MaizeGDB: The Maize Genetics and Genomics Database.

USDA-ARS?s Scientific Manuscript database

MaizeGDB is the community database for biological information about the crop plant Zea mays. Genomic, genetic, sequence, gene product, functional characterization, literature reference, and person/organization contact information are among the datatypes stored at MaizeGDB. At the project’s website...

Plant Reactome: a resource for plant pathways and comparative analysis.

PubMed

Naithani, Sushma; Preece, Justin; D'Eustachio, Peter; Gupta, Parul; Amarasinghe, Vindhya; Dharmawardhana, Palitha D; Wu, Guanming; Fabregat, Antonio; Elser, Justin L; Weiser, Joel; Keays, Maria; Fuentes, Alfonso Munoz-Pomer; Petryszak, Robert; Stein, Lincoln D; Ware, Doreen; Jaiswal, Pankaj

2017-01-04

Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes. Two hundred twenty-two rice pathways, 1025 reactions associated with 1173 proteins, 907 small molecules and 256 literature references have been curated to date. These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology. Database users can search and browse various components of the database, visualize curated baseline expression of pathway-associated genes provided by the Expression Atlas and upload and analyze their Omics datasets. The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Hydrocarbon Spectral Database

National Institute of Standards and Technology Data Gateway

SRD 115 Hydrocarbon Spectral Database (Web, free access)   All of the rotational spectral lines observed and reported in the open literature for 91 hydrocarbon molecules have been tabulated. The isotopic molecular species, assigned quantum numbers, observed frequency, estimated measurement uncertainty and reference are given for each transition reported.

Diatomic Spectral Database

National Institute of Standards and Technology Data Gateway

SRD 114 Diatomic Spectral Database (Web, free access)   All of the rotational spectral lines observed and reported in the open literature for 121 diatomic molecules have been tabulated. The isotopic molecular species, assigned quantum numbers, observed frequency, estimated measurement uncertainty, and reference are given for each transition reported.

Triatomic Spectral Database

National Institute of Standards and Technology Data Gateway

SRD 117 Triatomic Spectral Database (Web, free access)   All of the rotational spectral lines observed and reported in the open literature for 55 triatomic molecules have been tabulated. The isotopic molecular species, assigned quantum numbers, observed frequency, estimated measurement uncertainty and reference are given for each transition reported.

Selected Reference Books of 1993-1994.

ERIC Educational Resources Information Center

McIlvaine, Eileen

1994-01-01

Offers brief, critical reviews of recent scholarly and general works of interest to reference workers in university libraries. Titles covered include dictionaries, databases, religion, literature, music, dance, art and architecture, business, political science, social issues, and history. Brief descriptions of new editions and supplements for…

A World Wide Web (WWW) server database engine for an organelle database, MitoDat.

PubMed

Lemkin, P F; Chipperfield, M; Merril, C; Zullo, S

1996-03-01

We describe a simple database search engine "dbEngine" which may be used to quickly create a searchable database on a World Wide Web (WWW) server. Data may be prepared from spreadsheet programs (such as Excel, etc.) or from tables exported from relationship database systems. This Common Gateway Interface (CGI-BIN) program is used with a WWW server such as available commercially, or from National Center for Supercomputer Algorithms (NCSA) or CERN. Its capabilities include: (i) searching records by combinations of terms connected with ANDs or ORs; (ii) returning search results as hypertext links to other WWW database servers; (iii) mapping lists of literature reference identifiers to the full references; (iv) creating bidirectional hypertext links between pictures and the database. DbEngine has been used to support the MitoDat database (Mendelian and non-Mendelian inheritance associated with the Mitochondrion) on the WWW.

Effectiveness of Motivational Interviewing Interventions for Adolescent Substance Use Behavior Change: A Meta-Analytic Review

ERIC Educational Resources Information Center

Jensen, Chad D.; Cushing, Christopher C.; Aylward, Brandon S.; Craig, James T.; Sorell, Danielle M.; Steele, Ric G.

2011-01-01

Objective: This study was designed to quantitatively evaluate the effectiveness of motivational interviewing (MI) interventions for adolescent substance use behavior change. Method: Literature searches of electronic databases were undertaken in addition to manual reference searches of identified review articles. Databases searched include…

FreeSolv: A database of experimental and calculated hydration free energies, with input files

PubMed Central

Mobley, David L.; Guthrie, J. Peter

2014-01-01

This work provides a curated database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations. We call this the Free Solvation Database, or FreeSolv. Experimental values were taken from prior literature and will continue to be curated, with updated experimental references and data added as they become available. Calculated values are based on alchemical free energy calculations using molecular dynamics simulations. These used the GAFF small molecule force field in TIP3P water with AM1-BCC charges. Values were calculated with the GROMACS simulation package, with full details given in references cited within the database itself. This database builds in part on a previous, 504-molecule database containing similar information. However, additional curation of both experimental data and calculated values has been done here, and the total number of molecules is now up to 643. Additional information is now included in the database, such as SMILES strings, PubChem compound IDs, accurate reference DOIs, and others. One version of the database is provided in the Supporting Information of this article, but as ongoing updates are envisioned, the database is now versioned and hosted online. In addition to providing the database, this work describes its construction process. The database is available free-of-charge via http://www.escholarship.org/uc/item/6sd403pz. PMID:24928188

MPD3: a useful medicinal plants database for drug designing.

PubMed

Mumtaz, Arooj; Ashfaq, Usman Ali; Ul Qamar, Muhammad Tahir; Anwar, Farooq; Gulzar, Faisal; Ali, Muhammad Amjad; Saari, Nazamid; Pervez, Muhammad Tariq

2017-06-01

Medicinal plants are the main natural pools for the discovery and development of new drugs. In the modern era of computer-aided drug designing (CADD), there is need of prompt efforts to design and construct useful database management system that allows proper data storage, retrieval and management with user-friendly interface. An inclusive database having information about classification, activity and ready-to-dock library of medicinal plant's phytochemicals is therefore required to assist the researchers in the field of CADD. The present work was designed to merge activities of phytochemicals from medicinal plants, their targets and literature references into a single comprehensive database named as Medicinal Plants Database for Drug Designing (MPD3). The newly designed online and downloadable MPD3 contains information about more than 5000 phytochemicals from around 1000 medicinal plants with 80 different activities, more than 900 literature references and 200 plus targets. The designed database is deemed to be very useful for the researchers who are engaged in medicinal plants research, CADD and drug discovery/development with ease of operation and increased efficiency. The designed MPD3 is a comprehensive database which provides most of the information related to the medicinal plants at a single platform. MPD3 is freely available at: http://bioinform.info .

Generating PubMed Chemical Queries for Consumer Health Literature

PubMed Central

Loo, Jeffery; Chang, Hua Florence; Hochstein, Colette; Sun, Ying

2005-01-01

Two popular NLM resources that provide information for consumers about chemicals and their safety are the Household Products Database and Haz-Map. Search queries to PubMed via web links were generated from these databases. The query retrieves consumer health-oriented literature about adverse effects of chemicals. The retrieval was limited to a manageable set of 20 to 60 citations, achieved by successively applying increasing limits to the search until the desired number of references was reached. PMID:16779322

Mapping selected general literature of international nursing.

PubMed

Shams, Marie-Lise Antoun; Dixon, Lana S

2007-01-01

This study, part of a wider project to map the literature of nursing, identifies core journals cited in non-US nursing journals and determines the extent of their coverage by indexing services. Four general English-language journals were analyzed for format types and publication dates. Core titles were identified and nine bibliographic databases were scanned for indexing coverage. Findings show that 57.5% (13,391/23,271) of the cited references from the 4 core journals were to journal articles, 27.8% (6,471/23,271) to books, 9.5% (2,208/23,271) to government documents, 4.9% (1,131/23,271) to miscellaneous sources, and less than 1% (70/23,271) to Internet resources. Eleven journals produced one-third of the citations; the next third included 146 journals, followed by a dispersion of 1,622 titles. PubMed received the best database coverage scores, followed by CINAHL and Science Citation Index. None of the databases provided complete coverage of all 11 core titles. The four source journals contain a diverse group of cited references. The currency of citations to government documents makes these journals a good source for regulatory and legislative awareness. Nurses consult nursing and biomedical journals and must search both nursing and biomedical databases to cover the literature.

The U.S. Dairy Forage Research Center (USDFRC) Condensed Tannin NMR Database.

PubMed

Zeller, Wayne E; Schatz, Paul F

2017-06-28

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, and 1 H and 13 C chemical shifts of the condensed tannins. Citations for all literature references are provided and should serve as valuable resource for scientists working in the field of condensed tannin research. The database will be periodically updated as additional information becomes available, typically on a yearly basis and is available for use, free of charge, from the U.S. Dairy Forage Research Center (USDFRC) Website.

The Protein Information Resource: an integrated public resource of functional annotation of proteins

PubMed Central

Wu, Cathy H.; Huang, Hongzhan; Arminski, Leslie; Castro-Alvear, Jorge; Chen, Yongxing; Hu, Zhang-Zhi; Ledley, Robert S.; Lewis, Kali C.; Mewes, Hans-Werner; Orcutt, Bruce C.; Suzek, Baris E.; Tsugita, Akira; Vinayaka, C. R.; Yeh, Lai-Su L.; Zhang, Jian; Barker, Winona C.

2002-01-01

The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. The PIR, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the PIR-International Protein Sequence Database (PSD), the major annotated protein sequence database in the public domain, containing about 250 000 proteins. To improve protein annotation and the coverage of experimentally validated data, a bibliography submission system is developed for scientists to submit, categorize and retrieve literature information. Comprehensive protein information is available from iProClass, which includes family classification at the superfamily, domain and motif levels, structural and functional features of proteins, as well as cross-references to over 40 biological databases. To provide timely and comprehensive protein data with source attribution, we have introduced a non-redundant reference protein database, PIR-NREF. The database consists of about 800 000 proteins collected from PIR-PSD, SWISS-PROT, TrEMBL, GenPept, RefSeq and PDB, with composite protein names and literature data. To promote database interoperability, we provide XML data distribution and open database schema, and adopt common ontologies. The PIR web site (http://pir.georgetown.edu/) features data mining and sequence analysis tools for information retrieval and functional identification of proteins based on both sequence and annotation information. The PIR databases and other files are also available by FTP (ftp://nbrfa.georgetown.edu/pir_databases). PMID:11752247

Selecting a database for literature searches in nursing: MEDLINE or CINAHL?

PubMed

Brazier, H; Begley, C M

1996-10-01

This study compares the usefulness of the MEDLINE and CINAHL databases for students on post-registration nursing courses. We searched for nine topics, using title words only. Identical searches of the two databases retrieved 1162 references, of which 88% were in MEDLINE, 33% in CINAHL and 20% in both sources. The relevance of the references was assessed by student reviewers. The positive predictive value of CINAHL (70%) was higher than that of MEDLINE (54%), but MEDLINE produced more than twice as many relevant references as CINAHL. The sensitivity of MEDLINE was 85% (95% CI 82-88%), and that of CINAHL was 41% (95% CI 37-45%). To assess the ease of obtaining the references, we developed an index of accessibility, based on the holdings of a number of Irish and British libraries. Overall, 47% of relevant references were available in the students' own library, and 64% could be obtained within 48 hours. There was no difference between the two databases overall, but when two topics relating specifically to the organization of nursing were excluded, references found in MEDLINE were significantly more accessible. We recommend that MEDLINE should be regarded as the first choice of bibliographic database for any subject other than one related strictly to the organization of nursing.

Database citation in full text biomedical articles.

PubMed

Kafkas, Şenay; Kim, Jee-Hyub; McEntyre, Johanna R

2013-01-01

Molecular biology and literature databases represent essential infrastructure for life science research. Effective integration of these data resources requires that there are structured cross-references at the level of individual articles and biological records. Here, we describe the current patterns of how database entries are cited in research articles, based on analysis of the full text Open Access articles available from Europe PMC. Focusing on citation of entries in the European Nucleotide Archive (ENA), UniProt and Protein Data Bank, Europe (PDBe), we demonstrate that text mining doubles the number of structured annotations of database record citations supplied in journal articles by publishers. Many thousands of new literature-database relationships are found by text mining, since these relationships are also not present in the set of articles cited by database records. We recommend that structured annotation of database records in articles is extended to other databases, such as ArrayExpress and Pfam, entries from which are also cited widely in the literature. The very high precision and high-throughput of this text-mining pipeline makes this activity possible both accurately and at low cost, which will allow the development of new integrated data services.

Database Citation in Full Text Biomedical Articles

PubMed Central

Kafkas, Şenay; Kim, Jee-Hyub; McEntyre, Johanna R.

2013-01-01

Molecular biology and literature databases represent essential infrastructure for life science research. Effective integration of these data resources requires that there are structured cross-references at the level of individual articles and biological records. Here, we describe the current patterns of how database entries are cited in research articles, based on analysis of the full text Open Access articles available from Europe PMC. Focusing on citation of entries in the European Nucleotide Archive (ENA), UniProt and Protein Data Bank, Europe (PDBe), we demonstrate that text mining doubles the number of structured annotations of database record citations supplied in journal articles by publishers. Many thousands of new literature-database relationships are found by text mining, since these relationships are also not present in the set of articles cited by database records. We recommend that structured annotation of database records in articles is extended to other databases, such as ArrayExpress and Pfam, entries from which are also cited widely in the literature. The very high precision and high-throughput of this text-mining pipeline makes this activity possible both accurately and at low cost, which will allow the development of new integrated data services. PMID:23734176

A guide to experimental particle physics literature, 1991-1996

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ezhela, V.V.; Filimonov, B.B.; Lugovsky, S.B.

1996-10-01

We present an indexed guide to experimental particle physics literature for the years 1991 - 1996. Approximately 4200 papers are indexed by (1) Beam/Target/Momentum (2) Reaction/Momentum/Data-Descriptor (including the final state) (3) Particle/Decay (4) Accelerator/Experiment/Detector. All indices are cross-referenced to the paper`s title and references in the ID/Reference/Title index. The information presented in this guide is also publicly available on a regularly-updated DATAGUIDE database from the World Wide Web.

Locating grey literature on communication disorders.

PubMed

Shpilko, Inna

2005-01-01

This article provides an overview of selected Web-based resources containing grey literature in the area of communication disorders. It is geared to practitioners, researchers, students, and consumers seeking reliable, freely available scientific information. Grey (or gray) literature has been defined as "that which is produced on all levels of government, academics, business, and industry in print and electronic formats, but which is not controlled by commercial publishers."1 This paper reviews various general reference sources potentially containing grey literature on communication disorders. This review includes identification of the methods specialists in this field use to obtain this valuable, yet often overlooked, literature. Access points and search tools for identifying grey literature on communication disorders are recommended. Commercial databases containing grey literature are not included. Conclusions presented in this article are considered complementary to traditionally published information resources on communication disorders, such as scholarly journals, online databases, etc.

Newborn Screening: National Library of Medicine Literature Search, January 1980 through March 1987. No. 87-2.

ERIC Educational Resources Information Center

Patrias, Karen

This bibliography, prepared by the National Library of Medicine through a literature search of its online databases, covers all aspects of newborn screening. It includes references to screening for: inborn errors of metabolism, such as phenylketonuria and galactosemia; hemoglobinopathies, particularly sickle cell disease; congenital hypothyroidism…

University Library Virtual Reference Services: Best Practices and Continuous Improvement

ERIC Educational Resources Information Center

Shaw, Kate; Spink, Amanda

2009-01-01

The inclusion or not of chat services within Virtual Reference (VR) is an important topic for university libraries. Increasingly, email supported by a Frequently Asked Questions (FAQ) database is suggested in the scholarly literature as the preferred, cost-effective means for providing university VR services. This paper examines these issues and…

CORUM: the comprehensive resource of mammalian protein complexes

PubMed Central

Ruepp, Andreas; Brauner, Barbara; Dunger-Kaltenbach, Irmtraud; Frishman, Goar; Montrone, Corinna; Stransky, Michael; Waegele, Brigitte; Schmidt, Thorsten; Doudieu, Octave Noubibou; Stümpflen, Volker; Mewes, H. Werner

2008-01-01

Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The CORUM (http://mips.gsf.de/genre/proj/corum/index.html) database is a collection of experimentally verified mammalian protein complexes. Information is manually derived by critical reading of the scientific literature from expert annotators. Information about protein complexes includes protein complex names, subunits, literature references as well as the function of the complexes. For functional annotation, we use the FunCat catalogue that enables to organize the protein complex space into biologically meaningful subsets. The database contains more than 1750 protein complexes that are built from 2400 different genes, thus representing 12% of the protein-coding genes in human. A web-based system is available to query, view and download the data. CORUM provides a comprehensive dataset of protein complexes for discoveries in systems biology, analyses of protein networks and protein complex-associated diseases. Comparable to the MIPS reference dataset of protein complexes from yeast, CORUM intends to serve as a reference for mammalian protein complexes. PMID:17965090

Mapping the literature of perfusion.

PubMed Central

Hall, E F

1999-01-01

Perfusionists select and operate the equipment necessary for monitoring, supporting, or temporarily replacing the patient's circulatory or respiratory function. There are over 3,000 perfusionists working in U.S. hospitals, medical and perfusionist groups, and as independent contractors. The purpose of this study was to identify the core literature of perfusion and to determine which major databases provide the most thorough access to this literature. This paper is part of the Medical Library Association Nursing and Allied Health Resource Section's project to map the literature of the allied health professions. It uses a bibliometric methodology to identify core journals. A group of forty-three journals was determined to make up the core journal literature of perfusion. MEDLINE provided the best overall indexing coverage for these journals, but librarians and perfusionists will wish to supplement its use with the Cumulative Index to Nursing and Allied Health Literature in order to access the journals written primarily for perfusionists. The study results can guide purchasing and database searching decisions of collection development and reference librarians, encourage the database producer to increase coverage of titles that are unindexed or underindexed, and advise perfusionists of the best access to their core literature. PMID:10427432

Optimizing literature search in systematic reviews - are MEDLINE, EMBASE and CENTRAL enough for identifying effect studies within the area of musculoskeletal disorders?

PubMed

Aagaard, Thomas; Lund, Hans; Juhl, Carsten

2016-11-22

When conducting systematic reviews, it is essential to perform a comprehensive literature search to identify all published studies relevant to the specific research question. The Cochrane Collaborations Methodological Expectations of Cochrane Intervention Reviews (MECIR) guidelines state that searching MEDLINE, EMBASE and CENTRAL should be considered mandatory. The aim of this study was to evaluate the MECIR recommendations to use MEDLINE, EMBASE and CENTRAL combined, and examine the yield of using these to find randomized controlled trials (RCTs) within the area of musculoskeletal disorders. Data sources were systematic reviews published by the Cochrane Musculoskeletal Review Group, including at least five RCTs, reporting a search history, searching MEDLINE, EMBASE, CENTRAL, and adding reference- and hand-searching. Additional databases were deemed eligible if they indexed RCTs, were in English and used in more than three of the systematic reviews. Relative recall was calculated as the number of studies identified by the literature search divided by the number of eligible studies i.e. included studies in the individual systematic reviews. Finally, cumulative median recall was calculated for MEDLINE, EMBASE and CENTRAL combined followed by the databases yielding additional studies. Deemed eligible was twenty-three systematic reviews and the databases included other than MEDLINE, EMBASE and CENTRAL was AMED, CINAHL, HealthSTAR, MANTIS, OT-Seeker, PEDro, PsychINFO, SCOPUS, SportDISCUS and Web of Science. Cumulative median recall for combined searching in MEDLINE, EMBASE and CENTRAL was 88.9% and increased to 90.9% when adding 10 additional databases. Searching MEDLINE, EMBASE and CENTRAL was not sufficient for identifying all effect studies on musculoskeletal disorders, but additional ten databases did only increase the median recall by 2%. It is possible that searching databases is not sufficient to identify all relevant references, and that reviewers must rely upon additional sources in their literature search. However further research is needed.

Gender Dysphoria and Cross-Dressing in People with Intellectual Disability: A Literature Review

ERIC Educational Resources Information Center

Parkes, Georgina; Hall, Ian

2006-01-01

In clinical practice, we have come across people with intellectual disability who have gender dysphoria and cross-dress. Here, we review the literature on this subject and present an illustrative case example. We searched databases, followed-up references from relevant articles, and contacted colleagues in the field. We found nine papers with case…

Impact of Peer Nutrition Education on Dietary Behaviors and Health Outcomes among Latinos: A Systematic Literature Review

ERIC Educational Resources Information Center

Perez-Escamilla, Rafael; Hromi-Fiedler, Amber; Vega-Lopez, Sonia; Bermudez-Millan, Angela; Segura-Perez, Sofia

2008-01-01

Objective: This systematic review assesses the impact of peer education/counseling on nutrition and health outcomes among Latinos and identifies future research needs. Design: A systematic literature search was conducted by: (1) searching Internet databases; (2) conducting backward searches from reference lists of articles of interest; (3)…

Ranking the whole MEDLINE database according to a large training set using text indexing.

PubMed

Suomela, Brian P; Andrade, Miguel A

2005-03-24

The MEDLINE database contains over 12 million references to scientific literature, with about 3/4 of recent articles including an abstract of the publication. Retrieval of entries using queries with keywords is useful for human users that need to obtain small selections. However, particular analyses of the literature or database developments may need the complete ranking of all the references in the MEDLINE database as to their relevance to a topic of interest. This report describes a method that does this ranking using the differences in word content between MEDLINE entries related to a topic and the whole of MEDLINE, in a computational time appropriate for an article search query engine. We tested the capabilities of our system to retrieve MEDLINE references which are relevant to the subject of stem cells. We took advantage of the existing annotation of references with terms from the MeSH hierarchical vocabulary (Medical Subject Headings, developed at the National Library of Medicine). A training set of 81,416 references was constructed by selecting entries annotated with the MeSH term stem cells or some child in its sub tree. Frequencies of all nouns, verbs, and adjectives in the training set were computed and the ratios of word frequencies in the training set to those in the entire MEDLINE were used to score references. Self-consistency of the algorithm, benchmarked with a test set containing the training set and an equal number of references randomly selected from MEDLINE was better using nouns (79%) than adjectives (73%) or verbs (70%). The evaluation of the system with 6,923 references not used for training, containing 204 articles relevant to stem cells according to a human expert, indicated a recall of 65% for a precision of 65%. This strategy appears to be useful for predicting the relevance of MEDLINE references to a given concept. The method is simple and can be used with any user-defined training set. Choice of the part of speech of the words used for classification has important effects on performance. Lists of words, scripts, and additional information are available from the web address http://www.ogic.ca/projects/ks2004/.

Comparison of tiered formularies and reference pricing policies: a systematic review

PubMed Central

Morgan, Steve; Hanley, Gillian; Greyson, Devon

2009-01-01

Objectives To synthesize methodologically comparable evidence from the published literature regarding the outcomes of tiered formularies and therapeutic reference pricing of prescription drugs. Methods We searched the following electronic databases: ABI/Inform, CINAHL, Clinical Evidence, Digital Dissertations & Theses, Evidence-Based Medicine Reviews (which incorporates ACP Journal Club, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, Cochrane Methodology Register, Database of Abstracts of Reviews of Effectiveness, Health Technology Assessments and NHS Economic Evaluation Database), EconLit, EMBASE, International Pharmaceutical Abstracts, MEDLINE, PAIS International and PAIS Archive, and the Web of Science. We also searched the reference lists of relevant articles and several grey literature sources. We sought English-language studies published from 1986 to 2007 that examined the effects of either therapeutic reference pricing or tiered formularies, reported on outcomes relevant to patient care and cost-effectiveness, and employed quantitative study designs that included concurrent or historical comparison groups. We abstracted and assessed potentially appropriate articles using a modified version of the data abstraction form developed by the Cochrane Effective Practice and Organisation of Care Group. Results From an initial list of 2964 citations, 12 citations (representing 11 studies) were deemed eligible for inclusion in our review: 3 studies (reported in 4 articles) of reference pricing and 8 studies of tiered formularies. The introduction of reference pricing was associated with reduced plan spending, switching to preferred medicines, reduced overall drug utilization and short-term increases in the use of physician services. Reference pricing was not associated with adverse health impacts. The introduction of tiered formularies was associated with reduced plan expenditures, greater patient costs and increased rates of non-compliance with prescribed drug therapy. From the data available, we were unable to examine the hypothesis that tiered formulary policies result in greater use of physician services and potentially worse health outcomes. Conclusion The available evidence does not clearly differentiate between reference pricing and tiered formularies in terms of policy outcomes. Reference pricing appears to have a slight evidentiary advantage, given that patients’ health outcomes under tiered formularies have not been well studied and that tiered formularies are associated with increased rates of medicine discontinuation. PMID:21603047

Identifying known unknowns using the US EPA's CompTox ...

EPA Pesticide Factsheets

Chemical features observed using high-resolution mass spectrometry can be tentatively identified using online chemical reference databases by searching molecular formulae and monoisotopic masses and then rank-ordering of the hits using appropriate relevance criteria. The most likely candidate “known unknowns,” which are those chemicals unknown to an investigator but contained within a reference database or literature source, rise to the top of a chemical list when rank-ordered by the number of associated data sources. The U.S. EPA’s CompTox Chemistry Dashboard is a curated and freely available resource for chemistry and computational toxicology research, containing more than 720,000 chemicals of relevance to environmental health science. In this research, the performance of the Dashboard for identifying “known unknowns” was evaluated against that of the online ChemSpider database, one of the primary resources used by mass spectrometrists, using multiple previously studied datasets reported in the peer-reviewed literature totaling 162 chemicals. These chemicals were examined using both applications via molecular formula and monoisotopic mass searches followed by rank-ordering of candidate compounds by associated references or data sources. A greater percentage of chemicals ranked in the top position when using the Dashboard, indicating an advantage of this application over ChemSpider for identifying known unknowns using data source ranking. Addition

Assessing telemedicine: a systematic review of the literature.

PubMed

Roine, R; Ohinmaa, A; Hailey, D

2001-09-18

To clarify the current status of telemedicine, we carried out a systematic review of the literature. We identified controlled assessment studies of telemedicine that reported patient outcomes, administrative changes or economic assessments and assessed the quality of that literature. We carried out a systematic electronic search for articles published from 1966 to early 2000 using the MEDLINE (1966-April 2000), HEALTHSTAR (1975-January 2000), EMBASE (1988-February 2000) and CINALH (1982-January 2000) databases. In addition, the HSTAT database (Health Services/Technology Assessment Text, US National Library of Medicine), the Database of Abstracts of Reviews of Effectiveness (DARE, NHS Centre for Reviews and Dissemination, United Kingdom), the NHS Economic Evaluation Database and the Cochrane Controlled Trials Register were searched. We consulted experts in the field and did a manual search of the reference lists of review articles. A total of 1124 studies were identified. Based on a review of the abstracts, 133 full-text articles were obtained for closer inspection. Of these, 50 were deemed to represent assessment studies fulfilling the inclusion criteria of the review. Thirty-four of the articles assessed at least some clinical outcomes; the remaining 16 were mainly economic analyses. Most of the available literature referred only to pilot projects and short-term outcomes, and most of the studies were of low quality. Relatively convincing evidence of effectiveness was found only for teleradiology, teleneurosurgery, telepsychiatry, transmission of echocardiographic images, and the use of electronic referrals enabling e-mail consultations and video conferencing between primary and secondary health care providers. Economic analyses suggested that teleradiology, especially transmission of CT images, can be cost-saving. Evidence regarding the effectiveness or cost-effectiveness of telemedicine is still limited. Based on current scientific evidence, only a few telemedicine applications can be recommended for broader use.

Tone as a health concept: An analysis.

PubMed

McDowall, Donald; Emmanuel, Elizabeth; Grace, Sandra; Chaseling, Marilyn

2017-11-01

Concept analysis. This paper is a report on the analysis of the concept of tone in chiropractic. The purpose of this paper is to clarify the concept of tone as originally understood by Daniel David Palmer from 1895 to 1914 and to monitor its evolution over time. Data was sourced from Palmer's original work, published between 1895 and 1914. A literature search from 1980 to 2016 was also performed on the online databases CINHAL, PubMed and Scopus with key terms including 'tone', 'chiropractic', 'Palmer', 'vitalism', 'health', 'homeostasis', 'holism' and 'wellness'. Finally hand-searches were conducted through chiropractic books and professional literature from 1906 to 1980 for any references to 'tone'. Rodgers' evolutionary method of analysis was used to categorise the data in relation to the surrogates, attributes, references, antecedents and consequences of tone. A total of 49 references were found: five from publications by Palmer; three from the database searches, and; the remaining 41 from professional books, trade journals and websites. There is no clear interpretation of tone in the contemporary chiropractic literature. Tone is closely aligned with functional neurology and can be understood as an interface between the metaphysical and the biomedical. Using the concept of tone as a foundation for practice could strengthen the identity of the chiropractic profession. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Construction of chemical information database based on optical structure recognition technique].

PubMed

Lv, C Y; Li, M N; Zhang, L R; Liu, Z M

2018-04-18

To create a protocol that could be used to construct chemical information database from scientific literature quickly and automatically. Scientific literature, patents and technical reports from different chemical disciplines were collected and stored in PDF format as fundamental datasets. Chemical structures were transformed from published documents and images to machine-readable data by using the name conversion technology and optical structure recognition tool CLiDE. In the process of molecular structure information extraction, Markush structures were enumerated into well-defined monomer molecules by means of QueryTools in molecule editor ChemDraw. Document management software EndNote X8 was applied to acquire bibliographical references involving title, author, journal and year of publication. Text mining toolkit ChemDataExtractor was adopted to retrieve information that could be used to populate structured chemical database from figures, tables, and textual paragraphs. After this step, detailed manual revision and annotation were conducted in order to ensure the accuracy and completeness of the data. In addition to the literature data, computing simulation platform Pipeline Pilot 7.5 was utilized to calculate the physical and chemical properties and predict molecular attributes. Furthermore, open database ChEMBL was linked to fetch known bioactivities, such as indications and targets. After information extraction and data expansion, five separate metadata files were generated, including molecular structure data file, molecular information, bibliographical references, predictable attributes and known bioactivities. Canonical simplified molecular input line entry specification as primary key, metadata files were associated through common key nodes including molecular number and PDF number to construct an integrated chemical information database. A reasonable construction protocol of chemical information database was created successfully. A total of 174 research articles and 25 reviews published in Marine Drugs from January 2015 to June 2016 collected as essential data source, and an elementary marine natural product database named PKU-MNPD was built in accordance with this protocol, which contained 3 262 molecules and 19 821 records. This data aggregation protocol is of great help for the chemical information database construction in accuracy, comprehensiveness and efficiency based on original documents. The structured chemical information database can facilitate the access to medical intelligence and accelerate the transformation of scientific research achievements.

Mapping the literature of athletic training

PubMed Central

Delwiche, Frances A.; Hall, Ellen F.

2007-01-01

Purpose: This paper identifies the core literature of athletic training and determines which major databases provide the most thorough intellectual access to this literature. Methods: This study collected all cited references from 2002 to 2004 of three journals widely read by those in the athletic training field. Bradford's Law of Scattering was applied to the resulting list to determine the core journal titles in the discipline. Three major databases were reviewed for extent of their coverage of these core journals. Results: Of the total 8,678 citations, one-third referenced a compact group of 6 journals; another third of the citations referenced an additional 40 titles. The remaining 2,837 citations were scattered across 1,034 additional journal titles. Conclusions: The number and scatter of citations over a three-year period identified forty-six key journals in athletic training. The study results can inform athletic trainers of the core literature in their field, encourage database producers (e.g., MEDLINE, SPORTDiscus, CINAHL) to increase coverage of titles that are not indexed or underindexed, and guide purchasing decisions for libraries serving athletic training programs. PMID:17443253

Identifying the effective evidence sources to use in developing Clinical Guidelines for Acute Stroke Management: lived experiences of the search specialist and project manager.

PubMed

Parkhill, Anne; Hill, Kelvin

2009-03-01

The Australian National Stroke Foundation appointed a search specialist to find the best available evidence for the second edition of its Clinical Guidelines for Acute Stroke Management. To identify the relative effectiveness of differing evidence sources for the guideline update. We searched and reviewed references from five valid evidence sources for clinical and economic questions: (i) electronic databases; (ii) reference lists of relevant systematic reviews, guidelines, and/or primary studies; (iii) table of contents of a number of key journals for the last 6 months; (iv) internet/grey literature; and (v) experts. Reference sources were recorded, quantified, and analysed. In the clinical portion of the guidelines document, there was a greater use of previous knowledge and sources other than electronic databases for evidence, while there was a greater use of electronic databases for the economic section. The results confirmed that searchers need to be aware of the context and range of sources for evidence searches. For best available evidence, searchers cannot rely solely on electronic databases and need to encompass many different media and sources.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alekhin, S.I.; Ezhela, V.V.; Filimonov, B.B.

We present an indexed guide to the literature experimental particle physics for the years 1988--1992. About 4,000 papers are indexed by Beam/Target/Momentum, Reaction Momentum (including the final state), Final State Particle, and Accelerator/Detector/Experiment. All indices are cross-referenced to the paper`s title and reference in the ID/Reference/Title Index. The information in this guide is also publicly available from a regularly updated computer database.

Mapping the literature of physical therapy.

PubMed Central

Wakiji, E M

1997-01-01

Physical therapy is a fast growing profession because of the aging population, medical advances, and the public's interest in health promotion. This study is part of the Medical Library Association (MLA) Nursing and Allied Health Resources Section's project to map the allied health literature. It identifies the core journals in physical therapy by analyzing the cited references of articles in two established physical therapy journals, Physical Therapy and Archives of Physical Medicine and Rehabilitation, during the period 1991 through 1993. This bibliometric analysis also determines the extent to which these journals are covered by the primary indexing sources, Allied and Alternative Medicine (AMED), the Cumulative Index to Nursing and Allied Health Literature, EMBASE, and MEDLINE. In this study, fourteen journals were found to supply one-third of all references studied. Ninety-five journals provided an additional third of the references. MEDLINE rated the highest as the indexing tool of choice for these 109 journals. The study results can assist in collection development decisions, advise physical therapists as to the best access to their core literature, and influence database producers to increase their coverage of the literature important to physical therapy. PMID:9285129

Information sources for obesity prevention policy research: a review of systematic reviews.

