool designed to assist the heavy-atom derivatization of proteins. The conventional procedure for the preparation of derivatives is usually a time-consuming 'trial-and-error' process. The present program provides a solution for this problem using a database of known heavy-atom derivatives. A database search suggests potential heavy-atom reagents for any target protein based on its amino-acid sequence and crystallization conditions. A mining of the database identified 93 preferred motifs for heavy-atom binding. The motifs are observed frequently at the actual heavy-atom-binding sites encountered in the process of structure determination.

  2. A Hypervelocity Experimental Research Database (HERD): Support for the Wright Laboratory Armament Directorate Code Validation Program (COVAL)

    NASA Astrophysics Data System (ADS)

    Mullin, Scott A.; Anderson, Charles E., Jr.; Hertel, Eugene S., Jr.; Hunt, Ronald D.

    The Hypervelocity Experimental Research Database (HERD) described in this paper was developed to aid researchers with code validation for impacts that occur at velocities faster than the testable regime. Codes of concern include both hydrocodes and fast-running analytical or semi-empirical models used to predict the impact phenomenology and damage that results to projectiles and targets. There are several well documented experimental programs that can serve as benchmarks for code validation; these are identified and described. Recommendations for further experimentation (a canonical problem) to provide validation data are also discussed.

  3. A Hypervelocity Experimental Research Database (HERD): Support for the Wright Laboratory Armament Directorate Code Validation Program (COVAL)

    SciTech Connect

    Mullin, S.A.; Anderson, C.E. Jr.; Hertel, E.S. Jr.; Hunt, R.D.

    1994-10-01

    The Hypervelocity Experimental Research Database (HERD) described in this paper was developed to aid researchers with code validation for impacts that occur at velocities faster than the testable regime. Codes of concern include both hydrocodes and fast-running analytical or semi-empirical models used to predict the impact phenomenology and damage that results to projectiles and targets. There are several well documented experimental programs that can serve as benchmarks for code validation; these are identified and described. Recommendations for further experimentation (a canonical problem) to provide validation data are also discussed.

  4. What can we learn from a decade of database audits? The Duke Clinical Research Institute experience, 1997--2006.

    PubMed

    Rostami, Reza; Nahm, Meredith; Pieper, Carl F

    2009-04-01

    Despite a pressing and well-documented need for better sharing of information on clinical trials data quality assurance methods, many research organizations remain reluctant to publish descriptions of and results from their internal auditing and quality assessment methods. We present findings from a review of a decade of internal data quality audits performed at the Duke Clinical Research Institute, a large academic research organization that conducts data management for a diverse array of clinical studies, both academic and industry-sponsored. In so doing, we hope to stimulate discussions that could benefit the wider clinical research enterprise by providing insight into methods of optimizing data collection and cleaning, ultimately helping patients and furthering essential research. We present our audit methodologies, including sampling methods, audit logistics, sample sizes, counting rules used for error rate calculations, and characteristics of audited trials. We also present database error rates as computed according to two analytical methods, which we address in detail, and discuss the advantages and drawbacks of two auditing methods used during this 10-year period. Our review of the DCRI audit program indicates that higher data quality may be achieved from a series of small audits throughout the trial rather than through a single large database audit at database lock. We found that error rates trended upward from year to year in the period characterized by traditional audits performed at database lock (1997-2000), but consistently trended downward after periodic statistical process control type audits were instituted (2001-2006). These increases in data quality were also associated with cost savings in auditing, estimated at 1000 h per year, or the efforts of one-half of a full time equivalent (FTE). Our findings are drawn from retrospective analyses and are not the result of controlled experiments, and may therefore be subject to unanticipated confounding

  5. What can we learn from a decade of database audits? The Duke Clinical Research Institute experience, 1997–2006

    PubMed Central

    Rostami, Reza; Nahm, Meredith; Pieper, Carl F.

    2011-01-01

    Background Despite a pressing and well-documented need for better sharing of information on clinical trials data quality assurance methods, many research organizations remain reluctant to publish descriptions of and results from their internal auditing and quality assessment methods. Purpose We present findings from a review of a decade of internal data quality audits performed at the Duke Clinical Research Institute, a large academic research organization that conducts data management for a diverse array of clinical studies, both academic and industry-sponsored. In so doing, we hope to stimulate discussions that could benefit the wider clinical research enterprise by providing insight into methods of optimizing data collection and cleaning, ultimately helping patients and furthering essential research. Methods We present our audit methodologies, including sampling methods, audit logistics, sample sizes, counting rules used for error rate calculations, and characteristics of audited trials. We also present database error rates as computed according to two analytical methods, which we address in detail, and discuss the advantages and drawbacks of two auditing methods used during this ten-year period. Results Our review of the DCRI audit program indicates that higher data quality may be achieved from a series of small audits throughout the trial rather than through a single large database audit at database lock. We found that error rates trended upward from year to year in the period characterized by traditional audits performed at database lock (1997–2000), but consistently trended downward after periodic statistical process control type audits were instituted (2001–2006). These increases in data quality were also associated with cost savings in auditing, estimated at 1000 hours per year, or the efforts of one-half of a full time equivalent (FTE). Limitations Our findings are drawn from retrospective analyses and are not the result of controlled experiments, and

  6. Creation and use of a database in clinical and translational research.

    PubMed

    Smith, Janet P; Elliott, Alan C; Hynan, Linda S; Reisch, Joan S; Waddell, Stan A

    2010-03-01

    Often data collection for clinical studies is an afterthought. The results of such an approach are incomplete or confusing data that can, as a worst case, result in scrapping and restarting the entire study. We discuss the planning process for data collection and storage to include encounter form development; data flow and capture; data checking, verification, and validation; advantage of relational databases over spreadsheets; data security; and aspects of a complete data system.

  7. Inventory and Assessment of Databases Relevant for Social Science Research on Terrorism

    DTIC Science & Technology

    2003-11-01

    None; access to all information is by simply arranged links, with full range of movement among database segments. Original Purpose of the Study: “ ICT ...Hammarskjold Library Resource Page) 19 (www.un.org/depts/ dhl /resources/terrorism <http://www.un.org/Depts/ dhl /resources/terrorism>) - includes legal...agreements and UN actions against terrorism, and other conventions. (www.un.org/depts/ dhl /resources/terrorism/elinks.htm <http://www.un.org/depts/ dhl

  8. SPAM: A Canned Internet-Accessible Database of Interest to Solar Flare Researchers

    NASA Astrophysics Data System (ADS)

    Canfield, R. C.; Hudson, H. S.; Kiernan, E.; Metcalf, T. R.; Wulser, J.-P.

    1992-05-01

    We have established a searchable database, called SPAM (Spectroscopy and Polarimetry at Mees), which contains logs of observations made at Mees Solar Observatory (Haleakala, Maui). Of more general interest, the database also includes the Events List and Region Report from the Space Environment Laboratory (Boulder). Logs from YOHKOH are currently being added. Hence, SPAM can be used to determine, for example, whether Mees has vector magnetograms of a certain NOAA AR or whether YOHKOH has certain types of observations in specified time ranges. As well, it can be used to search the SEL database for flares with selected attributes. Included logs (and searchable attributes, in addition to date, day of year, and time) are: Mees Solar Observatory Log (instrument, NOAA AR, data type, observing setup), SEL Event List (NOAA AR, X-ray Class), SEL Region Report (NOAA AR), YOHKOH Orbit Summary, YOHKOH SXT Quiet Mode PFI Observations (latitude, longitude, X-ray and optical image size), YOHKOH Flare Observations (latitude, longitude, specific channel counts or ratios). SPAM runs on a Sun workstation at Mees Solar Observatory, and is available over Internet. Simply access (e.g., telnet) koa.ifa.hawaii.edu (128.171.167.1) from any vt100, Sun, or xterm emulator. Log on as spam (lower case); there is no password. New users are asked to read release notes and hints.

  9. The inherited ataxias: genetic heterogeneity, mutation databases, and future directions in research and clinical diagnostics.

    PubMed

    Hersheson, Joshua; Haworth, Andrea; Houlden, Henry

    2012-09-01

    The inherited cerebellar ataxias are a diverse group of clinically and genetically heterogeneous neurodegenerative disorders. Inheritance patterns of these disorders can be complex with autosomal dominant, autosomal recessive, X-linked, and mitochondrial inheritance demonstrated by one or more ataxic syndromes. The broad range of mutation types found in inherited ataxia contributes to the complex genetic etiology of these disorders. The majority of inherited ataxias are caused by repeat expansions; however, conventional mutations are important causes of the rarer dominant and recessive ataxias. Advances in sequencing technology have allowed for much broader testing of these rare ataxia genes. This is relevant to the aims of the Human Variome Project, which aims to collate and store gene variation data through mutation databases. Variant data is currently located in a range of public and commercial resources. Few locus-specific databases have been created to catalogue variation in the dominant ataxia genes although there are several databases for some recessive genes. Developing these resources will facilitate a better understanding of the complex genotype-phenotype relationships in these disorders and assist interpretation of gene variants as testing for rarer ataxia genes becomes commonplace.

  10. The phytophthora genome initiative database: informatics and analysis for distributed pathogenomic research.

    PubMed

    Waugh, M; Hraber, P; Weller, J; Wu, Y; Chen, G; Inman, J; Kiphart, D; Sobral, B

    2000-01-01

    The Phytophthora Genome Initiative (PGI) is a distributed collaboration to study the genome and evolution of a particularly destructive group of plant pathogenic oomycete, with the goal of understanding the mechanisms of infection and resistance. NCGR provides informatics support for the collaboration as well as a centralized data repository. In the pilot phase of the project, several investigators prepared Phytophthora infestans and Phytophthora sojae EST and Phytophthora sojae BAC libraries and sent them to another laboratory for sequencing. Data from sequencing reactions were transferred to NCGR for analysis and curation. An analysis pipeline transforms raw data by performing simple analyses (i.e., vector removal and similarity searching) that are stored and can be retrieved by investigators using a web browser. Here we describe the database and access tools, provide an overview of the data therein and outline future plans. This resource has provided a unique opportunity for the distributed, collaborative study of a genus from which relatively little sequence data are available. Results may lead to insight into how better to control these pathogens. The homepage of PGI can be accessed at http:www.ncgr.org/pgi, with database access through the database access hyperlink.

  11. Databases: Beyond the Basics.

    ERIC Educational Resources Information Center

    Whittaker, Robert

    This presented paper offers an elementary description of database characteristics and then provides a survey of databases that may be useful to the teacher and researcher in Slavic and East European languages and literatures. The survey focuses on commercial databases that are available, usable, and needed. Individual databases discussed include:…

  12. Databases: Beyond the Basics.

    ERIC Educational Resources Information Center

    Whittaker, Robert

    This presented paper offers an elementary description of database characteristics and then provides a survey of databases that may be useful to the teacher and researcher in Slavic and East European languages and literatures. The survey focuses on commercial databases that are available, usable, and needed. Individual databases discussed include:…

  13. [The research progress of succinic acid fermentation strains].

    PubMed

    Wang, Qing-Zhao; Zhao, Xue-Ming

    2007-07-01

    The potential of succinic acid as an important chemical intermediates had been realized and fermentation is one of the best ways to make it possible in economical aspect. Fermentation organism is the key part of the fermentation method. The updated research developments of fermentation organisms and the fermentation characteristics and problems of them were reviewed and analyzed in this paper. Finally,the development future of fermenation organism was forecasted.

  14. Mapping the Iranian Research Literature in the Field of Traditional Medicine in Scopus Database 2010-2014.

    PubMed

    GhaedAmini, Hossein; Okhovati, Maryam; Zare, Morteza; Saghafi, Zahra; Bazrafshan, Azam; GhaedAmini, Alireza; GhaedAmini, Mohammadreza

    2016-05-01

    The aim of this study was to provide research and collaboration overview of Iranian research efforts in the field of traditional medicine during 2010-2014. This is a bibliometric study using the Scopus database as data source, using search affiliation address relevant to traditional medicine and Iran as the search strategy. Subject and geographical overlay maps were also applied to visualize the network activities of the Iranian authors. Highly cited articles (citations >10) were further explored to highlight the impact of research domains more specifically. About 3,683 articles were published by Iranian authors in Scopus database. The compound annual growth rate of Iranian publications was 0.14% during 2010-2014. Tehran University of Medical Sciences (932 articles), Shiraz University of Medical Sciences (404 articles) and Tabriz Islamic Medical University (391 articles), were the leading institutions in the field of traditional medicine. Medicinal plants (72%), digestive system's disease (21%), basics of traditional medicine (13%), mental disorders (8%) were the major research topics. United States (7%), Netherlands (3%), and Canada (2.6%) were the most important collaborators of Iranian authors. Iranian research efforts in the field of traditional medicine have been increased slightly over the last years. Yet, joint multi-disciplinary collaborations are needed to cover inadequately described areas of traditional medicine in the country.

  15. Is the Quebec provincial administrative database a valid source for research on chronic non-cancer pain?

    PubMed

    Lacasse, Anaïs; Ware, Mark A; Dorais, Marc; Lanctôt, Hélène; Choinière, Manon

    2015-09-01

    The objective of this study was to evaluate the validity of diagnostic codes recorded in the Régie de l'assurance maladie du Québec (RAMQ) administrative database for identifying patients suffering from various types of chronic non-cancer pain. The validity of published International Classification of Diseases, Ninth Revision, coding algorithms for identifying patients with particular chronic pain syndromes in the RAMQ database was tested using pain specialist-established diagnostic data of 561 patients enrolled in the Quebec Pain Registry, which was used as the reference standard. Modified versions of these algorithms (i.e., adaptation of the number of healthcare encounters) were also tested. For each algorithm, sensitivity, specificity, positive/negative predictive values, and their respective 95% confidence intervals (95%CI) were calculated. In the RAMQ database, some previously published algorithms and modified versions of these algorithms were found to be valid for identifying patients suffering from chronic lumbar pain (sensitivity: 0.65, 95%CI: 0.59-0.71; specificity: 0.83, 95%CI: 0.79-0.87), chronic back pain (sensitivity: 0.70, 95%CI: 0.64-0.76; specificity: 0.73, 95%CI: 0.68-0.78), and chronic neck/back pain (sensitivity: 0.71, 95%CI: 0.65-0.76; specificity: 0.78, 95%CI: 0.72-0.82). Algorithms to identify patients with other types of chronic pain showed low sensitivity: complex regional pain syndrome (≤0.07), fibromyalgia (≤0.42), and neuropathic pain (≤0.39). Our study provides evidence supporting the value of the RAMQ administrative database for conducting research on certain types of chronic pain disorders including back and neck pain. Users should, however, be cautious about the limitations of this database for studying other types of chronic pain syndromes such as complex regional pain syndrome, fibromyalgia, and neuropathic pain. Copyright © 2015 John Wiley & Sons, Ltd.