PubMed

Hanneke, Rosie; Young, Sabrina K

2017-08-08

Systematic identification of evidence in health policy can be time-consuming and challenging. This study examines three questions pertaining to systematic reviews on obesity prevention policy, in order to identify the most efficient search methods: (1) What percentage of the primary studies selected for inclusion in the reviews originated in scholarly as opposed to gray literature? (2) How much of the primary scholarly literature in this topic area is indexed in PubMed/MEDLINE? (3) Which databases index the greatest number of primary studies not indexed in PubMed, and are these databases searched consistently across systematic reviews? We identified systematic reviews on obesity prevention policy and explored their search methods and citations. We determined the percentage of scholarly vs. gray literature cited, the most frequently cited journals, and whether each primary study was indexed in PubMed. We searched 21 databases for all primary study articles not indexed in PubMed to determine which database(s) indexed the highest number of these relevant articles. In total, 21 systematic reviews were identified. Ten of the 21 systematic reviews reported searching gray literature, and 12 reviews ultimately included gray literature in their analyses. Scholarly articles accounted for 577 of the 649 total primary study papers. Of these, 495 (76%) were indexed in PubMed. Google Scholar retrieved the highest number of the remaining 82 non-PubMed scholarly articles, followed by Scopus and EconLit. The Journal of the American Dietetic Association was the most-cited journal. Researchers can maximize search efficiency by searching a small yet targeted selection of both scholarly and gray literature resources. A highly sensitive search of PubMed and those databases that index the greatest number of relevant articles not indexed in PubMed, namely multidisciplinary and economics databases, could save considerable time and effort. When combined with a gray literature search and additional search methods, including cited reference searching and consulting with experts, this approach could help maintain broad retrieval of relevant studies while improving search efficiency. Findings also have implications for designing specialized databases for public health research.

Aquatic information and retrieval (AQUIRE) database system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hunter, R.; Niemi, G.; Pilli, A.

The AQUIRE database system is one of the foremost international resources for finding aquatic toxicity information. Information in the system is organized around the concept of an 'aquatic toxicity test.' A toxicity test record contains information about the chemical, species, endpoint, endpoint concentrations, and test conditions under which the toxicity test was conducted. For the past 10 years aquatic literature has been reviewed and entered into the system. Currently, the AQUIRE database system contains data on more than 2,400 species, 160 endpoints, 5,000 chemicals, 6,000 references, and 104,000 toxicity tests.

"Hyperstat": an educational and working tool in epidemiology.

PubMed

Nicolosi, A

1995-01-01

The work of a researcher in epidemiology is based on studying literature, planning studies, gathering data, analyzing data and writing results. Therefore he has need for performing, more or less, simple calculations, the need for consulting or quoting literature, the need for consulting textbooks about certain issues or procedures, and the need for looking at a specific formula. There are no programs conceived as a workstation to assist the different aspects of researcher work in an integrated fashion. A hypertextual system was developed which supports different stages of the epidemiologist's work. It combines database management, statistical analysis or planning, and literature searches. The software was developed on Apple Macintosh by using Hypercard 2.1 as a database and HyperTalk as a programming language. The program is structured in 7 "stacks" or files: Procedures; Statistical Tables; Graphs; References; Text; Formulas; Help. Each stack has its own management system with an automated Table of Contents. Stacks contain "cards" which make up the databases and carry executable programs. The programs are of four kinds: association; statistical procedure; formatting (input/output); database management. The system performs general statistical procedures, procedures applicable to epidemiological studies only (follow-up and case-control), and procedures for clinical trials. All commands are given by clicking the mouse on self-explanatory "buttons". In order to perform calculations, the user only needs to enter the data into the appropriate cells and then click on the selected procedure's button. The system has a hypertextual structure. The user can go from a procedure to other cards following the preferred order of succession and according to built-in associations. The user can access different levels of knowledge or information from any stack he is consulting or operating. From every card, the user can go to a selected procedure to perform statistical calculations, to the reference database management system, to the textbook in which all procedures and issues are discussed in detail, to the database of statistical formulas with automated table of contents, to statistical tables with automated table of contents, or to the help module. he program has a very user-friendly interface and leaves the user free to use the same format he would use on paper. The interface does not require special skills. It reflects the Macintosh philosophy of using windows, buttons and mouse. This allows the user to perform complicated calculations without losing the "feel" of data, weight alternatives, and simulations. This program shares many features in common with hypertexts. It has an underlying network database where the nodes consist of text, graphics, executable procedures, and combinations of these; the nodes in the database correspond to windows on the screen; the links between the nodes in the database are visible as "active" text or icons in the windows; the text is read by following links and opening new windows. The program is especially useful as an educational tool, directed to medical and epidemiology students. The combination of computing capabilities with a textbook and databases of formulas and literature references, makes the program versatile and attractive as a learning tool. The program is also helpful in the work done at the desk, where the researcher examines results, consults literature, explores different analytic approaches, plans new studies, or writes grant proposals or scientific articles.

Mapping the literature of occupational therapy: an update.

PubMed

Potter, Jonathan

2010-07-01

This study updated Reed's 1999 "Mapping the Literature of Occupational Therapy." An analysis of citation patterns and indexing coverage was undertaken to identify the core literature of occupational therapy and to determine access to that literature. Citations from three source journals for the years 2006 through 2008 were studied following the common methodology of the "Mapping the Literature of Allied Health Project." Bradford's Law of Scattering was applied to analyze the productivity of cited journals. A comparative analysis of indexing was conducted across three bibliographic databases. A total of 364 articles cited 10,425 references. Journals were the most frequently cited format, accounting for 65.3% of the references, an increase of 4.1% over the 1999 study. Approximately one-third of the journal references cited a cluster of 9 journals, with the American Journal of Occupational Therapy dominating the field. An additional 120 journals were identified as moderately important based on times cited. CINAHL provided the most comprehensive indexing of core journals, while MEDLINE provided the best overall coverage. Occupational therapy is a multidisciplinary field with a strong core identity and an increasingly diverse literature. Indexing has improved overall since 1999, but gaps in the coverage are still evident.

Composition-dependence of stacking fault energy in austenitic stainless steels through linear regression with random intercepts

NASA Astrophysics Data System (ADS)

Meric de Bellefon, G.; van Duysen, J. C.; Sridharan, K.

2017-08-01

The stacking fault energy (SFE) plays an important role in deformation behavior and radiation damage of FCC metals and alloys such as austenitic stainless steels. In the present communication, existing expressions to calculate SFE in those steels from chemical composition are reviewed and an improved multivariate linear regression with random intercepts is used to analyze a new database of 144 SFE measurements collected from 30 literature references. It is shown that the use of random intercepts can account for experimental biases in these literature references. A new expression to predict SFE from austenitic stainless steel compositions is proposed.

76 FR 51988 - Agency Information Collection Activities; Submission for Office of Management and Budget Review...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-19

... Medicines Agency (EMA) European Community Herbal Monographs, and World Health Organization (WHO) Monographs... that several authoritative labeling standards monographs for herbal products specify traditional use... the major scientific reference databases, such as the National Library of Medicine's literature...

The Corporate Library and Issues Management.

ERIC Educational Resources Information Center

Lancaster, F. W.; Loescher, Jane

1994-01-01

Discussion of corporate library services and the role of the librarian focuses on the recognition and tracking of issues of potential significance to the corporation, or issues management. Topics addressed include environmental scanning of relevant literature, and the use of databases to track issues. (16 references) (LRW)

Online Mendelian Inheritance in Man (OMIM).

PubMed

Hamosh, A; Scott, A F; Amberger, J; Valle, D; McKusick, V A

2000-01-01

Online Mendelian Inheritance In Man (OMIM) is a public database of bibliographic information about human genes and genetic disorders. Begun by Dr. Victor McKusick as the authoritative reference Mendelian Inheritance in Man, it is now distributed electronically by the National Center for Biotechnology Information (NCBI). Material in OMIM is derived from the biomedical literature and is written by Dr. McKusick and his colleagues at Johns Hopkins University and elsewhere. Each OMIM entry has a full text summary of a genetic phenotype and/or gene and has copious links to other genetic resources such as DNA and protein sequence, PubMed references, mutation databases, approved gene nomenclature, and more. In addition, NCBI's neighboring feature allows users to identify related articles from PubMed selected on the basis of key words in the OMIM entry. Through its many features, OMIM is increasingly becoming a major gateway for clinicians, students, and basic researchers to the ever-growing literature and resources of human genetics. Copyright 2000 Wiley-Liss, Inc.

Documentation for the CETACEA Database of Marine Mammal Literature References. Revision

DTIC Science & Technology

1990-06-01

interactions between birds and marine mammals. BT Mixed species 645 RT Fish marine mammal 941 Human marine mammal interraction 881 Birth 745 RT Foetus 405...817 -- 40 -- CETACEA Database SUBJECT HEADINGS Calf Age and growth 314 Birth 745 Care giving 201 Foetus 405 Growth rate 465 Juvenile 557 Lactation...Sound production 997 Visual, various subjects. Foetus 405 NT Multiplets 661 RT Acje and growth 314Brh745 Growth rate 465 Neonate 315 Sex ratio 921

Citation searches are more sensitive than keyword searches to identify studies using specific measurement instruments.

PubMed

Linder, Suzanne K; Kamath, Geetanjali R; Pratt, Gregory F; Saraykar, Smita S; Volk, Robert J

2015-04-01

To compare the effectiveness of two search methods in identifying studies that used the Control Preferences Scale (CPS), a health care decision-making instrument commonly used in clinical settings. We searched the literature using two methods: (1) keyword searching using variations of "Control Preferences Scale" and (2) cited reference searching using two seminal CPS publications. We searched three bibliographic databases [PubMed, Scopus, and Web of Science (WOS)] and one full-text database (Google Scholar). We report precision and sensitivity as measures of effectiveness. Keyword searches in bibliographic databases yielded high average precision (90%) but low average sensitivity (16%). PubMed was the most precise, followed closely by Scopus and WOS. The Google Scholar keyword search had low precision (54%) but provided the highest sensitivity (70%). Cited reference searches in all databases yielded moderate sensitivity (45-54%), but precision ranged from 35% to 75% with Scopus being the most precise. Cited reference searches were more sensitive than keyword searches, making it a more comprehensive strategy to identify all studies that use a particular instrument. Keyword searches provide a quick way of finding some but not all relevant articles. Goals, time, and resources should dictate the combination of which methods and databases are used. Copyright © 2015 Elsevier Inc. All rights reserved.

Citation searches are more sensitive than keyword searches to identify studies using specific measurement instruments

PubMed Central

Linder, Suzanne K.; Kamath, Geetanjali R.; Pratt, Gregory F.; Saraykar, Smita S.; Volk, Robert J.

2015-01-01

Objective To compare the effectiveness of two search methods in identifying studies that used the Control Preferences Scale (CPS), a healthcare decision-making instrument commonly used in clinical settings. Study Design & Setting We searched the literature using two methods: 1) keyword searching using variations of “control preferences scale” and 2) cited reference searching using two seminal CPS publications. We searched three bibliographic databases [PubMed, Scopus, Web of Science (WOS)] and one full-text database (Google Scholar). We report precision and sensitivity as measures of effectiveness. Results Keyword searches in bibliographic databases yielded high average precision (90%), but low average sensitivity (16%). PubMed was the most precise, followed closely by Scopus and WOS. The Google Scholar keyword search had low precision (54%) but provided the highest sensitivity (70%). Cited reference searches in all databases yielded moderate sensitivity (45–54%), but precision ranged from 35–75% with Scopus being the most precise. Conclusion Cited reference searches were more sensitive than keyword searches, making it a more comprehensive strategy to identify all studies that use a particular instrument. Keyword searches provide a quick way of finding some but not all relevant articles. Goals, time and resources should dictate the combination of which methods and databases are used. PMID:25554521

Whistleblowing: An integrative literature review of data-based studies involving nurses.

PubMed

Jackson, Debra; Hickman, Louise D; Hutchinson, Marie; Andrew, Sharon; Smith, James; Potgieter, Ingrid; Cleary, Michelle; Peters, Kath

2014-10-27

Abstract Aim To summarise and critique the research literature about whistleblowing and nurses. Background Whistleblowing is identified as a crucial issue in maintenance of healthcare standards and nurses are frequently involved in whistleblowing events. Despite the importance of this issue, to our knowledge an evaluation of this body of the data-based literature has not been undertaken. Method An integrative literature review approach was used to summarise and critique the research literature. A comprehensive search of five databases including Medline, CINAHL, PubMed and Health Science: Nursing/Academic Edition, and Google, were searched using terms including: 'whistleblow*', 'nurs*'. In addition, relevant journals were examined, as well as reference lists of retrieved papers. Papers published during the years 2007-2013 were selected for inclusion. Findings Fifteen papers were identified, capturing data from nurses in seven countries. The findings in this review demonstrate a growing body of research for the nursing profession at large to engage and respond appropriately to issues involving suboptimal patient care or organisational wrongdoing. Conclusions Nursing plays a key role in maintaining practice standards and in reporting care that is unacceptable although the repercussions to nurses who raise concerns are insupportable. Overall, whistleblowing and how it influences the individual, their family, work colleagues, nursing practice and policy overall, requires further national and international research attention.

Whistleblowing: An integrative literature review of data-based studies involving nurses.

PubMed

Jackson, Debra; Hickman, Louise D; Hutchinson, Marie; Andrew, Sharon; Smith, James; Potgieter, Ingrid; Cleary, Michelle; Peters, Kath

2014-01-01

Abstract Aim: To summarise and critique the research literature about whistleblowing and nurses. Whistleblowing is identified as a crucial issue in maintenance of healthcare standards and nurses are frequently involved in whistleblowing events. Despite the importance of this issue, to our knowledge an evaluation of this body of the data-based literature has not been undertaken. An integrative literature review approach was used to summarise and critique the research literature. A comprehensive search of five databases including Medline, CINAHL, PubMed and Health Science: Nursing/Academic Edition, and Google, were searched using terms including: 'Whistleblow*,' 'nurs*.' In addition, relevant journals were examined, as well as reference lists of retrieved papers. Papers published during the years 2007-2013 were selected for inclusion. Fifteen papers were identified, capturing data from nurses in seven countries. The findings in this review demonstrate a growing body of research for the nursing profession at large to engage and respond appropriately to issues involving suboptimal patient care or organisational wrongdoing. Nursing plays a key role in maintaining practice standards and in reporting care that is unacceptable although the repercussions to nurses who raise concerns are insupportable. Overall, whistleblowing and how it influences the individual, their family, work colleagues, nursing practice and policy overall, requires further national and international research attention.

Expert searching in public health

PubMed Central

Alpi, Kristine M.

2005-01-01

Objective: The article explores the characteristics of public health information needs and the resources available to address those needs that distinguish it as an area of searching requiring particular expertise. Methods: Public health searching activities from reference questions and literature search requests at a large, urban health department library were reviewed to identify the challenges in finding relevant public health information. Results: The terminology of the information request frequently differed from the vocabularies available in the databases. Searches required the use of multiple databases and/or Web resources with diverse interfaces. Issues of the scope and features of the databases relevant to the search questions were considered. Conclusion: Expert searching in public health differs from other types of expert searching in the subject breadth and technical demands of the databases to be searched, the fluidity and lack of standardization of the vocabulary, and the relative scarcity of high-quality investigations at the appropriate level of geographic specificity. Health sciences librarians require a broad exposure to databases, gray literature, and public health terminology to perform as expert searchers in public health. PMID:15685281

Parenting Interventions for Indigenous Child Psychosocial Functioning: A Scoping Review

ERIC Educational Resources Information Center

Macvean, Michelle; Shlonsky, Aron; Mildon, Robyn; Devine, Ben

2017-01-01

Objectives: To scope evaluations of Indigenous parenting programs designed to improve child psychosocial outcomes. Methods: Electronic databases, gray literature, Indigenous websites and journals, and reference lists were searched. The search was restricted to high-income countries with a history of colonialism. Results: Sixteen studies describing…

Identification of "Known Unknowns" Utilizing Accurate Mass Data and ChemSpider

NASA Astrophysics Data System (ADS)

Little, James L.; Williams, Antony J.; Pshenichnov, Alexey; Tkachenko, Valery

2012-01-01

In many cases, an unknown to an investigator is actually known in the chemical literature, a reference database, or an internet resource. We refer to these types of compounds as "known unknowns." ChemSpider is a very valuable internet database of known compounds useful in the identification of these types of compounds in commercial, environmental, forensic, and natural product samples. The database contains over 26 million entries from hundreds of data sources and is provided as a free resource to the community. Accurate mass mass spectrometry data is used to query the database by either elemental composition or a monoisotopic mass. Searching by elemental composition is the preferred approach. However, it is often difficult to determine a unique elemental composition for compounds with molecular weights greater than 600 Da. In these cases, searching by the monoisotopic mass is advantageous. In either case, the search results are refined by sorting the number of references associated with each compound in descending order. This raises the most useful candidates to the top of the list for further evaluation. These approaches were shown to be successful in identifying "known unknowns" noted in our laboratory and for compounds of interest to others.

Database systems for knowledge-based discovery.

PubMed

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

2009-01-01

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

The PMDB Protein Model Database

PubMed Central

Castrignanò, Tiziana; De Meo, Paolo D'Onorio; Cozzetto, Domenico; Talamo, Ivano Giuseppe; Tramontano, Anna

2006-01-01

The Protein Model Database (PMDB) is a public resource aimed at storing manually built 3D models of proteins. The database is designed to provide access to models published in the scientific literature, together with validating experimental data. It is a relational database and it currently contains >74 000 models for ∼240 proteins. The system is accessible at and allows predictors to submit models along with related supporting evidence and users to download them through a simple and intuitive interface. Users can navigate in the database and retrieve models referring to the same target protein or to different regions of the same protein. Each model is assigned a unique identifier that allows interested users to directly access the data. PMID:16381873

Mapping the literature of case management nursing.

PubMed

White, Pamela; Hall, Marilyn E

2006-04-01

Nursing case management provides a continuum of health care services for defined groups of patients. Its literature is multidisciplinary, emphasizing clinical specialties, case management methodology, and the health care system. This study is part of a project to map the literature of nursing, sponsored by the Nursing and Allied Health Resources Section of the Medical Library Association. The study identifies core journals cited in case management literature and indexing services that access those journals. Three source journals were identified based on established criteria, and cited references from each article published from 1997 to 1999 were analyzed. Nearly two-thirds of the cited references were from journals; others were from books, monographs, reports, government documents, and the Internet. Cited journal references were ranked in descending order, and Bradford's Law of Scattering was applied. The many journals constituting the top two zones reflect the diversity of this field. Zone 1 included journals from nursing administration, case management, general medicine, medical specialties, and social work. Two databases, PubMed/MEDLINE and OCLC ArticleFirst, provided the best indexing coverage. Collections that support case management require a relatively small group of core journals. Students and health care professionals will need to search across disciplines to identify appropriate literature.

Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants1[W][OA

PubMed Central

Zhang, Peifen; Dreher, Kate; Karthikeyan, A.; Chi, Anjo; Pujar, Anuradha; Caspi, Ron; Karp, Peter; Kirkup, Vanessa; Latendresse, Mario; Lee, Cynthia; Mueller, Lukas A.; Muller, Robert; Rhee, Seung Yon

2010-01-01

Metabolic networks reconstructed from sequenced genomes or transcriptomes can help visualize and analyze large-scale experimental data, predict metabolic phenotypes, discover enzymes, engineer metabolic pathways, and study metabolic pathway evolution. We developed a general approach for reconstructing metabolic pathway complements of plant genomes. Two new reference databases were created and added to the core of the infrastructure: a comprehensive, all-plant reference pathway database, PlantCyc, and a reference enzyme sequence database, RESD, for annotating metabolic functions of protein sequences. PlantCyc (version 3.0) includes 714 metabolic pathways and 2,619 reactions from over 300 species. RESD (version 1.0) contains 14,187 literature-supported enzyme sequences from across all kingdoms. We used RESD, PlantCyc, and MetaCyc (an all-species reference metabolic pathway database), in conjunction with the pathway prediction software Pathway Tools, to reconstruct a metabolic pathway database, PoplarCyc, from the recently sequenced genome of Populus trichocarpa. PoplarCyc (version 1.0) contains 321 pathways with 1,807 assigned enzymes. Comparing PoplarCyc (version 1.0) with AraCyc (version 6.0, Arabidopsis [Arabidopsis thaliana]) showed comparable numbers of pathways distributed across all domains of metabolism in both databases, except for a higher number of AraCyc pathways in secondary metabolism and a 1.5-fold increase in carbohydrate metabolic enzymes in PoplarCyc. Here, we introduce these new resources and demonstrate the feasibility of using them to identify candidate enzymes for specific pathways and to analyze metabolite profiling data through concrete examples. These resources can be searched by text or BLAST, browsed, and downloaded from our project Web site (http://plantcyc.org). PMID:20522724

Tests and Testing for Bilingual Children: A Bibliography of Literature.

ERIC Educational Resources Information Center

Kirsch, Judith, Comp.

This annotated listing cites tests, guides, dissertations, journal articles, research reports, reference materials, and conference papers and proceedings regarding tests and testing for bilingual children. Items cited were published between 1964-81. The listing is one of a series of bibliographies from a computerized database, Bilingual Education…

Searching for disability in electronic databases of published literature.

PubMed

Walsh, Emily S; Peterson, Jana J; Judkins, Dolores Z

2014-01-01

As researchers in disability and health conduct systematic reviews with greater frequency, the definition of disability used in these reviews gains importance. Translating a comprehensive conceptual definition of "disability" into an operational definition that utilizes electronic databases in the health sciences is a difficult step necessary for performing systematic literature reviews in the field. Consistency of definition across studies will help build a body of evidence that is comparable and amenable to synthesis. To illustrate a process for operationalizing the World Health Organization's International Classification of Disability, Functioning, and Health concept of disability for MEDLINE, PsycINFO, and CINAHL databases. We created an electronic search strategy in conjunction with a reference librarian and an expert panel. Quality control steps included comparison of search results to results of a search for a specific disabling condition and to articles nominated by the expert panel. The complete search strategy is presented. Results of the quality control steps indicated that our strategy was sufficiently sensitive and specific. Our search strategy will be valuable to researchers conducting literature reviews on broad populations with disabilities. Copyright © 2014 Elsevier Inc. All rights reserved.

Mapping the literature of occupational therapy: an update

PubMed Central

Potter, Jonathan

2010-01-01

Objectives: This study updated Reed's 1999 “Mapping the Literature of Occupational Therapy.” An analysis of citation patterns and indexing coverage was undertaken to identify the core literature of occupational therapy and to determine access to that literature. Methods: Citations from three source journals for the years 2006 through 2008 were studied following the common methodology of the “Mapping the Literature of Allied Health Project.” Bradford's Law of Scattering was applied to analyze the productivity of cited journals. A comparative analysis of indexing was conducted across three bibliographic databases. Results: A total of 364 articles cited 10,425 references. Journals were the most frequently cited format, accounting for 65.3% of the references, an increase of 4.1% over the 1999 study. Approximately one-third of the journal references cited a cluster of 9 journals, with the American Journal of Occupational Therapy dominating the field. An additional 120 journals were identified as moderately important based on times cited. CINAHL provided the most comprehensive indexing of core journals, while MEDLINE provided the best overall coverage. Conclusions: Occupational therapy is a multidisciplinary field with a strong core identity and an increasingly diverse literature. Indexing has improved overall since 1999, but gaps in the coverage are still evident. PMID:20648258

Computerized literature reference system: use of an optical scanner and optical character recognition software.

PubMed

Lossef, S V; Schwartz, L H

1990-09-01

A computerized reference system for radiology journal articles was developed by using an IBM-compatible personal computer with a hand-held optical scanner and optical character recognition software. This allows direct entry of scanned text from printed material into word processing or data-base files. Additionally, line diagrams and photographs of radiographs can be incorporated into these files. A text search and retrieval software program enables rapid searching for keywords in scanned documents. The hand scanner and software programs are commercially available, relatively inexpensive, and easily used. This permits construction of a personalized radiology literature file of readily accessible text and images requiring minimal typing or keystroke entry.

Use of patient safety culture instruments in operating rooms: A systematic literature review.

PubMed

Zhao, Pujng; Li, Yaqin; Li, Zhi; Jia, Pengli; Zhang, Longhao; Zhang, Mingming

2017-05-01

To identify and qualitatively describe, in a literature review, how the instruments were used to evaluate patient safety culture in the operating rooms of published studies. Systematic searches of the literature were conducted using the major database including MEDLINE, EMbase, The Cochrane Library, and four Chinese databases including Chinese Biomedical Literature Database (CBM), Wanfang Data, Chinese Scientific Journal Database (VIP), and Chinese Journals Full-text Database (CNKI) for studies published up to March 2016. We summarized and analyzed the country scope, the instrument utilized in the study, the year when the instrument was used, and fields of operating rooms. Study populations, study settings, and the time span between baseline and follow-up phase were evaluated according to the study design. We identified 1025 references, of which 99 were obtained for full-text assessment; 47 of these studies were deemed relevant and included in the literature review. Most of the studies were from the USA. The most commonly used patient safety culture instrument was Safety Attitude Questionnaire. All identified instruments were used after 2002 and across many fields. Most included studies on patient safety culture were conducted in teaching hospitals or university hospitals. The study population in the cross-sectional studies was much more than that in the before-after studies. The time span between baseline and follow-up phase of before-after studies were almost over three months. Although patient safety culture is considered important in health care and patient safety, the number of studies in which patient safety culture has been estimated using the instruments in operating rooms, is fairly small. © 2017 Chinese Cochrane Center, West China Hospital of Sichuan University and John Wiley & Sons Australia, Ltd.

TMDB: a literature-curated database for small molecular compounds found from tea.

PubMed

Yue, Yi; Chu, Gang-Xiu; Liu, Xue-Shi; Tang, Xing; Wang, Wei; Liu, Guang-Jin; Yang, Tao; Ling, Tie-Jun; Wang, Xiao-Gang; Zhang, Zheng-Zhu; Xia, Tao; Wan, Xiao-Chun; Bao, Guan-Hu

2014-09-16

Tea is one of the most consumed beverages worldwide. The healthy effects of tea are attributed to a wealthy of different chemical components from tea. Thousands of studies on the chemical constituents of tea had been reported. However, data from these individual reports have not been collected into a single database. The lack of a curated database of related information limits research in this field, and thus a cohesive database system should necessarily be constructed for data deposit and further application. The Tea Metabolome database (TMDB), a manually curated and web-accessible database, was developed to provide detailed, searchable descriptions of small molecular compounds found in Camellia spp. esp. in the plant Camellia sinensis and compounds in its manufactured products (different kinds of tea infusion). TMDB is currently the most complete and comprehensive curated collection of tea compounds data in the world. It contains records for more than 1393 constituents found in tea with information gathered from 364 published books, journal articles, and electronic databases. It also contains experimental 1H NMR and 13C NMR data collected from the purified reference compounds or collected from other database resources such as HMDB. TMDB interface allows users to retrieve tea compounds entries by keyword search using compound name, formula, occurrence, and CAS register number. Each entry in the TMDB contains an average of 24 separate data fields including its original plant species, compound structure, formula, molecular weight, name, CAS registry number, compound types, compound uses including healthy benefits, reference literatures, NMR, MS data, and the corresponding ID from databases such as HMDB and Pubmed. Users can also contribute novel regulatory entries by using a web-based submission page. The TMDB database is freely accessible from the URL of http://pcsb.ahau.edu.cn:8080/TCDB/index.jsp. The TMDB is designed to address the broad needs of tea biochemists, natural products chemists, nutritionists, and members of tea related research community. The TMDB database provides a solid platform for collection, standardization, and searching of compounds information found in tea. As such this database will be a comprehensive repository for tea biochemistry and tea health research community.

Health information technology in primary health care in developing countries: a literature review.

PubMed Central

Tomasi, Elaine; Facchini, Luiz Augusto; Maia, Maria de Fatima Santos

2004-01-01

This paper explores the debate and initiatives concerning the use of information technology (IT) in primary health care in developing countries. The literature from 1992-2002 was identified from searches of the MEDLINE, Latin American and Caribbean Health Science Literature Database (LILACS), Cochrane Library and Web of Science databases. The search identified 884 references, 350 of which were classified according to the scheme described by the Pan American Health Organization (PAHO). For the analysis of advantages, problems and perspectives of IT applications and systems, 52 articles were selected according to their potential contribution to the primary health-care processes in non-developed countries. These included: 10 on electronic patient registries (EPR), 22 on process and programmatic action evaluation and management systems (PPAEM) and 20 on clinical decision-support systems (CDS). The main advantages, limitations and perspectives are discussed. PMID:15640923

Search of medical literature for indoor carbon monoxide exposure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brennan, T.; Ivanovich, M.

1995-12-01

This report documents a literature search on carbon monoxide. The search was limited to the medical and toxicological databases at the National Library of Medicine (MEDLARS). The databases searched were Medline, Toxline and TOXNET. Searches were performed using a variety of strategies. Combinations of the following keywords were used: carbon, monoxide, accidental, residential, occult, diagnosis, misdiagnosis, heating, furnace, and indoor. The literature was searched from 1966 to the present. Over 1000 references were identified and summarized using the following abbreviations: The major findings of the search are: (1) Acute and subacute carbon monoxide exposures result in a large number ofmore » symptoms affecting the brain, kidneys, respiratory system, retina, and motor functions. (2) Acute and subacute carbon monoxide (CO) poisonings have been misdiagnosed on many occasions. (3) Very few systematic investigations have been made into the frequency and consequences of carbon monoxide poisonings.« less

Development of a biomarkers database for the National Children's Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lobdell, Danelle T.; Mendola, Pauline

The National Children's Study (NCS) is a federally-sponsored, longitudinal study of environmental influences on the health and development of children across the United States (www.nationalchildrensstudy.gov). Current plans are to study approximately 100,000 children and their families beginning before birth up to age 21 years. To explore potential biomarkers that could be important measurements in the NCS, we compiled the relevant scientific literature to identify both routine or standardized biological markers as well as new and emerging biological markers. Although the search criteria encouraged examination of factors that influence the breadth of child health and development, attention was primarily focused onmore » exposure, susceptibility, and outcome biomarkers associated with four important child health outcomes: autism and neurobehavioral disorders, injury, cancer, and asthma. The Biomarkers Database was designed to allow users to: (1) search the biomarker records compiled by type of marker (susceptibility, exposure or effect), sampling media (e.g., blood, urine, etc.), and specific marker name; (2) search the citations file; and (3) read the abstract evaluations relative to our search criteria. A searchable, user-friendly database of over 2000 articles was created and is publicly available at: http://cfpub.epa.gov/ncea/cfm/recordisplay.cfm?deid=85844. PubMed was the primary source of references with some additional searches of Toxline, NTIS, and other reference databases. Our initial focus was on review articles, beginning as early as 1996, supplemented with searches of the recent primary research literature from 2001 to 2003. We anticipate this database will have applicability for the NCS as well as other studies of children's environmental health.« less

mirPub: a database for searching microRNA publications.

PubMed

Vergoulis, Thanasis; Kanellos, Ilias; Kostoulas, Nikos; Georgakilas, Georgios; Sellis, Timos; Hatzigeorgiou, Artemis; Dalamagas, Theodore

2015-05-01

Identifying, amongst millions of publications available in MEDLINE, those that are relevant to specific microRNAs (miRNAs) of interest based on keyword search faces major obstacles. References to miRNA names in the literature often deviate from standard nomenclature for various reasons, since even the official nomenclature evolves. For instance, a single miRNA name may identify two completely different molecules or two different names may refer to the same molecule. mirPub is a database with a powerful and intuitive interface, which facilitates searching for miRNA literature, addressing the aforementioned issues. To provide effective search services, mirPub applies text mining techniques on MEDLINE, integrates data from several curated databases and exploits data from its user community following a crowdsourcing approach. Other key features include an interactive visualization service that illustrates intuitively the evolution of miRNA data, tag clouds summarizing the relevance of publications to particular diseases, cell types or tissues and access to TarBase 6.0 data to oversee genes related to miRNA publications. mirPub is freely available at http://www.microrna.gr/mirpub/. vergoulis@imis.athena-innovation.gr or dalamag@imis.athena-innovation.gr Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

HNdb: an integrated database of gene and protein information on head and neck squamous cell carcinoma

PubMed Central

Henrique, Tiago; José Freitas da Silveira, Nelson; Henrique Cunha Volpato, Arthur; Mioto, Mayra Mataruco; Carolina Buzzo Stefanini, Ana; Bachir Fares, Adil; Gustavo da Silva Castro Andrade, João; Masson, Carolina; Verónica Mendoza López, Rossana; Daumas Nunes, Fabio; Paulo Kowalski, Luis; Severino, Patricia; Tajara, Eloiza Helena

2016-01-01

The total amount of scientific literature has grown rapidly in recent years. Specifically, there are several million citations in the field of cancer. This makes it difficult, if not impossible, to manually retrieve relevant information on the mechanisms that govern tumor behavior or the neoplastic process. Furthermore, cancer is a complex disease or, more accurately, a set of diseases. The heterogeneity that permeates many tumors is particularly evident in head and neck (HN) cancer, one of the most common types of cancer worldwide. In this study, we present HNdb, a free database that aims to provide a unified and comprehensive resource of information on genes and proteins involved in HN squamous cell carcinoma, covering data on genomics, transcriptomics, proteomics, literature citations and also cross-references of external databases. Different literature searches of MEDLINE abstracts were performed using specific Medical Subject Headings (MeSH terms) for oral, oropharyngeal, hypopharyngeal and laryngeal squamous cell carcinomas. A curated gene-to-publication assignment yielded a total of 1370 genes related to HN cancer. The diversity of results allowed identifying novel and mostly unexplored gene associations, revealing, for example, that processes linked to response to steroid hormone stimulus are significantly enriched in genes related to HN carcinomas. Thus, our database expands the possibilities for gene networks investigation, providing potential hypothesis to be tested. Database URL: http://www.gencapo.famerp.br/hndb PMID:27013077

FINDbase: a relational database recording frequencies of genetic defects leading to inherited disorders worldwide.

PubMed

van Baal, Sjozef; Kaimakis, Polynikis; Phommarinh, Manyphong; Koumbi, Daphne; Cuppens, Harry; Riccardino, Francesca; Macek, Milan; Scriver, Charles R; Patrinos, George P

2007-01-01

Frequency of INherited Disorders database (FINDbase) (http://www.findbase.org) is a relational database, derived from the ETHNOS software, recording frequencies of causative mutations leading to inherited disorders worldwide. Database records include the population and ethnic group, the disorder name and the related gene, accompanied by links to any corresponding locus-specific mutation database, to the respective Online Mendelian Inheritance in Man entries and the mutation together with its frequency in that population. The initial information is derived from the published literature, locus-specific databases and genetic disease consortia. FINDbase offers a user-friendly query interface, providing instant access to the list and frequencies of the different mutations. Query outputs can be either in a table or graphical format, accompanied by reference(s) on the data source. Registered users from three different groups, namely administrator, national coordinator and curator, are responsible for database curation and/or data entry/correction online via a password-protected interface. Databaseaccess is free of charge and there are no registration requirements for data querying. FINDbase provides a simple, web-based system for population-based mutation data collection and retrieval and can serve not only as a valuable online tool for molecular genetic testing of inherited disorders but also as a non-profit model for sustainable database funding, in the form of a 'database-journal'.

Classifying the bacterial gut microbiota of termites and cockroaches: A curated phylogenetic reference database (DictDb).