  16. Databases and Geographical Information Systems at the research/teaching interface: palaeoclimate proxies, freshwater biodiversity and the OMEGA project

    NASA Astrophysics Data System (ADS)

    Horne, David

    2013-04-01

    The Mutual Ostracod Temperature Range (MOTR) method provides Quaternary palaeotemperature range estimates based on fossil ostracod assemblages calibrated using modern distributional databases and climate data. Over the past five years, aspects of the development and application of the MOTR method have been incorporated into undergraduate teaching in two second-year modules (Global Environmental Change and Digital Worlds: Cartography, Geographical Information Systems and Modelling) via lectures and practical exercises. Consequently, several students became sufficiently interested and enthused to undertake successful major projects aimed at developing, testing and applying aspects of the method, leading in turn to postgraduate work on the same topic in two cases and in a third case to co-authorship of a research publication. Thus both research and teaching have benefited from the integration of an innovative geoscience application with undergraduate coursework. The scope of MOTR applications is being expanded from European to global via the Ostracod Metadatabase of Environmental and Geographical Attributes (OMEGA) project; the current focus is on harmonising North American and European datasets, supported by the EU-funded (FP7) BioFresh project which is building a global information platform with access to all available databases of freshwater biodiversity. Undergraduate participation will be sought to underpin a Citizen Science initiative aimed at checking, correcting and validating the geographic referencing of species' records in the databases, using datasets exported as Keyhole Markup Language files for use in Google Earth.

  17. Development of prostate cancer research database with the clinical data warehouse technology for direct linkage with electronic medical record system.

    PubMed

    Choi, In Young; Park, Seungho; Park, Bumjoon; Chung, Byung Ha; Kim, Choung-Soo; Lee, Hyun Moo; Byun, Seok-Soo; Lee, Ji Youl

    2013-01-01

    In spite of increased prostate cancer patients, little is known about the impact of treatments for prostate cancer patients and outcome of different treatments based on nationwide data. In order to obtain more comprehensive information for Korean prostate cancer patients, many professionals urged to have national system to monitor the quality of prostate cancer care. To gain its objective, the prostate cancer database system was planned and cautiously accommodated different views from various professions. This prostate cancer research database system incorporates information about a prostate cancer research including demographics, medical history, operation information, laboratory, and quality of life surveys. And, this system includes three different ways of clinical data collection to produce a comprehensive data base; direct data extraction from electronic medical record (EMR) system, manual data entry after linking EMR documents like magnetic resonance imaging findings and paper-based data collection for survey from patients. We implemented clinical data warehouse technology to test direct EMR link method with St. Mary's Hospital system. Using this method, total number of eligible patients were 2,300 from 1997 until 2012. Among them, 538 patients conducted surgery and others have different treatments. Our database system could provide the infrastructure for collecting error free data to support various retrospective and prospective studies.

  18. Development of prostate cancer research database with the clinical data warehouse technology for direct linkage with electronic medical record system

    PubMed Central

    Choi, In Young; Park, Seungho; Park, Bumjoon; Chung, Byung Ha; Kim, Choung-Soo; Lee, Hyun Moo; Byun, Seok-Soo; Lee, Ji Youl

    2013-01-01

    Purpose: In spite of increased prostate cancer patients, little is known about the impact of treatments for prostate cancer patients and outcome of different treatments based on nationwide data. In order to obtain more comprehensive information for Korean prostate cancer patients, many professionals urged to have national system to monitor the quality of prostate cancer care. To gain its objective, the prostate cancer database system was planned and cautiously accommodated different views from various professions. Methods: This prostate cancer research database system incorporates information about a prostate cancer research including demographics, medical history, operation information, laboratory, and quality of life surveys. And, this system includes three different ways of clinical data collection to produce a comprehensive data base; direct data extraction from electronic medical record (EMR) system, manual data entry after linking EMR documents like magnetic resonance imaging findings and paper-based data collection for survey from patients. Results: We implemented clinical data warehouse technology to test direct EMR link method with St. Mary’s Hospital system. Using this method, total number of eligible patients were 2,300 from 1997 until 2012. Among them, 538 patients conducted surgery and others have different treatments. Conclusions: Our database system could provide the infrastructure for collecting error free data to support various retrospective and prospective studies. PMID:24223403

  19. Using online databases to find journal articles on injury prevention and safety promotion research: key journals and the databases that index them.

    PubMed

    Lawrence, D W; Laflamme, L

    2008-04-01

    (1) To determine the trends of the number of journals that publish injury prevention and safety promotion (IPSP) articles and the number of articles published each year from 1900 through 2006; (2) to determine the coverage of key IPSP journals in widely used literature databases. Journals were identified through a structured procedure that included hand-searching selected classification categories of two major listings of periodicals that publish four or more IPSP-relevant articles per year. Article relevance was assessed using the inclusion criteria for SafetyLit (a database of scholarly literature selected for its relevance to the IPSP field). Each identified journal was hand-searched from its first issue, and IPSP-relevant articles were added to the SafetyLit archive database. A MySQL database was used to perform basic queries and statistical summary analyses for journals published 1900-2006. The number of IPSP journals and journal articles was plotted for these years to identify publication trends. The publication year range of each IPSP journal was compared with the coverage, if any, of the journals in each of the five databases. Of the 17 839 journals assessed, 597 met the threshold for inclusion in this study. This amounts to thousands of IPSP-related articles published each year: 6100 in 2006. Only 160 (26.8%) of the journals are included in all five databases, and none have all publication years included in all of the databases. Some key IPSP journals are completely excluded from some of the databases. Thus, a search in a single database may miss key information from one of the many disciplines that publish IPSP-relevant information.

  20. Overall Similar Infection Rates Reported in the Physician-reported Scoliosis Research Society Database and the Chart-abstracted American College of Surgeons National Surgical Quality Improvement Program Database.

    PubMed

    Webb, Matthew L; Lukasiewicz, Adam M; Samuel, Andre M; Bohl, Daniel D; Basques, Bryce A; Varthi, Arya G; Grauer, Jonathan N

    2015-09-15

    This is a retrospective cohort study. To compare the infection rates in the Scoliosis Research Society (SRS) morbidity and mortality database to those in the American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP) database. Surgical databases have demonstrated value in orthopaedic surgery. However, few studies in the literature have used the SRS database relative to other available databases. To validate the surgeon-reported data of the SRS database, we compared the rate of postoperative infection in this database to that in the chart-abstracted ACS-NSQIP database. International Classification of Disease, ninth revision (ICD-9) codes were used to group patients from the 2012 and 2013 ACS-NSQIP database into groups corresponding to spinal deformity diagnoses delineated by SRS. Postoperative infection rates after surgical correction of these deformities compared with those reported in the 2012 and 2013 SRS database using χ tests. The overall rate of acute postoperative infection was slightly lower in the SRS database than in the ACS-NSQIP database (1.21% compared to 2.05% in ACS-NSQIP, a difference of only 0.84%, statistically significant, P < 0.001).The infection rates of most diagnoses did not differ; these included scoliosis (idiopathic <10 yr of age/congenital/neuromuscular/other scoliosis), spondylolisthesis (isthmic/dysplastic), and kyphosis (congenital and other). The only differences noted were in Scheuermann kyphosis (difference of 5.49%, P = 0.003), degenerative spondylolithesis (difference of 0.69%, P = 0.003), and idiopathic scoliosis in the age 10 to18 yr and adult age ranges (differences of 1.10% and 1.28%, P < 0.001 for both). Although some statistical differences were found in infection rates between the surgeon-reported SRS database and the chart-abstracted ACS-NSQIP database, these small differences likely reflect differences in surgical cases and data collection methods. This finding supports the validity of the

  1. Costs associated with treatment of chronic low back pain: an analysis of the UK General Practice Research Database.

    PubMed

    Hong, Jihyung; Reed, Catherine; Novick, Diego; Happich, Michael

    2013-01-01

    Retrospective cohort study of health care costs associated with the treatment of chronic low back pain (CLBP) in the United Kingdom. To assess 12-month health care costs associated with the treatment of CLBP, using the UK General Practice Research Database. CLBP is a common health problem. Data were obtained from the General Practice Research Database, a computerized database of UK primary care patient data. Patients with CLBP were identified for the study period (January 1, 2007, to December 31, 2009) using diagnostic records and pain relief prescriptions (n = 64,167), and 1:1 matched to patients without CLBP (n = 52,986) on the basis of age, sex, and general practitioner's practice. Index date was defined as the first date of CLBP record; the same index date was assigned to matched controls. Multivariate analyses were performed to compare resource use costs (2009 values) in the 12 months after the index date between patients with and without CLBP. A sensitivity analysis was carried out with a more stringent definition for the control group by excluding a broad range of pain conditions. Total health care costs for patients with CLBP were double those of the matched controls (£1074 vs. £516; P < 0.05). Of the cost difference, 58.8% was accounted for by general practitioner's consultations, 22.3% by referrals to secondary care, and the rest by pain relief medications. The sensitivity analysis revealed an even greater cost difference between the 2 groups (£1052 vs. £304; P < 0.05). Because of the use of a retrospective administrative claims database, this study is subject to selection bias between study cohorts, misidentification of comorbidities, and an inability to confirm adherence to therapy or assess indirect costs and costs of over-the-counter medications. Our findings confirm the substantial economic burden of CLBP, even with direct costs only.

  2. Designing and recruiting to UK autism spectrum disorder research databases: do they include representative children with valid ASD diagnoses?

    PubMed Central

    Warnell, F; George, B; McConachie, H; Johnson, M; Hardy, R; Parr, J R

    2015-01-01

    Objectives (1) Describe how the Autism Spectrum Database-UK (ASD-UK) was established; (2) investigate the representativeness of the first 1000 children and families who participated, compared to those who chose not to; (3) investigate the reliability of the parent-reported Autism Spectrum Disorder (ASD) diagnoses, and present evidence about the validity of diagnoses, that is, whether children recruited actually have an ASD; (4) present evidence about the representativeness of the ASD-UK children and families, by comparing their characteristics with the first 1000 children and families from the regional Database of children with ASD living in the North East (Daslne), and children and families identified from epidemiological studies. Setting Recruitment through a network of 50 UK child health teams and self-referral. Patients Parents/carers with a child with ASD, aged 2–16 years, completed questionnaires about ASD and some gave professionals’ reports about their children. Results 1000 families registered with ASD-UK in 30 months. Children of families who participated, and of the 208 who chose not to, were found to be very similar on: gender ratio, year of birth, ASD diagnosis and social deprivation score. The reliability of parent-reported ASD diagnoses of children was very high when compared with clinical reports (over 96%); no database child without ASD was identified. A comparison of gender, ASD diagnosis, age at diagnosis, school placement, learning disability, and deprivation score of children and families from ASD-UK with 1084 children and families from Daslne, and families from population studies, showed that ASD-UK families are representative of families of children with ASD overall. Conclusions ASD-UK includes families providing parent-reported data about their child and family, who appear to be broadly representative of UK children with ASD. Families continue to join the databases and more than 3000 families can now be contacted by researchers

  3. Identification of Oxygenated Fatty Acid as a Side Chain of Lipo-Alkaloids in Aconitum carmichaelii by UHPLC-Q-TOF-MS and a Database.

    PubMed

    Liang, Ying; Wu, Jian-Lin; Leung, Elaine Lai-Han; Zhou, Hua; Liu, Zhongqiu; Yan, Guanyu; Liu, Ying; Liu, Liang; Li, Na

    2016-03-31

    Lipo-alkaloid is a kind of C19-norditerpenoid alkaloid usually found in Aconitum species. Structurally, they contain an aconitane skeleton and one or two fatty acid moieties of 3-25 carbon chains with 1-6 unsaturated degrees. Analysis of the lipo-alkaloids in roots of Aconitum carmichaelii resulted in the isolation of six known pure lipo-alkaloids (A1-A6) and a lipo-alkaloid mixture (A7). The mixture shared the same aconitane skeleton of 14-benzoylmesaconine, but their side chains were determined to be 9-hydroxy-octadecadienoic acid, 13-hydroxy-octadecadienoic acid and 10-hydroxy-octadecadienoic acid, respectively, by MS/MS analysis after alkaline hydrolysis. To our knowledge, this is the first time of the reporting of the oxygenated fatty acids as the side chains in naturally-occurring lipo-alkaloids. In order to identify more lipo-alkaloids, a compound database was established based on various combinations between the aconitane skeleton and the fatty acid chain, and then, the identification of lipo-alkaloids was conducted using the database, UHPLC-Q-TOF-MS and MS/MS. Finally, 148 lipo-alkaloids were identified from A. carmichaelii after intensive MS/MS analysis, including 93 potential new compounds and 38 compounds with oxygenated fatty acid moieties.

  4. An Integrated Sequence-Structure Database incorporating matching mRNA sequence, amino acid sequence and protein three-dimensional structure data.

    PubMed Central

    Adzhubei, I A; Adzhubei, A A; Neidle, S

    1998-01-01

    We have constructed a non-homologous database, termed the Integrated Sequence-Structure Database (ISSD) which comprises the coding sequences of genes, amino acid sequences of the corresponding proteins, their secondary structure and straight phi,psi angles assignments, and polypeptide backbone coordinates. Each protein entry in the database holds the alignment of nucleotide sequence, amino acid sequence and the PDB three-dimensional structure data. The nucleotide and amino acid sequences for each entry are selected on the basis of exact matches of the source organism and cell environment. The current version 1.0 of ISSD is available on the WWW at http://www.protein.bio.msu.su/issd/ and includes 107 non-homologous mammalian proteins, of which 80 are human proteins. The database has been used by us for the analysis of synonymous codon usage patterns in mRNA sequences showing their correlation with the three-dimensional structure features in the encoded proteins. Possible ISSD applications include optimisation of protein expression, improvement of the protein structure prediction accuracy, and analysis of evolutionary aspects of the nucleotide sequence-protein structure relationship. PMID:9399866

  5. PGSB PlantsDB: updates to the database framework for comparative plant genome research

    PubMed Central

    Spannagl, Manuel; Nussbaumer, Thomas; Bader, Kai C.; Martis, Mihaela M.; Seidel, Michael; Kugler, Karl G.; Gundlach, Heidrun; Mayer, Klaus F.X.

    2016-01-01

    PGSB (Plant Genome and Systems Biology: formerly MIPS) PlantsDB (http://pgsb.helmholtz-muenchen.de/plant/index.jsp) is a database framework for the comparative analysis and visualization of plant genome data. The resource has been updated with new data sets and types as well as specialized tools and interfaces to address user demands for intuitive access to complex plant genome data. In its latest incarnation, we have re-worked both the layout and navigation structure and implemented new keyword search options and a new BLAST sequence search functionality. Actively involved in corresponding sequencing consortia, PlantsDB has dedicated special efforts to the integration and visualization of complex triticeae genome data, especially for barley, wheat and rye. We enhanced CrowsNest, a tool to visualize syntenic relationships between genomes, with data from the wheat sub-genome progenitor Aegilops tauschii and added functionality to the PGSB RNASeqExpressionBrowser. GenomeZipper results were integrated for the genomes of barley, rye, wheat and perennial ryegrass and interactive access is granted through PlantsDB interfaces. Data exchange and cross-linking between PlantsDB and other plant genome databases is stimulated by the transPLANT project (http://transplantdb.eu/). PMID:26527721

  6. Pressure ulcer research funding in America: creation and analysis of an on-line database.

    PubMed

    Zanca, Jeanne M; Brienza, David M; Berlowitz, Dan; Bennett, Richard G; Lyder, Courtney H

    2003-01-01

    To systematically collect information on active research grants to characterize pressure ulcer research funding in the United States and to identify potential targets for future research and funding initiatives. DESIGN A descriptive study. The investigators identified 32 grants, representing 16,444,117 US dollars in research funding. The majority of this funding came from federal sources, including the National Institutes of Health (90%), the Department of Veterans Affairs (7%), the National Institute on Disability and Rehabilitation Research (2%), and the Agency for Healthcare Research and Quality (1%). One quarter of pressure ulcer research grants related to quality improvement. Additional topic areas included risk factors or risk assessment tools (19%), adjunctive therapy (16%), mobilization (13%), and pressure management in foot care for patients with diabetes mellitus (9%). Further grants were in the areas of incidence, assessing tissue damage or healing, support surfaces, dressings and topical agents, nutrition, economic evaluation, and pain. The investment in pressure ulcer research is minute compared with pressure ulcer treatment expenditures. Policy makers are urged to encourage increased federal and foundation funding for research concerning pressure ulcers. Researchers are also encouraged to develop well-designed proposals to obtain available research funding. Additional research is needed in the areas of pressure ulcer incidence and prevalence, support surface design and use, pain, operative treatment, economic impact, and education strategies for caregivers and patients.

  7. iSTAR First Light: Characterizing Astronomy Education Research Dissertations in the iSTAR Database

    ERIC Educational Resources Information Center

    Slater, Stephanie J.; Tatge, Coty B.; Bretones, Paulo S.; Slater, Timothy F.; Schleigh, Sharon P.; McKinnon, David; Heyer, Inge

    2016-01-01

    There is widespread interest among discipline-based science education researchers to situate their research in the existing scholarly literature base. Unfortunately, traditional approaches to conducting a thorough literature review are unduly hindered in astronomy education research as the venues in which scholarship is reported are fragmented and…

  8. Research Update: Highlights from the Out-of-School Time Database. Number 3

    ERIC Educational Resources Information Center

    Harris, Erin

    2008-01-01

    This "Research Update" explores two major themes: (1) Using evaluation to shape program improvement and planning; and (2) Out-of-school time benefits to older youth and their families. Themes were culled from 13 research and evaluation reports added to the Out-of-School Time (OST) Program Research and Evaluation Bibliography in September 2008.…

  9. Bibliometric analysis of nutrition and dietetics research activity in Arab countries using ISI Web of Science database.

    PubMed

    Sweileh, Waleed M; Al-Jabi, Samah W; Sawalha, Ansam F; Zyoud, Sa'ed H

    2014-01-01

    Reducing nutrition-related health problems in Arab countries requires an understanding of the performance of Arab countries in the field of nutrition and dietetics research. Assessment of research activity from a particular country or region could be achieved through bibliometric analysis. This study was carried out to investigate research activity in "nutrition and dietetics" in Arab countries. Original and review articles published from Arab countries in "nutrition and dietetics" Web of Science category up until 2012 were retrieved and analyzed using the ISI Web of Science database. The total number of documents published in "nutrition and dietetics" category from Arab countries was 2062. This constitutes 1% of worldwide research activity in the field. Annual research productivity showed a significant increase after 2005. Approximately 60% of published documents originated from three Arab countries, particularly Egypt, Kingdom of Saudi Arabia, and Tunisia. However, Kuwait has the highest research productivity per million inhabitants. Main research areas of published documents were in "Food Science/Technology" and "Chemistry" which constituted 75% of published documents compared with 25% for worldwide documents in nutrition and dietetics. A total of 329 (15.96%) nutrition - related diabetes or obesity or cancer documents were published from Arab countries compared with 21% for worldwide published documents. Interest in nutrition and dietetics research is relatively recent in Arab countries. Focus of nutrition research is mainly toward food technology and chemistry with lesser activity toward nutrition-related health research. International cooperation in nutrition research will definitely help Arab researchers in implementing nutrition research that will lead to better national policies regarding nutrition.

  10. YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research.

    PubMed

    Cheng, Wei-Chung; Chung, I-Fang; Tsai, Cheng-Fong; Huang, Tse-Shun; Chen, Chen-Yang; Wang, Shao-Chuan; Chang, Ting-Yu; Sun, Hsing-Jen; Chao, Jeffrey Yung-Chuan; Cheng, Cheng-Chung; Wu, Cheng-Wen; Wang, Hsei-Wei

    2015-01-01

    We previously presented YM500, which is an integrated database for miRNA quantification, isomiR identification, arm switching discovery and novel miRNA prediction from 468 human smRNA-seq datasets. Here in this updated YM500v2 database (http://ngs.ym.edu.tw/ym500/), we focus on the cancer miRNome to make the database more disease-orientated. New miRNA-related algorithms developed after YM500 were included in YM500v2, and, more significantly, more than 8000 cancer-related smRNA-seq datasets (including those of primary tumors, paired normal tissues, PBMC, recurrent tumors, and metastatic tumors) were incorporated into YM500v2. Novel miRNAs (miRNAs not included in the miRBase R21) were not only predicted by three independent algorithms but also cleaned by a new in silico filtration strategy and validated by wetlab data such as Cross-Linked ImmunoPrecipitation sequencing (CLIP-seq) to reduce the false-positive rate. A new function 'Meta-analysis' is additionally provided for allowing users to identify real-time differentially expressed miRNAs and arm-switching events according to customer-defined sample groups and dozens of clinical criteria tidying up by proficient clinicians. Cancer miRNAs identified hold the potential for both basic research and biotech applications.

  11. Nucleic acid aptamers: research tools in disease diagnostics and therapeutics.

    PubMed

    Santosh, Baby; Yadava, Pramod K

    2014-01-01

    Aptamers are short sequences of nucleic acid (DNA or RNA) or peptide molecules which adopt a conformation and bind cognate ligands with high affinity and specificity in a manner akin to antibody-antigen interactions. It has been globally acknowledged that aptamers promise a plethora of diagnostic and therapeutic applications. Although use of nucleic acid aptamers as targeted therapeutics or mediators of targeted drug delivery is a relatively new avenue of research, one aptamer-based drug "Macugen" is FDA approved and a series of aptamer-based drugs are in clinical pipelines. The present review discusses the aspects of design, unique properties, applications, and development of different aptamers to aid in cancer diagnosis, prevention, and/or treatment under defined conditions.

  12. Nucleic Acid Aptamers: Research Tools in Disease Diagnostics and Therapeutics

    PubMed Central

    Yadava, Pramod K.

    2014-01-01

    Aptamers are short sequences of nucleic acid (DNA or RNA) or peptide molecules which adopt a conformation and bind cognate ligands with high affinity and specificity in a manner akin to antibody-antigen interactions. It has been globally acknowledged that aptamers promise a plethora of diagnostic and therapeutic applications. Although use of nucleic acid aptamers as targeted therapeutics or mediators of targeted drug delivery is a relatively new avenue of research, one aptamer-based drug “Macugen” is FDA approved and a series of aptamer-based drugs are in clinical pipelines. The present review discusses the aspects of design, unique properties, applications, and development of different aptamers to aid in cancer diagnosis, prevention, and/or treatment under defined conditions. PMID:25050359

  13. The Energy Science and Technology Database on a local library system: A case study at the Los Alamos National Research Library

    SciTech Connect

    Holtkamp, I.S.

    1994-10-01

    This paper presents an overview of efforts at Los Alamos National Laboratory to acquire and mount the Energy Science and Technology Database (EDB) as a citation database on the Research Library`s Geac Advance system. The rationale for undertaking this project and expected benefits are explained. Significant issues explored are loading non-USMARC records into a MARC-based library system, the use of EDB records to replace or supplement in-house cataloging of technical reports, the impact of different cataloging standards and database size on searching and retrieval, and how integrating an external database into the library`s online catalog may affect staffing and workflow.

  14. BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types

    PubMed Central

    Howe, E.A.; de Souza, A.; Lahr, D.L.; Chatwin, S.; Montgomery, P.; Alexander, B.R.; Nguyen, D.-T.; Cruz, Y.; Stonich, D.A.; Walzer, G.; Rose, J.T.; Picard, S.C.; Liu, Z.; Rose, J.N.; Xiang, X.; Asiedu, J.; Durkin, D.; Levine, J.; Yang, J.J.; Schürer, S.C.; Braisted, J.C.; Southall, N.; Southern, M.R.; Chung, T.D.Y.; Brudz, S.; Tanega, C.; Schreiber, S.L.; Bittker, J.A.; Guha, R.; Clemons, P.A.

    2015-01-01

    BARD, the BioAssay Research Database (https://bard.nih.gov/) is a public database and suite of tools developed to provide access to bioassay data produced by the NIH Molecular Libraries Program (MLP). Data from 631 MLP projects were migrated to a new structured vocabulary designed to capture bioassay data in a formalized manner, with particular emphasis placed on the description of assay protocols. New data can be submitted to BARD with a user-friendly set of tools that assist in the creation of appropriately formatted datasets and assay definitions. Data published through the BARD application program interface (API) can be accessed by researchers using web-based query tools or a desktop client. Third-party developers wishing to create new tools can use the API to produce stand-alone tools or new plug-ins that can be integrated into BARD. The entire BARD suite of tools therefore supports three classes of researcher: those who wish to publish data, those who wish to mine data for testable hypotheses, and those in the developer community who wish to build tools that leverage this carefully curated chemical biology resource. PMID:25477388

  15. The Use of Research Electronic Data Capture (REDCap) Software to Create a Database of Librarian-Mediated Literature Searches

    PubMed Central

    LYON, JENNIFER A.; GARCIA-MILIAN, ROLANDO; NORTON, HANNAH F.; TENNANT, MICHELE R.

    2015-01-01

    Expert-mediated literature searching, a keystone service in biomedical librarianship, would benefit significantly from regular methodical review. This paper describes the novel use of Research Electronic Data Capture (REDCap) software to create a database of literature searches conducted at a large academic health sciences library. An archive of paper search requests was entered into REDCap, and librarians now prospectively enter records for current searches. Having search data readily available allows librarians to reuse search strategies and track their workload. In aggregate, this data can help guide practice and determine priorities by identifying users’ needs, tracking librarian effort, and focusing librarians’ continuing education. PMID:25023012

  16. Effect of competition bias in safety signal generation: analysis of a research database of spontaneous reports in France.

    PubMed

    Pariente, Antoine; Avillach, Paul; Salvo, Francesco; Thiessard, Frantz; Miremont-Salamé, Ghada; Fourrier-Reglat, Annie; Haramburu, Françoise; Bégaud, Bernard; Moore, Nicholas

    2012-10-01

    Automated disproportionality analysis of spontaneous reporting is increasingly used routinely. It can theoretically be influenced by a competition bias for signal detection owing to the presence of reports related to well-established drug-event associations. The aim of the study was to explore the effects of competition bias on safety signals generated from a large spontaneous reporting research database. Using the case/non-case approach in the French spontaneous reporting research database, which includes data of reporting in France from January 1986 to December 2001, the effects of the competition bias were explored by generating safety signals associated with six events of interest (gastric and oesophageal haemorrhages, central nervous system haemorrhage and cerebrovascular accidents, ischaemic coronary disorders, migraine headaches, muscle pains, and hepatic enzymes and function abnormalities) before and after removing from the database reports relating to drugs known to be strongly associated with these events, whether they constituted cases or non-cases. As this study was performed on a closed database (last data entered 31 December 2001), potential signals unmasked by removal were considered as real signals if no or only incomplete knowledge about the association was available from the literature before 1 January 2002. For gastric and oesophageal haemorrhages, after removing reports involving antithrombotic agents or NSAIDs, three potential signals were unmasked (prednisone, rivastigmine and isotretinoin). For central nervous system haemorrhage and cerebrovascular accidents, after removing reports involving antithrombotic agents, three potential signals were unmasked (ethinylestradiol, interferon-α-2B and methylprednisolone). For ischaemic coronary disorders, after removing reports involving anthracyclines, bleomycine, anti-HIV drugs or triptans, one potential signal was unmasked (ondansetron). For migraine headaches, after removing reports involving

  17. A spatial classification and database for management, research, and policy making: The Great Lakes aquatic habitat framework

    USGS Publications Warehouse

    Wang, Lizhu; Riseng, Catherine M.; Mason, Lacey; Werhrly, Kevin; Rutherford, Edward; McKenna, James E.; Castiglione, Chris; Johnson, Lucinda B.; Infante, Dana M.; Sowa, Scott P.; Robertson, Mike; Schaeffer, Jeff; Khoury, Mary; Gaiot, John; Hollenhurst, Tom; Brooks, Colin N.; Coscarelli, Mark

    2015-01-01

    Managing the world's largest and most complex freshwater ecosystem, the Laurentian Great Lakes, requires a spatially hierarchical basin-wide database of ecological and socioeconomic information that is comparable across the region. To meet such a need, we developed a spatial classification framework and database — Great Lakes Aquatic Habitat Framework (GLAHF). GLAHF consists of catchments, coastal terrestrial, coastal margin, nearshore, and offshore zones that encompass the entire Great Lakes Basin. The catchments captured in the database as river pour points or coastline segments are attributed with data known to influence physicochemical and biological characteristics of the lakes from the catchments. The coastal terrestrial zone consists of 30-m grid cells attributed with data from the terrestrial region that has direct connection with the lakes. The coastal margin and nearshore zones consist of 30-m grid cells attributed with data describing the coastline conditions, coastal human disturbances, and moderately to highly variable physicochemical and biological characteristics. The offshore zone consists of 1.8-km grid cells attributed with data that are spatially less variable compared with the other aquatic zones. These spatial classification zones and their associated data are nested within lake sub-basins and political boundaries and allow the synthesis of information from grid cells to classification zones, within and among political boundaries, lake sub-basins, Great Lakes, or within the entire Great Lakes Basin. This spatially structured database could help the development of basin-wide management plans, prioritize locations for funding and specific management actions, track protection and restoration progress, and conduct research for science-based decision making.

  18. The Starkey habitat database for ungulate research: construction, documentation, and use.

    Treesearch

    Mary M. Rowland; Priscilla K. Coe; Rosemary J. Stussy; [and others].

    1998-01-01

    The Starkey Project, a large-scale, multidisciplinary research venture, began in 1987 in the Starkey Experimental Forest and Range in northeast Oregon. Researchers are studying effects of forest management on interactions and habitat use of mule deer (Odocoileus hemionus hemionus), elk (Cervus elaphus nelsoni), and cattle. A...

  19. Immediate Dissemination of Student Discoveries to a Model Organism Database Enhances Classroom-Based Research Experiences

    ERIC Educational Resources Information Center

    Wiley, Emily A.; Stover, Nicholas A.

    2014-01-01

    Use of inquiry-based research modules in the classroom has soared over recent years, largely in response to national calls for teaching that provides experience with scientific processes and methodologies. To increase the visibility of in-class studies among interested researchers and to strengthen their impact on student learning, we have…

  20. Immediate Dissemination of Student Discoveries to a Model Organism Database Enhances Classroom-Based Research Experiences

    ERIC Educational Resources Information Center

    Wiley, Emily A.; Stover, Nicholas A.