PubMed

Mikaelyan, Aram; Köhler, Tim; Lampert, Niclas; Rohland, Jeffrey; Boga, Hamadi; Meuser, Katja; Brune, Andreas

2015-10-01

Recent developments in sequencing technology have given rise to a large number of studies that assess bacterial diversity and community structure in termite and cockroach guts based on large amplicon libraries of 16S rRNA genes. Although these studies have revealed important ecological and evolutionary patterns in the gut microbiota, classification of the short sequence reads is limited by the taxonomic depth and resolution of the reference databases used in the respective studies. Here, we present a curated reference database for accurate taxonomic analysis of the bacterial gut microbiota of dictyopteran insects. The Dictyopteran gut microbiota reference Database (DictDb) is based on the Silva database but was significantly expanded by the addition of clones from 11 mostly unexplored termite and cockroach groups, which increased the inventory of bacterial sequences from dictyopteran guts by 26%. The taxonomic depth and resolution of DictDb was significantly improved by a general revision of the taxonomic guide tree for all important lineages, including a detailed phylogenetic analysis of the Treponema and Alistipes complexes, the Fibrobacteres, and the TG3 phylum. The performance of this first documented version of DictDb (v. 3.0) using the revised taxonomic guide tree in the classification of short-read libraries obtained from termites and cockroaches was highly superior to that of the current Silva and RDP databases. DictDb uses an informative nomenclature that is consistent with the literature also for clades of uncultured bacteria and provides an invaluable tool for anyone exploring the gut community structure of termites and cockroaches. Copyright © 2015 Elsevier GmbH. All rights reserved.

[Interpretation in the Danish health-care system].

PubMed

Lund Hansen, Marianne Taulo; Nielsen, Signe Smith

2013-03-04

Communication between health professional and patient is central for treatment and patient safety in the health-care system. This systematic review examines the last ten years of specialist literature concerning interpretation in the Danish health-care system. Structural search in two databases, screening of references and recommended literature from two scientists led to identification of seven relevant articles. The review showed that professional interpreters were not used consistently when needed. Family members were also used as interpreters. These results were supported by international investigations.

Planned Parenthood Federation of America: Its Role as Provider of Information Services.

ERIC Educational Resources Information Center

Roberts, Gloria A.

1985-01-01

Planned Parenthood Federation of America was established in 1916 to fulfill the need to provide family planning information and services to women. The Katharine Dexter McCormick Library serves organizational goals by publishing family planning bibliographies, performing literature searches on in-house database, and providing reference services to…

Business Ethics. Focused Access to Selected Topics (FAST) Bibliography No. 17.

ERIC Educational Resources Information Center

Shermis, Michael

Addressing the needs of students who choose careers in business, this annotated bibliography contains 30 references of articles and papers in the ERIC database dealing with ethics in business. Sources cited in the first section, "Business Instruction," deal with teaching ethics in business communication, business literature, and other areas of the…

BADERI: an online database to coordinate handsearching activities of controlled clinical trials for their potential inclusion in systematic reviews.

PubMed

Pardo-Hernandez, Hector; Urrútia, Gerard; Barajas-Nava, Leticia A; Buitrago-Garcia, Diana; Garzón, Julieth Vanessa; Martínez-Zapata, María José; Bonfill, Xavier

2017-06-13

Systematic reviews provide the best evidence on the effect of health care interventions. They rely on comprehensive access to the available scientific literature. Electronic search strategies alone may not suffice, requiring the implementation of a handsearching approach. We have developed a database to provide an Internet-based platform from which handsearching activities can be coordinated, including a procedure to streamline the submission of these references into CENTRAL, the Cochrane Collaboration Central Register of Controlled Trials. We developed a database and a descriptive analysis. Through brainstorming and discussion among stakeholders involved in handsearching projects, we designed a database that met identified needs that had to be addressed in order to ensure the viability of handsearching activities. Three handsearching teams pilot tested the proposed database. Once the final version of the database was approved, we proceeded to train the staff involved in handsearching. The proposed database is called BADERI (Database of Iberoamerican Clinical Trials and Journals, by its initials in Spanish). BADERI was officially launched in October 2015, and it can be accessed at www.baderi.com/login.php free of cost. BADERI has an administration subsection, from which the roles of users are managed; a references subsection, where information associated to identified controlled clinical trials (CCTs) can be entered; a reports subsection, from which reports can be generated to track and analyse the results of handsearching activities; and a built-in free text search engine. BADERI allows all references to be exported in ProCite files that can be directly uploaded into CENTRAL. To date, 6284 references to CCTs have been uploaded to BADERI and sent to CENTRAL. The identified CCTs were published in a total of 420 journals related to 46 medical specialties. The year of publication ranged between 1957 and 2016. BADERI allows the efficient management of handsearching activities across different countries and institutions. References to all CCTs available in BADERI can be readily submitted to CENTRAL for their potential inclusion in systematic reviews.

Mapping the literature of case management nursing

PubMed Central

White, Pamela; Hall, Marilyn E.

2006-01-01

Objectives: Nursing case management provides a continuum of health care services for defined groups of patients. Its literature is multidisciplinary, emphasizing clinical specialties, case management methodology, and the health care system. This study is part of a project to map the literature of nursing, sponsored by the Nursing and Allied Health Resources Section of the Medical Library Association. The study identifies core journals cited in case management literature and indexing services that access those journals. Methods: Three source journals were identified based on established criteria, and cited references from each article published from 1997 to 1999 were analyzed. Results: Nearly two-thirds of the cited references were from journals; others were from books, monographs, reports, government documents, and the Internet. Cited journal references were ranked in descending order, and Bradford's Law of Scattering was applied. The many journals constituting the top two zones reflect the diversity of this field. Zone 1 included journals from nursing administration, case management, general medicine, medical specialties, and social work. Two databases, PubMed/MEDLINE and OCLC ArticleFirst, provided the best indexing coverage. Conclusion: Collections that support case management require a relatively small group of core journals. Students and health care professionals will need to search across disciplines to identify appropriate literature. PMID:16710470

Suicide in elderly people: a literature review.

PubMed

Minayo, Maria Cecília de Souza; Cavalcante, Fátima Gonçalves

2010-08-01

A literature review was carried out focusing on the main factors associated with suicidal ideation, attempts and completed suicide in elders. The following databases were searched: MEDLINE, PsychINFO, SciELO and Biblioteca Virtual em Violência e Saúde da BIREME (BIREME's Violence and Health Virtual Library), referring to the period from 1980 to 2008. Fifty-two references were selected and analyzed. They showed a strong relationship among suicide ideation, attempt and completion in elderly individuals, which results from the interaction of complex physical, mental, neurobiological and social factors. Suicide associated with depression in the elderly can be prevented, provided the person is properly treated. In Brazil, it is necessary to invest in research, given the persistent increase in suicide rates among aged people, especially among males.

The use of grey literature in health sciences: a preliminary survey.

PubMed Central

Alberani, V; De Castro Pietrangeli, P; Mazza, A M

1990-01-01

The paper describes some initiatives in the field of grey literature (GL) and the activities, from 1985, of the Italian Library Association Study Group. The major categories of GL are defined; a survey that evaluates the use of GL by end users in the health sciences is described. References in selected periodicals and databases have been analyzed for the years 1987-1988 to determine the number of articles citing GL, the number of GL citations found in selected periodicals, the various types of GL found, and the number of technical reports cited and their country of origin and intergovernmental issuing organization. Selected databases were also searched to determine the presence of GL during those same years. The paper presents the first results obtained. Images PMID:2224298

Gene annotation from scientific literature using mappings between keyword systems.

PubMed

Pérez, Antonio J; Perez-Iratxeta, Carolina; Bork, Peer; Thode, Guillermo; Andrade, Miguel A

2004-09-01

The description of genes in databases by keywords helps the non-specialist to quickly grasp the properties of a gene and increases the efficiency of computational tools that are applied to gene data (e.g. searching a gene database for sequences related to a particular biological process). However, the association of keywords to genes or protein sequences is a difficult process that ultimately implies examination of the literature related to a gene. To support this task, we present a procedure to derive keywords from the set of scientific abstracts related to a gene. Our system is based on the automated extraction of mappings between related terms from different databases using a model of fuzzy associations that can be applied with all generality to any pair of linked databases. We tested the system by annotating genes of the SWISS-PROT database with keywords derived from the abstracts linked to their entries (stored in the MEDLINE database of scientific references). The performance of the annotation procedure was much better for SWISS-PROT keywords (recall of 47%, precision of 68%) than for Gene Ontology terms (recall of 8%, precision of 67%). The algorithm can be publicly accessed and used for the annotation of sequences through a web server at http://www.bork.embl.de/kat

Searching CINAHL did not add value to clinical questions posed in NICE guidelines.

PubMed

Beckles, Zosia; Glover, Sarah; Ashe, Joanna; Stockton, Sarah; Boynton, Janette; Lai, Rosalind; Alderson, Philip

2013-09-01

This study aims to quantify the unique useful yield from the Cumulative Index to Nursing and Allied Health Literature (CINAHL) database to National Institute for Health and Clinical Excellence (NICE) clinical guidelines. A secondary objective is to investigate the relationship between this yield and different clinical question types. It is hypothesized that the unique useful yield from CINAHL is low, and this database can therefore be relegated to selective rather than routine searching. A retrospective sample of 15 NICE guidelines published between 2005 and 2009 was taken. Information on clinical review question type, number of references, and reference source was extracted. Only 0.33% (95% confidence interval: 0.01-0.64%) of references per guideline were unique to CINAHL. Nursing- or allied health (AH)-related questions were nearly three times as likely to have references unique to CINAHL as non-nursing- or AH-related questions (14.89% vs. 5.11%), and this relationship was found to be significant (P<0.05). No significant relationship was found between question type and unique CINAHL yield for drug-related questions. The very low proportion of references unique to CINAHL strongly suggests that this database can be safely relegated to selective rather than routine searching. Nursing- and AH-related questions would benefit from selective searching of CINAHL. Copyright © 2013 Elsevier Inc. All rights reserved.

MaizeGDB: The Maize Genetics and Genomics Database.

PubMed

Harper, Lisa; Gardiner, Jack; Andorf, Carson; Lawrence, Carolyn J

2016-01-01

MaizeGDB is the community database for biological information about the crop plant Zea mays. Genomic, genetic, sequence, gene product, functional characterization, literature reference, and person/organization contact information are among the datatypes stored at MaizeGDB. At the project's website ( http://www.maizegdb.org ) are custom interfaces enabling researchers to browse data and to seek out specific information matching explicit search criteria. In addition, pre-compiled reports are made available for particular types of data and bulletin boards are provided to facilitate communication and coordination among members of the community of maize geneticists.

Literature review of the potential effects of formalin on nitrogen oxidation efficiency of the biofilters of recirculating aquaculture systems (RAS) for freshwater finfish

USGS Publications Warehouse

Fredricks, Kim T.

2015-01-01

After the initial screening, the remaining 1,287 papers underwent a second screening. Titles and abstracts (when available) were again read to verify that the topic of the paper was related to RAS. During the second screening, a second person verified that the papers proposed for elimination were not related to RAS. A combined reference list of the 443 remaining papers was created and submitted to the U.S. Geological Survey (USGS) Upper Midwest Environmental Sciences Center (UMESC) librarian to obtain the actual papers; electronic copies of those citations were obtained and reviewed. The UMESC librarian also would receive weekly updates from Scopus (a bibliographic database containing abstracts and citations for academic journal articles) using the search terms. Any resulting papers from those updates also were screened using the inclusion criteria, and any relevant papers were requested. From those, 82 were cited in the literature review. An additional 10 references were obtained from weekly updates or reference mining other sources and were incorporated into the final literature review.

Properties of publications on anatomy in medical education literature.

PubMed

Vorstenbosch, Marc; Bolhuis, Sanneke; van Kuppeveld, Sascha; Kooloos, Jan; Laan, Roland

2011-01-01

Publications on anatomy in medical education appear to be largely anecdotal. To explore this, we investigated the literature on anatomy in medical education, aiming first to evaluate the contribution of the literature on anatomy in medical education to "best evidence medical education" (BEME) and second to evaluate the development of this literature toward more "best evidence" between 1985 and 2009. Four databases were searched for publications on anatomy in medical education published between 1985 and 2009, resulting in 525 references. Hundred publications were characterized by five variables (journal category, paper subject, paper category, author perspective, and paper perspective). Statements from these publications were characterized by two variables (category and foundation). The publications contained 797 statements that involved the words "anatomy," "anatomical," or "anatomist." Forty-five percent of the publications contained no explicit research question. Forty percent of the statements made were about "teaching methods" and 17% about "teaching content," 8% referred to "practical value," and 10% to "side effects" of anatomy education. Ten percent of the statements were "positional," five percent "traditional," four percent "self-evident," and two percent referred to "quality of care." Fifty-six percent of the statements had no foundation, 17% were founded on empirical data, and 27% by references. These results substantiated the critical comments about the anecdotal nature of the literature. However, it is encouraging to see that between 1985 and 2009 the number of publications is rising that these publications increasingly focus on teaching methods and that an academic writing style is developing. This suggests a growing body of empirical literature about anatomy education. Copyright © 2011 American Association of Anatomists.

Teachers' Perceptions of Students' Needs for Family Counseling and Attitudes toward School-Based Family Counseling

ERIC Educational Resources Information Center

Star Snyder, Marjorie

2010-01-01

A comprehensive search of multiple databases for references to the connection between families and schools yields a rich representation from family therapy, school counseling, school psychology, and education literature supporting the idea that schools must serve not only students, but students' families as well. One of the common themes emerging…

Children of Parents with Intellectual Disability: Facing Poor Outcomes or Faring Okay?

ERIC Educational Resources Information Center

Collings, Susan; Llewellyn, Gwynnyth

2012-01-01

Background: Children of parents with intellectual disability are assumed to be at risk of poor outcomes but a comprehensive review of the literature has not previously been undertaken. Method: A database and reference search from March 2010 to March 2011 resulted in 26 studies for review. Results: Two groups of studies were identified. The first…

Cyberbullying: A Research-Based Content Analysis of the Psychological Literature

ERIC Educational Resources Information Center

Piotrowski, Chris

2012-01-01

Research on the topic of cyber-bullying has proliferated over the past decade, particularly on its impact on children through adolescents. Thus, it would be of interest to examine the scope and extent of research interest on the topic in scholarly publications. This paper reports on a reference citation analysis of the database PsycINFO, using the…

Assessing Preferences for AAC Options in Communication Interventions for Individuals with Developmental Disabilities: A Review of the Literature

ERIC Educational Resources Information Center

van der Meer, Larah; Sigafoos, Jeff; O'Reilly, Mark F.; Lancioni, Giulio E.

2011-01-01

We synthesized studies that assessed preference for using different augmentative and alternative communication (AAC) options. Studies were identified via systematic searches of electronic databases, journals, and reference lists. Studies were evaluated in terms of: (a) participants, (b) setting, (c) communication options assessed, (d) design, (e)…

STRBase: a short tandem repeat DNA database for the human identity testing community

PubMed Central

Ruitberg, Christian M.; Reeder, Dennis J.; Butler, John M.

2001-01-01

The National Institute of Standards and Technology (NIST) has compiled and maintained a Short Tandem Repeat DNA Internet Database (http://www.cstl.nist.gov/biotech/strbase/) since 1997 commonly referred to as STRBase. This database is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. STRBase consolidates and organizes the abundant literature on this subject to facilitate on-going efforts in DNA typing. Observed alleles and annotated sequence for each STR locus are described along with a review of STR analysis technologies. Additionally, commercially available STR multiplex kits are described, published polymerase chain reaction (PCR) primer sequences are reported, and validation studies conducted by a number of forensic laboratories are listed. To supplement the technical information, addresses for scientists and hyperlinks to organizations working in this area are available, along with the comprehensive reference list of over 1300 publications on STRs used for DNA typing purposes. PMID:11125125

Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders.

PubMed

Hamosh, Ada; Scott, Alan F; Amberger, Joanna S; Bocchini, Carol A; McKusick, Victor A

2005-01-01

Online Mendelian Inheritance in Man (OMIM) is a comprehensive, authoritative and timely knowledgebase of human genes and genetic disorders compiled to support human genetics research and education and the practice of clinical genetics. Started by Dr Victor A. McKusick as the definitive reference Mendelian Inheritance in Man, OMIM (http://www.ncbi.nlm.nih.gov/omim/) is now distributed electronically by the National Center for Biotechnology Information, where it is integrated with the Entrez suite of databases. Derived from the biomedical literature, OMIM is written and edited at Johns Hopkins University with input from scientists and physicians around the world. Each OMIM entry has a full-text summary of a genetically determined phenotype and/or gene and has numerous links to other genetic databases such as DNA and protein sequence, PubMed references, general and locus-specific mutation databases, HUGO nomenclature, MapViewer, GeneTests, patient support groups and many others. OMIM is an easy and straightforward portal to the burgeoning information in human genetics.

[Characteristics of acupoint application for the sub-healthy condition treated with ancient and modern acupuncture based on data mining exploration].

PubMed

Cai, Liyan; Wu, Jie; Ma, Tingting; Yang, Lijie

2015-10-01

The acupoint selection was retrieved from the ancient and modern literature on the treatment of sub-healthy condition with acupuncture. The law of acupoint application was analyzed so as to provide a certain reference to the determination of acupoint prescription in clinical acupuncture. The ancient literature was retrieved from Chinese basic ancient literature database. The modern literature was retrieved from Cochrane Library, Medline, PubMed, Ovid evidence-based medicine database, Chinese biomedical literature database, China journal full-text database, VIP journal full-text database and Wanfang database. The database mining software was adopted to explore the law of acupoint application in treatment of sub-healthy conditions with ancient and modern acupuncture. The acupoint use frequency, compatibility association rule, law for meridian use and the use regularity of specific points were analyzed. In the ancient treatment for sub-healthy condition, the top five commonly used acupoints are Shenmen (HT 7), Zhaohai (KI 6), Taibai (SP 3), Daling (PC 7) and Taixi (KI 3). The most commonly combined points are Zhangmen (LR 13), Taibai (SP 3) and Zhaohai (KI 6). The most commonly used meridians are the bladder meridian of foot-taiyang, kidney meridian of foot-shaoyin and liver meridian of foot-jueyin. The most commonly used specific points are the five-shu points. The most commonly used acupoints are located in the lower limbs. In the modern treatment, the top five commonly used acupoints are Zusanli (ST 36), Sanyinjiao (SP 6), Baihui (GV 20), Shenshu (BL 23) and Guanyuan (CV 4). The most commonly supplemented points are Hegu (LI 4) and Taichong (LR 3). The most commonly used meridians are the bladder meridian of foot-taiyang, the conception vessel and the governor vessel. The most commonly used specific points are the back-shu points. The most commonly used acupoints are located in the lower limbs. After the systematic comprehension of the relevant ancient and modern literature, the most commonly used acupoints are selected along the bladder meridian of foot-taiyang, and the most commonly used specific points are the back-shu points, the five-shu points and the front-mu-points. the acupoints are mostly located in the lower limbs.

The Universal Protein Resource (UniProt): an expanding universe of protein information.

PubMed

Wu, Cathy H; Apweiler, Rolf; Bairoch, Amos; Natale, Darren A; Barker, Winona C; Boeckmann, Brigitte; Ferro, Serenella; Gasteiger, Elisabeth; Huang, Hongzhan; Lopez, Rodrigo; Magrane, Michele; Martin, Maria J; Mazumder, Raja; O'Donovan, Claire; Redaschi, Nicole; Suzek, Baris

2006-01-01

The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at http://www.uniprot.org or downloaded at ftp://ftp.uniprot.org/pub/databases/.

The Effect of Orthodontic Therapy on Periodontal Health: A Review of the Literature

PubMed Central

Alfuriji, Samah; Alhazmi, Nora; Alhamlan, Nasir; Al-Ehaideb, Ali; Alruwaithi, Moatazbellah; Alkatheeri, Nasser; Geevarghese, Amrita

2014-01-01

Objectives. This review aims to evaluate the effect of orthodontic therapy on periodontal health. Data. Original articles that reported on the effect of orthodontic therapy on periodontal health were included. The reference lists of potentially relevant review articles were also sought. Sources. A literature search was conducted using the databases, Medline, EMBASE, Cochrane Library, Web of Science, Google Scholar, and Scopus databases for relevant studies. The search was carried out by using a combined text and the MeSH search strategies: using the key words in different combinations: “periodontal disease,” “orthodontics” and “root resorption.” This was supplemented by hand-searching in peer-reviewed journals and cross-referenced with the articles accessed. Articles published only in English language were included. Letters to the Editor, historical reviews and unpublished articles were not sought. Conclusions. Within the limitations of the present literature review, it was observed that there is a very close inter-relationship between the periodontal health and the outcome of orthodontic therapy. PMID:24991214

Full Text Searching and Customization in the NASA ADS Abstract Service

NASA Technical Reports Server (NTRS)

Eichhorn, G.; Accomazzi, A.; Grant, C. S.; Kurtz, M. J.; Henneken, E. A.; Thompson, D. M.; Murray, S. S.

2004-01-01

The NASA-ADS Abstract Service provides a sophisticated search capability for the literature in Astronomy, Planetary Sciences, Physics/Geophysics, and Space Instrumentation. The ADS is funded by NASA and access to the ADS services is free to anybody worldwide without restrictions. It allows the user to search the literature by author, title, and abstract text. The ADS database contains over 3.6 million references, with 965,000 in the Astronomy/Planetary Sciences database, and 1.6 million in the Physics/Geophysics database. 2/3 of the records have full abstracts, the rest are table of contents entries (titles and author lists only). The coverage for the Astronomy literature is better than 95% from 1975. Before that we cover all major journals and many smaller ones. Most of the journal literature is covered back to volume 1. We now get abstracts on a regular basis from most journals. Over the last year we have entered basically all conference proceedings tables of contents that are available at the Harvard Smithsonian Center for Astrophysics library. This has greatly increased the coverage of conference proceedings in the ADS. The ADS also covers the ArXiv Preprints. We download these preprints every night and index all the preprints. They can be searched either together with the other abstracts or separately. There are currently about 260,000 preprints in that database. In January 2004 we have introduced two new services, full text searching and a personal notification service called "myADS". As all other ADS services, these are free to use for anybody.

Bibliographical database of radiation biological dosimetry and risk assessment: Part 1, through June 1988

DOE Office of Scientific and Technical Information (OSTI.GOV)

Straume, T.; Ricker, Y.; Thut, M.

1988-08-29

This database was constructed to support research in radiation biological dosimetry and risk assessment. Relevant publications were identified through detailed searches of national and international electronic databases and through our personal knowledge of the subject. Publications were numbered and key worded, and referenced in an electronic data-retrieval system that permits quick access through computerized searches on publication number, authors, key words, title, year, and journal name. Photocopies of all publications contained in the database are maintained in a file that is numerically arranged by citation number. This report of the database is provided as a useful reference and overview. Itmore » should be emphasized that the database will grow as new citations are added to it. With that in mind, we arranged this report in order of ascending citation number so that follow-up reports will simply extend this document. The database cite 1212 publications. Publications are from 119 different scientific journals, 27 of these journals are cited at least 5 times. It also contains reference to 42 books and published symposia, and 129 reports. Information relevant to radiation biological dosimetry and risk assessment is widely distributed among the scientific literature, although a few journals clearly dominate. The four journals publishing the largest number of relevant papers are Health Physics, Mutation Research, Radiation Research, and International Journal of Radiation Biology. Publications in Health Physics make up almost 10% of the current database.« less

Choosing and using citation and bibliographic database software (BDS).

PubMed

Hernandez, David A; El-Masri, Maher M; Hernandez, Cheri Ann

2008-01-01

The diabetes educator/researcher is faced with a proliferation of diabetes articles in various journals, both online and in print. Keeping track of cited references and remembering how to cite the references in text and the bibliography can be a daunting task for the new researcher and a tedious task for the experienced researcher. The challenge is to find and use a technology, such as bibliographic database software (BDS), which can help to manage this information overload. This article focuses on the use of BDS for the diabetes educator who is undertaking research. BDS can help researchers access and organize literature and make literature searches more efficient and less time consuming. Moreover, the use of such programs tends to reduce errors associated with the complexity of bibliographic citations and can increase the productivity of scholarly publications. The purpose of this article is to provide an overview of BDS currently available, describe how it can be used to aid researchers in their work, and highlight the features of different programs. It is important for diabetes educators and researchers to explore the many benefits of such BDS programs and consider their use to enhance the accuracy and efficiency of accessing and citing references of their research work and publications. Armed with this knowledge, researchers will be able to make informed decisions about selecting BDS which will meet their usage requirements.

Identifying known unknowns using the US EPA's CompTox Chemistry Dashboard.

PubMed

McEachran, Andrew D; Sobus, Jon R; Williams, Antony J

2017-03-01

Chemical features observed using high-resolution mass spectrometry can be tentatively identified using online chemical reference databases by searching molecular formulae and monoisotopic masses and then rank-ordering of the hits using appropriate relevance criteria. The most likely candidate "known unknowns," which are those chemicals unknown to an investigator but contained within a reference database or literature source, rise to the top of a chemical list when rank-ordered by the number of associated data sources. The U.S. EPA's CompTox Chemistry Dashboard is a curated and freely available resource for chemistry and computational toxicology research, containing more than 720,000 chemicals of relevance to environmental health science. In this research, the performance of the Dashboard for identifying known unknowns was evaluated against that of the online ChemSpider database, one of the primary resources used by mass spectrometrists, using multiple previously studied datasets reported in the peer-reviewed literature totaling 162 chemicals. These chemicals were examined using both applications via molecular formula and monoisotopic mass searches followed by rank-ordering of candidate compounds by associated references or data sources. A greater percentage of chemicals ranked in the top position when using the Dashboard, indicating an advantage of this application over ChemSpider for identifying known unknowns using data source ranking. Additional approaches are being developed for inclusion into a non-targeted analysis workflow as part of the CompTox Chemistry Dashboard. This work shows the potential for use of the Dashboard in exposure assessment and risk decision-making through significant improvements in non-targeted chemical identification. Graphical abstract Identifying known unknowns in the US EPA's CompTox Chemistry Dashboard from molecular formula and monoisotopic mass inputs.

Energy science and technology database (on the internet). Online data

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

The Energy Science and Technology Database (EDB) is a multidisciplinary file containing worldwide references to basic and applied scientific and technical research literature. The information is collected for use by government managers, researchers at the national laboratories, and other research efforts sponsored by the U.S. Department of Energy, and the results of this research are transferred to the public. Abstracts are included for records from 1976 to the present. The EDB also contains the Nuclear Science Abstracts which is a comprehensive abstract and index collection to the international nuclear science and technology literature for the period 1948 through 1976. Includedmore » are scientific and technical reports of the U.S. Atomic Energy Commission, U.S. Energy Research and Development Administration and its contractors, other agencies, universities, and industrial and research organizations. Approximately 25% of the records in the file contain abstracts. Nuclear Science Abstracts contains over 900,000 bibliographic records. The entire Energy Science and Technology Database contains over 3 million bibliographic records. This database is now available for searching through the GOV. Research-Center (GRC) service. GRC is a single online web-based search service to well known Government databases. Featuring powerful search and retrieval software, GRC is an important research tool. The GRC web site is at http://grc.ntis.gov.« less

MIPS: curated databases and comprehensive secondary data resources in 2010.

PubMed

Mewes, H Werner; Ruepp, Andreas; Theis, Fabian; Rattei, Thomas; Walter, Mathias; Frishman, Dmitrij; Suhre, Karsten; Spannagl, Manuel; Mayer, Klaus F X; Stümpflen, Volker; Antonov, Alexey

2011-01-01

The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological data. Selected data sets of high relevance, such as model genomes, are subjected to careful manual curation, while the bulk of high-throughput data is annotated by automatic means. High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). More recent projects are PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38,000,000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis. All databases described here, as well as the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.helmholtz-muenchen.de).

MIPS: curated databases and comprehensive secondary data resources in 2010

PubMed Central

Mewes, H. Werner; Ruepp, Andreas; Theis, Fabian; Rattei, Thomas; Walter, Mathias; Frishman, Dmitrij; Suhre, Karsten; Spannagl, Manuel; Mayer, Klaus F.X.; Stümpflen, Volker; Antonov, Alexey

2011-01-01

The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological data. Selected data sets of high relevance, such as model genomes, are subjected to careful manual curation, while the bulk of high-throughput data is annotated by automatic means. High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). More recent projects are PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38 000 000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis. All databases described here, as well as the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.helmholtz-muenchen.de). PMID:21109531

CCDB: a curated database of genes involved in cervix cancer.

PubMed

Agarwal, Subhash M; Raghav, Dhwani; Singh, Harinder; Raghava, G P S

2011-01-01

The Cervical Cancer gene DataBase (CCDB, http://crdd.osdd.net/raghava/ccdb) is a manually curated catalog of experimentally validated genes that are thought, or are known to be involved in the different stages of cervical carcinogenesis. In spite of the large women population that is presently affected from this malignancy still at present, no database exists that catalogs information on genes associated with cervical cancer. Therefore, we have compiled 537 genes in CCDB that are linked with cervical cancer causation processes such as methylation, gene amplification, mutation, polymorphism and change in expression level, as evident from published literature. Each record contains details related to gene like architecture (exon-intron structure), location, function, sequences (mRNA/CDS/protein), ontology, interacting partners, homology to other eukaryotic genomes, structure and links to other public databases, thus augmenting CCDB with external data. Also, manually curated literature references have been provided to support the inclusion of the gene in the database and establish its association with cervix cancer. In addition, CCDB provides information on microRNA altered in cervical cancer as well as search facility for querying, several browse options and an online tool for sequence similarity search, thereby providing researchers with easy access to the latest information on genes involved in cervix cancer.

The multiple personalities of Watson and Crick strands.

PubMed

Cartwright, Reed A; Graur, Dan

2011-02-08

In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two terms, and the many usages contradict one another as well as the original definition. Here, we review the history of the terminology and suggest retaining a single sense that is currently the most useful and consistent. The Saccharomyces Genome Database defines the Watson strand as the strand which has its 5'-end at the short-arm telomere and the Crick strand as its complement. The Watson strand is always used as the reference strand in their database. Using this as the basis of our standard, we recommend that Watson and Crick strand terminology only be used in the context of genomics. When possible, the centromere or other genomic feature should be used as a reference point, dividing the chromosome into two arms of unequal lengths. Under our proposal, the Watson strand is standardized as the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. Furthermore, the Watson strand should be retained as the reference (plus) strand in a genomic database. This usage not only makes the determination of Watson and Crick unambiguous, but also allows unambiguous selection of reference stands for genomics. This article was reviewed by John M. Logsdon, Igor B. Rogozin (nominated by Andrey Rzhetsky), and William Martin.

Catalog of open clusters and associated interstellar matter

NASA Technical Reports Server (NTRS)

Leisawitz, David

1988-01-01

The Catalog of Open Clusters and Associated Interstellar Matter summarizes observations of 128 open clusters and their associated ionized, atomic, and molecular iinterstellar matter. Cluster sizes, distances, radial velocities, ages, and masses, and the radial velocities and masses of associated interstellar medium components, are given. The database contains information from approximately 400 references published in the scientific literature before 1988.

Searching for Music's Potential: A Critical Examination of Research on Music Therapy with Individuals with Autism

ERIC Educational Resources Information Center

Accordino, Robert; Comer, Ronald; Heller, Wendy B.

2007-01-01

The authors conducted a literature review on music therapy for individuals with autism because of the frequent use of music therapy for those with autism and recent research on the musical abilities of this population. To accomplish this narrative review, articles were searched from relevant databases, reference lists from articles, and book…

Second chronological supplement to the Carcinogenic Potency Database: standardized results of animal bioassays published through December 1984 and by the National Toxicology Program through May 1986.

PubMed Central

Gold, L S; Slone, T H; Backman, G M; Magaw, R; Da Costa, M; Lopipero, P; Blumenthal, M; Ames, B N

1987-01-01

This paper is the second chronological supplement to the Carcinogenic Potency Database, published earlier in this journal (1,2,4). We report here results of carcinogenesis bioassays published in the general literature between January 1983 and December 1984, and in Technical Reports of the National Cancer Institute/National Toxicology Program between January 1983 and May 1986. This supplement includes results of 525 long-term, chronic experiments of 199 test compounds, and reports the same information about each experiment in the same plot format as the earlier papers: e.g., the species and strain of test animal, the route and duration of compound administration, dose level and other aspects of experimental protocol, histopathology and tumor incidence, TD50 (carcinogenic potency) and its statistical significance, dose response, author's opinion about carcinogenicity, and literature citation. We refer the reader to the 1984 publications for a description of the numerical index of carcinogenic potency (TD50), a guide to the plot of the database, and a discussion of the sources of data, the rationale for the inclusion of particular experiments and particular target sites, and the conventions adopted in summarizing the literature. The three plots of the database are to be used together, since results of experiments published in earlier plots are not repeated. Taken together, the three plots include results for more than 3500 experiments on 975 chemicals. Appendix 14 is an index to all chemicals in the database and indicates which plot(s) each chemical appears in. PMID:3691431

US and foreign alloy cross-reference database

NASA Technical Reports Server (NTRS)

Springer, John M.; Morgan, Steven H.

1991-01-01

Marshall Space Flight Center and other NASA installations have a continuing requirement for materials data from other countries involved with the development of joint international Spacelab experiments and other hardware. This need includes collecting data for common alloys to ascertain composition, physical properties, specifications, and designations. This data is scattered throughout a large number of specification statements, standards, handbooks, and other technical literature which make a manual search both tedious and often limited in extent. In recognition of this problem, a computerized database of information on alloys was developed along with the software necessary to provide the desired functions to access this data. The intention was to produce an initial database covering aluminum alloys, along with the program to provide a user-interface to the data, and then later to extend and refine the database to include other nonferrous and ferrous alloys.

[Nursing knowledge production in Argentina, Chile, Paraguay and Uruguay].

PubMed

Lange, C; Meincke, S M; Schwartz, E

2001-07-01

Research is being pointed out as a path to nursing recognition. The knowledge production concerning the tendencies of research lines in nursing during the 90's, in Argentina, Chile, Paraguay and Uruguay, took part of a study that had the purpose to know the impact of the nursing profession practice on health in Latin America and in the Caribbean Islands. The methodology used was the exploratory quantitative research, and the database used were Lilacs and Medline. The most frequent investigation themes refer to nursing profession (up to 13.2%). Regarding the lines of investigation in nursing, we found out that the nursing professional stood out with 41%, being technique and methodology the main approaches. Chile was the country that produced the largest amount of research, 86.8% of the summaries. Referring to the financing source, no reference is made in 86.8% of the summaries. With reference to the number of authors involved with the published literature, 50.7% of the literature have only one author. The nurses should be aware to invest in the enlargement of this production.