    2014-01-01

    Use of inquiry-based research modules in the classroom has soared over recent years, largely in response to national calls for teaching that provides experience with scientific processes and methodologies. To increase the visibility of in-class studies among interested researchers and to strengthen their impact on student learning, we have…

  1. Slim-Prim: A Biomedical Informatics Database to Promote Translational Research

    PubMed Central

    Viangteeravat, Teeradache; Brooks, Ian M; Smith, Ebony J; Furlotte, Nicolas; Vuthipadadon, Somchan; Reynolds, Rebecca; McDonald, Chanchai Singhanayok

    2009-01-01

    With the current national emphasis on translational research, data-exchange systems that can bridge the basic and clinical sciences are vital. To meet this challenge, we have developed Slim-Prim, an integrated data system (IDS) for collecting, processing, archiving, and distributing basic and clinical research data. Slim-Prim is accessed via user-friendly Web-based applications, thus increasing data accessibility and eliminating the security risks inherent with office or laboratory servers. Slim-Prim serves as a laboratory management interface and archival data repository for institutional projects. Importantly, multiple levels of controlled access allow HIPAA-compliant sharing of de-identified information to facilitate data sharing and analysis across research domains; thus Slim-Prim encourages collaboration between researchers and clinicians, an essential factor in the development of translational research. Slim-Prim is an example of utilizing an IDS to improve organizational efficiency and to bridge the gap between laboratory discovery and practice. PMID:19471646

  2. Slim-prim: a biomedical informatics database to promote translational research.

    PubMed

    Viangteeravat, Teeradache; Brooks, Ian M; Smith, Ebony J; Furlotte, Nicolas; Vuthipadadon, Somchan; Reynolds, Rebecca; McDonald, Chanchai Singhanayok

    2009-05-08

    With the current national emphasis on translational research, data-exchange systems that can bridge the basic and clinical sciences are vital. To meet this challenge, we have developed Slim-Prim, an integrated data system (IDS) for collecting, processing, archiving, and distributing basic and clinical research data. Slim-Prim is accessed via user-friendly Web-based applications, thus increasing data accessibility and eliminating the security risks inherent with office or laboratory servers. Slim-Prim serves as a laboratory management interface and archival data repository for institutional projects. Importantly, multiple levels of controlled access allow HIPAA-compliant sharing of de-identified information to facilitate data sharing and analysis across research domains; thus Slim-Prim encourages collaboration between researchers and clinicians, an essential factor in the development of translational research. Slim-Prim is an example of utilizing an IDS to improve organizational efficiency and to bridge the gap between laboratory discovery and practice.

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

    PubMed

    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.

  4. Comparison of Indian Council for Medical Research and Lunar Databases for Categorization of Male Bone Mineral Density.

    PubMed

    Singh, Surya K; Patel, Vivek H; Gupta, Balram

    2017-06-19

    The mainstay of diagnosis of osteoporosis is dual-energy X-ray absorptiometry (DXA) scan measuring areal bone mineral density (BMD) (g/cm(2)). The aim of the present study was to compare the Indian Council of Medical Research database (ICMRD) and the Lunar ethnic reference database of DXA scans in the diagnosis of osteoporosis in male patients. In this retrospective study, all male patients who underwent a DXA scan were included. The areal BMD (g/cm(2)) was measured at either the lumbar spine (L1-L4) or the total hip using the Lunar DXA machine (software version 8.50) manufactured by GE Medical Systems (Shanghai, China). The Indian Council of Medical Research published a reference data for BMD in the Indian population derived from the population-based study conducted in healthy Indian individuals, which was used to analyze the BMD result by Lunar DXA scan. The 2 results were compared for various values using statistical software SPSS for Windows (version 16; SPSS Inc., Chicago, IL). A total 238 male patients with a mean age of 57.2 yr (standard deviation ±15.9) were included. Overall, 26.4% (66/250) and 2.8% (7/250) of the subjects were classified in the osteoporosis group according to the Lunar database and the ICMRD, respectively. Out of the 250 sites of the DXA scan, 28.8% (19/66) and 60.0% (40/66) of the cases classified as osteoporosis by the Lunar database were reclassified as normal and osteopenia by ICMRD, respectively. In conclusion, the Indian Council of Medical Research data underestimated the degree of osteoporosis in male subjects that might result in deferring of treatment. In view of the discrepancy, the decision on the treatment of osteoporosis should be based on the multiple fracture risk factors and less reliably on the BMD T-score. Copyright © 2017 The International Society for Clinical Densitometry. Published by Elsevier Inc. All rights reserved.

  5. RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database.

    PubMed

    Miao, Zhichao; Westhof, Eric

    2016-07-08

    RBscore&NBench combines a web server, RBscore and a database, NBench. RBscore predicts RNA-/DNA-binding residues in proteins and visualizes the prediction scores and features on protein structures. The scoring scheme of RBscore directly links feature values to nucleic acid binding probabilities and illustrates the nucleic acid binding energy funnel on the protein surface. To avoid dataset, binding site definition and assessment metric biases, we compared RBscore with 18 web servers and 3 stand-alone programs on 41 datasets, which demonstrated the high and stable accuracy of RBscore. A comprehensive comparison led us to develop a benchmark database named NBench. The web server is available on: http://ahsoka.u-strasbg.fr/rbscorenbench/.

  6. NeuPAT: an intranet database supporting translational research in neuroblastic tumors.

    PubMed

    Villamón, Eva; Piqueras, Marta; Meseguer, Javier; Blanquer, Ignacio; Berbegall, Ana P; Tadeo, Irene; Hernández, Vicente; Navarro, Samuel; Noguera, Rosa

    2013-03-01

    Translational research in oncology is directed mainly towards establishing a better risk stratification and searching for appropriate therapeutic targets. This research generates a tremendous amount of complex clinical and biological data needing speedy and effective management. The authors describe the design, implementation and early experiences of a computer-aided system for the integration and management of data for neuroblastoma patients. NeuPAT facilitates clinical and translational research, minimizes the workload in consolidating the information, reduces errors and increases correlation of data through extensive coding. This design can also be applied to other tumor types. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. Asthma research performance in Asia-Pacific: a bibliometric analysis by searching PubMed database.

    PubMed

    Klaewsongkram, Jettanong; Reantragoon, Rangsima

    2009-12-01

    Countries in the Asia-Pacific region have experienced an increase in the prevalence of asthma, and they have been actively involved in asthma research recently. This study aimed to analyze asthma research from Asia-Pacific in the last decade by bibliometric method. Asthma articles from Asia-Pacific countries published between 1998 and 2007 were retrieved from PubMed by searching MeSH for "asthma." Most of published asthma articles in Asia-Pacific are from affluent countries in northeast Asia and Oceania. Australia and Japan have been the regional powerhouses since they contributed more than half of regional articles on asthma. Asthma publications from emerging economies in Asia such as South Korea, Taiwan, Hong Kong, and Singapore, have dramatically increased in the last decade in terms of quantity and quality aspects and were considerable sources of basic and translational research in the region. Mainland China and India have significantly increased their research capacity as well, but quality needs to be improved. Asthma publications from New Zealand and Australia, countries with the highest asthma prevalence rates in the world, yielded highest citation counts per articles and were published in journals with high impact factor. Asthma research parameters per million population correlate well with gross domestic product per capita. Almost half (41%) of total articles were produced from only 25 institutions in the region and almost half of them (47%) were published in 20 journals. Asthma research in Asia-Pacific were mainly conducted in countries in Oceania and Northeast Asia and research performance strongly correlated with the nation's wealth. Interesting asthma research projects in the region were recommended.

  8. [Research and development of medical case database: a novel medical case information system integrating with biospecimen management].

    PubMed

    Pan, Shiyang; Mu, Yuan; Wang, Hong; Wang, Tong; Huang, Peijun; Ma, Jianfeng; Jiang, Li; Zhang, Jie; Gu, Bing; Yi, Lujiang

    2010-04-01

    To meet the needs of management of medical case information and biospecimen simultaneously, we developed a novel medical case information system integrating with biospecimen management. The database established by MS SQL Server 2000 covered, basic information, clinical diagnosis, imaging diagnosis, pathological diagnosis and clinical treatment of patient; physicochemical property, inventory management and laboratory analysis of biospecimen; users log and data maintenance. The client application developed by Visual C++ 6.0 was used to implement medical case and biospecimen management, which was based on Client/Server model. This system can perform input, browse, inquest, summary of case and related biospecimen information, and can automatically synthesize case-records based on the database. Management of not only a long-term follow-up on individual, but also of grouped cases organized according to the aim of research can be achieved by the system. This system can improve the efficiency and quality of clinical researches while biospecimens are used coordinately. It realizes synthesized and dynamic management of medical case and biospecimen, which may be considered as a new management platform.

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

    NASA Astrophysics Data System (ADS)

    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.

  10. Meteor Databases in Astronomy

    NASA Astrophysics Data System (ADS)

    Kolomiyets, Svitlana V.

    2017-06-01

    There are specific problems of databases in meteor science such as making meteor databases into the modern research tools. Special institutes and virtual observatories exist for the meteor data storage where the data is online and in open access. However, there are also numerous databases without the open access, such as for example, three radar databases: Kharkiv database with 250,000 meteor orbits in Ukraine, New Zealand database with 500,000 meteor orbits, and Canadian database with more than 3 million meteor orbits. One of the reasons the open access is absent for these databases could be the complexity in the copyright compliance. In the framework of the creation of the modern effective research tool in the meteor science, we discuss here the case of the Kharkiv meteor database.

  11. Evidence for ASD recurrence rates and reproductive stoppage from large UK ASD research family databases.

    PubMed

    Wood, Claire L; Warnell, Frances; Johnson, Mary; Hames, Annette; Pearce, Mark S; McConachie, Helen; Parr, Jeremy R

    2015-02-01

    Following a diagnosis of a developmental disorder such as autism spectrum disorder (ASD) in early childhood, parents may decide to have fewer children than previously planned. The tendency for families to halt reproduction after receiving a diagnosis for one child is known as reproductive stoppage. Stoppage may lead to an underestimate of recurrence risk estimates of parents having more than one child with ASD. Using two large UK ASD family databases, we investigated recurrence rates for ASD and evidence for reproductive stoppage for both ASD and undiagnosed ASD/broader autism phenotype in a subgroup of families. Reproductive stoppage was tested for using the Mann-Whitney U-test to disprove the null hypothesis that affected and nonaffected children were distributed randomly by birth order. Dahlberg's later-sib method was used to estimate recurrence risk and take stoppage into account. Data were available from 299 families (660 children) including 327 with ASD. Ten percent of the complete families had more than one child with an ASD. Using Dahlberg's later-sib method, the recurrence risk for ASD was 24.7% overall and 50.0% in families with two or more older siblings with ASD. Children with ASD were born significantly later in families than those without ASD in all sibship combinations. This study shows strong evidence that ASD is associated with reproductive stoppage. These data have important implications for family planning and genetic counseling.

  12. Propulsion System Airframe Integration Issues and Aerodynamic Database Development for the Hyper-X Flight Research Vehicle

    NASA Technical Reports Server (NTRS)

    Engelund, Walter C.; Holland, Scott D.; Cockrell, Charles E., Jr.; Bittner, Robert D.

    1999-01-01

    NASA's Hyper-X Research Vehicle will provide a unique opportunity to obtain data on an operational airframe integrated scramjet propulsion system at true flight conditions. The airframe integrated nature of the scramjet engine with the Hyper-X vehicle results in a strong coupling effect between the propulsion system operation and the airframe s basic aerodynamic characteristics. Comments on general airframe integrated scramjet propulsion system effects on vehicle aerodynamic performance, stability, and control are provided, followed by examples specific to the Hyper-X research vehicle. An overview is provided of the current activities associated with the development of the Hyper-X aerodynamic database, including wind tunnel test activities and parallel CFD analysis efforts. A brief summary of the Hyper-X aerodynamic characteristics is provided, including the direct and indirect effects of the airframe integrated scramjet propulsion system operation on the basic airframe stability and control characteristics.

  13. Assessing worldwide research activity on probiotics in pediatrics using Scopus database: 1994-2014.

    PubMed

    Sweileh, Waleed M; Shraim, Naser Y; Al-Jabi, Samah W; Sawalha, Ansam F; Rahhal, Belal; Khayyat, Rasha A; Zyoud, Sa'ed H

    2016-01-01

    A wide variety of probiotic products has been introduced into the market in the past decade. Research trends and activity on probiotics help understand how these products were evolved and their potential future role in medicine. The objective of this study was to assess the research activity on probiotics in pediatrics using bibliometric indicators and network visualization. Original and review articles on probiotics in pediatrics published worldwide were retrieved from SciVerse, Scopus (1994-2014) and analyzed. VOSviewer was used for network visualization. The total number of documents published on probiotics in pediatrics was 2817. Research activity on probiotics in pediatrics showed approximately 90- fold increase during the study period. Approximately 22 % of published articles originated from USA and has the greatest share, however, Finland ranked first when data were stratified by population or income. The most productive institution in this field was Turku University in Finland with 82 (2.91 %) articles. Half of the prolific authors were also from Finland. Most of the published research activity appeared in Journal of Pediatric Gastroenterology and Nutrition. Most frequently encountered title terms include nutrition, infant formula, necrotizing enetrocolitis, allergy, and diarrhea. The total number of citations for the retreived documents documents was 70991, and the average citation per article was 25.20. Interest in probiotic research and its potential benefits in pediatric ailments is relatively recent but significantly increasing. Bibliometric analysis can be used as an indicator of the importance and growth of probiotic use in pediatrics.

  14. Phynx: an open source software solution supporting data management and web-based patient-level data review for drug safety studies in the general practice research database and other health care databases.

    PubMed

    Egbring, Marco; Kullak-Ublick, Gerd A; Russmann, Stefan

    2010-01-01

    To develop a software solution that supports management and clinical review of patient data from electronic medical records databases or claims databases for pharmacoepidemiological drug safety studies. We used open source software to build a data management system and an internet application with a Flex client on a Java application server with a MySQL database backend. The application is hosted on Amazon Elastic Compute Cloud. This solution named Phynx supports data management, Web-based display of electronic patient information, and interactive review of patient-level information in the individual clinical context. This system was applied to a dataset from the UK General Practice Research Database (GPRD). Our solution can be setup and customized with limited programming resources, and there is almost no extra cost for software. Access times are short, the displayed information is structured in chronological order and visually attractive, and selected information such as drug exposure can be blinded. External experts can review patient profiles and save evaluations and comments via a common Web browser. Phynx provides a flexible and economical solution for patient-level review of electronic medical information from databases considering the individual clinical context. It can therefore make an important contribution to an efficient validation of outcome assessment in drug safety database studies.

  15. Designing and recruiting to UK autism spectrum disorder research databases: do they include representative children with valid ASD diagnoses?

    PubMed

    Warnell, F; George, B; McConachie, H; Johnson, M; Hardy, R; Parr, J R

    2015-09-04

    (1) Describe how the Autism Spectrum Database-UK (ASD-UK) was established; (2) investigate the representativeness of the first 1000 children and families who participated, compared to those who chose not to; (3) investigate the reliability of the parent-reported Autism Spectrum Disorder (ASD) diagnoses, and present evidence about the validity of diagnoses, that is, whether children recruited actually have an ASD; (4) present evidence about the representativeness of the ASD-UK children and families, by comparing their characteristics with the first 1000 children and families from the regional Database of children with ASD living in the North East (Dasl(n)e), and children and families identified from epidemiological studies. Recruitment through a network of 50 UK child health teams and self-referral. Parents/carers with a child with ASD, aged 2-16 years, completed questionnaires about ASD and some gave professionals' reports about their children. 1000 families registered with ASD-UK in 30 months. Children of families who participated, and of the 208 who chose not to, were found to be very similar on: gender ratio, year of birth, ASD diagnosis and social deprivation score. The reliability of parent-reported ASD diagnoses of children was very high when compared with clinical reports (over 96%); no database child without ASD was identified. A comparison of gender, ASD diagnosis, age at diagnosis, school placement, learning disability, and deprivation score of children and families from ASD-UK with 1084 children and families from Dasl(n)e, and families from population studies, showed that ASD-UK families are representative of families of children with ASD overall. ASD-UK includes families providing parent-reported data about their child and family, who appear to be broadly representative of UK children with ASD. Families continue to join the databases and more than 3000 families can now be contacted by researchers about UK autism research. Published by the BMJ

  16. Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies

    PubMed Central

    Bouwman, Jildau; Dragsted, Lars O.; Drevon, Christian A.; Elliott, Ruan; de Groot, Philip; Kaput, Jim; Mathers, John C.; Müller, Michael; Pepping, Fre; Saito, Jahn; Scalbert, Augustin; Radonjic, Marijana; Rocca-Serra, Philippe; Travis, Anthony; Wopereis, Suzan; Evelo, Chris T.

    2010-01-01

    The challenge of modern nutrition and health research is to identify food-based strategies promoting life-long optimal health and well-being. This research is complex because it exploits a multitude of bioactive compounds acting on an extensive network of interacting processes. Whereas nutrition research can profit enormously from the revolution in ‘omics’ technologies, it has discipline-specific requirements for analytical and bioinformatic procedures. In addition to measurements of the parameters of interest (measures of health), extensive description of the subjects of study and foods or diets consumed is central for describing the nutritional phenotype. We propose and pursue an infrastructural activity of constructing the “Nutritional Phenotype database” (dbNP). When fully developed, dbNP will be a research and collaboration tool and a publicly available data and knowledge repository. Creation and implementation of the dbNP will maximize benefits to the research community by enabling integration and interrogation of data from multiple studies, from different research groups, different countries and different—omics levels. The dbNP is designed to facilitate storage of biologically relevant, pre-processed—omics data, as well as study descriptive and study participant phenotype data. It is also important to enable the combination of this information at different levels (e.g. to facilitate linkage of data describing participant phenotype, genotype and food intake with information on study design and—omics measurements, and to combine all of this with existing knowledge). The biological information stored in the database (i.e. genetics, transcriptomics, proteomics, biomarkers, metabolomics, functional assays, food intake and food composition) is tailored to nutrition research and embedded in an environment of standard procedures and protocols, annotations, modular data-basing, networking and integrated bioinformatics. The dbNP is an evolving enterprise

  17. Neodymium in the oceans: a global database, a regional comparison and implications for palaeoceanographic research

    PubMed Central

    Griffiths, Alexander M.; Lambelet, Myriam; Little, Susan H.; Stichel, Torben; Wilson, David J.

    2016-01-01

    The neodymium (Nd) isotopic composition of seawater has been used extensively to reconstruct ocean circulation on a variety of time scales. However, dissolved neodymium concentrations and isotopes do not always behave conservatively, and quantitative deconvolution of this non-conservative component can be used to detect trace metal inputs and isotopic exchange at ocean–sediment interfaces. In order to facilitate such comparisons for historical datasets, we here provide an extended global database for Nd isotopes and concentrations in the context of hydrography and nutrients. Since 2010, combined datasets for a large range of trace elements and isotopes are collected on international GEOTRACES section cruises, alongside classical nutrient and hydrography measurements. Here, we take a first step towards exploiting these datasets by comparing high-resolution Nd sections for the western and eastern North Atlantic in the context of hydrography, nutrients and aluminium (Al) concentrations. Evaluating those data in tracer–tracer space reveals that North Atlantic seawater Nd isotopes and concentrations generally follow the patterns of advection, as do Al concentrations. Deviations from water mass mixing are observed locally, associated with the addition or removal of trace metals in benthic nepheloid layers, exchange with ocean margins (i.e. boundary exchange) and/or exchange with particulate phases (i.e. reversible scavenging). We emphasize that the complexity of some of the new datasets cautions against a quantitative interpretation of individual palaeo Nd isotope records, and indicates the importance of spatial reconstructions for a more balanced approach to deciphering past ocean changes. This article is part of the themed issue ‘Biological and climatic impacts of ocean trace element chemistry’.

  18. Neodymium in the oceans: a global database, a regional comparison and implications for palaeoceanographic research

    NASA Astrophysics Data System (ADS)

    van de Flierdt, Tina; Griffiths, Alexander M.; Lambelet, Myriam; Little, Susan H.; Stichel, Torben; Wilson, David J.

    2016-11-01

    The neodymium (Nd) isotopic composition of seawater has been used extensively to reconstruct ocean circulation on a variety of time scales. However, dissolved neodymium concentrations and isotopes do not always behave conservatively, and quantitative deconvolution of this non-conservative component can be used to detect trace metal inputs and isotopic exchange at ocean-sediment interfaces. In order to facilitate such comparisons for historical datasets, we here provide an extended global database for Nd isotopes and concentrations in the context of hydrography and nutrients. Since 2010, combined datasets for a large range of trace elements and isotopes are collected on international GEOTRACES section cruises, alongside classical nutrient and hydrography measurements. Here, we take a first step towards exploiting these datasets by comparing high-resolution Nd sections for the western and eastern North Atlantic in the context of hydrography, nutrients and aluminium (Al) concentrations. Evaluating those data in tracer-tracer space reveals that North Atlantic seawater Nd isotopes and concentrations generally follow the patterns of advection, as do Al concentrations. Deviations from water mass mixing are observed locally, associated with the addition or removal of trace metals in benthic nepheloid layers, exchange with ocean margins (i.e. boundary exchange) and/or exchange with particulate phases (i.e. reversible scavenging). We emphasize that the complexity of some of the new datasets cautions against a quantitative interpretation of individual palaeo Nd isotope records, and indicates the importance of spatial reconstructions for a more balanced approach to deciphering past ocean changes. This article is part of the themed issue 'Biological and climatic impacts of ocean trace element chemistry'.

  19. U.S. Department of Agriculture Agricultural Research Service Mahantango Creek Watershed, Pennsylvania, United States: long-term stream discharge database

    USDA-ARS?s Scientific Manuscript database

    A long-term streamflow discharge database has been developed by the U.S. Department of Agriculture, Agricultural Research Service, Pasture Systems and Watershed Management Research Unit (PSWMRU) to support intensive hydrologic and water quality research within WE-38, a 7.3 km**2 experimental watersh...

  20. U.S. Department of Agriculture Agricultural Research Service Mahantango Creek Watershed, Pennsylvania, United States: long-term water quality database

    USDA-ARS?s Scientific Manuscript database

    The U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Pasture Systems and Watershed Management Research Unit (PSWMRU) has developed a long-term water quality database to support water quality research within the 7.3 km**2 WE-38 experimental watershed in east-central Pennsyl...

  1. Gypsy moths: Pest control research. (Latest citations from the Life Sciences Collection database). Published Search

    SciTech Connect

    Not Available

    1993-06-01

    The bibliography contains citations concerning control and research regarding gypsy moths or lymantria dispar. Both natural and synthetic controls are discussed, including parasites, viral diseases, fungal diseases, bird predation, bacterial diseases, pheromone trapping, insecticides, and physical and chemical localized protection. Laboratory and field studies on sex pheromones, environmental effects on life cycles, effects of feeding behavior, plant-insect interactions, and other research relating to the control of this forest pest are considered. (Contains 250 citations and includes a subject term index and title list.)

  2. Recycling rubber wastes. (Latest citations from the Rubber and Plastics Research Association database). Published Search

    SciTech Connect

    1995-02-01

    The bibliography contains citations concerning research and innovations in the recycling of rubber wastes. Recycling methods and equipment, applications of recycled rubber, and energy recovery systems and performance are among the topics discussed. Recycling methods compared and contrasted with various rubber waste disposal techniques are also included. (Contains a minimum of 96 citations and includes a subject term index and title list.)

  3. National databases and rheumatology research II: the National Health and Nutrition Examination Surveys.

    PubMed

    Sokka, Tuulikki; Krishnan, Eswar

    2004-11-01

    Three National Health and Nutrition Examination Surveys were conducted in the United States between 1971 and 1994 to provide data on the nutritional and health status of the population and on specific target conditions. This article describes features of the surveys and provides examples of research on musculoskeletal disorders that used the survey data.

  4. "How Obvious": Personal Reflections on the Database of Educational Psychology and Effective Teaching Research

    ERIC Educational Resources Information Center

    Yates, Gregory C. R.

    2005-01-01

    From a personal perspective, the author reflects upon the notion that many research findings appear falsely to possess the quality of being "obvious". Specific attention is given to the topic of teacher effectiveness. The feeling that findings are obvious can be related to the following: the false consensus effect, selfserving cognition, hindsight…

  5. Linking CALL and SLA: Using the IRIS Database to Locate Research Instruments

    ERIC Educational Resources Information Center

    Handley, Zöe; Marsden, Emma

    2014-01-01

    To establish an evidence base for future computer-assisted language learning (CALL) design, CALL research needs to move away from CALL versus non-CALL comparisons, and focus on investigating the differential impact of individual coding elements, that is, specific features of a technology which might have an impact on learning (Pederson, 1987).…

  6. Recycling rubber wastes. (Latest citations from the rubber and plastics research association database). Published Search

    SciTech Connect

    Not Available

    1994-05-01

    The bibliography contains citations concerning research and innovations in the recycling of rubber wastes. Recycling methods and equipment, applications of recycled rubber, and energy recovery systems and performance are among the topics discussed. Recycling methods compared and contrasted with various rubber waste disposal techniques are also included. (Contains a minimum of 89 citations and includes a subject term index and title list.)

  7. "How Obvious": Personal Reflections on the Database of Educational Psychology and Effective Teaching Research

    ERIC Educational Resources Information Center

    Yates, Gregory C. R.

    2005-01-01

    From a personal perspective, the author reflects upon the notion that many research findings appear falsely to possess the quality of being "obvious". Specific attention is given to the topic of teacher effectiveness. The feeling that findings are obvious can be related to the following: the false consensus effect, selfserving cognition, hindsight…

  8. Current concepts in clinical research: web-based, automated, arthroscopic surgery prospective database registry.

    PubMed

    Lubowitz, James H; Smith, Patrick A

    2012-03-01

    In 2011, postsurgical patient outcome data may be compiled in a research registry, allowing comparative-effectiveness research and cost-effectiveness analysis by use of Health Insurance Portability and Accountability Act-compliant, institutional review board-approved, Food and Drug Administration-approved, remote, Web-based data collection systems. Computerized automation minimizes cost and minimizes surgeon time demand. A research registry can be a powerful tool to observe and understand variations in treatment and outcomes, to examine factors that influence prognosis and quality of life, to describe care patterns, to assess effectiveness, to monitor safety, and to change provider practice through feedback of data. Registry of validated, prospective outcome data is required for arthroscopic and related researchers and the public to advocate with governments and health payers. The goal is to develop evidence-based data to determine the best methods for treating patients. Copyright © 2012 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

  9. Association Between Age and Complications in Adult Scoliosis Surgery: An Analysis of the Scoliosis Research Society Morbidity and Mortality Database.

    PubMed

    Shaw, Richard; Skovrlj, Branko; Cho, Samuel K

    2016-03-01

    Retrospective review. To assess the relationship between age and complications, and report age-stratified complication rates for the surgical treatment of adult scoliosis. Literature examining age and complication rates for adult scoliosis surgery is conflicting. The Scoliosis Research Society (SRS) morbidity and mortality (M&M) database contains a large series of adult scoliosis patients that can be utilized to investigate this relationship. The SRS M&M database was queried from 2004 to 2007 to identify all cases of adult scoliosis. Data pertaining to patient age, complications, scoliosis, and surgery type were extracted from the database. Age-based analyses of clinical parameters were conducted using age as both a stratified categorical variable and as a continuous variable. In our cohort of 5470 adult scoliosis patients, the overall complication rate was 13.5% and there was a 0.3% mortality rate. Patients who experienced complications were significantly older than those without complications (55.9 ± 16.5 yrs vs. 51.2 ± 18.7 yrs, P < 0.001). When complications were stratified according to decade of age, there was also a statistically significant trend of increasing complication rates with each decade of life (P < 0.001). Dural tears were the most common complication in patients over 50 years, whereas implant-related complications were the most common in patients less than 50 years. There was a clear association between increasing age and higher rates of major short-term complications, a factor that ought to be taken into account during treatment decision making and patient counseling.

  10. The epidemiology and burden of Alzheimer’s disease in Taiwan utilizing data from the National Health Insurance Research Database

    PubMed Central

    Hung, Yen-Ni; Kadziola, Zbigniew; Brnabic, Alan JM; Yeh, Ju-Fen; Fuh, Jong-Ling; Hwang, Jen-Ping; Montgomery, William

    2016-01-01

    Purpose The objectives of this study were to estimate the incidence, cumulative incidence, and economic burden of Alzheimer’s disease (AD) in Taiwan, using data from the National Health Insurance Research Database (NHIRD). Materials and methods This was a retrospective, longitudinal, observational study using data from the Longitudinal Health Insurance Database of the NHIRD. Patients were included in this study if they were 50 years of age or older and their records included a primary or secondary diagnosis of AD. New patients who met inclusion criteria were followed up longitudinally from 2005 to 2010. Costs were calculated for the first year following the diagnosis of AD. Results Overall, a higher percentage of women than men were diagnosed with AD (54% vs 46%, respectively). The first AD diagnosis occurred most frequently in the age of 75–84 years. The person-year incidence rate increased from 5.63/1,000 persons (95% CI, 5.32–5.94) in 2005 to 8.17/1,000 persons (95% CI, 7.78–8.57) in 2010. The cumulative incidence rate was 33.54/1,000 persons (95% CI, 32.76–34.33) in 2005–2010. The total mean inflated annual costs per patient in new Taiwan dollars (NT$) in the first year of diagnosis ranged from NT$205,413 (2009) to NT$227,110 (2005), with hospitalization representing the largest component. Conclusion AD represents a substantial burden in Taiwan, and based on the observed increase in incidence rate over time, it is likely that this burden will continue to increase. The findings reported here are consistent with previous research. The NHIRD contains extensive real-world information that can be used to conduct research, allowing us to expand our understanding of the incidence, prevalence, and burden of disease in Taiwan. PMID:27536149

  11. Linking Swedish health data registers to establish a research database and a shared decision-making tool in hip replacement.