Humanization policy in primary health care: a systematic review

PubMed Central

Nora, Carlise Rigon Dalla; Junges, José Roque

2013-01-01

OBJECTIVE To analyze humanization practices in primary health care in the Brazilian Unified Health System according to the principles of the National Humanization Policy. METHODS A systematic review of the literature was carried out, followed by a meta-synthesis, using the following databases: BDENF (nursing database), BDTD (Brazilian digital library of theses and dissertations), CINAHL (Cumulative Index to nursing and allied health literature), LILACS (Latin American and Caribbean health care sciences literature), MedLine (International health care sciences literature), PAHO (Pan-American Health Care Organization Library) and SciELO (Scientific Electronic Library Online). The following descriptors were used: Humanization; Humanizing Health Care; Reception: Humanized care: Humanization in health care; Bonding; Family Health Care Program; Primary Care; Public Health and Sistema Único de Saúde (the Brazilian public health care system). Research articles, case studies, reports of experiences, dissertations, theses and chapters of books written in Portuguese, English or Spanish, published between 2003 and 2011, were included in the analysis. RESULTS Among the 4,127 publications found on the topic, 40 studies were evaluated and included in the analysis, producing three main categories: the first referring to the infrastructure and organization of the primary care service, made clear the dissatisfaction with the physical structure and equipment of the services and with the flow of attendance, which can facilitate or make difficult the access. The second, referring to the health work process, showed issues about the insufficient number of professionals, fragmentation of the work processes, the professional profile and responsibility. The third category, referring to the relational technologies, indicated the reception, bonding, listening, respect and dialog with the service users. CONCLUSIONS Although many practices were cited as humanizing they do not produce changes in the health services because of the lack of more profound analysis of the work processes and ongoing education in the health care services. PMID:24626556

Sexual Abuse of Older Nursing Home Residents: A Literature Review

PubMed Central

Malmedal, Wenche; Iversen, Maria Helen; Kilvik, Astrid

2015-01-01

Despite an increasing literature related to elder abuse, sexual abuse of older persons in general and of vulnerable adults living in nursing homes in particular is still sparsely described. The purpose of this study was to assess the state of knowledge on the subject of sexual abuse against older nursing home residents through a literature review. Systematic searches in reference databases including Cinahl, Medline, OVID Nursing Database, ISI Web of Science, PsycINFO, Cochrane Library, and SveMed + were conducted. Through several phases of selection of the articles, using strict inclusion and exclusion criteria, six articles were chosen for a deeper examination. Findings from the review show that sexual abuse occurs in nursing homes and that both older women and men are victims of sexual abuse. Perpetrators appear mainly to be staff and other residents and mainly to be men, but also women abuse both older men and older women. Findings from the literature review show that there is a need for knowledge and further research on the topic of sexual abuse against older residents in nursing homes. Furthermore, there is a need for good policies and reporting systems, as an important step in seriously addressing sexual abuse against older persons. PMID:25642347

A carcinogenic potency database of the standardized results of animal bioassays

PubMed Central

Gold, Lois Swirsky; Sawyer, Charles B.; Magaw, Renae; Backman, Georganne M.; De Veciana, Margarita; Levinson, Robert; Hooper, N. Kim; Havender, William R.; Bernstein, Leslie; Peto, Richard; Pike, Malcolm C.; Ames, Bruce N.

1984-01-01

The preceding paper described our numerical index of carcinogenic potency, the TD50 and the statistical procedures adopted for estimating it from experimental data. This paper presents the Carcinogenic Potency Database, which includes results of about 3000 long-term, chronic experiments of 770 test compounds. Part II is a discussion of the sources of our data, the rationale for the inclusion of particular experiments and particular target sites, and the conventions adopted in summarizing the literature. Part III is a guide to the plot of results presented in Part IV. A number of appendices are provided to facilitate use of the database. The plot includes information about chronic cancer tests in mammals, such as dose and other aspects of experimental protocol, histopathology and tumor incidence, TD50 and its statistical significance, dose response, author's opinion and literature reference. The plot readily permits comparisons of carcinogenic potency and many other aspects of cancer tests; it also provides quantitative information about negative tests. The range of carcinogenic potency is over 10 million-fold. PMID:6525996

Ipsilateral femur and tibia fractures in pediatric patients: A systematic review

PubMed Central

Anari, Jason B; Neuwirth, Alexander L; Horn, B David; Baldwin, Keith D

2017-01-01

AIM To better understand how pediatric floating knee injuries are managed after the wide spread use of new orthopaedic technology. METHODS We searched EMBASE, COCHRANE and MEDLINE computerized literature databases from the earliest date available in the databases to February 2017 using the following search term including variants and pleural counterparts: Pediatric floating knee. All studies were thoroughly reviewed by multiple authors. Reference lists from all articles were scrutinized to identify any additional studies of interest. A final database of individual patients was assembled from the literature. Univariate and multivariate statistical tests were applied to the assembled database to assess differences in outcomes. RESULTS The English language literature contains series with a total of 97 pediatric patients who sustained floating knee injuries. Patients averaged 9.3 years of age and were mostly male (73). Approximately 25% of the fractures were open injuries, more tibia (27) than femur (10). Over 75% of the fractures of both the tibia and the femur involved the diaphysis. More than half (52) of the patients were treated non-operatively for both fractures. As a sequela of the injury 32 (33%) patients were left with a limb length discrepancy, 24 (25%) patients had lengthening of the injured limb at follow up, while 8 (8%) had shortening of the affected limb. Infection developed in 9 patients and 3 had premature physeal closure. Younger patients were more likely to be treated non-operatively (P < 0.001) and patients treated with operative intervention had statistically significant shorter hospital length of stays (P = 0.001). CONCLUSION Given the predominance of non-operative management in published studies, the available literature is not clinically relevant since the popularization of internal fixation for pediatric long-bone fractures PMID:28875130

The fifth plot of the Carcinogenic Potency Database: results of animal bioassays published in the general literature through 1988 and by the National Toxicology Program through 1989.

PubMed Central

Gold, L S; Manley, N B; Slone, T H; Garfinkel, G B; Rohrbach, L; Ames, B N

1993-01-01

This paper is the fifth plot of the Carcinogenic Potency Database (CPDB) that first appeared in this journal in 1984 (1-5). We report here results of carcinogenesis bioassays published in the general literature between January 1987 and December 1988, and in technical reports of the National Toxicology Program between July 1987 and December 1989. This supplement includes results of 412 long-term, chronic experiments of 147 test compounds and reports the same information about each experiment in the same plot format as the earlier papers: the species and strain of test animal, the route and duration of compound administration, dose level and other aspects of experimental protocol, histopathology and tumor incidence, TD50 (carcinogenic potency) and its statistical significance, dose response, author's opinion about carcinogenicity, and literature citation. We refer the reader to the 1984 publications (1,5,6) for a guide to the plot of the database, a complete description of the numerical index of carcinogenic potency, and a discussion of the sources of data, the rationale for the inclusion of particular experiments and particular target sites, and the conventions adopted in summarizing the literature. The five plots of the database are to be used together, as results of individual experiments that were published earlier are not repeated. In all, the five plots include results of 4487 experiments on 1136 chemicals. Several analyses based on the CPDB that were published earlier are described briefly, and updated results based on all five plots are given for the following earlier analyses: the most potent TD50 value by species, reproducibility of bioassay results, positivity rates, and prediction between species.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8354183

Ipsilateral femur and tibia fractures in pediatric patients: A systematic review.

PubMed

Anari, Jason B; Neuwirth, Alexander L; Horn, B David; Baldwin, Keith D

2017-08-18

To better understand how pediatric floating knee injuries are managed after the wide spread use of new orthopaedic technology. We searched EMBASE, COCHRANE and MEDLINE computerized literature databases from the earliest date available in the databases to February 2017 using the following search term including variants and pleural counterparts: Pediatric floating knee. All studies were thoroughly reviewed by multiple authors. Reference lists from all articles were scrutinized to identify any additional studies of interest. A final database of individual patients was assembled from the literature. Univariate and multivariate statistical tests were applied to the assembled database to assess differences in outcomes. The English language literature contains series with a total of 97 pediatric patients who sustained floating knee injuries. Patients averaged 9.3 years of age and were mostly male (73). Approximately 25% of the fractures were open injuries, more tibia (27) than femur (10). Over 75% of the fractures of both the tibia and the femur involved the diaphysis. More than half (52) of the patients were treated non-operatively for both fractures. As a sequela of the injury 32 (33%) patients were left with a limb length discrepancy, 24 (25%) patients had lengthening of the injured limb at follow up, while 8 (8%) had shortening of the affected limb. Infection developed in 9 patients and 3 had premature physeal closure. Younger patients were more likely to be treated non-operatively ( P < 0.001) and patients treated with operative intervention had statistically significant shorter hospital length of stays ( P = 0.001). Given the predominance of non-operative management in published studies, the available literature is not clinically relevant since the popularization of internal fixation for pediatric long-bone fractures.

PubMed searches: overview and strategies for clinicians.

PubMed

Lindsey, Wesley T; Olin, Bernie R

2013-04-01

PubMed is a biomedical and life sciences database maintained by a division of the National Library of Medicine known as the National Center for Biotechnology Information (NCBI). It is a large resource with more than 5600 journals indexed and greater than 22 million total citations. Searches conducted in PubMed provide references that are more specific for the intended topic compared with other popular search engines. Effective PubMed searches allow the clinician to remain current on the latest clinical trials, systematic reviews, and practice guidelines. PubMed continues to evolve by allowing users to create a customized experience through the My NCBI portal, new arrangements and options in search filters, and supporting scholarly projects through exportation of citations to reference managing software. Prepackaged search options available in the Clinical Queries feature also allow users to efficiently search for clinical literature. PubMed also provides information regarding the source journals themselves through the Journals in NCBI Databases link. This article provides an overview of the PubMed database's structure and features as well as strategies for conducting an effective search.

Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders.

PubMed

Hamosh, Ada; Scott, Alan F; Amberger, Joanna; Bocchini, Carol; Valle, David; McKusick, Victor A

2002-01-01

Online Mendelian Inheritance in Man (OMIM) is a comprehensive, authoritative and timely knowledgebase of human genes and genetic disorders compiled to support research and education in human genomics and the practice of clinical genetics. Started by Dr Victor A. McKusick as the definitive reference Mendelian Inheritance in Man, OMIM (www.ncbi.nlm.nih.gov/omim) is now distributed electronically by the National Center for Biotechnology Information (NCBI), where it is integrated with the Entrez suite of databases. Derived from the biomedical literature, OMIM is written and edited at Johns Hopkins University with input from scientists and physicians around the world. Each OMIM entry has a full-text summary of a genetically determined phenotype and/or gene and has numerous links to other genetic databases such as DNA and protein sequence, PubMed references, general and locus-specific mutation databases, approved gene nomenclature, and the highly detailed mapviewer, as well as patient support groups and many others. OMIM is an easy and straightforward portal to the burgeoning information in human genetics.

Comparative study of minutiae selection algorithms for ISO fingerprint templates

NASA Astrophysics Data System (ADS)

Vibert, B.; Charrier, C.; Le Bars, J.-M.; Rosenberger, C.

2015-03-01

We address the selection of fingerprint minutiae given a fingerprint ISO template. Minutiae selection plays a very important role when a secure element (i.e. a smart-card) is used. Because of the limited capability of computation and memory, the number of minutiae of a stored reference in the secure element is limited. We propose in this paper a comparative study of 6 minutiae selection methods including 2 methods from the literature and 1 like reference (No Selection). Experimental results on 3 fingerprint databases from the Fingerprint Verification Competition show their relative efficiency in terms of performance and computation time.

Sixth plot of the carcinogenic potency database: results of animal bioassays published in the General Literature 1989 to 1990 and by the National Toxicology Program 1990 to 1993.

PubMed Central

Gold, L S; Manley, N B; Slone, T H; Garfinkel, G B; Ames, B N; Rohrbach, L; Stern, B R; Chow, K

1995-01-01

This paper presents two types of information from the Carcinogenic Potency Database (CPDB): (a) the sixth chronological plot of analyses of long-term carcinogenesis bioassays, and (b) an index to chemicals in all six plots, including a summary compendium of positivity and potency for each chemical (Appendix 14). The five earlier plots of the CPDB have appeared in this journal, beginning in 1984 (1-5). Including the plot in this paper, the CPDB reports results of 5002 experiments on 1230 chemicals. This paper includes bioassay results published in the general literature between January 1989 and December 1990, and in Technical Reports of the National Toxicology Program between January 1990 and June 1993. Analyses are included on 17 chemicals tested in nonhuman primates by the Laboratory of Chemical Pharmacology, National Cancer Institute. This plot presents results of 531 long-term, chronic experiments of 182 test compounds and includes the same information about each experiment in the same plot format as the earlier papers: the species and strain of test animal, the route and duration of compound administration, dose level and other aspects of experimental protocol, histopathology and tumor incidence, TD50 (carcinogenic potency) and its statistical significance, dose response, author's opinion about carcinogenicity, and literature citation. We refer the reader to the 1984 publications (1,6,7) for a detailed guide to the plot of the database, a complete description of the numerical index of carcinogenic potency, and a discussion of the sources of data, the rationale for the inclusion of particular experiments and particular target sites, and the conventions adopted in summarizing the literature. The six plots of the CPDB are to be used together since results of individual experiments that were published earlier are not repeated. Appendix 14 is designed to facilitate access to results on all chemicals. References to the published papers that are the source of experimental data are reported in each of the published plots. For readers using the CPDB extensively, a combined plot is available of all results from the six separate plot papers, ordered alphabetically by chemical; the combined plot in printed form or on computer tape or diskette is available from the first author. A SAS database is also available. PMID:8741772

Development of a PubMed Based Search Tool for Identifying Sex and Gender Specific Health Literature.

PubMed

Song, Michael M; Simonsen, Cheryl K; Wilson, Joanna D; Jenkins, Marjorie R

2016-02-01

An effective literature search strategy is critical to achieving the aims of Sex and Gender Specific Health (SGSH): to understand sex and gender differences through research and to effectively incorporate the new knowledge into the clinical decision making process to benefit both male and female patients. The goal of this project was to develop and validate an SGSH literature search tool that is readily and freely available to clinical researchers and practitioners. PubMed, a freely available search engine for the Medline database, was selected as the platform to build the SGSH literature search tool. Combinations of Medical Subject Heading terms, text words, and title words were evaluated for optimal specificity and sensitivity. The search tool was then validated against reference bases compiled for two disease states, diabetes and stroke. Key sex and gender terms and limits were bundled to create a search tool to facilitate PubMed SGSH literature searches. During validation, the search tool retrieved 50 of 94 (53.2%) stroke and 62 of 95 (65.3%) diabetes reference articles selected for validation. A general keyword search of stroke or diabetes combined with sex difference retrieved 33 of 94 (35.1%) stroke and 22 of 95 (23.2%) diabetes reference base articles, with lower sensitivity and specificity for SGSH content. The Texas Tech University Health Sciences Center SGSH PubMed Search Tool provides higher sensitivity and specificity to sex and gender specific health literature. The tool will facilitate research, clinical decision-making, and guideline development relevant to SGSH.

Development of a PubMed Based Search Tool for Identifying Sex and Gender Specific Health Literature

PubMed Central

Song, Michael M.; Simonsen, Cheryl K.; Wilson, Joanna D.

2016-01-01

Abstract Background: An effective literature search strategy is critical to achieving the aims of Sex and Gender Specific Health (SGSH): to understand sex and gender differences through research and to effectively incorporate the new knowledge into the clinical decision making process to benefit both male and female patients. The goal of this project was to develop and validate an SGSH literature search tool that is readily and freely available to clinical researchers and practitioners. Methods: PubMed, a freely available search engine for the Medline database, was selected as the platform to build the SGSH literature search tool. Combinations of Medical Subject Heading terms, text words, and title words were evaluated for optimal specificity and sensitivity. The search tool was then validated against reference bases compiled for two disease states, diabetes and stroke. Results: Key sex and gender terms and limits were bundled to create a search tool to facilitate PubMed SGSH literature searches. During validation, the search tool retrieved 50 of 94 (53.2%) stroke and 62 of 95 (65.3%) diabetes reference articles selected for validation. A general keyword search of stroke or diabetes combined with sex difference retrieved 33 of 94 (35.1%) stroke and 22 of 95 (23.2%) diabetes reference base articles, with lower sensitivity and specificity for SGSH content. Conclusions: The Texas Tech University Health Sciences Center SGSH PubMed Search Tool provides higher sensitivity and specificity to sex and gender specific health literature. The tool will facilitate research, clinical decision-making, and guideline development relevant to SGSH. PMID:26555409

The multiple personalities of Watson and Crick strands

PubMed Central

2011-01-01

Background In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two terms, and the many usages contradict one another as well as the original definition. Here, we review the history of the terminology and suggest retaining a single sense that is currently the most useful and consistent. Proposal The Saccharomyces Genome Database defines the Watson strand as the strand which has its 5'-end at the short-arm telomere and the Crick strand as its complement. The Watson strand is always used as the reference strand in their database. Using this as the basis of our standard, we recommend that Watson and Crick strand terminology only be used in the context of genomics. When possible, the centromere or other genomic feature should be used as a reference point, dividing the chromosome into two arms of unequal lengths. Under our proposal, the Watson strand is standardized as the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. Furthermore, the Watson strand should be retained as the reference (plus) strand in a genomic database. This usage not only makes the determination of Watson and Crick unambiguous, but also allows unambiguous selection of reference stands for genomics. Reviewers This article was reviewed by John M. Logsdon, Igor B. Rogozin (nominated by Andrey Rzhetsky), and William Martin. PMID:21303550

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

[Neuropsychomotor developmental delay: conceptual map, term definitions, uses and limitations].

PubMed

Dornelas, Lílian de Fátima; Duarte, Neuza Maria de Castro; Magalhães, Lívia de Castro

2015-01-01

To retrieve the origin of the term neuropsychomotor developmental delay" (NPMD), its conceptual evolution over time, and to build a conceptual map based on literature review. A literature search was performed in the SciELO Brazil, Web of Science, Science Direct, OneFile (GALE), Pubmed (Medline), Whiley Online, and Springer databases, from January of 1940 to January of 2013, using the following keywords NPMD delay, NPMD retardation, developmental delay, and global developmental delay. A total of 71 articles were selected, which were used to build the conceptual map of the term. Of the 71 references, 55 were international and 16 national. The terms developmental delay and global developmental delay were the most frequently used in the international literature and, in Brazil, delayed NPMD was the most often used. The term developmental delay emerged in the mid 1940s, gaining momentum in the 1990 s. In Brazil, the term delayed NPMD started to be used in the 1980s, and has been frequently cited and published in the literature. Delayed development was a characteristic of 13 morbidities described in 23 references. Regarding the type of use, 19 references were found, with seven forms of use. Among the references, 34 had definitions of the term, and 16 different concepts were identified. Developmental delay is addressed in the international and national literature under different names, various applications, and heterogeneous concepts. Internationally, ways to improve communication between professionals have been indicated, with standardized definition of the term and use in very specific situations up to the fifth year of life, which was not found in Brazilian publications. Copyright © 2014 Associação de Pediatria de São Paulo. Publicado por Elsevier Editora Ltda. All rights reserved.

Neuropsychomotor developmental delay: conceptual map, term definitions, uses and limitations

PubMed Central

Dornelas, Lílian de Fátima; Duarte, Neuza Maria de Castro; Magalhães, Lívia de Castro

2015-01-01

OBJECTIVE: To retrieve the origin of the term neuropsychomotor developmental delay" (NPMD), its conceptual evolution over time, and to build a conceptual map based on literature review. DATA SOURCE: A literature search was performed in the SciELO Brazil, Web of Science, Science Direct, OneFile (GALE), Pubmed (Medline), Whiley Online, and Springer databases, from January of 1940 to January of 2013, using the following keywords: NPMD delay, NPMD retardation, developmental delay, and global developmental delay. A total of 71 articles were selected, which were used to build the conceptual map of the term. DATA SYNTHESIS: Of the 71 references, 55 were international and 16 national. The terms developmental delay and global developmental delay were the most frequently used in the international literature and, in Brazil, delayed NPMD was the most often used. The term developmental delay emerged in the mid 1940s, gaining momentum in the 1990s. In Brazil, the term delayed NPMD started to be used in the 1980s, and has been frequently cited and published in the literature. Delayed development was a characteristic of 13 morbidities described in 23 references. Regarding the type of use, 19 references were found, with seven forms of use. Among the references, 34 had definitions of the term, and 16 different concepts were identified. CONCLUSIONS: Developmental delay is addressed in the international and national literature under different names, various applications, and heterogeneous concepts. Internationally, ways to improve communication between professionals have been indicated, with standardized definition of the term and use in very specific situations up to the fifth year of life, which was not found in Brazilian publications. PMID:25662016

Third chronological supplement to the carcinogenic potency database: standardized results of animal bioassays published through December 1986 and by the National Toxicology Program through June 1987.

PubMed Central

Gold, L S; Slone, T H; Backman, G M; Eisenberg, S; Da Costa, M; Wong, M; Manley, N B; Rohrbach, L; Ames, B N

1990-01-01

This paper is the third chronological supplement to the Carcinogenic Potency Database that first appeared in this journal in 1984. We report here results of carcinogenesis bioassays published in the general literature between January 1985 and December 1986, and in Technical Reports of the National Toxicology Program between June 1986 and June 1987. This supplement includes results of 337 long-term, chronic experiments of 121 compounds, and reports the same information about each experiment in the same plot format as the earlier papers, e.g., the species and strain of animal, the route and duration of compound administration, dose level, and other aspects of experimental protocol, histopathology, and tumor incidence, TD50 (carcinogenic potency) and its statistical significance, dose response, opinion of the author about carcinogenicity, and literature citation. The reader needs to refer to the 1984 publication for a guide to the plot of the database, a complete description of the numerical index of carcinogenic potency, and a discussion of the sources of data, the rationale for the inclusion of particular experiments and particular target sites, and the conventions adopted in summarizing the literature. The four plots of the database are to be used together as results published earlier are not repeated. In all, the four plots include results for approximately 4000 experiments on 1050 chemicals. Appendix 14 of this paper is an alphabetical index to all chemicals in the database and indicates which plot(s) each chemical appears in. A combined plot of all results from the four separate papers, that is ordered alphabetically by chemical, is available from the first author, in printed form or on computer tape or diskette. PMID:2351123

Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.

PubMed

Sakai, Hiroaki; Lee, Sung Shin; Tanaka, Tsuyoshi; Numa, Hisataka; Kim, Jungsok; Kawahara, Yoshihiro; Wakimoto, Hironobu; Yang, Ching-chia; Iwamoto, Masao; Abe, Takashi; Yamada, Yuko; Muto, Akira; Inokuchi, Hachiro; Ikemura, Toshimichi; Matsumoto, Takashi; Sasaki, Takuji; Itoh, Takeshi

2013-02-01

The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics.

A curated database of cyanobacterial strains relevant for modern taxonomy and phylogenetic studies.

PubMed

Ramos, Vitor; Morais, João; Vasconcelos, Vitor M

2017-04-25

The dataset herein described lays the groundwork for an online database of relevant cyanobacterial strains, named CyanoType (http://lege.ciimar.up.pt/cyanotype). It is a database that includes categorized cyanobacterial strains useful for taxonomic, phylogenetic or genomic purposes, with associated information obtained by means of a literature-based curation. The dataset lists 371 strains and represents the first version of the database (CyanoType v.1). Information for each strain includes strain synonymy and/or co-identity, strain categorization, habitat, accession numbers for molecular data, taxonomy and nomenclature notes according to three different classification schemes, hierarchical automatic classification, phylogenetic placement according to a selection of relevant studies (including this), and important bibliographic references. The database will be updated periodically, namely by adding new strains meeting the criteria for inclusion and by revising and adding up-to-date metadata for strains already listed. A global 16S rDNA-based phylogeny is provided in order to assist users when choosing the appropriate strains for their studies.

A curated database of cyanobacterial strains relevant for modern taxonomy and phylogenetic studies

PubMed Central

Ramos, Vitor; Morais, João; Vasconcelos, Vitor M.

2017-01-01

The dataset herein described lays the groundwork for an online database of relevant cyanobacterial strains, named CyanoType (http://lege.ciimar.up.pt/cyanotype). It is a database that includes categorized cyanobacterial strains useful for taxonomic, phylogenetic or genomic purposes, with associated information obtained by means of a literature-based curation. The dataset lists 371 strains and represents the first version of the database (CyanoType v.1). Information for each strain includes strain synonymy and/or co-identity, strain categorization, habitat, accession numbers for molecular data, taxonomy and nomenclature notes according to three different classification schemes, hierarchical automatic classification, phylogenetic placement according to a selection of relevant studies (including this), and important bibliographic references. The database will be updated periodically, namely by adding new strains meeting the criteria for inclusion and by revising and adding up-to-date metadata for strains already listed. A global 16S rDNA-based phylogeny is provided in order to assist users when choosing the appropriate strains for their studies. PMID:28440791

Mapping the literature of occupational therapy.

PubMed Central

Reed, K L

1999-01-01

Occupational therapy, formally organized in the United States in 1917, is considered an allied health field. Mapping occupational therapy literature is part of a bibliometric project of the Medical Library Association's Nursing and Allied Health Resources Section's project for mapping the literature of allied health. Three core journals were selected from the years 1995 and 1996 and a determination was made of the extent to which the cited journal references were covered by standard indexing sources. Using Bradford's Law of Scattering three zones were created, each containing approximately one-third of the cited journal references. The results showed that three journals made up the first zone, 117 journals the second, and 657 the third. The most cited journal was the American Journal of Occupational Therapy. In the second zone, journals from twelve disciplines were identified. While MEDLINE provided the best overall indexing, the Cumulative Index to Nursing and Allied Health Literature (CINAHL) was the only database that indexed the three most cited journals plus nine of the currently active titles in occupational therapy. MEDLINE could improve its coverage of occupational therapy by indexing the journals of the British, Canadian, and Australian national associations. PMID:10427431

Taking control of your digital library: how modern citation managers do more than just referencing.

PubMed

Mahajan, Amit K; Hogarth, D Kyle

2013-12-01

Physicians are constantly navigating the overwhelming body of medical literature available on the Internet. Although early citation managers were capable of limited searching of index databases and tedious bibliography production, modern versions of citation managers such as EndNote, Zotero, and Mendeley are powerful web-based tools for searching, organizing, and sharing medical literature. Effortless point-and-click functions provide physicians with the ability to develop robust digital libraries filled with literature relevant to their fields of interest. In addition to easily creating manuscript bibliographies, various citation managers allow physicians to readily access medical literature, share references for teaching purposes, collaborate with colleagues, and even participate in social networking. If physicians are willing to invest the time to familiarize themselves with modern citation managers, they will reap great benefits in the future.

Economic Considerations on the Follow-Up Practice in Gynecologic Cancers: Few Lights and Many Shadows From a Literature Review.

PubMed

Pagano, Eva; Sobrero, Simona; Cavallero, Camilla; Zola, Paolo; Ciccone, Giovannino

2015-09-01

The aim of this review was to analyze the existing literature on the cost of follow-up in gynecology oncology. We performed a literature search in Medline and NHS CRD (University of Oxford) databases. Research strings were mainly based on MESH terms referring to economic studies and to neoplasms follow-up/aftercare and cancer recurrences. Two independent searches were performed for ovarian neoplasm and uterine neoplasm. Some studies were also identified among the references of the selected articles. Potentially relevant studies were identified based on the title and abstract by 2 independent readers. Finally, the reviewing process selected 2 studies on gynecologic cancers in general, including uterine and ovarian cancers, 3 specific on ovarian cancer, 7 on endometrium, and 9 on cervix. The identified economic literature on economic evaluation of gynecologic cancer follow-up procedures showed to be based on weak evidence of effectiveness and to lack formal methodological approaches. In general, such literature is quite recent, relies on small sample observational studies, and suffers from a lack of financial support. There are few available lights in economic considerations on gynecologic cancer follow-up, represented by all the published studies, and many shadows that require to be clarified by properly designed randomized trials including cost-effectiveness analysis.

Is There a Potential of Misuse for Quetiapine?: Literature Review and Analysis of the European Medicines Agency/European Medicines Agency Adverse Drug Reactions' Database.

PubMed

Chiappini, Stefania; Schifano, Fabrizio

2018-02-01

A recent years' increase in both prescribing and availability of second-generation antipsychotics (SGAs) has been observed. According to the literature, typically made up by case studies/series, quetiapine seems to be the most commonly misused SGA, with both intranasal and intravenous intake modalities having been described. Another SGA that has been anecdotally reported to be misused is olanzapine. For these molecules, both a previous history of drug misuse and being an inmate have been described as factors associated with misuse. Hence, while providing here an updated literature review of the topic, we aimed at assessing all cases of quetiapine misuse/abuse/dependence/withdrawal as reported to the European Medicines Agency's EudraVigilance (EV) database; this was carried out in comparison with the reference drug olanzapine. All spontaneous, European Medicines Agency database reports relating to both quetiapine (2005-2016) and olanzapine (2004-2016) misuse/abuse/dependence/withdrawal issues were retrieved, and a descriptive analysis was performed. From the EV database, 18,112 (8.64% of 209,571) and 4178 (7.58% of 55,100) adverse drug reaction reports of misuse/abuse/dependence/withdrawal were associated with quetiapine and olanzapine, respectively. The resulting proportional reporting ratio values suggested that the misuse/abuse-, dependence-, and withdrawal-related adverse drug reactions were more frequently reported for quetiapine (1.07, 1.01, and 5.25, respectively) in comparison with olanzapine. Despite data collection limitations, present EV data may suggest that, at least in comparison with olanzapine, quetiapine misuse may be a cause for concern.

HRGFish: A database of hypoxia responsive genes in fishes

NASA Astrophysics Data System (ADS)

Rashid, Iliyas; Nagpure, Naresh Sahebrao; Srivastava, Prachi; Kumar, Ravindra; Pathak, Ajey Kumar; Singh, Mahender; Kushwaha, Basdeo

2017-02-01

Several studies have highlighted the changes in the gene expression due to the hypoxia response in fishes, but the systematic organization of the information and the analytical platform for such genes are lacking. In the present study, an attempt was made to develop a database of hypoxia responsive genes in fishes (HRGFish), integrated with analytical tools, using LAMPP technology. Genes reported in hypoxia response for fishes were compiled through literature survey and the database presently covers 818 gene sequences and 35 gene types from 38 fishes. The upstream fragments (3,000 bp), covered in this database, enables to compute CG dinucleotides frequencies, motif finding of the hypoxia response element, identification of CpG island and mapping with the reference promoter of zebrafish. The database also includes functional annotation of genes and provides tools for analyzing sequences and designing primers for selected gene fragments. This may be the first database on the hypoxia response genes in fishes that provides a workbench to the scientific community involved in studying the evolution and ecological adaptation of the fish species in relation to hypoxia.

Reconsidering the conceptualization of nursing workload: literature review.

PubMed

Morris, Roisin; MacNeela, Padraig; Scott, Anne; Treacy, Pearl; Hyde, Abbey

2007-03-01

This paper reports a literature review that aimed to analyse the way in which nursing intensity and patient dependency have been considered to be conceptually similar to nursing workload, and to propose a model to show how these concepts actually differ in both theoretical and practical terms. The literature on nursing workload considers the concepts of patient 'dependency' and nursing 'intensity' in the realm of nursing workload. These concepts differ by definition but are used to measure the same phenomenon, i.e. nursing workload. The literature search was undertaken in 2004 using electronic databases, reference lists and other available literature. Papers were sourced from the Medline, Psychlit, CINAHL and Cochrane databases and through the general search engine Google. The keywords focussed on nursing workload, nursing intensity and patient dependency. Nursing work and workload concepts and labels are defined and measured in different and often contradictory ways. It is vitally important to understand these differences when using such conceptualizations to measure nursing workload. A preliminary model is put forward to clarify the relationships between nursing workload concepts. In presenting a preliminary model of nursing workload, it is hoped that nursing workload might be better understood so that it becomes more visible and recognizable. Increasing the visibility of nursing workload should have a positive impact on nursing workload management and on the provision of patient care.

Building a protein name dictionary from full text: a machine learning term extraction approach.

PubMed

Shi, Lei; Campagne, Fabien

2005-04-07

The majority of information in the biological literature resides in full text articles, instead of abstracts. Yet, abstracts remain the focus of many publicly available literature data mining tools. Most literature mining tools rely on pre-existing lexicons of biological names, often extracted from curated gene or protein databases. This is a limitation, because such databases have low coverage of the many name variants which are used to refer to biological entities in the literature. We present an approach to recognize named entities in full text. The approach collects high frequency terms in an article, and uses support vector machines (SVM) to identify biological entity names. It is also computationally efficient and robust to noise commonly found in full text material. We use the method to create a protein name dictionary from a set of 80,528 full text articles. Only 8.3% of the names in this dictionary match SwissProt description lines. We assess the quality of the dictionary by studying its protein name recognition performance in full text. This dictionary term lookup method compares favourably to other published methods, supporting the significance of our direct extraction approach. The method is strong in recognizing name variants not found in SwissProt.

Building a protein name dictionary from full text: a machine learning term extraction approach

PubMed Central

Shi, Lei; Campagne, Fabien

2005-01-01

Background The majority of information in the biological literature resides in full text articles, instead of abstracts. Yet, abstracts remain the focus of many publicly available literature data mining tools. Most literature mining tools rely on pre-existing lexicons of biological names, often extracted from curated gene or protein databases. This is a limitation, because such databases have low coverage of the many name variants which are used to refer to biological entities in the literature. Results We present an approach to recognize named entities in full text. The approach collects high frequency terms in an article, and uses support vector machines (SVM) to identify biological entity names. It is also computationally efficient and robust to noise commonly found in full text material. We use the method to create a protein name dictionary from a set of 80,528 full text articles. Only 8.3% of the names in this dictionary match SwissProt description lines. We assess the quality of the dictionary by studying its protein name recognition performance in full text. Conclusion This dictionary term lookup method compares favourably to other published methods, supporting the significance of our direct extraction approach. The method is strong in recognizing name variants not found in SwissProt. PMID:15817129

Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database

PubMed Central

Drabkin, Harold J.; Blake, Judith A.

2012-01-01

The Mouse Genome Database, the Gene Expression Database and the Mouse Tumor Biology database are integrated components of the Mouse Genome Informatics (MGI) resource (http://www.informatics.jax.org). The MGI system presents both a consensus view and an experimental view of the knowledge concerning the genetics and genomics of the laboratory mouse. From genotype to phenotype, this information resource integrates information about genes, sequences, maps, expression analyses, alleles, strains and mutant phenotypes. Comparative mammalian data are also presented particularly in regards to the use of the mouse as a model for the investigation of molecular and genetic components of human diseases. These data are collected from literature curation as well as downloads of large datasets (SwissProt, LocusLink, etc.). MGI is one of the founding members of the Gene Ontology (GO) and uses the GO for functional annotation of genes. Here, we discuss the workflow associated with manual GO annotation at MGI, from literature collection to display of the annotations. Peer-reviewed literature is collected mostly from a set of journals available electronically. Selected articles are entered into a master bibliography and indexed to one of eight areas of interest such as ‘GO’ or ‘homology’ or ‘phenotype’. Each article is then either indexed to a gene already contained in the database or funneled through a separate nomenclature database to add genes. The master bibliography and associated indexing provide information for various curator-reports such as ‘papers selected for GO that refer to genes with NO GO annotation’. Once indexed, curators who have expertise in appropriate disciplines enter pertinent information. MGI makes use of several controlled vocabularies that ensure uniform data encoding, enable robust analysis and support the construction of complex queries. These vocabularies range from pick-lists to structured vocabularies such as the GO. All data associations are supported with statements of evidence as well as access to source publications. PMID:23110975

Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database.