    PubMed

    Cnudde, Peter; Rolfson, Ola; Nemes, Szilard; Kärrholm, Johan; Rehnberg, Clas; Rogmark, Cecilia; Timperley, John; Garellick, Göran

    2016-10-04

    Sweden offers a unique opportunity to researchers to construct comprehensive databases that encompass a wide variety of healthcare related data. Statistics Sweden and the National Board of Health and Welfare collect individual level data for all Swedish residents that ranges from medical diagnoses to socioeconomic information. In addition to the information collected by governmental agencies the medical profession has initiated nationwide Quality Registers that collect data on specific diagnoses and interventions. The Quality Registers analyze activity within healthcare institutions, with the aims of improving clinical care and fostering clinical research. The Swedish Hip Arthroplasty Register (SHAR) has been collecting data since 1979. Joint replacement in general and hip replacement in particular is considered a success story with low mortality and complication rate. It is credited to the pioneering work of the SHAR that the revision rate following hip replacement surgery in Sweden is amongst the lowest in the world. This has been accomplished by the diligent follow-up of patients with feedback of outcomes to the providers of the healthcare along with post market surveillance of individual implant performance. During its existence SHAR has experienced a constant organic growth. One major development was the introduction of the Patient Reported Outcome Measures program, giving a voice to the patients in healthcare performance evaluation. The next aim for SHAR is to integrate patients' wishes and expectations with the surgeons' expertise in the form of a Shared Decision-Making (SDM) instrument. The first step in building such an instrument is to assemble the necessary data. This involves linking the SHARs database with the two aforementioned governmental agencies. The linkage is done by the 10-digit personal identity number assigned at birth (or immigration) for every Swedish resident. The anonymized data is stored on encrypted serves and can only be accessed after

  12. Independent Review of Aviation Technology and Research Information Analysis System (ATRIAS) Database

    DTIC Science & Technology

    1994-02-01

    capability to support the Federal Aviation Administration (FAA)/ Aviation Security Research and Development Service’s (ACA) Explosive Detection...Systems (EDS) programs and Aviation Security Human Factors Program (ASHFP). This review was conducted by an independent consultant selected by the FAA...sections 2 and 3 of the report. Overall, ATRIAS was found to address many technology application areas relevant to the FAA’s aviation security programs

  13. The process of installing REDCap, a web based database supporting biomedical research: the first year.

    PubMed

    Klipin, M; Mare, I; Hazelhurst, S; Kramer, B

    2014-01-01

    Clinical and research data are essential for patient care, research and healthcare system planning. REDCapTM is a web-based tool for research data curatorship developed at Vanderbilt University in Nashville, USA. The Faculty of Health Sciences at the University of the Witwatersrand, Johannesburg South Africa identified the need for a cost effective data management instrument. REDCap was installed as per the user agreement with Vanderbilt University in August 2012. In order to assist other institutions that may lack the in-house Information Technology capacity, this paper describes the installation and support of REDCap and incorporates an analysis of user uptake over the first year of use. We reviewed the staffing requirements, costs of installation, process of installation and necessary infrastructure and end-user requests following the introduction of REDCap at Wits. The University Legal Office and Human Research Ethics Committee were consulted regarding the REDCap end-user agreement. Bi-monthly user meetings resulted in a training workshop in August 2013. We compared our REDCap software user numbers and records before and after the first training workshop. Human resources were recruited from existing staff. Installation costs were limited to servers and security certificates. The total costs to provide a functional REDCap platform was less than $9000. Eighty-one (81) users were registered in the first year. After the first training workshop the user numbers increased by 59 in one month and the total number of active users to 140 by the end of August 2013. Custom software applications for REDCap were created by collaboration between clinicians and software developers. REDCap was installed and maintained at limited cost. A small number of people with defined skills can support multiple REDCap users in two to four hours a week. End user training increased in the number of users, number of projects created and the number of projects moved to production.

  14. Recycling rubber wastes. (Latest citations from the Rubber and Plastics Research Association database). Published Search

    SciTech Connect

    1996-04-01

    The bibliography contains citations concerning research and innovations in the recycling of rubber wastes. Recycling methods and equipment, applications of recycled rubber, and energy recovery systems and performance are among the topics discussed. Recycling methods compared and contrasted with various rubber waste disposal techniques are also included. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  15. The Process of Installing REDCap, a Web Based Database Supporting Biomedical Research

    PubMed Central

    Mare, I.; Hazelhurst, S.; Kramer, B.

    2014-01-01

    Summary Background Clinical and research data are essential for patient care, research and healthcare system planning. REDCapTM is a web-based tool for research data curatorship developed at Vanderbilt University in Nashville, USA. The Faculty of Health Sciences at the University of the Witwatersrand, Johannesburg South Africa identified the need for a cost effective data management instrument. REDCap was installed as per the user agreement with Vanderbilt University in August 2012. Objectives In order to assist other institutions that may lack the in-house Information Technology capacity, this paper describes the installation and support of REDCap and incorporates an analysis of user uptake over the first year of use. Methods We reviewed the staffing requirements, costs of installation, process of installation and necessary infrastructure and end-user requests following the introduction of REDCap at Wits. The University Legal Office and Human Research Ethics Committee were consulted regarding the REDCap end-user agreement. Bi-monthly user meetings resulted in a training workshop in August 2013. We compared our REDCap software user numbers and records before and after the first training workshop. Results Human resources were recruited from existing staff. Installation costs were limited to servers and security certificates. The total costs to provide a functional REDCap platform was less than $9000. Eighty-one (81) users were registered in the first year. After the first training workshop the user numbers increased by 59 in one month and the total number of active users to 140 by the end of August 2013. Custom software applications for REDCap were created by collaboration between clinicians and software developers. Conclusion REDCap was installed and maintained at limited cost. A small number of people with defined skills can support multiple REDCap users in two to four hours a week. End user training increased in the number of users, number of projects created and

  16. Update on the profile of the EUSTAR cohort: an analysis of the EULAR Scleroderma Trials and Research group database.

    PubMed

    Meier, Florian M P; Frommer, Klaus W; Dinser, Robert; Walker, Ulrich A; Czirjak, Laszlo; Denton, Christopher P; Allanore, Yannick; Distler, Oliver; Riemekasten, Gabriela; Valentini, Gabriele; Müller-Ladner, Ulf

    2012-08-01

    Systemic sclerosis (SSc) is a rare disease requiring multicentre collaboration to reveal comprehensive details of disease-related causes for morbidity and mortality. The European League Against Rheumatism (EULAR) Scleroderma Trials and Research (EUSTAR) group initiated a database to prospectively gather key data of patients with SSc using a minimal essential dataset that was reorganised in 2008 introducing new items. Baseline visit data of patients who were registered between 2004 and 2011 were analysed using descriptive statistics. In June 2011, 7655 patients (2838 with diffuse cutaneous (dc) and 4481 with limited cutaneous (lc) SSc who fulfilled the American College of Rheumatology diagnostic criteria had been registered in 174 centres, mainly European. The most prominent hallmarks of disease were Raynaud's phenomenon (96.3%), antinuclear antibodies (93.4%) and a typical capillaroscopic pattern (90.9%). Scleroderma was more common on fingers and hands than on any other part of the skin. Proton pump inhibitors (65.2%), calcium channel blockers (52.7%), and corticosteroids (45.3%) were most often prescribed. Among the immunosuppressant agents, cyclophosphamide was used more often in dcSSc than in lcSSc. The EUSTAR database provides an abundance of information on the true clinical face of SSc that will be helpful in improving the classification of SSc and its subsets and for developing more specific therapeutic recommendations.

  17. Djeen (Database for Joomla!'s Extensible Engine): a research information management system for flexible multi-technology project administration.

    PubMed

    Stahl, Olivier; Duvergey, Hugo; Guille, Arnaud; Blondin, Fanny; Vecchio, Alexandre Del; Finetti, Pascal; Granjeaud, Samuel; Vigy, Oana; Bidaut, Ghislain

    2013-06-06

    With the advance of post-genomic technologies, the need for tools to manage large scale data in biology becomes more pressing. This involves annotating and storing data securely, as well as granting permissions flexibly with several technologies (all array types, flow cytometry, proteomics) for collaborative work and data sharing. This task is not easily achieved with most systems available today. We developed Djeen (Database for Joomla!'s Extensible Engine), a new Research Information Management System (RIMS) for collaborative projects. Djeen is a user-friendly application, designed to streamline data storage and annotation collaboratively. Its database model, kept simple, is compliant with most technologies and allows storing and managing of heterogeneous data with the same system. Advanced permissions are managed through different roles. Templates allow Minimum Information (MI) compliance. Djeen allows managing project associated with heterogeneous data types while enforcing annotation integrity and minimum information. Projects are managed within a hierarchy and user permissions are finely-grained for each project, user and group.Djeen Component source code (version 1.5.1) and installation documentation are available under CeCILL license from http://sourceforge.net/projects/djeen/files and supplementary material.

  18. The Cerebral Blood Flow Biomedical Informatics Research Network (CBFBIRN) database and analysis pipeline for arterial spin labeling MRI data

    PubMed Central

    Shin, David D.; Ozyurt, I. Burak; Liu, Thomas T.

    2013-01-01

    Arterial spin labeling (ASL) is a magnetic resonance imaging technique that provides a non-invasive and quantitative measure of cerebral blood flow (CBF). After more than a decade of active research, ASL is now emerging as a robust and reliable CBF measurement technique with increased availability and ease of use. There is a growing number of research and clinical sites using ASL for neuroscience research and clinical care. In this paper, we present an online CBF Database and Analysis Pipeline, collectively called the Cerebral Blood Flow Biomedical Informatics Research Network (CBFBIRN) that allows researchers to upload and share ASL and clinical data. In addition to serving the role as a central data repository, the CBFBIRN provides a streamlined data processing infrastructure for CBF quantification and group analysis, which has the potential to accelerate the discovery of new scientific and clinical knowledge. All capabilities and features built into the CBFBIRN are accessed online using a web browser through a secure login. In this work, we begin with a general description of the CBFBIRN system data model and its architecture, then devote the remainder of the paper to the CBFBIRN capabilities. The latter part of our work is divided into two processing modules: (1) Data Upload and CBF Quantification Module; (2) Group Analysis Module that supports three types of analysis commonly used in neuroscience research. To date, the CBFBIRN hosts CBF maps and associated clinical data from more than 1,300 individual subjects. The data have been contributed by more than 20 different research studies, investigating the effect of various conditions on CBF including Alzheimer’s, schizophrenia, bipolar disorder, depression, traumatic brain injury, HIV, caffeine usage, and methamphetamine abuse. Several example results, generated by the CBFBIRN processing modules, are presented. We conclude with the lessons learned during implementation and deployment of the CBFBIRN and our

  19. Heart research advances using database search engines, Human Protein Atlas and the Sydney Heart Bank.

    PubMed

    Li, Amy; Estigoy, Colleen; Raftery, Mark; Cameron, Darryl; Odeberg, Jacob; Pontén, Fredrik; Lal, Sean; Dos Remedios, Cristobal G

    2013-10-01

    This Methodological Review is intended as a guide for research students who may have just discovered a human "novel" cardiac protein, but it may also help hard-pressed reviewers of journal submissions on a "novel" protein reported in an animal model of human heart failure. Whether you are an expert or not, you may know little or nothing about this particular protein of interest. In this review we provide a strategic guide on how to proceed. We ask: How do you discover what has been published (even in an abstract or research report) about this protein? Everyone knows how to undertake literature searches using PubMed and Medline but these are usually encyclopaedic, often producing long lists of papers, most of which are either irrelevant or only vaguely relevant to your query. Relatively few will be aware of more advanced search engines such as Google Scholar and even fewer will know about Quertle. Next, we provide a strategy for discovering if your "novel" protein is expressed in the normal, healthy human heart, and if it is, we show you how to investigate its subcellular location. This can usually be achieved by visiting the website "Human Protein Atlas" without doing a single experiment. Finally, we provide a pathway to discovering if your protein of interest changes its expression level with heart failure/disease or with ageing.

  20. Research on an expert system for database operation of simulation-emulation math models. Volume 1, Phase 1: Results

    NASA Technical Reports Server (NTRS)

    Kawamura, K.; Beale, G. O.; Schaffer, J. D.; Hsieh, B. J.; Padalkar, S.; Rodriguez-Moscoso, J. J.

    1985-01-01

    The results of the first phase of Research on an Expert System for Database Operation of Simulation/Emulation Math Models, is described. Techniques from artificial intelligence (AI) were to bear on task domains of interest to NASA Marshall Space Flight Center. One such domain is simulation of spacecraft attitude control systems. Two related software systems were developed to and delivered to NASA. One was a generic simulation model for spacecraft attitude control, written in FORTRAN. The second was an expert system which understands the usage of a class of spacecraft attitude control simulation software and can assist the user in running the software. This NASA Expert Simulation System (NESS), written in LISP, contains general knowledge about digital simulation, specific knowledge about the simulation software, and self knowledge.

  1. DISCONTOOLS: a database to identify research gaps on vaccines, pharmaceuticals and diagnostics for the control of infectious diseases of animals.

    PubMed

    O'Brien, Declan; Scudamore, Jim; Charlier, Johannes; Delavergne, Morgane

    2017-01-03

    The public and private sector in the EU spend around €800 million per year on animal health and welfare related research. An objective process to identify critical gaps in knowledge and available control tools should aid the prioritisation of research in order to speed up the development of new or improved diagnostics, vaccines and pharmaceuticals and reduce the burden of animal diseases. Here, we describe the construction of a database based on expert consultation for 52 infectious diseases of animals. For each disease, an expert group produced a disease and product analysis document that formed the basis for gap analysis and prioritisation. The prioritisation model was based on a closed scoring system, employing identical weights for six evaluation criteria (disease knowledge; impact on animal health and welfare; impact on public health; impact on wider society; impact on trade; control tools). The diseases were classified into three groups: epizootic diseases, food-producing animal complexes or zoonotic diseases. The highly ranked diseases in the prioritisation model comprised mostly zoonotic and epizootic diseases with important gaps identified in vaccine development and pharmaceuticals, respectively. The most important outcome is the identification of key research needs by disease. The rankings and research needs by disease are provided on a public website ( www.discontools.eu ) which is currently being updated based on new expert consultations. As such, it can become a reference point for funders of research including the European Commission, member states, foundations, trusts along with private industry to prioritise research. This will deliver benefits in terms of animal health and welfare but also public health, societal benefits and a safe and secure food supply.

  2. Veterans Administration Databases

    Cancer.gov

    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.

  3. Scopus database: a review.

    PubMed

    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.

  4. Scopus database: a review

    PubMed Central

    Burnham, Judy F

    2006-01-01

    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. PMID:16522216

  5. Pediatric critical care physician-administered procedural sedation using propofol: a report from the Pediatric Sedation Research Consortium Database.

    PubMed

    Kamat, Pradip P; McCracken, Courtney E; Gillespie, Scott E; Fortenberry, James D; Stockwell, Jana A; Cravero, Joseph P; Hebbar, Kiran B

    2015-01-01

    Increasing demand for pediatric procedural sedation has resulted in a marked increase in provision of pediatric procedural sedation by pediatric critical care physicians both inside and outside of the ICU. Reported experience of pediatric critical care physicians-administered pediatric procedural sedation is limited. We used the Pediatric Sedation Research Consortium database to evaluate a multicenter experience with propofol by pediatric critical care physicians in all settings. Review of national Pediatric Sedation Research Consortium database to identify pediatric procedural sedation provided by pediatric critical care physicians from 2007 to 2012. Demographic and clinical data were collected to describe pediatric procedural sedation selection, location, and delivery. Multivariable logistic regression analysis was performed to identify risk factors associated with pediatric procedural sedation-related adverse events and complications. A total of 91,189 pediatric procedural sedation performed by pediatric critical care physicians using propofol were included in the database. Median age was 60.0 months (range, 0-264 months; interquartile range, 34.0-132.0); 81.9% of patients were American Society of Anesthesiologists class I or II. Most sedations were performed in dedicated sedation or radiology units (80.9%). Procedures were successfully completed in 99.9% of patients. A propofol bolus alone was used in 52.8%, and 41.7% received bolus plus continuous infusion. Commonly used adjunctive medications were lidocaine (35.3%), opioids (23.3%), and benzodiazepines (16.4%). Overall adverse event incidence was 5.0% (95% CI, 4.9-5.2%), which included airway obstruction (1.6%), desaturation (1.5%), coughing (1.0%), and emergent airway intervention (0.7%). No deaths occurred; a single cardiac arrest was reported in a 13-month-old child receiving propofol and ketamine, with no untoward neurologic sequelae. Risk factors associated with adverse event included: location of

  6. [Research on compatibility chemistry of acid-alkaline pair medicines in formulas of traditional Chinese medicine].

    PubMed

    Pei, Miaorong; Duan, Xiujun; Pei, Xiangping; Xuan, Chunsheng; Wang, Xiaoying; Zhao, Lina; Zhang, Shurong; Liu, Bingchen; Wang, Shimin

    2009-08-01

    Compatibility chemistry of acid-alkaline pair medicines in formulas of traditional Chinese medicine (TCM) is an important research field which should merit to pay attention. The ideas and methods in prescription compatibility research on formulas containing alkaline-acid pair medicines were summarized from the aspect of chemical groups of alkaline and acid ingredients; the research results were introduced and analyzed; the research meaning was elaborated; and the expectation of the field was viewed.

  7. Pathway — Using a State-of-the-Art Digital Video Database for Research and Development in Teacher Education

    NASA Astrophysics Data System (ADS)

    Adrian, Brian; Zollman, Dean; Stevens, Scott

    2006-02-01

    To demonstrate how state-of-the-art video databases can address issues related to the lack of preparation of many physics teachers, we have created the prototype Physics Teaching Web Advisory (Pathway). Pathway's Synthetic Interviews and related video materials are beginning to provide pre-service and out-of-field in-service teachers with much-needed professional development and well-prepared teachers with new perspectives on teaching physics. The prototype was limited to a demonstration of the systems. Now, with an additional grant we will extend the system and conduct research and evaluation on its effectiveness. This project will provide virtual expert help on issues of pedagogy and content. In particular, the system will convey, by example and explanation, contemporary ideas about the teaching of physics and applications of physics education research. The research effort will focus on the value of contemporary technology to address the continuing education of teachers who are teaching in a field in which they have not been trained.

  8. Research on the corrosion inhibitors of zinc in hydrochloric acid

    NASA Astrophysics Data System (ADS)

    Sun, C. X.; Chen, Y. M.; Xu, H. W.; Huang, C. S.; Zhang, M.; Wu, J. Y.; Chen, M.; Xue, M.

    2017-06-01

    Three organic compounds were tested as zinc corrosion inhibitors in hydrochloric acid: cetyltrimethyl ammonium bromide (CTAB), nicotini acid, bromohexadecyl pyridine. The static coupon test results indicate that CTAB and bromohexadecyl pyridine offer the best zinc corrosion protection, while nicotinic acid accelerates zinc corrosion. The polarization results indicate that CTAB, nicotinic acid and bromohexadecyl pyridine induce a positive shift in the E0 of zinc in hydrochloric acid. A complex of CTAB and bromohexadecyl pyridine inhibits the corrosion of zinc in hydrochloric acid. SEM results indicate that the CTAB and bromohexadecyl pyridine formed a uniform and compact membrane on the surface of zinc that subsequently protects the zinc from effective corrosion.

  9. Biological Macromolecule Crystallization Database

    National Institute of Standards and Technology Data Gateway

    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.

  10. Reduction in database search space by utilization of amino acid composition information from electron transfer dissociation and higher-energy collisional dissociation mass spectra.

    PubMed

    Hansen, Thomas A; Kryuchkov, Fedor; Kjeldsen, Frank

    2012-08-07

    With high-mass accuracy and consecutively obtained electron transfer dissociation (ETD) and higher-energy collisional dissociation (HCD) tandem mass spectrometry (MS/MS), reliable (≥97%) and sensitive fragment ions have been extracted for identification of specific amino acid residues in peptide sequences. The analytical benefit of these specific amino acid composition (AAC) ions is to restrict the database search space and provide identification of peptides with higher confidence and reduced false negative rates. The 6706 uniquely identified peptide sequences determined with a conservative Mascot score of >30 were used to characterize the AAC ions. The loss of amino acid side chains (small neutral losses, SNLs) from the charge reduced peptide radical cations was studied using ETD. Complementary AAC information from HCD spectra was provided by immonium ions. From the ETD/HCD mass spectra, 5162 and 6720 reliable SNLs and immonium ions were successfully extracted, respectively. Automated application of the AAC information during database searching resulted in an average 3.5-fold higher confidence level of peptide identification. In addition, 4% and 28% more peptides were identified above the significance level in a standard and extended search space, respectively.

  11. An open-database of Grape Harvest dates for climate research: data description and quality assessment

    NASA Astrophysics Data System (ADS)

    Daux, V.; Garcia de Cortazar-Atauri, I.; Yiou, P.; Chuine, I.; Garnier, E.; Ladurie, E. Le Roy; Mestre, O.; Tardaguila, J.

    2011-11-01

    during a two-century long time-window from the early 17th to the early 19th century, while extremely early years are frequent during the 16th and since the mid-19th century. The dataset is made accessible for climate research through the Internet. It should allow a variety of climate studies, including reconstructions of atmospheric circulation over Western Europe.

  12. Atomic Databases

    NASA Astrophysics Data System (ADS)

    Mendoza, Claudio

    2000-10-01

    Atomic and molecular data are required in a variety of fields ranging from the traditional astronomy, atmospherics and fusion research to fast growing technologies such as lasers, lighting, low-temperature plasmas, plasma assisted etching and radiotherapy. In this context, there are some research groups, both theoretical and experimental, scattered round the world that attend to most of this data demand, but the implementation of atomic databases has grown independently out of sheer necessity. In some cases the latter has been associated with the data production process or with data centers involved in data collection and evaluation; but sometimes it has been the result of individual initiatives that have been quite successful. In any case, the development and maintenance of atomic databases call for a number of skills and an entrepreneurial spirit that are not usually associated with most physics researchers. In the present report we present some of the highlights in this area in the past five years and discuss what we think are some of the main issues that have to be addressed.

  13. Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

    PubMed Central

    Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.

    2013-01-01

    We introduce a Python-based program that utilizes the large database of 13C and 15N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D 13C–13C, 15N–13C, or 3D 15N–13C–13C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D 13C–13C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40–60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO–Cα–Cβ or N–Cα–Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination. PMID:23625364

  14. The research on conformal acid etching process of glass ceramic

    NASA Astrophysics Data System (ADS)

    Wang, Kepeng; Guo, Peiji

    2014-08-01

    A series of experiments have been done to explore the effect of different conditions on the hydrofluoric acid etching. The hydrofluoric acid was used to etch the glass ceramic called "ZERODUR", which is invented by SCHOTT in Germany. The glass ceramic was processed into cylindrical samples. The hydrofluoric acid etching was done in a plastic beaker. The concentration of hydrofluoric acid and the etching time were changed to measure the changes of geometric tolerance and I observed the surface using a microscope in order to find an appropriate condition of hydrofluoric acid etching.

  15. Assessment of research productivity of Arab countries in the field of infectious diseases using Web of Science database.

    PubMed

    Sweileh, Waleed M; Al-Jabi, Samah W; Abuzanat, Alaeddin; Sawalha, Ansam F; AbuTaha, Adham S; Ghanim, Mustafa A; Zyoud, Sa'ed H

    2015-01-01

    To meet the future challenges of infectious diseases and limit the spread of multidrug resistant microorganisms, a better understanding of published studies in the field of infectious diseases is needed. The objective of this study was to analyze the quantity and quality of research activity in the field of infectious diseases in Arab countries and compare it with that in non-Arab countries. Documents published in Arab countries within the research category of "infectious diseases" were extracted and analyzed using the Web of Science database. The data analyzed represent research productivity during the time interval between 1900 - 2012. Worldwide, the total number of documents published in the field of infectious diseases up to 2012 was 227,188. A total of 2,408 documents in the field of infectious diseases were published in Arab countries, which represents 1.06% of worldwide research output. Research output from Arab countries in the field of infectious diseases was low for decades. However, approximately a five-fold increase was observed in the past decade. Arab countries ranked 56(th) to 218(th) on the standard competition ranking (SCR) in worldwide publications in the field of infectious diseases. Egypt, with a total publication of 464 (19.27%) documents ranked first among Arab countries, while Kuwait University was the most productive institution with a total of 158 (6.56%) documents. Average citation per document published in Arab countries was 13.25 and the h-index was 64. Tuberculosis (230; 9.55%), malaria (223; 9.26%), and hepatitis (189; 7.8%) were the top three infectious diseases studied as according to the retrieved documents. The present data reveals that some Arab countries contribute significantly to the field of infectious diseases. However, Arab countries need to work harder to bridge the gap in this field. Compared with non-Arab countries in the Middle East, research output from Arab countries was high, but more efforts are needed to enhance the

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

    NASA Astrophysics Data System (ADS)

    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.

  17. Comparison between the phi distribution of the amino acids in the protein database and NMR data indicates that amino acids have various phi propensities in the random coil conformation.

    PubMed

    Serrano, L

    1995-11-24

    It has been indicated that amino acids have various intrinsic phi and psi propensities, as demonstrated from the comparison between experimental secondary structure propensities and their relative statistical distribution in the protein database for the appropriate region of the Ramachandran plot. However, this does not eliminate the possibility that these experimental propensities are the result of context effects due to the secondary structure environment of the mutated position. To demonstrate that there are at least real intrinsic phi propensities, independent of context effects, we have used two different nuclear magnetic resonance parameters related to the phi dihedral angle (J3 alpha HN coupling constants and the chemical shift of the C alpha H proton), determined in random-coil tetra- and pentapeptides, and/or in proteins. Comparison of the experimentally determined values for these parameters with the theoretical ones determined from the analysis by different empirical and theoretical equations of the phi dihedral angle statistical distribution of the amino acids in the protein database, supports the idea that each amino acid has, at least, different phi intrinsic propensities. Consideration of all conformations, or only coil conformations, in the protein database produces similar results. The reasonable correlation between these experimental and theoretical data and the hydrogen-exchange data in random-coil peptides suggests that maximisation of hydrophobic surface-buried and hydrogen-bond formation with the solvent could be responsible for these different random-coil conformational preferences. Analysis of the intrinsic propensities for beta-strand, alpha-helix and polyproline II dihedral angles of the 20 amino acids in coil conformations, indicates that the side-chain of the amino acids is mainly determining the relative preferences for the phi angle.

  18. Recent data on obesity research: β-aminoisobutyric acid.

    PubMed

    Ginter, E; Simko, V

    2014-01-01

    The world-wide epidemic of obesity is now affecting up to a third of the adult population. Research attempting to contribute to management of this health scourge has been recently refocused on the essential role of physical activity. Muscle activity induces a dramatic increase in transcription of the peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α). This protein is a regulator of mitochondrial biogenesis and function. Very recently, in 2014 it was revealed that the mediator of this metabolic process is a low molecular myokine, the beta- aminoisobutyric acid (BAIBA). This compound with a simple molecular structure has a key metabolic role: it converts the cells of white adipose tissue into brown fat. The brown adipocytes contain a protein thermogenin. This substance turns off the energy stores, among others the adenosine triphosphate (ATP), thereby accelerating the breakdown of lipids into heat, water and CO2. We may be at the threshold of new and effective management of obesity. The world eagerly expects to see how the BAIBA will compare with other recently reported agents to fight the overweight (Fig. 2, Ref. 6).

  19. Association between teriparatide treatment persistence and adherence, and fracture incidence in Taiwan: analysis using the National Health Insurance Research Database.

    PubMed

    Chan, D-C; Chang, C H-C; Lim, L-C; Brnabic, A J M; Tsauo, J-Y; Burge, R; Hsiao, F-Y; Jin, L; Gürbüz, S; Yang, R-S

    2016-09-01

    Medication persistence and adherence are critical for osteoporosis outcomes. Using the Taiwan National Health Insurance Research Database, we found that persistence and adherence to teriparatide were low in Taiwanese patients with osteoporosis and that greater persistence and adherence were associated with a lower incidence of hip and other nonvertebral fractures. The purpose of this study was to determine the persistence and adherence to teriparatide treatment in Taiwanese patients with osteoporosis, and to examine the association between persistence and adherence to teriparatide with fracture risks. Medical and pharmacy claims for 4,692 patients with vertebral or hip fractures and teriparatide prescriptions between 2005 and 2008 were identified (Taiwan National Health Insurance Research Database). Persistence was the time from the start of treatment to the first 90-day gap between two teriparatide prescriptions. Adherence was the number of teriparatide pens (each pen is used over 1 month) prescribed over 24 months. Association of persistence and adherence to teriparatide with fracture incidence was assessed using adjusted Cox proportional hazards models. The proportion of patients persisting with teriparatide for >6 months and >12 months was 44.6 and 24.9 %, respectively. Over 24 months, 53.6 % of patients were adherent for >6 months and 33.9 % were adherent for >12 months. Patients persisting for >12 months had a significantly lower incidence of hip (adjusted hazard ratio [HR], 0.61 [95 % confidence interval (CI), 0.40-0.93], P = 0.0229) and nonvertebral fracture (HR, 0.79 [95 % CI, 0.63-0.99], P = 0.0462) compared with those who persisted for ≤12 months. Patients adherent for >12 months had a lower incidence of hip (HR, 0.66 [95 % CI, 0.46-0.96], P = 0.0286) and nonvertebral fracture (HR, 0.81 [95 % CI, 0.66-0.99], P = 0.0377) compared with those adherent for ≤12 months. Persistence and adherence to teriparatide over 24

  20. Cloud-Based NoSQL Open Database of Pulmonary Nodules for Computer-Aided Lung Cancer Diagnosis and Reproducible Research.

    PubMed

    Ferreira Junior, José Raniery; Oliveira, Marcelo Costa; de Azevedo-Marques, Paulo Mazzoncini

    2016-12-01

    Lung cancer is the leading cause of cancer-related deaths in the world, and its main manifestation is pulmonary nodules. Detection and classification of pulmonary nodules are challenging tasks that must be done by qualified specialists, but image interpretation errors make those tasks difficult. In order to aid radiologists on those hard tasks, it is important to integrate the computer-based tools with the lesion detection, pathology diagnosis, and image interpretation processes. However, computer-aided diagnosis research faces the problem of not having enough shared medical reference data for the development, testing, and evaluation of computational methods for diagnosis. In order to minimize this problem, this paper presents a public nonrelational document-oriented cloud-based database of pulmonary nodules characterized by 3D texture attributes, identified by experienced radiologists and classified in nine different subjective characteristics by the same specialists. Our goal with the development of this database is to improve computer-aided lung cancer diagnosis and pulmonary nodule detection and classification research through the deployment of this database in a cloud Database as a Service framework. Pulmonary nodule data was provided by the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI), image descriptors were acquired by a volumetric texture analysis, and database schema was developed using a document-oriented Not only Structured Query Language (NoSQL) approach. The proposed database is now with 379 exams, 838 nodules, and 8237 images, 4029 of them are CT scans and 4208 manually segmented nodules, and it is allocated in a MongoDB instance on a cloud infrastructure.