PubMed

Drabkin, Harold J; Blake, Judith A

2012-01-01

The Mouse Genome Database, the Gene Expression Database and the Mouse Tumor Biology database are integrated components of the Mouse Genome Informatics (MGI) resource (http://www.informatics.jax.org). The MGI system presents both a consensus view and an experimental view of the knowledge concerning the genetics and genomics of the laboratory mouse. From genotype to phenotype, this information resource integrates information about genes, sequences, maps, expression analyses, alleles, strains and mutant phenotypes. Comparative mammalian data are also presented particularly in regards to the use of the mouse as a model for the investigation of molecular and genetic components of human diseases. These data are collected from literature curation as well as downloads of large datasets (SwissProt, LocusLink, etc.). MGI is one of the founding members of the Gene Ontology (GO) and uses the GO for functional annotation of genes. Here, we discuss the workflow associated with manual GO annotation at MGI, from literature collection to display of the annotations. Peer-reviewed literature is collected mostly from a set of journals available electronically. Selected articles are entered into a master bibliography and indexed to one of eight areas of interest such as 'GO' or 'homology' or 'phenotype'. Each article is then either indexed to a gene already contained in the database or funneled through a separate nomenclature database to add genes. The master bibliography and associated indexing provide information for various curator-reports such as 'papers selected for GO that refer to genes with NO GO annotation'. Once indexed, curators who have expertise in appropriate disciplines enter pertinent information. MGI makes use of several controlled vocabularies that ensure uniform data encoding, enable robust analysis and support the construction of complex queries. These vocabularies range from pick-lists to structured vocabularies such as the GO. All data associations are supported with statements of evidence as well as access to source publications.

Patent Databases. . .A Survey of What Is Available from DIALOG, Questel, SDC, Pergamon and INPADOC.

ERIC Educational Resources Information Center

Kulp, Carol S.

1984-01-01

Presents survey of two groups of databases covering patent literature: patent literature only and general literature that includes patents relevant to subject area of database. Description of databases and comparison tables for patent and general databases (cost, country coverage, years covered, update frequency, file size, and searchable data…

Managing equipment innovations in mining: A review.

PubMed

Trudel, Bryan; Nadeau, Sylvie; Zaras, Kazimierz; Deschamps, Isabelle

2015-01-01

Technological innovations in mining equipment have led to increased productivity and occupational health and safety (OHS) performance, but their introduction also brings new risks for workers. The aim of this study is to provide support for mining industry managers who are required to reconcile equipment choices with OHS and productivity. Examination of the literature through interdisciplinary digital databases. Databases were searched using specific combinations of keywords and limited to studies dating back no farther than 1992. The ``snowball'' technique was also used to examining the references listed in research articles initially identified with the databases. A total of 19 contextual factors were identified as having the potential to influence the OHS and productivity leverage of equipment innovations. The most often cited among these factors are the level of training provided to the equipment operators, operator experience and age, supervisor leadership abilities, and maintaining good relations within work crews. Interactions between these factors are not discussed in mining innovation literature. It would be helpful to use a systems thinking approach which incorporates interaction between relevant actors and factors to define properly the most sensitive aspects of innovation management as it applies to mining equipment.

Database of Geoscientific References Through 2007 for Afghanistan, Version 2

USGS Publications Warehouse

Eppinger, Robert G.; Sipeki, Julianna; Scofield, M.L. Sco

2007-01-01

This report describes an accompanying database of geoscientific references for the country of Afghanistan. Included is an accompanying Microsoft? Access 2003 database of geoscientific references for the country of Afghanistan. The reference compilation is part of a larger joint study of Afghanistan's energy, mineral, and water resources, and geologic hazards, currently underway by the U.S. Geological Survey, the British Geological Survey, and the Afghanistan Geological Survey. The database includes both published (n = 2,462) and unpublished (n = 174) references compiled through September, 2007. The references comprise two separate tables in the Access database. The reference database includes a user-friendly, keyword-searchable, interface and only minimum knowledge of the use of Microsoft? Access is required.

Effects of therapy for dysphagia in Parkinson's disease: systematic review.

PubMed

Baijens, Laura W J; Speyer, Renée

2009-03-01

This systematic review explores the effects of dysphagia treatment for Parkinson's disease. The review includes rehabilitative, surgical, pharmacologic, and other treatments. Only oropharyngeal dysphagia is selected for this literature search, excluding dysphagia due to esophageal or gastric disorders. The effects of deep brain stimulation on dysphagia are not included. In general, the literature concerning dysphagia treatment in Parkinson's disease is rather limited. Most effect studies show diverse methodologic problems. Multiple case studies and trials are identified by searching biomedical literature databases PubMed and Embase, and by hand-searching reference lists. The conclusions of most studies cannot be compared with one another because of heterogeneous therapy methods and outcome measures. Further research based on randomized controlled trials to determine the effectiveness of different therapies for dysphagia in Parkinson's disease is required.

Concept analysis: lack of anonymity.

PubMed

Swan, Marilyn A; Hobbs, Barbara B

2017-05-01

To re-examine and expand understanding of the concept 'lack of anonymity' as a component of rural nursing theory. Early healthcare literature reports lack of anonymity as part of social and working environments, particularly rural nursing. Rural nursing theory included the first published concept analysis on lack of anonymity but lacked empirical referents. Workforce, societal and rural healthcare changes support an updated analysis. To further understand lack of anonymity, its present day use and applicability to diverse environments, research from multiple disciplines was reviewed. Concept analysis. A literature search using eight terms in eleven databases was conducted of literature published between 2008-2013. Walker and Avant's concept analysis methodology guided the analysis. The previous concept analysis is supported in part by current literature. The defining attributes, 'identifiable', 'establishing boundaries for public and private self and interconnectedness' in a community were updated. Updated antecedents include: (i) environmental context; (ii) opportunities to become visible; (iii) developing relationships and (iv) unconscious or limited awareness of public or personal privacy. Consequences are: (i) familiarity; (ii) visibility; (iii) awareness of privacy and (iv) manage or balance of lack of anonymity. Cases were constructed and empirical referents identified. The concept of lack of anonymity was updated; portions of the original definition remain unchanged. Empirical referents reveal the defining attributes in daily life and may guide future research on the effect of lack of anonymity on nursing practice. This analysis advances the conceptual understanding of rural nursing theory. © 2016 John Wiley & Sons Ltd.

DMTB: the magnetotactic bacteria database

NASA Astrophysics Data System (ADS)

Pan, Y.; Lin, W.

2012-12-01

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

Work injury management model and implication in Hong Kong: a literature review.

PubMed

Chong, Cecilia Suk-Mei; Cheng, Andy Shu-Kei

2010-01-01

The objective of this review is to explore the work injury management models in literatures and the essential components in different models. The resulting information could be used to develop an integrated holistic model that could be applied in the work injury management system in Hong Kong. A keyword search of MEDLINE and CINAHL databases was conducted. A total of 68 studies related to the management of an injury were found within the above mentioned electronic database. Together with the citation tracking, there were 13 studies left for selection after the exclusion screening. Only 7 out of those 13 studies met the inclusion criteria for review. It is noticeable that the most important component in the injury management model in the reviewed literatures is early intervention. Because of limitations in Employees' Compensation Ordinance in Hong Kong, there is an impetus to have a model and practice guideline for work injury management in Hong Kong to ensure the quality of injury management services. At the end of this paper, the authors propose a work injury management model based on the employees' compensation system in Hong Kong. This model can be used as a reference for those countries adopting similar legislation as in Hong Kong.

Cervical Spine Involvement in Mild Traumatic Brain Injury: A Review

PubMed Central

Morin, Michael; Langevin, Pierre

2016-01-01

Background. There is a lack of scientific evidence in the literature on the involvement of the cervical spine in mTBI; however, its involvement is clinically accepted. Objective. This paper reviews evidence for the involvement of the cervical spine in mTBI symptoms, the mechanisms of injury, and the efficacy of therapy for cervical spine with concussion-related symptoms. Methods. A keyword search was conducted on PubMed, ICL, SportDiscus, PEDro, CINAHL, and Cochrane Library databases for articles published since 1990. The reference lists of articles meeting the criteria (original data articles, literature reviews, and clinical guidelines) were also searched in the same databases. Results. 4,854 records were screened and 43 articles were retained. Those articles were used to describe different subjects such as mTBI's signs and symptoms, mechanisms of injury, and treatments of the cervical spine. Conclusions. The hypothesis of cervical spine involvement in post-mTBI symptoms and in PCS (postconcussion syndrome) is supported by increasing evidence and is widely accepted clinically. For the management and treatment of mTBIs, few articles were available in the literature, and relevant studies showed interesting results about manual therapy and exercises as efficient tools for health care practitioners. PMID:27529079

Systematic review of serum steroid reference intervals developed using mass spectrometry.

PubMed

Tavita, Nevada; Greaves, Ronda F

2017-12-01

The aim of this study was to perform a systematic review of the published literature to determine the available serum/plasma steroid reference intervals generated by mass spectrometry (MS) methods across all age groups in healthy subjects and to suggest recommendations to achieve common MS based reference intervals for serum steroids. MEDLINE, EMBASE and PubMed databases were used to conduct a comprehensive search for English language, MS-based reference interval studies for serum/plasma steroids. Selection of steroids to include was based on those listed in the Royal College of Pathologists of Australasia Quality Assurance Programs, Chemical Pathology, Endocrine Program. This methodology has been registered onto the PROSPERO International prospective register of systematic reviews (ID number: CRD42015029637). After accounting for duplicates, a total of 60 manuscripts were identified through the search strategy. Following critical evaluation, a total of 16 studies were selected. Of the 16 studies, 12 reported reference intervals for testosterone, 11 for 17 hydroxy-progesterone, nine for androstenedione, six for cortisol, three for progesterone, two for dihydrotestosterone and only one for aldosterone and dehydroepiandrosterone sulphate. No studies established MS-based reference intervals for oestradiol. As far as we are aware, this report provides the first comparison of the peer reviewed literature for serum/plasma steroid reference intervals generated by MS-based methods. The reference intervals based on these published studies can be used to inform the process to develop common reference intervals, and agreed reporting units for mass spectrometry based steroid methods. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Mapping the literature of maternal-child/gynecologic nursing.

PubMed

Jacobs, Susan Kaplan

2006-04-01

As part of a project to map the literature of nursing, sponsored by the Nursing and Allied Health Resources Section of the Medical Library Association, this study identifies core journals cited in maternal-child/gynecologic nursing and the indexing services that access the cited journals. Three source journals were selected and subjected to a citation analysis of articles from 1996 to 1998. Journals were the most frequently cited format (74.1%), followed by books (19.7%), miscellaneous (4.2%), and government documents (1.9%). Bradford's Law of Scattering was applied to the results, ranking cited journal references in descending order. One-third of the citations were found in a core of 14 journal titles; one-third were dispersed among a middle zone of 100 titles; and the remaining third were scattered in a larger zone of 1,194 titles. Indexing coverage for the core titles was most comprehensive in PubMed/MEDLINE, followed by Science Citation Index and CINAHL. The core of journals cited in this nursing specialty revealed a large number of medical titles, thus, the biomedical databases provide the best access. The interdisciplinary nature of maternal-child/ gynecologic nursing topics dictates that social sciences databases are an important adjunct. The study results will assist librarians in collection development, provide end users with guidelines for selecting databases, and influence database producers to consider extending coverage to identified titles.

Mapping the literature of maternal-child/gynecologic nursing

PubMed Central

Jacobs, Susan Kaplan

2006-01-01

Objectives: As part of a project to map the literature of nursing, sponsored by the Nursing and Allied Health Resources Section of the Medical Library Association, this study identifies core journals cited in maternal-child/gynecologic nursing and the indexing services that access the cited journals. Methods: Three source journals were selected and subjected to a citation analysis of articles from 1996 to 1998. Results: Journals were the most frequently cited format (74.1%), followed by books (19.7%), miscellaneous (4.2%), and government documents (1.9%). Bradford's Law of Scattering was applied to the results, ranking cited journal references in descending order. One-third of the citations were found in a core of 14 journal titles; one-third were dispersed among a middle zone of 100 titles; and the remaining third were scattered in a larger zone of 1,194 titles. Indexing coverage for the core titles was most comprehensive in PubMed/MEDLINE, followed by Science Citation Index and CINAHL. Conclusion: The core of journals cited in this nursing specialty revealed a large number of medical titles, thus, the biomedical databases provide the best access. The interdisciplinary nature of maternal-child/ gynecologic nursing topics dictates that social sciences databases are an important adjunct. The study results will assist librarians in collection development, provide end users with guidelines for selecting databases, and influence database producers to consider extending coverage to identified titles. PMID:16710464

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

PubMed Central

Caspi, Ron; Altman, Tomer; Dale, Joseph M.; Dreher, Kate; Fulcher, Carol A.; Gilham, Fred; Kaipa, Pallavi; Karthikeyan, Athikkattuvalasu S.; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Mueller, Lukas A.; Paley, Suzanne; Popescu, Liviu; Pujar, Anuradha; Shearer, Alexander G.; Zhang, Peifen; Karp, Peter D.

2010-01-01

The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs also contain additional features, such as predicted operons, transport systems, and pathway hole-fillers. The BioCyc Web site offers several tools for the analysis of the PGDBs, including Omics Viewers that enable visualization of omics datasets on two different genome-scale diagrams and tools for comparative analysis. The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism. PMID:19850718

The search for reliable aqueous solubility (Sw) and octanol-water partition coefficient (Kow) data for hydrophobic organic compounds; DDT and DDE as a case study

USGS Publications Warehouse

Pontolillo, James; Eganhouse, R.P.

2001-01-01

The accurate determination of an organic contaminant?s physico-chemical properties is essential for predicting its environmental impact and fate. Approximately 700 publications (1944?2001) were reviewed and all known aqueous solubilities (Sw) and octanol-water partition coefficients (Kow) for the organochlorine pesticide, DDT, and its persistent metabolite, DDE were compiled and examined. Two problems are evident with the available database: 1) egregious errors in reporting data and references, and 2) poor data quality and/or inadequate documentation of procedures. The published literature (particularly the collative literature such as compilation articles and handbooks) is characterized by a preponderance of unnecessary data duplication. Numerous data and citation errors are also present in the literature. The percentage of original Sw and Kow data in compilations has decreased with time, and in the most recent publications (1994?97) it composes only 6?26 percent of the reported data. The variability of original DDT/DDE Sw and Kow data spans 2?4 orders of magnitude, and there is little indication that the uncertainty in these properties has declined over the last 5 decades. A criteria-based evaluation of DDT/DDE Sw and Kow data sources shows that 95?100 percent of the database literature is of poor or unevaluatable quality. The accuracy and reliability of the vast majority of the data are unknown due to inadequate documentation of the methods of determination used by the authors. [For example, estimates of precision have been reported for only 20 percent of experimental Sw data and 10 percent of experimental Kow data.] Computational methods for estimating these parameters have been increasingly substituted for direct or indirect experimental determination despite the fact that the data used for model development and validation may be of unknown reliability. Because of the prevalence of errors, the lack of methodological documentation, and unsatisfactory data quality, the reliability of the DDT/ DDE Sw and Kow database is questionable. The nature and extent of the errors documented in this study are probably indicative of a more general problem in the literature of hydrophobic organic compounds. Under these circumstances, estimation of critical environmental parameters on the basis of Sw and Kow (for example, bioconcentration factors, equilibrium partition coefficients) is inadvisable because it will likely lead to incorrect environmental risk assessments. The current state of the database indicates that much greater efforts are needed to: 1) halt the proliferation of erroneous data and references, 2) initiate a coordinated program to develop improved methods of property determination, 3) establish and maintain consistent reporting requirements for physico-chemical property data, and 4) create a mechanism for archiving reliable data for widespread use in the scientific/regulatory community.

Evaluation of unique identifiers used as keys to match identical publications in Pure and SciVal - a case study from health science.

PubMed

Madsen, Heidi Holst; Madsen, Dicte; Gauffriau, Marianne

2016-01-01

Unique identifiers (UID) are seen as an effective key to match identical publications across databases or identify duplicates in a database. The objective of the present study is to investigate how well UIDs work as match keys in the integration between Pure and SciVal, based on a case with publications from the health sciences. We evaluate the matching process based on information about coverage, precision, and characteristics of publications matched versus not matched with UIDs as the match keys. We analyze this information to detect errors, if any, in the matching process. As an example we also briefly discuss how publication sets formed by using UIDs as the match keys may affect the bibliometric indicators number of publications, number of citations, and the average number of citations per publication.  The objective is addressed in a literature review and a case study. The literature review shows that only a few studies evaluate how well UIDs work as a match key. From the literature we identify four error types: Duplicate digital object identifiers (DOI), incorrect DOIs in reference lists and databases, DOIs not registered by the database where a bibliometric analysis is performed, and erroneous optical or special character recognition. The case study explores the use of UIDs in the integration between the databases Pure and SciVal. Specifically journal publications in English are matched between the two databases. We find all error types except erroneous optical or special character recognition in our publication sets. In particular the duplicate DOIs constitute a problem for the calculation of bibliometric indicators as both keeping the duplicates to improve the reliability of citation counts and deleting them to improve the reliability of publication counts will distort the calculation of average number of citations per publication. The use of UIDs as a match key in citation linking is implemented in many settings, and the availability of UIDs may become critical for the inclusion of a publication or a database in a bibliometric analysis.

Evaluation of unique identifiers used as keys to match identical publications in Pure and SciVal – a case study from health science

PubMed Central

Madsen, Heidi Holst; Madsen, Dicte; Gauffriau, Marianne

2016-01-01

Unique identifiers (UID) are seen as an effective key to match identical publications across databases or identify duplicates in a database. The objective of the present study is to investigate how well UIDs work as match keys in the integration between Pure and SciVal, based on a case with publications from the health sciences. We evaluate the matching process based on information about coverage, precision, and characteristics of publications matched versus not matched with UIDs as the match keys. We analyze this information to detect errors, if any, in the matching process. As an example we also briefly discuss how publication sets formed by using UIDs as the match keys may affect the bibliometric indicators number of publications, number of citations, and the average number of citations per publication.  The objective is addressed in a literature review and a case study. The literature review shows that only a few studies evaluate how well UIDs work as a match key. From the literature we identify four error types: Duplicate digital object identifiers (DOI), incorrect DOIs in reference lists and databases, DOIs not registered by the database where a bibliometric analysis is performed, and erroneous optical or special character recognition. The case study explores the use of UIDs in the integration between the databases Pure and SciVal. Specifically journal publications in English are matched between the two databases. We find all error types except erroneous optical or special character recognition in our publication sets. In particular the duplicate DOIs constitute a problem for the calculation of bibliometric indicators as both keeping the duplicates to improve the reliability of citation counts and deleting them to improve the reliability of publication counts will distort the calculation of average number of citations per publication. The use of UIDs as a match key in citation linking is implemented in many settings, and the availability of UIDs may become critical for the inclusion of a publication or a database in a bibliometric analysis. PMID:27635223

[Analysis of on medication rules for Qi-deficiency and blood-stasis syndrome of chronic heart failure based on data mining technology].

PubMed

Wang, Qian; Yao, Geng-Zhen; Pan, Guang-Ming; Huang, Jing-Yi; An, Yi-Pei; Zou, Xu

2017-01-01

To analyze the medication features and the regularity of prescriptions of traditional Chinese medicine in treating patients with Qi-deficiency and blood-stasis syndrome of chronic heart failure based on modern literature. In this article, CNKI Chinese academic journal database, Wanfang Chinese academic journal database and VIP Chinese periodical database were all searched from January 2000 to December 2015 for the relevant literature on traditional Chinese medicine treatment for Qi-deficiency and blood-stasis syndrome of chronic heart failure. Then a normalized database was established for further data mining and analysis. Subsequently, the medication features and the regularity of prescriptions were mined by using traditional Chinese medicine inheritance support system(V2.5), association rules, improved mutual information algorithm, complex system entropy clustering and other mining methods. Finally, a total of 171 articles were included, involving 171 prescriptions, 140 kinds of herbs, with a total frequency of 1 772 for the herbs. As a result, 19 core prescriptions and 7 new prescriptions were mined. The most frequently used herbs included Huangqi(Astragali Radix), Danshen(Salviae Miltiorrhizae Radix et Rhizoma), Fuling(Poria), Renshen(Ginseng Radix et Rhizoma), Tinglizi(Semen Lepidii), Baizhu(Atractylodis Macrocephalae Rhizoma), and Guizhi(Cinnamomum Ramulus). The core prescriptions were composed of Huangqi(Astragali Radix), Danshen(Salviae Miltiorrhizae Radix et Rhizoma) and Fuling(Poria), etc. The high frequent herbs and core prescriptions not only highlight the medication features of Qi-invigorating and blood-circulating therapy, but also reflect the regularity of prescriptions of blood-circulating, Yang-warming, and urination-promoting therapy based on syndrome differentiation. Moreover, the mining of the new prescriptions provide new reference and inspiration for clinical treatment of various accompanying symptoms of chronic heart failure. In conclusion, this article provides new reference for traditional Chinese medicine in the treatment of chronic heart failure. Copyright© by the Chinese Pharmaceutical Association.

Influence of gender in the recognition of basic facial expressions: A critical literature review

PubMed Central

Forni-Santos, Larissa; Osório, Flávia L

2015-01-01

AIM: To conduct a systematic literature review about the influence of gender on the recognition of facial expressions of six basic emotions. METHODS: We made a systematic search with the search terms (face OR facial) AND (processing OR recognition OR perception) AND (emotional OR emotion) AND (gender or sex) in PubMed, PsycINFO, LILACS, and SciELO electronic databases for articles assessing outcomes related to response accuracy and latency and emotional intensity. The articles selection was performed according to parameters set by COCHRANE. The reference lists of the articles found through the database search were checked for additional references of interest. RESULTS: In respect to accuracy, women tend to perform better than men when all emotions are considered as a set. Regarding specific emotions, there seems to be no gender-related differences in the recognition of happiness, whereas results are quite heterogeneous in respect to the remaining emotions, especially sadness, anger, and disgust. Fewer articles dealt with the parameters of response latency and emotional intensity, which hinders the generalization of their findings, especially in the face of their methodological differences. CONCLUSION: The analysis of the studies conducted to date do not allow for definite conclusions concerning the role of the observer’s gender in the recognition of facial emotion, mostly because of the absence of standardized methods of investigation. PMID:26425447

Grappling with the Literature of Education Research and Practice

PubMed Central

2007-01-01

The absence of a central database and use of specialized language hinder nonexperts in becoming familiar with the science teaching and learning literature and using it to inform their work. The challenge of locating articles related to a specific question or problem, coupled with the difficulty of comprehending findings based on a variety of different perspectives and practices, can be prohibitively difficult. As I have transitioned from bench to classroom-based research, I have become familiar with how to locate, decipher, and evaluate the education research literature. In this essay, I point out analogies to the literature of science research and practice, and I reference some of the literature that I have found useful in becoming an education researcher. I also introduce a new regular feature, “Current Insights: Recent Research in Science Teaching and Learning,” which is designed to point CBE—Life Sciences Education (CBE-LSE) readers to current articles of interest in life sciences education, as well as more general and noteworthy publications in education research. PMID:18056300

Grappling with the literature of education research and practice.

PubMed

Dolan, Erin L

2007-01-01

The absence of a central database and use of specialized language hinder nonexperts in becoming familiar with the science teaching and learning literature and using it to inform their work. The challenge of locating articles related to a specific question or problem, coupled with the difficulty of comprehending findings based on a variety of different perspectives and practices, can be prohibitively difficult. As I have transitioned from bench to classroom-based research, I have become familiar with how to locate, decipher, and evaluate the education research literature. In this essay, I point out analogies to the literature of science research and practice, and I reference some of the literature that I have found useful in becoming an education researcher. I also introduce a new regular feature, "Current Insights: Recent Research in Science Teaching and Learning," which is designed to point CBE--Life Sciences Education (CBE-LSE) readers to current articles of interest in life sciences education, as well as more general and noteworthy publications in education research.

Quantified trends in the history of verbal behavior research

PubMed Central

Eshleman, John W.

1991-01-01

The history of scientific research about verbal behavior research, especially that based on Verbal Behavior (Skinner, 1957), can be assessed on the basis of a frequency and celeration analysis of the published and presented literature. In order to discover these quantified trends, a comprehensive bibliographical database was developed. Based on several literature searches, the bibliographic database included papers pertaining to verbal behavior that were published in the Journal of the Experimental Analysis of Behavior, the Journal of Applied Behavior Analysis, Behaviorism, The Behavior Analyst, and The Analysis of Verbal Behavior. A nonbehavioral journal, the Journal of Verbal Learning and Verbal Behavior was assessed as a nonexample comparison. The bibliographic database also included a listing of verbal behavior papers presented at the meetings of the Association for Behavior Analysis. Papers were added to the database if they (a) were about verbal behavior, (b) referenced B.F. Skinner's (1957) book Verbal Behavior, or (c) did both. Because the references indicated the year of publication or presentation, a count per year of them was measured. These yearly frequencies were plotted on Standard Celeration Charts. Once plotted, various celeration trends in the literature became visible, not the least of which was the greater quantity of verbal behavior research than is generally acknowledged. The data clearly show an acceleration of research across the past decade. The data also question the notion that a “paucity” of research based on Verbal Behavior currently exists. Explanations of the acceleration of verbal behavior research are suggested, and plausible reasons are offered as to why a relative lack of verbal behavior research extended through the mid 1960s to the latter 1970s. PMID:22477630

Systematic review of the literature on the effectiveness of product reformulation measures to reduce the sugar content of food and drink on the population's sugar consumption and health: a study protocol

PubMed Central

Hashem, Kawther M; He, Feng J; MacGregor, Graham A

2016-01-01

Introduction Obesity, type 2 diabetes and dental caries are all major public health problems in the UK, with significant costs to the healthcare service. We aim to conduct a systematic review to summarise the evidence on the effectiveness of product reformulation measures to reduce the sugar content of food and drink on the population's sugar consumption and health. Methods and analysis Electronic database will be systematically searched using a combination of terms, tailored to optimise sensitivity, specificity, and the syntax and functionality of each database. The databases searched will include the Cochrane Library, EMBASE, MEDLINE (Ovid) and Scopus. The bibliographies of those papers that match inclusion criteria will be searched by hand to identify any further, relevant references, which will be subject to the same screening and selection process. The database search results will be supplemented by hand searches. In addition to the peer-reviewed literature, a number of grey literature searches will be undertaken using the broad search terms ‘sugar’ and ‘food’ or ‘drink’ and ‘reduction’, these searches will include key government and organisation websites as well as general searches in Google. The selection of the studies, data collection and quality appraisal will be performed independently by 2 reviewers. Data will be initially analysed through a narrative synthesis method. If a subset of data we analyse appears comparable, we will investigate the possibility of performing a meta-analysis. Ethics and dissemination Ethics approval will not be required as this is a protocol for a systematic review. The findings will be disseminated widely through conference presentations and published in a peer-reviewed journal. PROSPERO registration number CRD42016034022. PMID:27288379

The COG database: new developments in phylogenetic classification of proteins from complete genomes

PubMed Central

Tatusov, Roman L.; Natale, Darren A.; Garkavtsev, Igor V.; Tatusova, Tatiana A.; Shankavaram, Uma T.; Rao, Bachoti S.; Kiryutin, Boris; Galperin, Michael Y.; Fedorova, Natalie D.; Koonin, Eugene V.

2001-01-01

The database of Clusters of Orthologous Groups of proteins (COGs), which represents an attempt on a phylogenetic classification of the proteins encoded in complete genomes, currently consists of 2791 COGs including 45 350 proteins from 30 genomes of bacteria, archaea and the yeast Saccharomyces cerevisiae (http://www.ncbi.nlm.nih.gov/COG). In addition, a supplement to the COGs is available, in which proteins encoded in the genomes of two multicellular eukaryotes, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, and shared with bacteria and/or archaea were included. The new features added to the COG database include information pages with structural and functional details on each COG and literature references, improvements of the COGNITOR program that is used to fit new proteins into the COGs, and classification of genomes and COGs constructed by using principal component analysis. PMID:11125040

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baer, M.R.; Hobbs, M.L.; McGee, B.C.

Exponential-13,6 (EXP-13,6) potential pammeters for 750 gases composed of 48 elements were determined and assembled in a database, referred to as the JCZS database, for use with the Jacobs Cowperthwaite Zwisler equation of state (JCZ3-EOS)~l) The EXP- 13,6 force constants were obtained by using literature values of Lennard-Jones (LJ) potential functions, by using corresponding states (CS) theory, by matching pure liquid shock Hugoniot data, and by using molecular volume to determine the approach radii with the well depth estimated from high-pressure isen- tropes. The JCZS database was used to accurately predict detonation velocity, pressure, and temperature for 50 dif- 3more » Accurate predictions were also ferent explosives with initial densities ranging from 0.25 glcm3 to 1.97 g/cm . obtained for pure liquid shock Hugoniots, static properties of nitrogen, and gas detonations at high initial pressures.« less

[Exploration and construction of the full-text database of acupuncture literature in the Republic of China].

PubMed

Fei, Lin; Zhao, Jing; Leng, Jiahao; Zhang, Shujian

2017-10-12

The ALIPORC full-text database is targeted at a specific full-text database of acupuncture literature in the Republic of China. Starting in 2015, till now, the database has been getting completed, focusing on books relevant with acupuncture, articles and advertising documents, accomplished or published in the Republic of China. The construction of this database aims to achieve the source sharing of acupuncture medical literature in the Republic of China through the retrieval approaches to diversity and accurate content presentation, contributes to the exchange of scholars, reduces the paper damage caused by paging and simplify the retrieval of the rare literature. The writers have made the explanation of the database in light of sources, characteristics and current situation of construction; and have discussed on improving the efficiency and integrity of the database and deepening the development of acupuncture literature in the Republic of China.

Literature information in PubChem: associations between PubChem records and scientific articles.

PubMed

Kim, Sunghwan; Thiessen, Paul A; Cheng, Tiejun; Yu, Bo; Shoemaker, Benjamin A; Wang, Jiyao; Bolton, Evan E; Wang, Yanli; Bryant, Stephen H

2016-01-01

PubChem is an open archive consisting of a set of three primary public databases (BioAssay, Compound, and Substance). It contains information on a broad range of chemical entities, including small molecules, lipids, carbohydrates, and (chemically modified) amino acid and nucleic acid sequences (including siRNA and miRNA). Currently (as of Nov. 2015), PubChem contains more than 150 million depositor-provided chemical substance descriptions, 60 million unique chemical structures, and 225 million biological activity test results provided from over 1 million biological assay records. Many PubChem records (substances, compounds, and assays) include depositor-provided cross-references to scientific articles in PubMed. Some PubChem contributors provide bioactivity data extracted from scientific articles. Literature-derived bioactivity data complement high-throughput screening (HTS) data from the concluded NIH Molecular Libraries Program and other HTS projects. Some journals provide PubChem with information on chemicals that appear in their newly published articles, enabling concurrent publication of scientific articles in journals and associated data in public databases. In addition, PubChem links records to PubMed articles indexed with the Medical Subject Heading (MeSH) controlled vocabulary thesaurus. Literature information, both provided by depositors and derived from MeSH annotations, can be accessed using PubChem's web interfaces, enabling users to explore information available in literature related to PubChem records beyond typical web search results. Graphical abstractLiterature information for PubChem records is derived from various sources.

What do we know about sibling attended birth? An integrative literature review.

PubMed

Naber, Nora L; Miller, Suzanne; Baddock, Sally A

2018-05-08

to consolidate existing research in the field of sibling attended birth (SAB) into a body of knowledge to inform decision-making processes and guide midwifery practice throughout the sibling attended birth experience. An integrative literature review. CINAHL Complete, Cochrane Library, PubMed, Index New Zealand, Australia/New Zealand Reference Centre, grey literature databases REVIEW METHODS: An extensive search of five electronic databases as well as 17 grey literature databases was conducted. Abstracts of 2340 papers and full texts of 39 papers were scrutinised for inclusion criteria leading to 22 studies being included in this review. The Crowe Critical Appraisal Tool was used to facilitate a systematic quality appraisal process. This review included 22 studies (13 qualitative, 4 quantitative and 5 mixed methods). Studies were analysed using a narrative synthesis approach. Publications mainly focussed on families' motivations for choosing SAB, the preparation for the event, and the impact of SAB on children's behaviour and the infant/sibling relationship. This review identified that children experienced birth as a positive, exciting and important life event and parents viewed their SAB experiences as overwhelmingly positive and reported a heightened sense of family unity. Included studies did not address the long term effects of sibling attended birth, however, in the short-term, children did not show signs of trauma or severe distress, though differing levels of transient fear and anxiety were described. Families could benefit from receiving evidence based information to enable an informed decision regarding their children's involvement during pregnancy, birth and the immediate postpartum. Information shared by the midwife could focus on how families can achieve an optimal SAB experience for all family members. Copyright © 2018 Elsevier Ltd. All rights reserved.

Fish Karyome: A karyological information network database of Indian Fishes.

PubMed

Nagpure, Naresh Sahebrao; Pathak, Ajey Kumar; Pati, Rameshwar; Singh, Shri Prakash; Singh, Mahender; Sarkar, Uttam Kumar; Kushwaha, Basdeo; Kumar, Ravindra

2012-01-01

'Fish Karyome', a database on karyological information of Indian fishes have been developed that serves as central source for karyotype data about Indian fishes compiled from the published literature. Fish Karyome has been intended to serve as a liaison tool for the researchers and contains karyological information about 171 out of 2438 finfish species reported in India and is publically available via World Wide Web. The database provides information on chromosome number, morphology, sex chromosomes, karyotype formula and cytogenetic markers etc. Additionally, it also provides the phenotypic information that includes species name, its classification, and locality of sample collection, common name, local name, sex, geographical distribution, and IUCN Red list status. Besides, fish and karyotype images, references for 171 finfish species have been included in the database. Fish Karyome has been developed using SQL Server 2008, a relational database management system, Microsoft's ASP.NET-2008 and Macromedia's FLASH Technology under Windows 7 operating environment. The system also enables users to input new information and images into the database, search and view the information and images of interest using various search options. Fish Karyome has wide range of applications in species characterization and identification, sex determination, chromosomal mapping, karyo-evolution and systematics of fishes.

Public Health Policies and Practices of the Ottoman Empire with Special Reference to the Gallipoli Campaign.