  1. Native Health Research Database

    MedlinePlus

    ... Nova Scotia Nunavut NW Territories Ohio Oklahoma Ontario Oregon Pennsylvania Quebec Rhode Island Saskatchewan South Carolina South ... Rhode Island, Vermont Northwestern United States Idaho, Montana, Oregon, Washington, Wyoming Pacific States Alaska, California, Hawaii, Oregon, ...

  2. Acid precipitation: Effects on fresh water ecosystems. (Latest citations from the Life Sciences Collection database). Published Search

    SciTech Connect

    Not Available

    1993-05-01

    The bibliography contains citations concerning the effects of acidification on fresh water ecosystems. Algae and diatom distribution, survival and reproduction rates of specific fish species under acid lake conditions, and tolerance to stress caused by acidic conditions in fresh water ecosystems are studied. Effects of water pH on trace metal toxicity to fresh water organisms are briefly considered. Control and reduction of acidification are excluded from this bibliography. (Contains 250 citations and includes a subject term index and title list.)

  3. www.kanjidatabase.com: a new interactive online database for psychological and linguistic research on Japanese kanji and their compound words.

    PubMed

    Tamaoka, Katsuo; Makioka, Shogo; Sanders, Sander; Verdonschot, Rinus G

    2017-05-01

    Most experimental research making use of the Japanese language has involved the 1945 officially standardized kanji (Japanese logographic characters) in the Jōyō kanji list (originally announced by the Japanese government in 1981). However, this list was extensively modified in 2010: five kanji were removed and 196 kanji were added; the latest revision of the list now has a total of 2136 kanji. Using an up-to-date corpus consisting of 11 years' worth of articles printed in the Mainichi Newspaper (2000-2010), we have constructed two novel databases that can be used in psychological research using the Japanese language: (1) a database containing a wide variety of properties on the latest 2136 Jōyō kanji, and (2) a novel database containing 27,950 two-kanji compound words (or jukugo). Based on these two databases, we have created an interactive website ( www.kanjidatabase.com ) to retrieve and store linguistic information to be used in psychological and linguistic experiments. The present paper reports the most important characteristics for the new databases, as well as their value for experimental psychological and linguistic research.

  4. ZIKV – CDB: A Collaborative Database to Guide Research Linking SncRNAs and ZIKA Virus Disease Symptoms

    PubMed Central

    Morais, Daniel Kumazawa; Cuadros-Orellana, Sara; Pais, Fabiano Sviatopolk-Mirsky; Medeiros, Julliane Dutra; Geraldo, Juliana Assis; Gilbert, Jack; Volpini, Angela Cristina; Fernandes, Gabriel Rocha

    2016-01-01

    Background In early 2015, a ZIKA Virus (ZIKV) infection outbreak was recognized in northeast Brazil, where concerns over its possible links with infant microcephaly have been discussed. Providing a causal link between ZIKV infection and birth defects is still a challenge. MicroRNAs (miRNAs) are small noncoding RNAs (sncRNAs) that regulate post-transcriptional gene expression by translational repression, and play important roles in viral pathogenesis and brain development. The potential for flavivirus-mediated miRNA signalling dysfunction in brain-tissue development provides a compelling hypothesis to test the perceived link between ZIKV and microcephaly. Methodology/Principal Findings Here, we applied in silico analyses to provide novel insights to understand how Congenital ZIKA Syndrome symptoms may be related to an imbalance in miRNAs function. Moreover, following World Health Organization (WHO) recommendations, we have assembled a database to help target investigations of the possible relationship between ZIKV symptoms and miRNA-mediated human gene expression. Conclusions/Significance We have computationally predicted both miRNAs encoded by ZIKV able to target genes in the human genome and cellular (human) miRNAs capable of interacting with ZIKV genomes. Our results represent a step forward in the ZIKV studies, providing new insights to support research in this field and identify potential targets for therapy. PMID:27332714

  5. Preliminary results of the Social Impact Research Group of MEDEX: the request database (2000-2002) of two Meteorological Services

    NASA Astrophysics Data System (ADS)

    Amaro, J.; Gayà, M.; Aran, M.; Llasat, M. C.

    2010-12-01

    One of the aims of the MEDEX project is to improve the knowledge of high-impact weather events in the Mediterranean. According to the guidelines of this project, a pilot study was carried out in two regions of Spain (the Balearic Islands and Catalonia) by the Social Impact Research group of MEDEX. The main goal is to suggest some general and suitable criteria about how to analyse requests received in Meteorological Services arising out of the damage caused by weather events. Thus, all the requests received between 2000 and 2002 at the Servei Meteorològic de Catalunya as well as at the Division of AEMET in the Balearic Islands were analysed. Firstly, the proposed criteria in order to build the database are defined and discussed. Secondly, the temporal distribution of the requests for damage claims is analysed. On average, almost half of them were received during the first month after the event happened. During the first six months, the percentage increases by 90%. Thirdly, various factors are taken into account to determine the impact of specific events on society. It is remarkable that the greatest number of requests is for those episodes with simultaneous heavy rain and strong wind, and finally, those that are linked to high population density.

  6. TREC Document Database: Disk 4

    National Institute of Standards and Technology Data Gateway

    NIST TREC Document Database: Disk 4 (PC database for purchase)   NIST TREC Document Databases (Special Database 22) are distributed for the development and testing of information retrieval (IR) systems and related natural language processing research. The document collections consist of the full text of various newspaper and newswire articles plus government proceedings.

  7. TREC Document Database: Disk 5

    National Institute of Standards and Technology Data Gateway

    NIST TREC Document Database: Disk 5 (PC database for purchase)   NIST TREC Document Databases (Special Database 23) are distributed for the development and testing of information retrieval (IR) systems and related natural language processing research. The document collections consist of the full text of various newspaper and newswire articles plus government proceedings.

  8. Changes in Trans Fatty Acid Profiles for Selected Snack Foods in the USDA National Nutrient Database for Standard Reference

    USDA-ARS?s Scientific Manuscript database

    Historically, many snack foods had been formulated with partially hydrogenated vegetable oils, the primary contributor of trans fatty acids (TFA) in the US diet. Health concerns about TFA and saturated fat intake and increased risk for chronic health disorders have prompted some manufacturers to ref...

  9. Changes in Trans Fatty Acid Profiles for Selected Snack Foods in the USDA National Nutrient Database for Standard Reference

    USDA-ARS?s Scientific Manuscript database

    : Historically, many snack foods had been formulated with partially hydrogenated vegetable oils, the primary contributor of trans fatty acids (TFA) in the US diet. Health concerns about TFA and saturated fat intake and increased risk for chronic health disorders have prompted some manufacturers to r...

  10. Providing Database Services in a Nationwide Research Organisation--Coexistence of Traditional Information Services and a Modern CD-ROM/Online Hybrid Solution.

    ERIC Educational Resources Information Center

    Bowman, Benjamin F.

    For the past two decades the central Information Retrieval Services of the Max Planck Society has been providing database searches for scientists in Max Planck Institutes and Research Groups throughout Germany. As a supplement to traditional search services offered by professional intermediaries, they have recently fostered the introduction of a…

  11. Exploiting the potential of large databases of electronic health records for research using rapid search algorithms and an intuitive query interface

    PubMed Central

    Tate, A Rosemary; Beloff, Natalia; Al-Radwan, Balques; Wickson, Joss; Puri, Shivani; Williams, Timothy; Van Staa, Tjeerd; Bleach, Adrian

    2014-01-01

    Objective UK primary care databases, which contain diagnostic, demographic and prescribing information for millions of patients geographically representative of the UK, represent a significant resource for health services and clinical research. They can be used to identify patients with a specified disease or condition (phenotyping) and to investigate patterns of diagnosis and symptoms. Currently, extracting such information manually is time-consuming and requires considerable expertise. In order to exploit more fully the potential of these large and complex databases, our interdisciplinary team developed generic methods allowing access to different types of user. Materials and methods Using the Clinical Practice Research Datalink database, we have developed an online user-focused system (TrialViz), which enables users interactively to select suitable medical general practices based on two criteria: suitability of the patient base for the intended study (phenotyping) and measures of data quality. Results An end-to-end system, underpinned by an innovative search algorithm, allows the user to extract information in near real-time via an intuitive query interface and to explore this information using interactive visualization tools. A usability evaluation of this system produced positive results. Discussion We present the challenges and results in the development of TrialViz and our plans for its extension for wider applications of clinical research. Conclusions Our fast search algorithms and simple query algorithms represent a significant advance for users of clinical research databases. PMID:24272162

  12. Exploiting the potential of large databases of electronic health records for research using rapid search algorithms and an intuitive query interface.

    PubMed

    Tate, A Rosemary; Beloff, Natalia; Al-Radwan, Balques; Wickson, Joss; Puri, Shivani; Williams, Timothy; Van Staa, Tjeerd; Bleach, Adrian

    2014-01-01

    UK primary care databases, which contain diagnostic, demographic and prescribing information for millions of patients geographically representative of the UK, represent a significant resource for health services and clinical research. They can be used to identify patients with a specified disease or condition (phenotyping) and to investigate patterns of diagnosis and symptoms. Currently, extracting such information manually is time-consuming and requires considerable expertise. In order to exploit more fully the potential of these large and complex databases, our interdisciplinary team developed generic methods allowing access to different types of user. Using the Clinical Practice Research Datalink database, we have developed an online user-focused system (TrialViz), which enables users interactively to select suitable medical general practices based on two criteria: suitability of the patient base for the intended study (phenotyping) and measures of data quality. An end-to-end system, underpinned by an innovative search algorithm, allows the user to extract information in near real-time via an intuitive query interface and to explore this information using interactive visualization tools. A usability evaluation of this system produced positive results. We present the challenges and results in the development of TrialViz and our plans for its extension for wider applications of clinical research. Our fast search algorithms and simple query algorithms represent a significant advance for users of clinical research databases.

  13. Prototype of an Integrated Hurricane Information System for Research: Design and Implementation of the Database and Web Portal

    NASA Astrophysics Data System (ADS)

    Li, P. P.; Knosp, B.; Vu, Q. A.; Hristova-Veleva, S.; Chao, Y.; Vane, D.; Lambrigtsen, B.; Su, H.; Dang, V.; Fovell, R.; Willis, J.; Tanelli, S.; Fishbein, E.; Ao, C. O.; Poulsen, W. L.; Park, K. J.; Fetzer, E.; Vazquez, J.; Callahan, P. S.; Marcus, S.; Garay, M.; Kahn, R.; Haddad, Z.

    2007-12-01

    location placemark to see the time, location, and the intensity of the hurricane. Large scale datasets, such as SST or aerosol optical depth can be overlaid on top of the hurricane track in Google Map. In addition, available satellite and in-situ data during the hurricane period are displayed as little bars in a time line organized by datasets. When clicking a little bar, pre-generated plots for the selected dataset will be displayed in a separate window together with all other datasets co-located around the same time. The raw data in user-specified format can be downloaded for further analysis or model integration. As for the 3D model data, Live Access Server (LAS) is used to provide custom subsets and on-the-fly visualization. The site is dynamically configured using a backend relational database that is designed to let users easily browse through the website to find data and plots that are pertinent to their research. In this presentation, we will describe the current status of the integrated hurricane information system prototype, the design and the implementation of the hurricane database and portal, and future enhancements.

  14. Database for propagation models

    NASA Technical Reports Server (NTRS)

    Kantak, Anil V.

    1991-01-01

    A propagation researcher or a systems engineer who intends to use the results of a propagation experiment is generally faced with various database tasks such as the selection of the computer software, the hardware, and the writing of the programs to pass the data through the models of interest. This task is repeated every time a new experiment is conducted or the same experiment is carried out at a different location generating different data. Thus the users of this data have to spend a considerable portion of their time learning how to implement the computer hardware and the software towards the desired end. This situation may be facilitated considerably if an easily accessible propagation database is created that has all the accepted (standardized) propagation phenomena models approved by the propagation research community. Also, the handling of data will become easier for the user. Such a database construction can only stimulate the growth of the propagation research it if is available to all the researchers, so that the results of the experiment conducted by one researcher can be examined independently by another, without different hardware and software being used. The database may be made flexible so that the researchers need not be confined only to the contents of the database. Another way in which the database may help the researchers is by the fact that they will not have to document the software and hardware tools used in their research since the propagation research community will know the database already. The following sections show a possible database construction, as well as properties of the database for the propagation research.

  15. Biofuel Database

    National Institute of Standards and Technology Data Gateway

    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.

  16. [On the application of elements of data mining (the detection of useful knowledge in databases) in hygienic research and social-hygiene monitoring].

    PubMed

    Gudinova, Zh V

    2012-01-01

    In article necessity and possibility of application of Data Mining methods (detection of useful knowledge in databases) in modern hygienic researches and during the decision of practical problems of socially-hygienic monitoring is proved. As illustration for applications of Data Mining technologies for development of administrative decisions in sphere of sanitary-and-epidemiologic well-being of the population of region results of the cluster analysis of a database about medium and population health in districts of the Omsk region are presented.

  17. Database Administrator

    ERIC Educational Resources Information Center

    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. FIREMON Database

    Treesearch

    John F. Caratti

    2006-01-01

    The FIREMON database software allows users to enter data, store, analyze, and summarize plot data, photos, and related documents. The FIREMON database software consists of a Java application and a Microsoft® Access database. The Java application provides the user interface with FIREMON data through data entry forms, data summary reports, and other data management tools...

  19. Database Administrator

    ERIC Educational Resources Information Center

    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…

  20. Improving the Identification of Out-of-Hospital Sudden Cardiac Deaths in a General Practice Research Database.

    PubMed

    Varas-Lorenzo, Cristina; Arana, Alejandro; Johannes, Catherine B; McQuay, Lisa J; Rothman, Kenneth J; Fife, Daniel

    2016-09-01

    The ascertainment of sudden cardiac death (SCD) in electronic health databases is challenging. Our objective was to evaluate the applicability of the validated computer definition of SCD developed by Chung et al. in a retrospective study of SCD and domperidone exposure in the Clinical Practice Research Datalink (CPRD). We assessed out-of-hospital SCD by applying the validated computer definition and linking data with Hospital Episode Statistics and death certificates. We developed a separate algorithm to identify end-of-life care in noninstitutionalized patients and excluded associated deaths from the analysis to address their misclassification as SCD. Of the 681,104 patients in the study cohort, 3444 were initially classified as out-of-hospital SCD. Next, 163 deaths were identified as expected deaths by our algorithm for end-of-life home care. After review of patient profiles, 162 were classified as expected deaths because of evidence that the patient received palliative or end-of-life care, but one was a false negative. The exclusion of such cases appreciably changed the odds ratio for current exposure to domperidone compared with non-use of study medications from 2.09 (95 % confidence interval [CI] 1.16-3.74) to 1.71 (95 % CI 0.92-3.18). A similar effect on the odds ratio was observed for current exposure to metoclopramide but not to proton pump inhibitors. Our algorithm to identify end-of-life care at home in the CPRD performed well, with only one false negative. The exclusion of misclassified cases of SCD reduced the magnitude of the odds ratios for SCD associated with domperidone and metoclopramide exposure by controlling protopathic bias.