PubMed

Aboul-Enein, Basil; Puddy, William

2015-06-01

To review the selected historiographic and contemporary literature that examined the Ottoman public health practices and policies with special reference to the Gallipoli campaign during the First World War. To date, no work has been published surrounding the Ottoman public health policies and responses during the battle of Gallipoli. A historiographic methodology was used to examine relevant primary and secondary publications using ten academic electronic databases. The literature discussed pre-war Hapsburg efforts to improve the Ottoman medical infrastructure, the activities of military medical students and units at Gallipoli, quarantine and vaccination procedures, and general medical issues throughout the empire during the war. Access to the official Turkish archives and translating relevant official documents into English are warranted. This represents an opportunity for military and public health historians to examine and identify relevant public health practices and policies that the Ottoman Empire implemented during the First World War and, in particular, the Gallipoli campaign.

Combined semantic and similarity search in medical image databases

NASA Astrophysics Data System (ADS)

Seifert, Sascha; Thoma, Marisa; Stegmaier, Florian; Hammon, Matthias; Kramer, Martin; Huber, Martin; Kriegel, Hans-Peter; Cavallaro, Alexander; Comaniciu, Dorin

2011-03-01

The current diagnostic process at hospitals is mainly based on reviewing and comparing images coming from multiple time points and modalities in order to monitor disease progression over a period of time. However, for ambiguous cases the radiologist deeply relies on reference literature or second opinion. Although there is a vast amount of acquired images stored in PACS systems which could be reused for decision support, these data sets suffer from weak search capabilities. Thus, we present a search methodology which enables the physician to fulfill intelligent search scenarios on medical image databases combining ontology-based semantic and appearance-based similarity search. It enabled the elimination of 12% of the top ten hits which would arise without taking the semantic context into account.

A Systematic Literature Review of Studies Analyzing Inequalities in Health Expectancy among the Older Population

PubMed Central

Pongiglione, Benedetta; De Stavola, Bianca L.; Ploubidis, George B.

2015-01-01

Aim To collect, organize and appraise evidence of socioeconomic and demographic inequalities in health and mortality among the older population using a summary measure of population health: Health Expectancy. Methods A systematic literature review was conducted. Literature published in English before November 2014 was searched via two possible sources: three electronic databases (Web of Science, Medline and Embase), and references in selected articles. The search was developed combining terms referring to outcome, exposure and participants, consisting in health expectancy, socioeconomic and demographic groups, and older population, respectively. Results Of 256 references identified, 90 met the inclusion criteria. Six references were added after searching reference lists of included articles. Thirty-three studies were focused only on gender-based inequalities; the remaining sixty-three considered gender along with other exposures. Findings were organized according to two leading perspectives: the type of inequalities considered and the health indicators chosen to measure health expectancy. Evidence of gender-based differentials and a socioeconomic gradient were found in all studies. A remarkable heterogeneity in the choice of health indicators used to compute health expectancy emerged as well as a non-uniform way of defining same health conditions. Conclusions Health expectancy is a useful and convenient measure to monitor and assess the quality of ageing and compare different groups and populations. This review showed a general agreement of results obtained in different studies with regard to the existence of inequalities associated with several factors, such as gender, education, behaviors, and race. However, the lack of a standardized definition of health expectancy limits its comparability across studies. The need of conceiving health expectancy as a comparable and repeatable measure was highlighted as fundamental to make it an informative instrument for policy makers. PMID:26115099

Mapping the literature of pediatric nursing: update and implications for library services

PubMed Central

Watwood, Carol L.

2016-01-01

Objective The purpose of this study was to identify core journals and other types of literature cited in four major pediatric nursing journals and to characterize coverage of these resources in major bibliographic databases. The study was part of the “Mapping the Literature of Nursing Project” of the Medical Library Association's Nursing and Allied Health Resource Section. It updates a similar analysis published in 2006 and determines whether citation patterns have changed over time. Methods Cited references from articles published in 4 pediatric nursing journals between 2011 and 2013 were collected. Cited journal titles were ranked according to number of times cited and analyzed according to Bradford's Law of Scattering and the 80/20 rule to identify the most frequently cited journals. Five databases were surveyed to assess the coverage of the most-often-cited journals. The most frequently cited non-journal sources were also identified. Results Journals were the most frequently cited sources, followed by books, government documents, Internet resources, and miscellaneous resources. Most cited sources were cited within ten years of their publication, which was particularly true for government documents and Internet resources. Scopus had complete coverage of the most frequently cited journals, whereas PubMed had nearly complete coverage. Conclusions Compared with the 2006 study, the list of top-cited journals referenced by pediatric nursing researchers has remained relatively stable, but the number of cited journal titles has increased. Book citations have declined, and Internet and government document references have increased. These findings suggest that librarians should retain subscriptions to frequently cited journal titles, provide efficient document delivery of articles from infrequently used journals, de-emphasize but not eliminate books, and connect patrons with useful open-access Internet resources. PMID:27822148

Mapping the literature of pediatric nursing: update and implications for library services.

PubMed

Watwood, Carol L

2016-10-01

The purpose of this study was to identify core journals and other types of literature cited in four major pediatric nursing journals and to characterize coverage of these resources in major bibliographic databases. The study was part of the "Mapping the Literature of Nursing Project" of the Medical Library Association's Nursing and Allied Health Resource Section. It updates a similar analysis published in 2006 and determines whether citation patterns have changed over time. Cited references from articles published in 4 pediatric nursing journals between 2011 and 2013 were collected. Cited journal titles were ranked according to number of times cited and analyzed according to Bradford's Law of Scattering and the 80/20 rule to identify the most frequently cited journals. Five databases were surveyed to assess the coverage of the most-often-cited journals. The most frequently cited non-journal sources were also identified. Journals were the most frequently cited sources, followed by books, government documents, Internet resources, and miscellaneous resources. Most cited sources were cited within ten years of their publication, which was particularly true for government documents and Internet resources. Scopus had complete coverage of the most frequently cited journals, whereas PubMed had nearly complete coverage. Compared with the 2006 study, the list of top-cited journals referenced by pediatric nursing researchers has remained relatively stable, but the number of cited journal titles has increased. Book citations have declined, and Internet and government document references have increased. These findings suggest that librarians should retain subscriptions to frequently cited journal titles, provide efficient document delivery of articles from infrequently used journals, de-emphasize but not eliminate books, and connect patrons with useful open-access Internet resources.

Frequent attenders in general practice care: a literature review with special reference to methodological considerations.

PubMed

Vedsted, P; Christensen, M B

2005-02-01

To describe the basis on which our knowledge of frequent attendance in general practice rests and to propose recommendations for further research on frequent attenders (FAs). The literature review (finished February 2004) encompassed peer-reviewed articles in English describing contacts with general practice in terms of frequency. Searches were performed in the Medline, CINAHL, EMBASE, PsycINFO, Social Sciences Expanded Index and ISI Citation databases with additional searches in reference lists and the 'related articles' function in the ISI Citation database and Medline. General practice. Sixty-one articles (54 studies). The articles were assessed according to the following design variables: setting; definition of FAs; sampling; sample size; control groups; study aim; study design; data sources; effect measure; and main results. There was no generally accepted definition of frequent attendance. Research designs differed substantially. Eight articles gave sufficient information on all design variables. The top 10% of attenders accounted for 30-50% of all contacts, and up to 40% of FAs were still FAs the following year. More than 50% of FAs had a physical disease, more than 50% of FAs suffered from psychological distress, social factors (low social support, unemployment, divorce) were associated with frequent attendance in more than 50% of FAs, multiproblems (physical, psychological and social) were found in one-third of FAs, and frequent attendance was associated with increasing age and female gender. The diversity of designs, definitions and methods in the current literature on FAs in general practice hampers comparison of their precision, validity and generalizability, and calls for cautious interpretation and adoption of a common, generally acceptable definition in future studies.

A User-Friendly, Keyword-Searchable Database of Geoscientific References Through 2007 for Afghanistan

USGS Publications Warehouse

Eppinger, Robert G.; Sipeki, Julianna; Scofield, M.L. Sco

2008-01-01

This report includes a document and accompanying Microsoft Access 2003 database of geoscientific references for the country of Afghanistan. The reference compilation is part of a larger joint study of Afghanistan?s energy, mineral, and water resources, and geologic hazards currently underway by the U.S. Geological Survey, the British Geological Survey, and the Afghanistan Geological Survey. The database includes both published (n = 2,489) and unpublished (n = 176) references compiled through calendar year 2007. The references comprise two separate tables in the Access database. The reference database includes a user-friendly, keyword-searchable interface and only minimum knowledge of the use of Microsoft Access is required.

Addressing unwarranted clinical variation: A rapid review of current evidence.

PubMed

Harrison, Reema; Manias, Elizabeth; Mears, Stephen; Heslop, David; Hinchcliff, Reece; Hay, Liz

2018-05-15

Unwarranted clinical variation (UCV) can be described as variation that can only be explained by differences in health system performance. There is a lack of clarity regarding how to define and identify UCV and, once identified, to determine whether it is sufficiently problematic to warrant action. As such, the implementation of systemic approaches to reducing UCV is challenging. A review of approaches to understand, identify, and address UCV was undertaken to determine how conceptual and theoretical frameworks currently attempt to define UCV, the approaches used to identify UCV, and the evidence of their effectiveness. Rapid evidence assessment (REA) methodology was used. A range of text words, synonyms, and subject headings were developed for the major concepts of unwarranted clinical variation, standards (and deviation from these standards), and health care environment. Two electronic databases (Medline and Pubmed) were searched from January 2006 to April 2017, in addition to hand searching of relevant journals, reference lists, and grey literature. Results were merged using reference-management software (Endnote) and duplicates removed. Inclusion criteria were independently applied to potentially relevant articles by 3 reviewers. Findings were presented in a narrative synthesis to highlight key concepts addressed in the published literature. A total of 48 relevant publications were included in the review; 21 articles were identified as eligible from the database search, 4 from hand searching published work and 23 from the grey literature. The search process highlighted the voluminous literature reporting clinical variation internationally; yet, there is a dearth of evidence regarding systematic approaches to identifying or addressing UCV. Wennberg's classification framework is commonly cited in relation to classifying variation, but no single approach is agreed upon to systematically explore and address UCV. The instances of UCV that warrant investigation and action are largely determined at a systems level currently, and stakeholder engagement in this process is limited. Lack of consensus on an evidence-based definition for UCV remains a substantial barrier to progress in this field. © 2018 John Wiley & Sons, Ltd.

"On-screen" writing and composing: two years experience with Manuscript Manager, Apple II and IBM-PC versions.

PubMed

Offerhaus, L

1989-06-01

The problems of the direct composition of a biomedical manuscript on a personal computer are discussed. Most word processing software is unsuitable because literature references, once stored, cannot be rearranged if major changes are necessary. These obstacles have been overcome in Manuscript Manager, a combination of word processing and database software. As it follows Council of Biology Editors and Vancouver rules, the printouts should be technically acceptable to most leading biomedical journals.

Loneliness: a concept analysis.

PubMed

Bekhet, Abir K; Zauszniewski, Jaclene A; Nakhla, Wagdy E

2008-01-01

Loneliness is a universal human experience recognized since the dawn of time, yet it is unique for every individual. Loneliness can lead to both depression and low self-esteem. This article explicates the concept of loneliness through the examination of its conceptual definition and uses, defining attributes, related concepts, and empirical referents. Literature review using hand search and database were used as sources of information. Because loneliness is commonly encountered in nursing situations, the information provided will serve as a framework for assessment, planning, intervention, and evaluation of clients.

Adapting the ISO 20462 softcopy ruler method for online image quality studies

NASA Astrophysics Data System (ADS)

Burns, Peter D.; Phillips, Jonathan B.; Williams, Don

2013-01-01

In this paper we address the problem of Image Quality Assessment of no reference metrics, focusing on JPEG corrupted images. In general no reference metrics are not able to measure with the same performance the distortions within their possible range and with respect to different image contents. The crosstalk between content and distortion signals influences the human perception. We here propose two strategies to improve the correlation between subjective and objective quality data. The first strategy is based on grouping the images according to their spatial complexity. The second one is based on a frequency analysis. Both the strategies are tested on two databases available in the literature. The results show an improvement in the correlations between no reference metrics and psycho-visual data, evaluated in terms of the Pearson Correlation Coefficient.

The economic impact of Clostridium difficile infection: a systematic review.

PubMed

Nanwa, Natasha; Kendzerska, Tetyana; Krahn, Murray; Kwong, Jeffrey C; Daneman, Nick; Witteman, William; Mittmann, Nicole; Cadarette, Suzanne M; Rosella, Laura; Sander, Beate

2015-04-01

With Clostridium difficile infection (CDI) on the rise, knowledge of the current economic burden of CDI can inform decisions on interventions related to CDI. We systematically reviewed CDI cost-of-illness (COI) studies. We performed literature searches in six databases: MEDLINE, Embase, the Health Technology Assessment Database, the National Health Service Economic Evaluation Database, the Cost-Effectiveness Analysis Registry, and EconLit. We also searched gray literature and conducted reference list searches. Two reviewers screened articles independently. One reviewer abstracted data and assessed quality using a modified guideline for economic evaluations. The second reviewer validated the abstraction and assessment. We identified 45 COI studies between 1988 and June 2014. Most (84%) of the studies were from the United States, calculating costs of hospital stays (87%), and focusing on direct costs (100%). Attributable mean CDI costs ranged from $8,911 to $30,049 for hospitalized patients. Few studies stated resource quantification methods (0%), an epidemiological approach (0%), or a justified study perspective (16%) in their cost analyses. In addition, few studies conducted sensitivity analyses (7%). Forty-five COI studies quantified and confirmed the economic impact of CDI. Costing methods across studies were heterogeneous. Future studies should follow standard COI methodology, expand study perspectives (e.g., patient), and explore populations least studied (e.g., community-acquired CDI).

The emergence and evolution of school psychology literature: A scientometric analysis from 1907 through 2014.

PubMed

Liu, Shuyan; Oakland, Thomas

2016-03-01

The objective of this current study is to identify the growth and development of scholarly literature that specifically references the term 'school psychology' in the Science Citation Index from 1907 through 2014. Documents from Web of Science were accessed and analyzed through the use of scientometric analyses, including HistCite and Pajek software, resulting in the identification of 4,806 scholars who contributed 3,260 articles in 311 journals. Whereas the database included journals from around the world, most articles were published by authors in the United States and in 20 journals, including the Journal of School Psychology, Psychology in the Schools, School Psychology Review, School Psychology International, and School Psychology Quarterly. Analyses of the database from the past century revealed that 20 of the most prolific scholars contributed 14% of all articles. Contributions from faculty and students at University of Minnesota-Twin Cities, University of Nebraska-Lincoln, University of South Carolina, University of Wisconsin-Madison, and University of Texas-Austin represented 10% of all articles including the term school psychology in the Science Citation Index. Relationships among some of the most highly cited articles are also described. Collectively, the series of analyses reported herein contribute to our understanding of scholarship in school psychology. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Assessment of the periodontal health status in patients undergoing orthodontic treatment with fixed appliances and Invisalign system: A meta-analysis.

PubMed

Lu, Haili; Tang, Haifang; Zhou, Tian; Kang, Na

2018-03-01

At present, many scholars have studied the periodontal health status of patients undergoing orthodontic treatment with fixed appliances and invisalign. However, those results are inconsistent. Therefore, we conducted this meta-analysis, and then provide reference for clinical treatment. Most databases, such as the Cochrane Library, EMBASE, PubMed, Medline, Chinese Biomedical Literature Database, CNKI, and Wan Fang Data were retrieved for related articles from the establishment of the database to October 2017. Meanwhile, we also searched the references of the related literatures manually, in order to increase the included literatures. Two researchers screened the related literatures according to the inclusion criteria and exclusion criteria. Stata 12.0 software was used for data analysis, and results are estimated by odds ratio (OR) and 95% confidence interval (CI). Finally, 7 articles, including 368 patients, were included into our meta-analysis. Meta-analysis results showed that there was no statistically significant difference of gingival index (GI) and sulcus probing depth (SPD) status between the invisalign group and the control group, including at 1, 3, and 6 months (all P > .05). When compared with the control group, the invisalign group presented a lower plaque index (PLI) and sulcus bleeding index (SBI) status at 1 month (OR = -0.53, 95% CI: -0.89 to -0.18; OR = -0.44, 95% CI: -0.70 to -0.19, respectively), 3 months (OR = -0.69, 95% CI: -1.12 to -0.27; OR = -0.49, 95% CI: -0.93 to -0.05, respectively), and 6 months (OR = -0.91, 95% CI: -1.47 to -0.35; OR = -0.40, 95% CI: -0.63 to -0.07, respectively). Subgroup analysis showed that the SPD status was lower in the invisalign group at 6 months when measured the teeth using Ramfjord index (OR = -0.74, 95% CI: -1.35 to -0.12). However, there was no statistically significant difference between the 2 groups when using other measure methods (OR = 0.12, 95% CI: -0.26 to 0.17). Our meta-analysis suggests that comparing with the traditional fixed appliances, patients treated with invisalign have a better periodontal health. However, more studies are needed to confirm this conclusion in the future.

How to construct and implement script concordance tests: insights from a systematic review.

PubMed

Dory, Valérie; Gagnon, Robert; Vanpee, Dominique; Charlin, Bernard

2012-06-01

Programmes of assessment should measure the various components of clinical competence. Clinical reasoning has been traditionally assessed using written tests and performance-based tests. The script concordance test (SCT) was developed to assess clinical data interpretation skills. A recent review of the literature examined the validity argument concerning the SCT. Our aim was to provide potential users with evidence-based recommendations on how to construct and implement an SCT. A systematic review of relevant databases (MEDLINE, ERIC [Education Resources Information Centre], PsycINFO, the Research and Development Resource Base [RDRB, University of Toronto]) and Google Scholar, medical education journals and conference proceedings was conducted for references in English or French. It was supplemented by ancestry searching and by additional references provided by experts. The search yielded 848 references, of which 80 were analysed. Studies suggest that tests with around 100 items (25-30 cases), of which 25% are discarded after item analysis, should provide reliable scores. Panels with 10-20 members are needed to reach adequate precision in terms of estimated reliability. Panellists' responses can be analysed by checking for moderate variability among responses. Studies of alternative scoring methods are inconclusive, but the traditional scoring method is satisfactory. There is little evidence on how best to determine a pass/fail threshold for high-stakes examinations. Our literature search was broad and included references from medical education journals not indexed in the usual databases, conference abstracts and dissertations. There is good evidence on how to construct and implement an SCT for formative purposes or medium-stakes course evaluations. Further avenues for research include examining the impact of various aspects of SCT construction and implementation on issues such as educational impact, correlations with other assessments, and validity of pass/fail decisions, particularly for high-stakes examinations. © Blackwell Publishing Ltd 2012.

Standards for Clinical Grade Genomic Databases.

PubMed

Yohe, Sophia L; Carter, Alexis B; Pfeifer, John D; Crawford, James M; Cushman-Vokoun, Allison; Caughron, Samuel; Leonard, Debra G B

2015-11-01

Next-generation sequencing performed in a clinical environment must meet clinical standards, which requires reproducibility of all aspects of the testing. Clinical-grade genomic databases (CGGDs) are required to classify a variant and to assist in the professional interpretation of clinical next-generation sequencing. Applying quality laboratory standards to the reference databases used for sequence-variant interpretation presents a new challenge for validation and curation. To define CGGD and the categories of information contained in CGGDs and to frame recommendations for the structure and use of these databases in clinical patient care. Members of the College of American Pathologists Personalized Health Care Committee reviewed the literature and existing state of genomic databases and developed a framework for guiding CGGD development in the future. Clinical-grade genomic databases may provide different types of information. This work group defined 3 layers of information in CGGDs: clinical genomic variant repositories, genomic medical data repositories, and genomic medicine evidence databases. The layers are differentiated by the types of genomic and medical information contained and the utility in assisting with clinical interpretation of genomic variants. Clinical-grade genomic databases must meet specific standards regarding submission, curation, and retrieval of data, as well as the maintenance of privacy and security. These organizing principles for CGGDs should serve as a foundation for future development of specific standards that support the use of such databases for patient care.

What is lost when searching only one literature database for articles relevant to injury prevention and safety promotion?

PubMed

Lawrence, D W

2008-12-01

To assess what is lost if only one literature database is searched for articles relevant to injury prevention and safety promotion (IPSP) topics. Serial textword (keyword, free-text) searches using multiple synonym terms for five key IPSP topics (bicycle-related brain injuries, ethanol-impaired driving, house fires, road rage, and suicidal behaviors among adolescents) were conducted in four of the bibliographic databases that are most used by IPSP professionals: EMBASE, MEDLINE, PsycINFO, and Web of Science. Through a systematic procedure, an inventory of articles on each topic in each database was conducted to identify the total unduplicated count of all articles on each topic, the number of articles unique to each database, and the articles available if only one database is searched. No single database included all of the relevant articles on any topic, and the database with the broadest coverage differed by topic. A search of only one literature database will return 16.7-81.5% (median 43.4%) of the available articles on any of five key IPSP topics. Each database contributed unique articles to the total bibliography for each topic. A literature search performed in only one database will, on average, lead to a loss of more than half of the available literature on a topic.

Reference point detection for camera-based fingerprint image based on wavelet transformation.

PubMed

Khalil, Mohammed S

2015-04-30

Fingerprint recognition systems essentially require core-point detection prior to fingerprint matching. The core-point is used as a reference point to align the fingerprint with a template database. When processing a larger fingerprint database, it is necessary to consider the core-point during feature extraction. Numerous core-point detection methods are available and have been reported in the literature. However, these methods are generally applied to scanner-based images. Hence, this paper attempts to explore the feasibility of applying a core-point detection method to a fingerprint image obtained using a camera phone. The proposed method utilizes a discrete wavelet transform to extract the ridge information from a color image. The performance of proposed method is evaluated in terms of accuracy and consistency. These two indicators are calculated automatically by comparing the method's output with the defined core points. The proposed method is tested on two data sets, controlled and uncontrolled environment, collected from 13 different subjects. In the controlled environment, the proposed method achieved a detection rate 82.98%. In uncontrolled environment, the proposed method yield a detection rate of 78.21%. The proposed method yields promising results in a collected-image database. Moreover, the proposed method outperformed compare to existing method.

NCBI Bookshelf: books and documents in life sciences and health care

PubMed Central

Hoeppner, Marilu A.

2013-01-01

Bookshelf (http://www.ncbi.nlm.nih.gov/books/) is a full-text electronic literature resource of books and documents in life sciences and health care at the National Center for Biotechnology Information (NCBI). Created in 1999 with a single book as an encyclopedic reference for resources such as PubMed and GenBank, it has grown to its current size of >1300 titles. Unlike other NCBI databases, such as GenBank and Gene, which have a strict data structure, books come in all forms; they are diverse in publication types, formats, sizes and authoring models. The Bookshelf data format is XML tagged in the NCBI Book DTD (Document Type Definition), modeled after the National Library of Medicine journal article DTDs. The book DTD has been used for systematically tagging the diverse data formats of books, a move that has set the foundation for the growth of this resource. Books at NCBI followed the route of journal articles in the PubMed Central project, using the PubMed Central architectural framework, workflows and processes. Through integration with other NCBI molecular databases, books at NCBI can be used to provide reference information for biological data and facilitate its discovery. This article describes Bookshelf at NCBI: its growth, data handling and retrieval and integration with molecular databases. PMID:23203889

NCBI Bookshelf: books and documents in life sciences and health care.

PubMed

Hoeppner, Marilu A

2013-01-01

Bookshelf (http://www.ncbi.nlm.nih.gov/books/) is a full-text electronic literature resource of books and documents in life sciences and health care at the National Center for Biotechnology Information (NCBI). Created in 1999 with a single book as an encyclopedic reference for resources such as PubMed and GenBank, it has grown to its current size of >1300 titles. Unlike other NCBI databases, such as GenBank and Gene, which have a strict data structure, books come in all forms; they are diverse in publication types, formats, sizes and authoring models. The Bookshelf data format is XML tagged in the NCBI Book DTD (Document Type Definition), modeled after the National Library of Medicine journal article DTDs. The book DTD has been used for systematically tagging the diverse data formats of books, a move that has set the foundation for the growth of this resource. Books at NCBI followed the route of journal articles in the PubMed Central project, using the PubMed Central architectural framework, workflows and processes. Through integration with other NCBI molecular databases, books at NCBI can be used to provide reference information for biological data and facilitate its discovery. This article describes Bookshelf at NCBI: its growth, data handling and retrieval and integration with molecular databases.

The Era of the Large Databases: Outcomes After Gastroesophageal Surgery According to NSQIP, NIS, and NCDB Databases. Systematic Literature Review.

PubMed

Batista Rodríguez, Gabriela; Balla, Andrea; Fernández-Ananín, Sonia; Balagué, Carmen; Targarona, Eduard M

2018-05-01

The term big data refers to databases that include large amounts of information used in various areas of knowledge. Currently, there are large databases that allow the evaluation of postoperative evolution, such as the American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP), the Healthcare Cost and Utilization Project (HCUP) National Inpatient Sample (NIS), and the National Cancer Database (NCDB). The aim of this review was to evaluate the clinical impact of information obtained from these registries regarding gastroesophageal surgery. A systematic review using the Meta-analysis of Observational Studies in Epidemiology guidelines was performed. The research was carried out using the PubMed database identifying 251 articles. All outcomes related to gastroesophageal surgery were analyzed. A total of 34 articles published between January 2007 and July 2017 were included, for a total of 345 697 patients. Studies were analyzed and divided according to the type of surgery and main theme in (1) esophageal surgery and (2) gastric surgery. The information provided by these databases is an effective way to obtain levels of evidence not obtainable by conventional methods. Furthermore, this information is useful for the external validation of previous studies, to establish benchmarks that allow comparisons between centers and have a positive impact on the quality of care.

Chapter 4 - The LANDFIRE Prototype Project reference database

Treesearch

John F. Caratti

2006-01-01

This chapter describes the data compilation process for the Landscape Fire and Resource Management Planning Tools Prototype Project (LANDFIRE Prototype Project) reference database (LFRDB) and explains the reference data applications for LANDFIRE Prototype maps and models. The reference database formed the foundation for all LANDFIRE tasks. All products generated by the...

A question-answer pair (QAP) database integrated with websites to answer complex questions submitted to the Regional Medicines Information and Pharmacovigilance Centres in Norway (RELIS): a descriptive study.

PubMed

Schjøtt, Jan; Reppe, Linda A; Roland, Pål-Didrik H; Westergren, Tone

2012-01-01

To assess a question-answer pair (QAP) database integrated with websites developed for drug information centres to answer complex questions effectively. Descriptive study with comparison of two subsequent 6-year periods (1995-2000 and 2001-2006). The Regional Medicines Information and Pharmacovigilance Centres in Norway (RELIS). A randomised sample of QAPs from the RELIS database. Answer time in days compared with Mann-Whitney U test. Number of drugs involved (one, two, three or more), complexity (judgemental and/or patient-related or not) and literature search (none, simple or advanced) compared with χ(2) tests. 842 QAPs (312 from 1995 to 2000 and 530 from 2001 to 2006) were compared. The fraction of judgemental and patient-related questions increased (66%-75% and 54%-72%, respectively, p<0.01). Number of drugs and literature search (>50% advanced) was similar in the two periods, but the fraction of answers referring to the RELIS database increased (13%-31%, p<0.01). Median answer time was reduced from 2 days to 1 (p<0.01), although the fraction of complex questions increased from the first to the second period. Furthermore, the mean number of questions per employee per year increased from 66 to 89 from the first to the second period. The authors conclude that RELIS has a potential to efficiently answer complex questions. The model is of relevance for organisation of drug information centres.

Normative Databases for Imaging Instrumentation.

PubMed

Realini, Tony; Zangwill, Linda M; Flanagan, John G; Garway-Heath, David; Patella, Vincent M; Johnson, Chris A; Artes, Paul H; Gaddie, Ian B; Fingeret, Murray

2015-08-01

To describe the process by which imaging devices undergo reference database development and regulatory clearance. The limitations and potential improvements of reference (normative) data sets for ophthalmic imaging devices will be discussed. A symposium was held in July 2013 in which a series of speakers discussed issues related to the development of reference databases for imaging devices. Automated imaging has become widely accepted and used in glaucoma management. The ability of such instruments to discriminate healthy from glaucomatous optic nerves, and to detect glaucomatous progression over time is limited by the quality of reference databases associated with the available commercial devices. In the absence of standardized rules governing the development of reference databases, each manufacturer's database differs in size, eligibility criteria, and ethnic make-up, among other key features. The process for development of imaging reference databases may be improved by standardizing eligibility requirements and data collection protocols. Such standardization may also improve the degree to which results may be compared between commercial instruments.

Normative Databases for Imaging Instrumentation

PubMed Central

Realini, Tony; Zangwill, Linda; Flanagan, John; Garway-Heath, David; Patella, Vincent Michael; Johnson, Chris; Artes, Paul; Ben Gaddie, I.; Fingeret, Murray

2015-01-01

Purpose To describe the process by which imaging devices undergo reference database development and regulatory clearance. The limitations and potential improvements of reference (normative) data sets for ophthalmic imaging devices will be discussed. Methods A symposium was held in July 2013 in which a series of speakers discussed issues related to the development of reference databases for imaging devices. Results Automated imaging has become widely accepted and used in glaucoma management. The ability of such instruments to discriminate healthy from glaucomatous optic nerves, and to detect glaucomatous progression over time is limited by the quality of reference databases associated with the available commercial devices. In the absence of standardized rules governing the development of reference databases, each manufacturer’s database differs in size, eligibility criteria, and ethnic make-up, among other key features. Conclusions The process for development of imaging reference databases may be improved by standardizing eligibility requirements and data collection protocols. Such standardization may also improve the degree to which results may be compared between commercial instruments. PMID:25265003

The impact of mHealth interventions on health systems: a systematic review protocol.

PubMed

Fortuin, Jill; Salie, Faatiema; Abdullahi, Leila H; Douglas, Tania S

2016-11-25

Mobile health (mHealth) has been described as a health enabling tool that impacts positively on the health system in terms of improved access, quality and cost of health care. The proposed systematic review will examine the impact of mHealth on health systems by assessing access, quality and cost of health care as indicators. The systematic review will include literature from various sources including published and unpublished/grey literature. The databases to be searched include: PubMed, Cochrane Library, Google Scholar, NHS Health Technology Assessment Database and Web of Science. The reference lists of studies will be screened and conference proceedings searched for additional eligible reports. Literature to be included will have mHealth as the primary intervention. Two authors will independently screen the search output, select studies and extract data; discrepancies will be resolved by consensus and discussion with the assistance of the third author. The systematic review will inform policy makers, investors, health professionals, technologists and engineers about the impact of mHealth in strengthening the health system. In particular, it will focus on three metrics to determine whether mHealth strengthens the health system, namely quality of, access to and cost of health care services. Systematic review registration: PROSPERO CRD42015026070.

Mapping the literature of nurse practitioners.

PubMed

Shams, Marie-Lise Antoun

2006-04-01

This study was designed to identify core journals for the nurse practitioner specialty and to determine the extent of their indexing in bibliographic databases. As part of a larger project for mapping the literature of nursing, this study followed a common methodology based on citation analysis. Four journals designated by nurse practitioners as sources for their practice information were selected. All cited references were analyzed to determine format types and publication years. Bradford's Law of Scattering was applied to identify core journals. Nine bibliographic databases were searched to estimate the index coverage of the core titles. The findings indicate that nurse practitioners rely primarily on journals (72.0%) followed by books (20.4%) for their professional knowledge. The majority of the identified core journals belong to non-nursing disciplines. This is reflected in the indexing coverage results: PubMed/MEDLINE more comprehensively indexes the core titles than CINAHL does. Nurse practitioners, as primary care providers, consult medical as well as nursing sources for their information. The implications of the citation analysis findings are significant for collection development librarians and indexing services.

New Features in the ADS Abstract Service

NASA Astrophysics Data System (ADS)

Eichhorn, G.; Accomazzi, A.; Grant, C. S.; Kurtz, M. J.; ReyBacaicoa, V.; Murray, S. S.

2001-11-01

The ADS Abstract Service contains over 2.3 million references in four databases: Astronomy/Astrophysics/Planetary Sciences, Instrumentation, Physics/Geophysics, and Preprints. We provide abstracts and articles free to the astronomical community for all major and many smaller astronomy journals, PhD theses, conference proceedings, and technical reports. These four databases can be queried either separately of jointly. The ADS also has scanned 1.3 million pages in 180,000 articles in the ADS Article Service. This literature archive contains all major Astronomy journals and many smaller journals, as well as conference proceedings, including the abstract books from all the LPSCs back to volume 2. A new feature gives our users the ability to see list of articles that were also read by the readers of a given article. This is a powerful tool to find out what current articles are relevant in a particular field of study. We have recently expanded the citation and reference query capabilities. It allows our users to select papers for which they want to see references or citations and then retrieve these citations/references. Another new capability is the ability to sort a list of articles by their citation count. As usual, users should be reminded that the citations in ADS are incomplete because we do not obtain reference lists from all publishers. In addition, we cannot match all references (e.g. in press, private communications, author errors, some conference papers, etc.). Anyone using the citations for analysis of publishing records should keep this in mind. More work on expanding the citation and reference features is planned over the next year. ADS Home Page http://ads.harvard.edu/

Biological network extraction from scientific literature: state of the art and challenges.

PubMed

Li, Chen; Liakata, Maria; Rebholz-Schuhmann, Dietrich

2014-09-01

Networks of molecular interactions explain complex biological processes, and all known information on molecular events is contained in a number of public repositories including the scientific literature. Metabolic and signalling pathways are often viewed separately, even though both types are composed of interactions involving proteins and other chemical entities. It is necessary to be able to combine data from all available resources to judge the functionality, complexity and completeness of any given network overall, but especially the full integration of relevant information from the scientific literature is still an ongoing and complex task. Currently, the text-mining research community is steadily moving towards processing the full body of the scientific literature by making use of rich linguistic features such as full text parsing, to extract biological interactions. The next step will be to combine these with information from scientific databases to support hypothesis generation for the discovery of new knowledge and the extension of biological networks. The generation of comprehensive networks requires technologies such as entity grounding, coordination resolution and co-reference resolution, which are not fully solved and are required to further improve the quality of results. Here, we analyse the state of the art for the extraction of network information from the scientific literature and the evaluation of extraction methods against reference corpora, discuss challenges involved and identify directions for future research. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Review: Abortion care in Ghana: A critical review of the literature

PubMed Central

Rominski, Sarah D; Lori, Jody R

2015-01-01

The Government of Ghana has taken important steps to mitigate the impact of unsafe abortion. However, the expected decline in maternal deaths is yet to be realized. This literature review aims to present findings from empirical research directly related to abortion provision in Ghana and identify gaps for future research. A total of four (4) databases were searched with the keywords “Ghana and abortion” and hand review of reference lists was conducted. All abstracts were reviewed. The final include sample was 39 articles. Abortion-related complications represent a large component of admissions to gynecological wards in hospitals in Ghana as well as a large contributor to maternal mortality. Almost half of the included studies were hospital-based, mainly chart reviews. This review has identified gaps in the literature including: interviewing women who have sought unsafe abortions and with healthcare providers who may act as gatekeepers to women wishing to access safe abortion services. PMID:25438507

The impact of occupational load carriage on carrier mobility: a critical review of the literature.

PubMed

Carlton, Simon D; Orr, Robin M

2014-01-01

Military personnel and firefighters are required to carry occupational loads and complete tasks in hostile and unpredictable environments where a lack of mobility may risk lives. This review critically examines the literature investigating the impacts of load carriage on the mobility of these specialist personnel. Several literature databases, reference lists, and subject matter experts were employed to identify relevant studies. Studies meeting the inclusion criteria were critiqued using the Downs and Black protocol. Inter-rater agreement was determined by Cohen's κ. Twelve original research studies, which included male and female participants from military and firefighting occupations, were critiqued (κ = .81). A review of these papers found that as the carried load weight increased, carrier mobility during aerobic tasks (like road marching) and anaerobic tasks (like obstacle course negotiation) decreased. As such, it can be concluded that the load carried by some specialist personnel may increase their occupational risk by reducing their mobility.

[Nursing in palliative care to children and adolescents with cancer: integrative literature review].

PubMed

da Costa, Thailly Faria; Ceolim, Maria Filomena

2010-12-01

Pediatric palliative care is a challenge for nursing because it requires emotional balance and knowledge about its specific features. This study is an integrative literature review that aims to identify nursing actions in palliative care for children and adolescents with cancer, considering peculiarities of the disease and dying process. The review was performed by searching for articles indexed in Biblioteca Virtual da Adolescência (Adolec), Cumulative Index to Nursing and Allied Health Literature (CINAHL), Literatura Latino-Americana e do Caribe em Ciências da Saúde (LILACS) and PubMed databases from January 2004 till May 2009. From 29 references found, six met inclusion criteria. Results show teamwork, home care, pain management, dialogue, family support and particularities of childhood cancer fundamental tools for nursing in palliative care. The complexity of care in this situation requires solidarity, compassion, support and relieving suffering.

Evaluation Instruments for Quality of Life Related to Melasma: An Integrative Review.

PubMed

Pollo, Camila Fernandes; Meneguin, Silmara; Miot, Helio Amante

2018-05-21

The aim of this study was to analyze scientific production concerning the validation and cultural adaptation of quality of life evaluation instruments for patients with melasma and to offer a critical reflection on these methods. A literature review was performed based on a search of the Web of Science, Bireme, PubMed, Elsevier Scopus, and Google Scholar databases. All published articles from indexed periodicals in these electronic databases up to December 2015 were included. Eight articles were identified, of which only one (12.5%) referred to the development and validation of a specific instrument for evaluation of the quality of life of melasma patients. An additional six articles (75%) referred to transcultural adjustment and validation of the same instrument in other languages, and another (12.5%) article reported the development of a generic instrument for evaluation of quality of life in patients with pigment disorders. This review revealed only one specific instrument developed and validated in different cultures. Despite being widely used, this instrument did not follow the classic construction steps for psychometric instruments, which paves the way for future studies to develop novel instruments.

Evaluation Instruments for Quality of Life Related to Melasma: An Integrative Review

PubMed Central

Pollo, Camila Fernandes; Meneguin, Silmara; Miot, Helio Amante

2018-01-01

The aim of this study was to analyze scientific production concerning the validation and cultural adaptation of quality of life evaluation instruments for patients with melasma and to offer a critical reflection on these methods. A literature review was performed based on a search of the Web of Science, Bireme, PubMed, Elsevier Scopus, and Google Scholar databases. All published articles from indexed periodicals in these electronic databases up to December 2015 were included. Eight articles were identified, of which only one (12.5%) referred to the development and validation of a specific instrument for evaluation of the quality of life of melasma patients. An additional six articles (75%) referred to transcultural adjustment and validation of the same instrument in other languages, and another (12.5%) article reported the development of a generic instrument for evaluation of quality of life in patients with pigment disorders. This review revealed only one specific instrument developed and validated in different cultures. Despite being widely used, this instrument did not follow the classic construction steps for psychometric instruments, which paves the way for future studies to develop novel instruments. PMID:29791603

Bibliography on propulsion airframe integration technologies for high-speed civil transport applications, 1980-1991

NASA Technical Reports Server (NTRS)

Anderson, David J.; Mizukami, Masashi

1993-01-01

NASA has initiated the High Speed Research (HSR) program with the goal to develop technologies for a new generation, economically viable, environmentally acceptable, supersonic transport (SST) called the High Speed Civil Transport (HSCT). A significant part of this effort is expected to be in multidisciplinary systems integration, such as in propulsion airframe integration (PAI). In order to assimilate the knowledge database on PAI for SST type aircraft, a bibliography on this subject was compiled. The bibliography with over 1200 entries, full abstracts, and indexes. Related topics are also covered, such as the following: engine inlets, engine cycles, nozzles, existing supersonic cruise aircraft, noise issues, computational fluid dynamics, aerodynamics, and external interference. All identified documents from 1980 through early 1991 are included; this covers the latter part of the NASA Supersonic Cruise Research (SCR) program and the beginnings of the HSR program. In addition, some pre-1980 documents of significant merit or reference value are also included. The references were retrieved via a computerized literature search using the NASA RECON database system.

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

PubMed Central

Jia, Baofeng; Raphenya, Amogelang R.; Alcock, Brian; Waglechner, Nicholas; Guo, Peiyao; Tsang, Kara K.; Lago, Briony A.; Dave, Biren M.; Pereira, Sheldon; Sharma, Arjun N.; Doshi, Sachin; Courtot, Mélanie; Lo, Raymond; Williams, Laura E.; Frye, Jonathan G.; Elsayegh, Tariq; Sardar, Daim; Westman, Erin L.; Pawlowski, Andrew C.; Johnson, Timothy A.; Brinkman, Fiona S.L.; Wright, Gerard D.; McArthur, Andrew G.

2017-01-01

The Comprehensive Antibiotic Resistance Database (CARD; http://arpcard.mcmaster.ca) is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis on the genes, proteins and mutations involved in AMR. CARD is ontologically structured, model centric, and spans the breadth of AMR drug classes and resistance mechanisms, including intrinsic, mutation-driven and acquired resistance. It is built upon the Antibiotic Resistance Ontology (ARO), a custom built, interconnected and hierarchical controlled vocabulary allowing advanced data sharing and organization. Its design allows the development of novel genome analysis tools, such as the Resistance Gene Identifier (RGI) for resistome prediction from raw genome sequence. Recent improvements include extensive curation of additional reference sequences and mutations, development of a unique Model Ontology and accompanying AMR detection models to power sequence analysis, new visualization tools, and expansion of the RGI for detection of emergent AMR threats. CARD curation is updated monthly based on an interplay of manual literature curation, computational text mining, and genome analysis. PMID:27789705

[Design and establishment of modern literature database about acupuncture Deqi].

PubMed

Guo, Zheng-rong; Qian, Gui-feng; Pan, Qiu-yin; Wang, Yang; Xin, Si-yuan; Li, Jing; Hao, Jie; Hu, Ni-juan; Zhu, Jiang; Ma, Liang-xiao

2015-02-01

A search on acupuncture Deqi was conducted using four Chinese-language biomedical databases (CNKI, Wan-Fang, VIP and CBM) and PubMed database and using keywords "Deqi" or "needle sensation" "needling feeling" "needle feel" "obtaining qi", etc. Then, a "Modern Literature Database for Acupuncture Deqi" was established by employing Microsoft SQL Server 2005 Express Edition, introducing the contents, data types, information structure and logic constraint of the system table fields. From this Database, detailed inquiries about general information of clinical trials, acupuncturists' experience, ancient medical works, comprehensive literature, etc. can be obtained. The present databank lays a foundation for subsequent evaluation of literature quality about Deqi and data mining of undetected Deqi knowledge.

MGDB: a comprehensive database of genes involved in melanoma.

PubMed

Zhang, Di; Zhu, Rongrong; Zhang, Hanqian; Zheng, Chun-Hou; Xia, Junfeng

2015-01-01

The Melanoma Gene Database (MGDB) is a manually curated catalog of molecular genetic data relating to genes involved in melanoma. The main purpose of this database is to establish a network of melanoma related genes and to facilitate the mechanistic study of melanoma tumorigenesis. The entries describing the relationships between melanoma and genes in the current release were manually extracted from PubMed abstracts, which contains cumulative to date 527 human melanoma genes (422 protein-coding and 105 non-coding genes). Each melanoma gene was annotated in seven different aspects (General Information, Expression, Methylation, Mutation, Interaction, Pathway and Drug). In addition, manually curated literature references have also been provided to support the inclusion of the gene in MGDB and establish its association with melanoma. MGDB has a user-friendly web interface with multiple browse and search functions. We hoped MGDB will enrich our knowledge about melanoma genetics and serve as a useful complement to the existing public resources. Database URL: http://bioinfo.ahu.edu.cn:8080/Melanoma/index.jsp. © The Author(s) 2015. Published by Oxford University Press.

MultitaskProtDB: a database of multitasking proteins.

PubMed

Hernández, Sergio; Ferragut, Gabriela; Amela, Isaac; Perez-Pons, JosepAntoni; Piñol, Jaume; Mozo-Villarias, Angel; Cedano, Juan; Querol, Enrique

2014-01-01

We have compiled MultitaskProtDB, available online at http://wallace.uab.es/multitask, to provide a repository where the many multitasking proteins found in the literature can be stored. Multitasking or moonlighting is the capability of some proteins to execute two or more biological functions. Usually, multitasking proteins are experimentally revealed by serendipity. This ability of proteins to perform multitasking functions helps us to understand one of the ways used by cells to perform many complex functions with a limited number of genes. Even so, the study of this phenomenon is complex because, among other things, there is no database of moonlighting proteins. The existence of such a tool facilitates the collection and dissemination of these important data. This work reports the database, MultitaskProtDB, which is designed as a friendly user web page containing >288 multitasking proteins with their NCBI and UniProt accession numbers, canonical and additional biological functions, monomeric/oligomeric states, PDB codes when available and bibliographic references. This database also serves to gain insight into some characteristics of multitasking proteins such as frequencies of the different pairs of functions, phylogenetic conservation and so forth.

Communities of practice and the construction of the professional identities of nurse educators: A review of the literature.

PubMed

Woods, Andrew; Cashin, Andrew; Stockhausen, Lynette

2016-02-01

To comprehensively review the Community of Practice literature from nursing contexts to explore whether and how these communities contribute to the social construction of nurse educator professional identity. Due to the wide scope of predominately qualitative literature on the topic, papers were analysed and themed inductively. CINAHL, MEDLINE, COCHRANE, EBSCO databases, Emerald, Proquest & Google Scholar. These online databases were searched for relevant peer-reviewed journal papers in the English language with no date range specified. The search terms 'nurs* educator' and 'nurs* teacher' were combined with each of the terms 'communit* of practice', 'identity' and 'role' resulting in 293 peer-reviewed journal papers. Where abstracts were missing, introductory and background sections were skimmed for related content. Papers that made incidental reference to either professional identity or a Community of Practice were excluded. In total, 63 primary study or discussion papers were found to have a focus on nurse educator identity and/or communities of practice in healthcare contexts. Papers specifically focused on communities of practice in nursing (n=33) could only be found from the last 10 years (2005-2015). Only five of these focused on nurse educators. Community of Practice theory and the professional teaching literature offers collaborative and active ways for nurse educators to further develop their professional identities. Despite the emergence of communities of practice in the nursing literature, further studies are required to explore how such a construct can facilitate the social construction of nurse educator professional identity. Copyright © 2015 Elsevier Ltd. All rights reserved.

LocSigDB: a database of protein localization signals

PubMed Central

Negi, Simarjeet; Pandey, Sanjit; Srinivasan, Satish M.; Mohammed, Akram; Guda, Chittibabu

2015-01-01

LocSigDB (http://genome.unmc.edu/LocSigDB/) is a manually curated database of experimental protein localization signals for eight distinct subcellular locations; primarily in a eukaryotic cell with brief coverage of bacterial proteins. Proteins must be localized at their appropriate subcellular compartment to perform their desired function. Mislocalization of proteins to unintended locations is a causative factor for many human diseases; therefore, collection of known sorting signals will help support many important areas of biomedical research. By performing an extensive literature study, we compiled a collection of 533 experimentally determined localization signals, along with the proteins that harbor such signals. Each signal in the LocSigDB is annotated with its localization, source, PubMed references and is linked to the proteins in UniProt database along with the organism information that contain the same amino acid pattern as the given signal. From LocSigDB webserver, users can download the whole database or browse/search for data using an intuitive query interface. To date, LocSigDB is the most comprehensive compendium of protein localization signals for eight distinct subcellular locations. Database URL: http://genome.unmc.edu/LocSigDB/ PMID:25725059

CamMedNP: building the Cameroonian 3D structural natural products database for virtual screening.

PubMed

Ntie-Kang, Fidele; Mbah, James A; Mbaze, Luc Meva'a; Lifongo, Lydia L; Scharfe, Michael; Hanna, Joelle Ngo; Cho-Ngwa, Fidelis; Onguéné, Pascal Amoa; Owono Owono, Luc C; Megnassan, Eugene; Sippl, Wolfgang; Efange, Simon M N

2013-04-16

Computer-aided drug design (CADD) often involves virtual screening (VS) of large compound datasets and the availability of such is vital for drug discovery protocols. We present CamMedNP - a new database beginning with more than 2,500 compounds of natural origin, along with some of their derivatives which were obtained through hemisynthesis. These are pure compounds which have been previously isolated and characterized using modern spectroscopic methods and published by several research teams spread across Cameroon. In the present study, 224 distinct medicinal plant species belonging to 55 plant families from the Cameroonian flora have been considered. About 80 % of these have been previously published and/or referenced in internationally recognized journals. For each compound, the optimized 3D structure, drug-like properties, plant source, collection site and currently known biological activities are given, as well as literature references. We have evaluated the "drug-likeness" of this database using Lipinski's "Rule of Five". A diversity analysis has been carried out in comparison with the ChemBridge diverse database. CamMedNP could be highly useful for database screening and natural product lead generation programs.

[Validation of interaction databases in psychopharmacotherapy].

PubMed

Hahn, M; Roll, S C

2018-03-01

Drug-drug interaction databases are an important tool to increase drug safety in polypharmacy. There are several drug interaction databases available but it is unclear which one shows the best results and therefore increases safety for the user of the databases and the patients. So far, there has been no validation of German drug interaction databases. Validation of German drug interaction databases regarding the number of hits, mechanisms of drug interaction, references, clinical advice, and severity of the interaction. A total of 36 drug interactions which were published in the last 3-5 years were checked in 5 different databases. Besides the number of hits, it was also documented if the mechanism was correct, clinical advice was given, primary literature was cited, and the severity level of the drug-drug interaction was given. All databases showed weaknesses regarding the hit rate of the tested drug interactions, with a maximum of 67.7% hits. The highest score in this validation was achieved by MediQ with 104 out of 180 points. PsiacOnline achieved 83 points, arznei-telegramm® 58, ifap index® 54 and the ABDA-database 49 points. Based on this validation MediQ seems to be the most suitable databank for the field of psychopharmacotherapy. The best results in this comparison were achieved by MediQ but this database also needs improvement with respect to the hit rate so that the users can rely on the results and therefore increase drug therapy safety.

Quality of pharmaceutical advertising and gender bias in medical journals (1998-2008): a review of the scientific literature.

PubMed

Cambronero Saiz, Belén; Ruiz Cantero, María Teresa; Papí Gálvez, Natalia

2012-01-01

To review the scientific literature on pharmaceutical advertising aimed at health professionals in order to determine whether gender bias has decreased and the quality of information in pharmaceutical advertising has improved over time. We performed a content analysis of original articles dealing with medical drug promotion (1998-2008), according to quality criteria such as (a) the number, validity and accessibility of bibliographic references provided in pharmaceutical advertising and (b) the extent to which gender representations were consistent with the prevalence of the diseases. Databases: PUBMED, Medline, Scopus, Sociological Abstract, Eric and LILACS. We reviewed 31 articles that analyzed advertising in medical journals from 1975-2005 and were published between 1998 and 2008. We found that the number of references used to support pharmaceutical advertising claims increased from 1975 but that 50% of these references were not valid. There was a tendency to depict men in paid productive roles, while women appeared inside the home or in non-occupational social contexts. Advertisements for psychotropic and cardiovascular drugs overrepresented women and men respectively. The use of bibliographic references increased between 1998 and 2008. However, representation of traditional male-female roles was similar in 1975 and 2005. Pharmaceutical advertisements may contribute to reinforcing the perception that certain diseases are associated with the most frequently portrayed sex. Copyright © 2011 SESPAS. Published by Elsevier Espana. All rights reserved.

Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets

PubMed Central

Aubry, Marc; Monnier, Annabelle; Chicault, Celine; de Tayrac, Marie; Galibert, Marie-Dominique; Burgun, Anita; Mosser, Jean

2006-01-01

Background Large-scale genomic studies based on transcriptome technologies provide clusters of genes that need to be functionally annotated. The Gene Ontology (GO) implements a controlled vocabulary organised into three hierarchies: cellular components, molecular functions and biological processes. This terminology allows a coherent and consistent description of the knowledge about gene functions. The GO terms related to genes come primarily from semi-automatic annotations made by trained biologists (annotation based on evidence) or text-mining of the published scientific literature (literature profiling). Results We report an original functional annotation method based on a combination of evidence and literature that overcomes the weaknesses and the limitations of each approach. It relies on the Gene Ontology Annotation database (GOA Human) and the PubGene biomedical literature index. We support these annotations with statistically associated GO terms and retrieve associative relations across the three GO hierarchies to emphasise the major pathways involved by a gene cluster. Both annotation methods and associative relations were quantitatively evaluated with a reference set of 7397 genes and a multi-cluster study of 14 clusters. We also validated the biological appropriateness of our hybrid method with the annotation of a single gene (cdc2) and that of a down-regulated cluster of 37 genes identified by a transcriptome study of an in vitro enterocyte differentiation model (CaCo-2 cells). Conclusion The combination of both approaches is more informative than either separate approach: literature mining can enrich an annotation based only on evidence. Text-mining of the literature can also find valuable associated MEDLINE references that confirm the relevance of the annotation. Eventually, GO terms networks can be built with associative relations in order to highlight cooperative and competitive pathways and their connected molecular functions. PMID:16674810

A mapping review of the literature on UK-focused health and social care databases.

PubMed

Cooper, Chris; Rogers, Morwenna; Bethel, Alison; Briscoe, Simon; Lowe, Jenny

2015-03-01

Bibliographic databases are a day-to-day tool of the researcher: they offer the researcher easy and organised access to knowledge, but how much is actually known about the databases on offer? The focus of this paper is UK health and social care databases. These databases are often small, specialised by topic, and provide a complementary literature to the large, international databases. There is, however, good evidence that these databases are overlooked in systematic reviews, perhaps because little is known about what they can offer. To systematically locate and map, published and unpublished literature on the key UK health and social care bibliographic databases. Systematic searching and mapping. Two hundred and forty-two items were identified which specifically related to the 24 of the 34 databases under review. There is little published or unpublished literature specifically analysing the key UK health and social care databases. Since several UK databases have closed, others are at risk, and some are overlooked in reviews, better information is required to enhance our knowledge. Further research on UK health and social care databases is required. This paper suggests the need to develop the evidence base through a series of case studies on each of the databases. © 2014 The authors. Health Information and Libraries Journal © 2014 Health Libraries Journal.

Mentoring models in neurosurgical training: Review of literature.

PubMed

Akhigbe, Taiwo; Zolnourian, Ardalan; Bulters, Diederik

2017-11-01

Effective mentoring is an invaluable element in the development of next generation of neurosurgeons. A mentor helps to develop professional core values, technical and non-technical skills, attitudes and disposition required to be qualified and competent neurosurgeon. Giving the invaluable significance of mentoring in neurosurgery, we undertook this literature review to identify mentoring models evaluating its success and relative benefit. Literature search identified using MeSH word 'mentor', mentoring, mentorship, mentoring model, neurosurgery' in MEDLINE, EMBASE and Scopus databases from 1990 to 2016. Literature reviewed to identify status of mentoring in neurosurgery, potential barriers, pitfalls and future framework for mentoring in neurosurgery. Additional articles identified through manual search of reference lists. A total of 247 studies were obtained from electronic databases, after removing duplicates, abstracts, letters to the editor and non-neurosurgery papers. Sixteen full text articles retrieved out of which five met the inclusion criteria. Generally, there is paucity of articles regarding mentoring in neurosurgery, all included papers were written in English Language, all of them described mentoring model used including simulation, distance, collaborative, facilitative tele-mentoring and peer mentoring. Mentoring in Neurosurgery is an important aspect of personal and professional development of neurosurgical trainees, currently there is decline in traditional apprenticeship due to increase demand for modern use of specialised technology, simulation and tele-medicine in neurosurgery practice. Effective and efficient mentoring will be an interplay of six mentoring models (collaborative, facilitative, distance, simulation, tele mentoring and peer mentoring) identified. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Automatic Recognition of Object Names in Literature

NASA Astrophysics Data System (ADS)

Bonnin, C.; Lesteven, S.; Derriere, S.; Oberto, A.

2008-08-01

SIMBAD is a database of astronomical objects that provides (among other things) their bibliographic references in a large number of journals. Currently, these references have to be entered manually by librarians who read each paper. To cope with the increasing number of papers, CDS develops a tool to assist the librarians in their work, taking advantage of the Dictionary of Nomenclature of Celestial Objects, which keeps track of object acronyms and of their origin. The program searches for object names directly in PDF documents by comparing the words with all the formats stored in the Dictionary of Nomenclature. It also searches for variable star names based on constellation names and for a large list of usual names such as Aldebaran or the Crab. Object names found in the documents often correspond to several astronomical objects. The system retrieves all possible matches, displays them with their object type given by SIMBAD, and lets the librarian make the final choice. The bibliographic reference can then be automatically added to the object identifiers in the database. Besides, the systematic usage of the Dictionary of Nomenclature, which is updated manually, permitted to automatically check it and to detect errors and inconsistencies. Last but not least, the program collects some additional information such as the position of the object names in the document (in the title, subtitle, abstract, table, figure caption...) and their number of occurrences. In the future, this will permit to calculate the 'weight' of an object in a reference and to provide SIMBAD users with an important new information, which will help them to find the most relevant papers in the object reference list.

A Comparison of Selected Bibliographic Database Subject Overlap for Agricultural Information

ERIC Educational Resources Information Center

Ritchie, Stephanie M.; Young, Lauren M.; Sigman, Jessica

2018-01-01

Agricultural researchers and science librarians must understand which research literature databases provide the most comprehensive coverage of agricultural subjects to support their inquiries. Once the domain of a few specialized databases, agricultural research literature is now covered by broad, multidisciplinary databases. The purpose of this…

A Database of Woody Vegetation Responses to Elevated Atmospheric CO2 (NDP-072)

DOE Data Explorer

Curtis, Peter S [The Ohio State Univ., Columbus, OH (United States); Cushman, Robert M [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Brenkert, Antoinette L [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

1999-01-01

To perform a statistically rigorous meta-analysis of research results on the response by woody vegetation to increased atmospheric CO2 levels, a multiparameter database of responses was compiled. Eighty-four independent CO2-enrichment studies, covering 65 species and 35 response parameters, met the necessary criteria for inclusion in the database: reporting mean response, sample size, and variance of the response (either as standard deviation or standard error). Data were retrieved from the published literature and unpublished reports. This numeric data package contains a 29-field data set of CO2-exposure experiment responses by woody plants (as both a flat ASCII file and a spreadsheet file), files listing the references to the CO2-exposure experiments and specific comments relevant to the data in the data set, and this documentation file (which includes SAS and Fortran codes to read the ASCII data file; SAS is a registered trademark of the SAS Institute, Inc., Cary, North Carolina 27511).

SFINX-a drug-drug interaction database designed for clinical decision support systems.

PubMed

Böttiger, Ylva; Laine, Kari; Andersson, Marine L; Korhonen, Tuomas; Molin, Björn; Ovesjö, Marie-Louise; Tirkkonen, Tuire; Rane, Anders; Gustafsson, Lars L; Eiermann, Birgit

2009-06-01

The aim was to develop a drug-drug interaction database (SFINX) to be integrated into decision support systems or to be used in website solutions for clinical evaluation of interactions. Key elements such as substance properties and names, drug formulations, text structures and references were defined before development of the database. Standard operating procedures for literature searches, text writing rules and a classification system for clinical relevance and documentation level were determined. ATC codes, CAS numbers and country-specific codes for substances were identified and quality assured to ensure safe integration of SFINX into other data systems. Much effort was put into giving short and practical advice regarding clinically relevant drug-drug interactions. SFINX includes over 8,000 interaction pairs and is integrated into Swedish and Finnish computerised decision support systems. Over 31,000 physicians and pharmacists are receiving interaction alerts through SFINX. User feedback is collected for continuous improvement of the content. SFINX is a potentially valuable tool delivering instant information on drug interactions during prescribing and dispensing.

The Molecule Pages database

PubMed Central

Saunders, Brian; Lyon, Stephen; Day, Matthew; Riley, Brenda; Chenette, Emily; Subramaniam, Shankar

2008-01-01

The UCSD-Nature Signaling Gateway Molecule Pages (http://www.signaling-gateway.org/molecule) provides essential information on more than 3800 mammalian proteins involved in cellular signaling. The Molecule Pages contain expert-authored and peer-reviewed information based on the published literature, complemented by regularly updated information derived from public data source references and sequence analysis. The expert-authored data includes both a full-text review about the molecule, with citations, and highly structured data for bioinformatics interrogation, including information on protein interactions and states, transitions between states and protein function. The expert-authored pages are anonymously peer reviewed by the Nature Publishing Group. The Molecule Pages data is present in an object-relational database format and is freely accessible to the authors, the reviewers and the public from a web browser that serves as a presentation layer. The Molecule Pages are supported by several applications that along with the database and the interfaces form a multi-tier architecture. The Molecule Pages and the Signaling Gateway are routinely accessed by a very large research community. PMID:17965093

The Molecule Pages database.

PubMed

Saunders, Brian; Lyon, Stephen; Day, Matthew; Riley, Brenda; Chenette, Emily; Subramaniam, Shankar; Vadivelu, Ilango

2008-01-01

The UCSD-Nature Signaling Gateway Molecule Pages (http://www.signaling-gateway.org/molecule) provides essential information on more than 3800 mammalian proteins involved in cellular signaling. The Molecule Pages contain expert-authored and peer-reviewed information based on the published literature, complemented by regularly updated information derived from public data source references and sequence analysis. The expert-authored data includes both a full-text review about the molecule, with citations, and highly structured data for bioinformatics interrogation, including information on protein interactions and states, transitions between states and protein function. The expert-authored pages are anonymously peer reviewed by the Nature Publishing Group. The Molecule Pages data is present in an object-relational database format and is freely accessible to the authors, the reviewers and the public from a web browser that serves as a presentation layer. The Molecule Pages are supported by several applications that along with the database and the interfaces form a multi-tier architecture. The Molecule Pages and the Signaling Gateway are routinely accessed by a very large research community.

Methodology and preliminary results of a systematic literature review of ante-mortem and post-mortem diagnostic tests for bovine tuberculosis.

PubMed

Downs, Sara H; Parry, Jessica E; Upton, Paul A; Broughan, Jennifer M; Goodchild, Anthony V; Nuñez-Garcia, Javier; Greiner, Matthias; Abernethy, Darrell A; Cameron, Angus R; Cook, Alasdair J; de la Rua-Domenech, Ricardo; Gunn, Jane; Pritchard, Elizabeth; Rhodes, Shelley; Rolfe, Simon; Sharp, Michael; Vordermeier, H Martin; Watson, Eamon; Welsh, Michael; Whelan, Adam O; Woolliams, John A; More, Simon J; Clifton-Hadley, Richard S

2018-05-01

A systematic review was conducted to identify studies with data for statistical meta-analyses of sensitivity (Se) and specificity (Sp) of ante-mortem and post-mortem diagnostic tests for bovine tuberculosis (bTB) in cattle. Members of a working group (WG) developed and tested search criteria and developed a standardised two-stage review process, to identify primary studies with numerator and denominator data for test performance and an agreed range of covariate data. No limits were applied to year, language, region or type of test in initial searches of electronic databases. In stage 1, titles and available abstracts were reviewed. References that complied with stage 1 selection criteria were reviewed in entirety and agreed data were extracted from references that complied with stage 2 selection criteria. At stage 1, 9782 references were reviewed and 261 (2.6%) passed through to stage 2 where 215 English language references were each randomly allocated to two of 18 WG reviewers and 46 references in other languages were allocated to native speakers. Agreement regarding eligibility between reviewers of the same reference at stage 2 was moderate (Kappa statistic = 0.51) and a resolution procedure was conducted. Only 119 references (published 1934-2009) were identified with eligible performance estimates for one or more of 14 different diagnostic test types; despite a comprehensive search strategy and the global impact of bTB. Searches of electronic databases for diagnostic test performance data were found to be nonspecific with regard to identifying references with diagnostic test Se or Sp data. Guidelines for the content of abstracts to research papers reporting diagnostic test performance are presented. The results of meta-analyses of the sensitivity and specificity of the tests, and of an evaluation of the methodological quality of the source references, are presented in accompanying papers (Nuñez-Garcia et al., 2017; Downs et al., 2017). Copyright © 2017. Published by Elsevier B.V.

Techniques for searching the CINAHL database using the EBSCO interface.

PubMed

Lawrence, Janna C

2007-04-01

The cumulative index to Nursing and Allied Health Literature (CINAHL) is a useful research tool for accessing articles of interest to nurses and health care professionals. More than 2,800 journals are indexed by CINAHL and can be searched easily using assigned subject headings. Detailed instructions about conducting, combining, and saving searches in CINAHL are provided in this article. Establishing an account at EBSCO further allows a nurse to save references and searches and to receive e-mail alerts when new articles on a topic of interest are published.

Concentrations of indoor pollutants database: User's manual

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1992-05-01

This manual describes the computer-based database on indoor air pollutants. This comprehensive database alloys helps utility personnel perform rapid searches on literature related to indoor air pollutants. Besides general information, it provides guidance for finding specific information on concentrations of indoor air pollutants. The manual includes information on installing and using the database as well as a tutorial to assist the user in becoming familiar with the procedures involved in doing bibliographic and summary section searches. The manual demonstrates how to search for information by going through a series of questions that provide search parameters such as pollutants type, year,more » building type, keywords (from a specific list), country, geographic region, author's last name, and title. As more and more parameters are specified, the list of references found in the data search becomes smaller and more specific to the user's needs. Appendixes list types of information that can be input into the database when making a request. The CIP database allows individual utilities to obtain information on indoor air quality based on building types and other factors in their own service territory. This information is useful for utilities with concerns about indoor air quality and the control of indoor air pollutants. The CIP database itself is distributed by the Electric Power Software Center and runs on IBM PC-compatible computers.« less

Concentrations of indoor pollutants database: User`s manual

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1992-05-01

This manual describes the computer-based database on indoor air pollutants. This comprehensive database alloys helps utility personnel perform rapid searches on literature related to indoor air pollutants. Besides general information, it provides guidance for finding specific information on concentrations of indoor air pollutants. The manual includes information on installing and using the database as well as a tutorial to assist the user in becoming familiar with the procedures involved in doing bibliographic and summary section searches. The manual demonstrates how to search for information by going through a series of questions that provide search parameters such as pollutants type, year,more » building type, keywords (from a specific list), country, geographic region, author`s last name, and title. As more and more parameters are specified, the list of references found in the data search becomes smaller and more specific to the user`s needs. Appendixes list types of information that can be input into the database when making a request. The CIP database allows individual utilities to obtain information on indoor air quality based on building types and other factors in their own service territory. This information is useful for utilities with concerns about indoor air quality and the control of indoor air pollutants. The CIP database itself is distributed by the Electric Power Software Center and runs on IBM PC-compatible computers.« less

Dietary transition difficulties in preterm infants: critical literature review.

PubMed

Pagliaro, Carla Lucchi; Bühler, Karina Elena Bernardis; Ibidi, Silvia Maria; Limongi, Suelly Cecília Olivan

2016-01-01

To analyze the scientific literature on dietary changes in preterm children during the first years of life. The PubMed database was used for article selection. The texts were analyzed according to their objectives, research design, and research group characteristics. The following were selected to comprise the criteria: (1) publications in the period from 1996 to 2014; (2) participation of infants and children from birth to 10 years of age; (3) development of oral motor skills necessary for feeding; (4) development of the feeding process; and (5) feeding difficulties during childhood. There were 282 studies identified, of which 17 were used in the review, and five more articles were identified through the reference list of selected articles, totaling 22 references. Very low birth weight preterm newborns are more likely to have feeding problems in early postnatal stages and during childhood when compared with full-term infants. Monitoring the feeding of these infants after hospital discharge is strictly recommended in an early intervention program aiming at better development of feeding skills. Copyright © 2015 Sociedade Brasileira de Pediatria. Published by Elsevier Editora Ltda. All rights reserved.

Literature review of the potential effects of hydrogen peroxide on nitrogen oxidation efficiency of the biofilters of recirculating aquaculture systems (RAS) for freshwater finfish

USGS Publications Warehouse

Fredricks, Kim T.

2015-01-01

After the initial screening, the remaining 1,405 papers underwent a second screening. Titles and abstracts (when available) were again read to verify that the topic of the paper was related to RAS. During the second screening, a second person verified that the papers proposed for elimination were not related to RAS. A combined reference list of the 512 remaining papers was created and submitted to the U.S. Geological Survey (USGS) Upper Midwest Environmental Sciences Center (UMESC) librarian in order to obtain the actual papers; electronic copies of those citations were obtained and reviewed. The UMESC librarian also received weekly updates from Scopus (a bibliographic database containing abstracts and citations for academic journal articles) using the search terms. Any resulting papers from those updates were screened using the inclusion criteria and relevant papers were requested. From those, 86 were cited in the literature review. An additional 11 papers from other search methods (e.g., mining references lists) also were obtained.

Research-based recommendations for implementing international service-learning.

PubMed

Amerson, Roxanne

2014-01-01

An increasing number of schools of nursing are incorporating international service-learning and/or immersion experiences into their curriculum to promote cultural competence. The purpose of this paper is to identify research-based recommendations for implementing an international service-learning program. A review of literature was conducted in the Cumulative Index of Nursing and Allied Health Literature database using the keywords international, immersion, cultural competence, nursing, and international service-learning. Additional references were located from the reference lists of related articles. Planning of international or immersion experiences requires consideration of the type of country, the length of time, and design of the program; the use of a service-learning framework; opportunities that require the student to live and work in the community, provide hands-on care, participate in unstructured activities, and make home visits; and a method of reflection. Increasing cultural competence does not require foreign travel, but it does necessitate that students are challenged to move outside their comfort zone and work directly with diverse populations. These research-based recommendations may be used either internationally or locally to promote the most effective service-learning opportunities for nursing students. © 2014.

SIMBAD quality-control

NASA Technical Reports Server (NTRS)

Lesteven, Soizick

1992-01-01

The astronomical database SIMBAD developed at the Centre de donnees astronomiques de Strasbourg presently contains 760,000 objects (stellar and non-stellar). It has the unique characteristic of being structured specifically for astronomical objects. All types of heterogeneous data (bibliographic references, measurements, and sets of identification) are connected with each object. The attributes that define quality of the database include the following. Reliability: cross-identification should not rely upon just exact values object coordinates. It also means that information attached to one simple object should be consistent. The existing data must be controlled in order to start with a reliable base and to cross-identify new data assuring the quality as data grows. Exhaustivity: delays between publication of new informations and their inclusion in the database should be as short as possible. The integrity of the database has to be maintained as data accumulates. Taking the amount of data into consideration and the rate of new data production, it is necessary to use automatic methods. One of the possibilities is to use multivariate data analysis. The factor-space is a n-dimensional relevancy space which is described by the n-axes representing a set of n subject matter headings; the words and phrases can be used to scale the axes and the documents are then a vector average of the terms within them. The application reported herein is based on the NASA-STI bibliographical database. The selected data concern astronomy, astrophysics, and space radiation (102,963 references from 1975 to 1991 included 8070 keywords). The F-space is built from this bibliographical data. By comparing the F-space position obtained from the NASA-STI keywords with the F-space position obtained from the SIMBAD references, the authors will be able to show whether it is possible to retrieve information with a restricted set of words only. If the comparison is valid, this will be a way to enter bibliographic information in the SIMBAD quality control process. Furthermore, it is possible to connect the physical measurements of stars from SIMBAD to literature concerning these stars from the NASA-STI abstracts. The physical properties of stars (e.g. UBV colors) are not randomly distributed. Stars are distributed among different clusters in a physical parameter space. The authors will show that there are some relations between this classification and the literature concerning these objects clusters in a factor space. They will investigate the nature of the relationship between the SIMBAD measurements and the bibliography. These would be new relationships that are not pre-established by an astronomer. In addition, the bibliography could be neutral information that can be used in combination with the measured parameters.

Nominal ISOMERs (Incorrect Spellings Of Medicines Eluding Researchers)—variants in the spellings of drug names in PubMed: a database review

PubMed Central

Aronson, Jeffrey K

2016-01-01

Objective To examine how misspellings of drug names could impede searches for published literature. Design Database review. Data source PubMed. Review methods The study included 30 drug names that are commonly misspelt on prescription charts in hospitals in Birmingham, UK (test set), and 30 control names randomly chosen from a hospital formulary (control set). The following definitions were used: standard names—the international non-proprietary names, variant names—deviations in spelling from standard names that are not themselves standard names in English language nomenclature, and hidden reference variants—variant spellings that identified publications in textword (tw) searches of PubMed or other databases, and which were not identified by textword searches for the standard names. Variant names were generated from standard names by applying letter substitutions, omissions, additions, transpositions, duplications, deduplications, and combinations of these. Searches were carried out in PubMed (30 June 2016) for “standard name[tw]” and “variant name[tw] NOT standard name[tw].” Results The 30 standard names of drugs in the test set gave 325 979 hits in total, and 160 hidden reference variants gave 3872 hits (1.17%). The standard names of the control set gave 470 064 hits, and 79 hidden reference variants gave 766 hits (0.16%). Letter substitutions (particularly i to y and vice versa) and omissions together accounted for 2924 (74%) of the variants. Amitriptyline (8530 hits) yielded 18 hidden reference variants (179 (2.1%) hits). Names ending in “in,” “ine,” or “micin” were commonly misspelt. Failing to search for hidden reference variants of “gentamicin,” “amitriptyline,” “mirtazapine,” and “trazodone” would miss at least 19 systematic reviews. A hidden reference variant related to Christmas, “No-el”, was rare; variants of “X-miss” were rarer. Conclusion When performing searches, researchers should include misspellings of drug names among their search terms. PMID:27974346

Nominal ISOMERs (Incorrect Spellings Of Medicines Eluding Researchers)-variants in the spellings of drug names in PubMed: a database review.

PubMed

Ferner, Robin E; Aronson, Jeffrey K

2016-12-14

 To examine how misspellings of drug names could impede searches for published literature.  Database review.  PubMed.  The study included 30 drug names that are commonly misspelt on prescription charts in hospitals in Birmingham, UK (test set), and 30 control names randomly chosen from a hospital formulary (control set). The following definitions were used: standard names-the international non-proprietary names, variant names-deviations in spelling from standard names that are not themselves standard names in English language nomenclature, and hidden reference variants-variant spellings that identified publications in textword (tw) searches of PubMed or other databases, and which were not identified by textword searches for the standard names. Variant names were generated from standard names by applying letter substitutions, omissions, additions, transpositions, duplications, deduplications, and combinations of these. Searches were carried out in PubMed (30 June 2016) for "standard name[tw]" and "variant name[tw] NOT standard name[tw]."  The 30 standard names of drugs in the test set gave 325 979 hits in total, and 160 hidden reference variants gave 3872 hits (1.17%). The standard names of the control set gave 470 064 hits, and 79 hidden reference variants gave 766 hits (0.16%). Letter substitutions (particularly i to y and vice versa) and omissions together accounted for 2924 (74%) of the variants. Amitriptyline (8530 hits) yielded 18 hidden reference variants (179 (2.1%) hits). Names ending in "in," "ine," or "micin" were commonly misspelt. Failing to search for hidden reference variants of "gentamicin," "amitriptyline," "mirtazapine," and "trazodone" would miss at least 19 systematic reviews. A hidden reference variant related to Christmas, "No-el", was rare; variants of "X-miss" were rarer.  When performing searches, researchers should include misspellings of drug names among their search terms. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Astrobib: A Literature Referencing System Compatible with the AAS/WGAS Latex Macros

NASA Astrophysics Data System (ADS)

Ferguson, H. C.

1993-12-01

Perhaps the most tedious part of preparing an article is dealing with the references: keeping track of which have been cited and formatting the reference section at the end of the paper in accordance with a particular journal's requirements. This package aims to simplify this task, while remaining compatible with the AAS/WGAS latex macros (as well as the latex styles distributed by A&A and MNRAS). For lack of a better name, we call this package Astrobib. The astrobib package can be used on two levels. The first uses the standard ``bibtex'' software to collect all the references cited in the text and format the reference list at the end of the paper according to the style requirements of the Journal. All we have done here is to modify the public-domain ``chicago.bst'' bibtex styles to produce citations in the formats required by ApJ, AJ, A&A, MNRAS, and PASP. All implement, to first order, the formats for references specified in 1992 or 1993 ``Instructions to Authors'' of the different journals. If the paper is rejected by MNRAS, changing three lines will allow it to be printed in ApJ format. The second level overcomes two drawbacks bibtex: the tedious use of braces and commas in bibliography database and the requirement that the author remember citation keys, typically constructed of the authors' initials and the date. With Astrobib the bibliography is kept in a much simpler database (based on the Unix `refer' style) and a couple of Unix-specific programs parse the database into bibtex format and preprocess the text to convert ``loose'' citations into bibtex citation keys. Loose citations allow the author to cite just a few authors (in any order) and perhaps the year or a word of the title of the conference proceedings. Documentation and instructions for electronic access to the package will be available at the meeting. Support for this work was provided by the SERC and by NASA through grant HF1043 awarded by the STScI which is operated by AURA, Inc., for NASA under contract NAS5-26555.

Systematic review of the literature on the effectiveness of product reformulation measures to reduce the sugar content of food and drink on the population's sugar consumption and health: a study protocol.

PubMed

Hashem, Kawther M; He, Feng J; MacGregor, Graham A

2016-06-09

Obesity, type 2 diabetes and dental caries are all major public health problems in the UK, with significant costs to the healthcare service. We aim to conduct a systematic review to summarise the evidence on the effectiveness of product reformulation measures to reduce the sugar content of food and drink on the population's sugar consumption and health. Electronic database will be systematically searched using a combination of terms, tailored to optimise sensitivity, specificity, and the syntax and functionality of each database. The databases searched will include the Cochrane Library, EMBASE, MEDLINE (Ovid) and Scopus. The bibliographies of those papers that match inclusion criteria will be searched by hand to identify any further, relevant references, which will be subject to the same screening and selection process. The database search results will be supplemented by hand searches. In addition to the peer-reviewed literature, a number of grey literature searches will be undertaken using the broad search terms 'sugar' and 'food' or 'drink' and 'reduction', these searches will include key government and organisation websites as well as general searches in Google. The selection of the studies, data collection and quality appraisal will be performed independently by 2 reviewers. Data will be initially analysed through a narrative synthesis method. If a subset of data we analyse appears comparable, we will investigate the possibility of performing a meta-analysis. Ethics approval will not be required as this is a protocol for a systematic review. The findings will be disseminated widely through conference presentations and published in a peer-reviewed journal. CRD42016034022. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

ITS-90 Thermocouple Database

National Institute of Standards and Technology Data Gateway

SRD 60 NIST ITS-90 Thermocouple Database (Web, free access)   Web version of Standard Reference Database 60 and NIST Monograph 175. The database gives temperature -- electromotive force (emf) reference functions and tables for the letter-designated thermocouple types B, E, J, K, N, R, S and T. These reference functions have been adopted as standards by the American Society for Testing and Materials (ASTM) and the International Electrotechnical Commission (IEC).

Educational technologies to encourage (self) care in postpartum women.

PubMed

Barbosa, Eryjosy Marculino Guerreiro; Sousa, Albertina Antonielly Sydney de; Vasconcelos, Mardênia Gomes Ferreira; Carvalho, Rhanna Emanuela Fontenele Lima de; Oriá, Mônica Oliveira Batista; Rodrigues, Dafne Paiva

2016-06-01

to evaluate national and international literature regarding the use of educational technologies to encourage self care in postpartum women. an integrative review of the literature. The articles were collected from the CINAHL, SCOPUS, PubMed, SciELO, LILACS and Cochrane databases; the time period for the articles referred to January/2004 to July/2014; the languages used in the articles were Portuguese, English, Spanish and French; the articles were selected from the following descriptors: postpartum care period, educational technology, nursing and self care. Twenty-seven articles were selected for analysis Results: based on the information found, the scales, counseling and home visits were among the most recommended educational technologies. the technologies promote communication, but are sometimes dependent on computer and internet access, which hinder their use by low-income women.

Gender dysphoria and cross-dressing in people with intellectual disability: a literature review.

PubMed

Parkes, Georgina; Hall, Ian

2006-08-01

In clinical practice, we have come across people with intellectual disability who have gender dysphoria and cross-dress. Here, we review the literature on this subject and present an illustrative case example. We searched databases, followed-up references from relevant articles, and contacted colleagues in the field. We found nine papers with case examples and one survey. Gender identity problems certainly occur in people with intellectual disabilities, and developmental perspectives are important in assessing and treating them. In some cases autistic spectrum disorder was co-morbid, for individuals with and those without intellectual disability. Aggression was also common. Documented treatments were primarily psychological and social and did not include hormones and sex reassignment surgery. Capacity to consent is a factor that determines treatment.

Data Model and Relational Database Design for Highway Runoff Water-Quality Metadata

USGS Publications Warehouse

Granato, Gregory E.; Tessler, Steven

2001-01-01

A National highway and urban runoff waterquality metadatabase was developed by the U.S. Geological Survey in cooperation with the Federal Highway Administration as part of the National Highway Runoff Water-Quality Data and Methodology Synthesis (NDAMS). The database was designed to catalog available literature and to document results of the synthesis in a format that would facilitate current and future research on highway and urban runoff. This report documents the design and implementation of the NDAMS relational database, which was designed to provide a catalog of available information and the results of an assessment of the available data. All the citations and the metadata collected during the review process are presented in a stratified metadatabase that contains citations for relevant publications, abstracts (or previa), and reportreview metadata for a sample of selected reports that document results of runoff quality investigations. The database is referred to as a metadatabase because it contains information about available data sets rather than a record of the original data. The database contains the metadata needed to evaluate and characterize how valid, current, complete, comparable, and technically defensible published and available information may be when evaluated for application to the different dataquality objectives as defined by decision makers. This database is a relational database, in that all information is ultimately linked to a given citation in the catalog of available reports. The main database file contains 86 tables consisting of 29 data tables, 11 association tables, and 46 domain tables. The data tables all link to a particular citation, and each data table is focused on one aspect of the information collected in the literature search and the evaluation of available information. This database is implemented in the Microsoft (MS) Access database software because it is widely used within and outside of government and is familiar to many existing and potential customers. The stratified metadatabase design for the NDAMS program is presented in the MS Access file DBDESIGN.mdb and documented with a data dictionary in the NDAMS_DD.mdb file recorded on the CD-ROM. The data dictionary file includes complete documentation of the table names, table descriptions, and information about each of the 419 fields in the database.

Analysis and comparison of NoSQL databases with an introduction to consistent references in big data storage systems

NASA Astrophysics Data System (ADS)

Dziedzic, Adam; Mulawka, Jan

2014-11-01

NoSQL is a new approach to data storage and manipulation. The aim of this paper is to gain more insight into NoSQL databases, as we are still in the early stages of understanding when to use them and how to use them in an appropriate way. In this submission descriptions of selected NoSQL databases are presented. Each of the databases is analysed with primary focus on its data model, data access, architecture and practical usage in real applications. Furthemore, the NoSQL databases are compared in fields of data references. The relational databases offer foreign keys, whereas NoSQL databases provide us with limited references. An intermediate model between graph theory and relational algebra which can address the problem should be created. Finally, the proposal of a new approach to the problem of inconsistent references in Big Data storage systems is introduced.

Observatory Bibliographies as Research Tools

NASA Astrophysics Data System (ADS)

Rots, Arnold H.; Winkelman, S. L.

2013-01-01

Traditionally, observatory bibliographies were maintained to provide insight in how successful a observatory is as measured by its prominence in the (refereed) literature. When we set up the bibliographic database for the Chandra X-ray Observatory (http://cxc.harvard.edu/cgi-gen/cda/bibliography) as part of the Chandra Data Archive ((http://cxc.harvard.edu/cda/), very early in the mission, our objective was to make it primarily a useful tool for our user community. To achieve this we are: (1) casting a very wide net in collecting Chandra-related publications; (2) including for each literature reference in the database a wealth of metadata that is useful for the users; and (3) providing specific links between the articles and the datasets in the archive that they use. As a result our users are able to browse the literature and the data archive simultaneously. As an added bonus, the rich metadata content and data links have also allowed us to assemble more meaningful statistics about the scientific efficacy of the observatory. In all this we collaborate closely with the Astrophysics Data System (ADS). Among the plans for future enhancement are the inclusion of press releases and the Chandra image gallery, linking with ADS semantic searching tools, full-text metadata mining, and linking with other observatories' bibliographies. This work is supported by NASA contract NAS8-03060 (CXC) and depends critically on the services provided by the ADS.

Fear of cancer recurrence: a systematic literature review of self-report measures.

PubMed

Thewes, Belinda; Butow, Phillis; Zachariae, Robert; Christensen, Soren; Simard, Sébastien; Gotay, Carolyn

2012-06-01

Prior research has shown that many cancer survivors experience ongoing fears of cancer recurrence (FCR) and that this chronic uncertainty of health status during and after cancer treatment can be a significant psychological burden. The field of research on FCR is an emerging area of investigation in the cancer survivorship literature, and several standardised instruments for its assessment have been developed. This review aims to identify all available FCR-specific questionnaires and subscales and critically appraise their properties. A systematic review was undertaken to identify instruments measuring FCR. Relevant studies were identified via Medline (1950-2010), CINAHL (1982-2010), PsycINFO (1967-2010) and AMED (1985-2010) databases, reference lists of articles and reviews, grey literature databases and consultation with experts in the field. The Medical Outcomes Trust criteria were used to examine the psychometric properties of the questionnaires. A total of 20 relevant multi-item measures were identified. The majority of instruments have demonstrated reliability and preliminary evidence of validity. Relatively few brief measures (2-10 items) were found to have comprehensive validation and reliability data available. Several valid and reliable longer measures (>10 items) are available. Three have developed short forms that may prove useful as screening tools. This analysis indicated that further refinement and validation of existing instruments is required. Valid and reliable instruments are needed for both research and clinical care. Copyright © 2011 John Wiley & Sons, Ltd.

Analysing patent landscapes in plant biotechnology and new plant breeding techniques.

PubMed

Parisi, Claudia; Rodríguez-Cerezo, Emilio; Thangaraj, Harry

2013-02-01

This article aims to inform the reader of the importance of searching patent landscapes in plant biotechnology and the use of basic tools to perform a patent search. The recommendations for a patent search strategy are illustrated with the specific example of zinc finger nuclease technology for genetic engineering in plants. Within this scope, we provide a general introduction to searching using two online and free-access patent databases esp@cenet and PatentScope. The essential features of the two databases, and their functionality is described, together with short descriptions to enable the reader to understand patents, searching, their content, patent families, and their territorial scope. We mostly stress the value of patent searching for mining scientific, rather than legal information. Search methods through the use of keywords and patent codes are elucidated together with suggestions about how to search with or combine codes with keywords and we also comment on limitations of each method. We stress the importance of patent literature to complement more mainstream scientific literature, and the relative complexities and difficulties in searching patents compared to the latter. A parallel online resource where we describe detailed search exercises is available through reference for those intending further exploration. In essence this is aimed at a novice patent searcher who may want to examine accessory patent literature to complement knowledge gained from mainstream journal resources.

A literature review of transmission effectiveness and electromagnetic compatibility in home telemedicine environments to evaluate safety and security.

PubMed

Carranza, Noemí; Ramos, Victoria; Lizana, Francisca G; García, Jorge; del Pozo, Alejando; Monteagudo, José Luis

2010-09-01

The objective of this study was to determine already reported cases of transmission/reception failure and interferences to evaluate the safety and security of the new mobile home telemedicine systems. The literature published in the last 10 years (1998-2009) has been reviewed, by searching in several databases. Searches on transmission effectiveness and electromagnetic compatibility were made manually through journals, conference proceedings, and also the healthcare technology assessment agencies' Web pages. Search strategies developed through electronic databases and manual search identified a total of 886 references, with 44 finally being included in the results. They have been divided by technology in the transmission/reception effectiveness studies, and according to the type of medical device in the case of electromagnetic interferences studies. The study reveals that there are numerous publications on telemedicine and home-monitoring systems using wireless networks. However, literature on effectiveness in terms of connectivity and transmission problems and electromagnetic interferences is limited. From the collected studies, it can be concluded that there are transmission failures, low-coverage areas, errors in the transmission of packets, and so on. Moreover, cases of serious interferences in medical instruments have also been reported. These facts highlight the lack of studies and specific recommendations to be followed in the implementation of biomonitoring systems in domestic environments using wireless networks.

NASA Scope and Subject Category Guide

NASA Technical Reports Server (NTRS)

2011-01-01

This guide provides a simple, effective tool to assist aerospace information analysts and database builders in the high-level subject classification of technical materials. Each of the 76 subject categories comprising the classification scheme is presented with a description of category scope, a listing of subtopics, cross references, and an indication of particular areas of NASA interest. The guide also includes an index of nearly 3,000 specific research topics cross referenced to the subject categories. The portable document format (PDF) version of the guide contains links in the index from each input subject to its corresponding categories. In addition to subject classification, the guide can serve as an aid to searching databases that use the classification scheme, and is also an excellent selection guide for those involved in the acquisition of aerospace literature. The CD-ROM contains both HTML and PDF versions.

Monitoring the Sodium Content of Restaurant Foods: Public Health Challenges and Opportunities

PubMed Central

Cogswell, Mary E.; Gunn, Janelle P.; Curtis, Christine J.; Rhodes, Donna; Hoy, Kathy; Pehrsson, Pamela; Nickle, Melissa; Merritt, Robert

2013-01-01

We reviewed methods of studies assessing restaurant foods’ sodium content and nutrition databases. We systematically searched the 1964–2012 literature and manually examined references in selected articles and studies. Twenty-six (5.2%) of the 499 articles we found met the inclusion criteria and were abstracted. Five were conducted nationally. Sodium content determination methods included laboratory analysis (n = 15), point-of-purchase nutrition information or restaurants’ Web sites (n = 8), and menu analysis with a nutrient database (n = 3). There is no comprehensive data system that provides all information needed to monitor changes in sodium or other nutrients among restaurant foods. Combining information from different sources and methods may help inform a comprehensive system to monitor sodium content reduction efforts in the US food supply and to develop future strategies. PMID:23865701

Transcriptome-wide selection of a reliable set of reference genes for gene expression studies in potato cyst nematodes (Globodera spp.).

PubMed

Sabeh, Michael; Duceppe, Marc-Olivier; St-Arnaud, Marc; Mimee, Benjamin

2018-01-01

Relative gene expression analyses by qRT-PCR (quantitative reverse transcription PCR) require an internal control to normalize the expression data of genes of interest and eliminate the unwanted variation introduced by sample preparation. A perfect reference gene should have a constant expression level under all the experimental conditions. However, the same few housekeeping genes selected from the literature or successfully used in previous unrelated experiments are often routinely used in new conditions without proper validation of their stability across treatments. The advent of RNA-Seq and the availability of public datasets for numerous organisms are opening the way to finding better reference genes for expression studies. Globodera rostochiensis is a plant-parasitic nematode that is particularly yield-limiting for potato. The aim of our study was to identify a reliable set of reference genes to study G. rostochiensis gene expression. Gene expression levels from an RNA-Seq database were used to identify putative reference genes and were validated with qRT-PCR analysis. Three genes, GR, PMP-3, and aaRS, were found to be very stable within the experimental conditions of this study and are proposed as reference genes for future work.

Assessment of the periodontal health status in patients undergoing orthodontic treatment with fixed appliances and Invisalign system

PubMed Central

Lu, Haili; Tang, Haifang; Zhou, Tian; Kang, Na

2018-01-01

Abstract Background: At present, many scholars have studied the periodontal health status of patients undergoing orthodontic treatment with fixed appliances and invisalign. However, those results are inconsistent. Therefore, we conducted this meta-analysis, and then provide reference for clinical treatment. Methods: Most databases, such as the Cochrane Library, EMBASE, PubMed, Medline, Chinese Biomedical Literature Database, CNKI, and Wan Fang Data were retrieved for related articles from the establishment of the database to October 2017. Meanwhile, we also searched the references of the related literatures manually, in order to increase the included literatures. Two researchers screened the related literatures according to the inclusion criteria and exclusion criteria. Stata 12.0 software was used for data analysis, and results are estimated by odds ratio (OR) and 95% confidence interval (CI). Results: Finally, 7 articles, including 368 patients, were included into our meta-analysis. Meta-analysis results showed that there was no statistically significant difference of gingival index (GI) and sulcus probing depth (SPD) status between the invisalign group and the control group, including at 1, 3, and 6 months (all P > .05). When compared with the control group, the invisalign group presented a lower plaque index (PLI) and sulcus bleeding index (SBI) status at 1 month (OR = −0.53, 95% CI: −0.89 to −0.18; OR = −0.44, 95% CI: −0.70 to −0.19, respectively), 3 months (OR = −0.69, 95% CI: −1.12 to −0.27; OR = −0.49, 95% CI: −0.93 to −0.05, respectively), and 6 months (OR = −0.91, 95% CI: −1.47 to −0.35; OR = −0.40, 95% CI: −0.63 to −0.07, respectively). Subgroup analysis showed that the SPD status was lower in the invisalign group at 6 months when measured the teeth using Ramfjord index (OR = −0.74, 95% CI: −1.35 to −0.12). However, there was no statistically significant difference between the 2 groups when using other measure methods (OR = 0.12, 95% CI: −0.26 to 0.17). Conclusion: Our meta-analysis suggests that comparing with the traditional fixed appliances, patients treated with invisalign have a better periodontal health. However, more studies are needed to confirm this conclusion in the future. PMID:29595680

Longitudinal analysis of meta-analysis literatures in the database of ISI Web of Science.

PubMed

Zhu, Changtai; Jiang, Ting; Cao, Hao; Sun, Wenguang; Chen, Zhong; Liu, Jinming

2015-01-01

The meta-analysis is regarded as an important evidence for making scientific decision. The database of ISI Web of Science collected a great number of high quality literatures including meta-analysis literatures. However, it is significant to understand the general characteristics of meta-analysis literatures to outline the perspective of meta-analysis. In this present study, we summarized and clarified some features on these literatures in the database of ISI Web of Science. We retrieved the meta-analysis literatures in the database of ISI Web of Science including SCI-E, SSCI, A&HCI, CPCI-S, CPCI-SSH, CCR-E, and IC. The annual growth rate, literature category, language, funding, index citation, agencies and countries/territories of the meta-analysis literatures were analyzed, respectively. A total of 95,719 records, which account for 0.38% (99% CI: 0.38%-0.39%) of all literatures, were found in the database. From 1997 to 2012, the annual growth rate of meta-analysis literatures was 18.18%. The literatures involved in many categories, languages, fundings, citations, publication agencies, and countries/territories. Interestingly, the index citation frequencies of the meta-analysis were significantly higher than that of other type literatures such as multi-centre study, randomize controlled trial, cohort study, case control study, and cases report (P<0.0001). The increasing numbers, intensively global influence and high citations revealed that the meta-analysis has been becoming more and more prominent in recent years. In future, in order to promote the validity of meta-analysis, the CONSORT and PRISMA standard should be continuously popularized in the field of evidence-based medicine.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abbott, Jennifer; Sandberg, Tami

The Wind-Wildlife Impacts Literature Database (WILD), formerly known as the Avian Literature Database, was created in 1997. The goal of the database was to begin tracking the research that detailed the potential impact of wind energy development on birds. The Avian Literature Database was originally housed on a proprietary platform called Livelink ECM from Open- Text and maintained by in-house technical staff. The initial set of records was added by library staff. A vital part of the newly launched Drupal-based WILD database is the Bibliography module. Many of the resources included in the database have digital object identifiers (DOI). Themore » bibliographic information for any item that has a DOI can be imported into the database using this module. This greatly reduces the amount of manual data entry required to add records to the database. The content available in WILD is international in scope, which can be easily discerned by looking at the tags available in the browse menu.« less

Prospects for the therapeutic application of sulfated polysaccharides of brown algae in diseases of the cardiovascular system: review.

PubMed

Zaporozhets, Tatyana; Besednova, Natalia

2016-12-01

Fucoidans are water-soluble, highly sulfated, branched homo- and hetero-polysaccharides derived from the fibrillar cell walls and intercellular spaces of brown seaweeds of the class Phaeophyceae. Fucoidans possess mimetic properties of the natural ligands of protein receptors and regulate functions of biological systems via key signaling molecules. The aim of this review was to collect and combine all available scientific literature about the potential use of the fucoidans for diseases of cardiovascular system. The review has been compiled using references from major databases such as Web of Science, PubMed, Scopus, Elsevier, Springer and Google Scholar (up to September 2015). After obtaining all reports from database (a total number is about 580), the papers were carefully analyzed in order to find data related to the topic of this review (129 references). An exhaustive survey of literature revealed that fucoidans possess a broad spectrum of biological activity, including anti-coagulant, hypolipidemic, anti-thrombotic, anti-inflammatory, immunomodulatory, anti-tumor, anti-adhesive and anti-hypertensive properties. Numerous investigations of fucoidans in diseases of the cardiovascular system mainly focus on pleiotropic anti-inflammatory effects. Fucoidans also possess pro-angiogenic and pro-vasculogenic properties. A great number of investigations in the past years have demonstrated that fucoidans has great potential for in-depth investigation of their effects on cardiovascular system. Through this review, the authors hope to attract the attention of researchers to use fucoidan as mimetic of natural ligand receptor protein with the view of developing new formulations with an improved therapeutic value.

IT-CARES: an interactive tool for case-crossover analyses of electronic medical records for patient safety.

PubMed

Caron, Alexandre; Chazard, Emmanuel; Muller, Joris; Perichon, Renaud; Ferret, Laurie; Koutkias, Vassilis; Beuscart, Régis; Beuscart, Jean-Baptiste; Ficheur, Grégoire

2017-03-01

The significant risk of adverse events following medical procedures supports a clinical epidemiological approach based on the analyses of collections of electronic medical records. Data analytical tools might help clinical epidemiologists develop more appropriate case-crossover designs for monitoring patient safety. To develop and assess the methodological quality of an interactive tool for use by clinical epidemiologists to systematically design case-crossover analyses of large electronic medical records databases. We developed IT-CARES, an analytical tool implementing case-crossover design, to explore the association between exposures and outcomes. The exposures and outcomes are defined by clinical epidemiologists via lists of codes entered via a user interface screen. We tested IT-CARES on data from the French national inpatient stay database, which documents diagnoses and medical procedures for 170 million inpatient stays between 2007 and 2013. We compared the results of our analysis with reference data from the literature on thromboembolic risk after delivery and bleeding risk after total hip replacement. IT-CARES provides a user interface with 3 columns: (i) the outcome criteria in the left-hand column, (ii) the exposure criteria in the right-hand column, and (iii) the estimated risk (odds ratios, presented in both graphical and tabular formats) in the middle column. The estimated odds ratios were consistent with the reference literature data. IT-CARES may enhance patient safety by facilitating clinical epidemiological studies of adverse events following medical procedures. The tool's usability must be evaluated and improved in further research. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association.

CLSI-based transference of the CALIPER database of pediatric reference intervals from Abbott to Beckman, Ortho, Roche and Siemens Clinical Chemistry Assays: direct validation using reference samples from the CALIPER cohort.

PubMed

Estey, Mathew P; Cohen, Ashley H; Colantonio, David A; Chan, Man Khun; Marvasti, Tina Binesh; Randell, Edward; Delvin, Edgard; Cousineau, Jocelyne; Grey, Vijaylaxmi; Greenway, Donald; Meng, Qing H; Jung, Benjamin; Bhuiyan, Jalaluddin; Seccombe, David; Adeli, Khosrow

2013-09-01

The CALIPER program recently established a comprehensive database of age- and sex-stratified pediatric reference intervals for 40 biochemical markers. However, this database was only directly applicable for Abbott ARCHITECT assays. We therefore sought to expand the scope of this database to biochemical assays from other major manufacturers, allowing for a much wider application of the CALIPER database. Based on CLSI C28-A3 and EP9-A2 guidelines, CALIPER reference intervals were transferred (using specific statistical criteria) to assays performed on four other commonly used clinical chemistry platforms including Beckman Coulter DxC800, Ortho Vitros 5600, Roche Cobas 6000, and Siemens Vista 1500. The resulting reference intervals were subjected to a thorough validation using 100 reference specimens (healthy community children and adolescents) from the CALIPER bio-bank, and all testing centers participated in an external quality assessment (EQA) evaluation. In general, the transferred pediatric reference intervals were similar to those established in our previous study. However, assay-specific differences in reference limits were observed for many analytes, and in some instances were considerable. The results of the EQA evaluation generally mimicked the similarities and differences in reference limits among the five manufacturers' assays. In addition, the majority of transferred reference intervals were validated through the analysis of CALIPER reference samples. This study greatly extends the utility of the CALIPER reference interval database which is now directly applicable for assays performed on five major analytical platforms in clinical use, and should permit the worldwide application of CALIPER pediatric reference intervals. Copyright © 2013 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Children's experiences of parental mental illness: a literature review.

PubMed

Gladstone, Brenda M; Boydell, Katherine M; Seeman, Mary V; McKeever, Patricia D

2011-11-01

This paper provides a review of published qualitative research on children's experiences of parental mental illness. We undertook a comprehensive search of Medical Literature Analysis and Retrieval System Online, PsycINFO, Cumulative Index to Nursing and Allied Health Literature, Sociological Abstracts and Applied Social Sciences Index and Abstracts databases, as well as citation searches in Web of Science and manual searches of other relevant journals and reference lists of primary papers. Although 20 studies met the search criteria, only 10 focused exclusively on children's descriptions of their experience--the remainder elicited adults' perspectives on children's experiences of parental mental illnesses. Findings are organized under three themes: the impact of illness on children's daily life, how children cope with their experiences and how children understand mental illness. Despite references to pervasive knowledge gaps in the literature, significant information has been accumulated about children's experiences of parental mental illness. Considerable variability in research findings and tensions remain unresolved. For example, evidence is mixed as to children's knowledge and understanding of mental illnesses and how best to deploy resources to help them acquire optimal information. Furthermore, children's desire to be recognized as important to their parents' well-being conflicted with adults' perceptions that children should be protected from too much responsibility. Nevertheless, the cumulative evidence remains a key reason for advocating for psychoeducation and peer-support group interventions for children, which are endorsed by child and adult study participants alike. © 2011 Blackwell Publishing Asia Pty Ltd.

Modelling emergency decisions: recognition-primed decision making. The literature in relation to an ophthalmic critical incident.

PubMed

Bond, Susan; Cooper, Simon

2006-08-01

To review and reflect on the literature on recognition-primed decision (RPD) making and influences on emergency decisions with particular reference to an ophthalmic critical incident involving the sub-arachnoid spread of local anaesthesia following the peribulbar injection. This paper critics the literature on recognition-primed decision making, with particular reference to emergency situations. It illustrates the findings by focussing on an ophthalmic critical incident. Systematic literature review with critical incident reflection. Medline, CINAHL and PsychINFO databases were searched for papers on recognition-primed decision making (1996-2004) followed by the 'snowball method'. Studies were selected in accordance with preset criteria. A total of 12 papers were included identifying the recognition-primed decision making as a good theoretical description of acute emergency decisions. In addition, cognitive resources, situational awareness, stress, team support and task complexity were identified as influences on the decision process. Recognition-primed decision-making theory describes the decision processes of experts in time-bound emergency situations and is the foundation for a model of emergency decision making (Fig. 2). Decision theory and models, in this case related to emergency situations, inform practice and enhance clinical effectiveness. The critical incident described highlights the need for nurses to have a comprehensive and in-depth understanding of anaesthetic techniques as well as an ability to manage and resuscitate patients autonomously. In addition, it illustrates how the critical incidents should influence the audit cycle with improvements in patient safety.

PrionHome: a database of prions and other sequences relevant to prion phenomena.

PubMed

Harbi, Djamel; Parthiban, Marimuthu; Gendoo, Deena M A; Ehsani, Sepehr; Kumar, Manish; Schmitt-Ulms, Gerold; Sowdhamini, Ramanathan; Harrison, Paul M

2012-01-01

Prions are units of propagation of an altered state of a protein or proteins; prions can propagate from organism to organism, through cooption of other protein copies. Prions contain no necessary nucleic acids, and are important both as both pathogenic agents, and as a potential force in epigenetic phenomena. The original prions were derived from a misfolded form of the mammalian Prion Protein PrP. Infection by these prions causes neurodegenerative diseases. Other prions cause non-Mendelian inheritance in budding yeast, and sometimes act as diseases of yeast. We report the bioinformatic construction of the PrionHome, a database of >2000 prion-related sequences. The data was collated from various public and private resources and filtered for redundancy. The data was then processed according to a transparent classification system of prionogenic sequences (i.e., sequences that can make prions), prionoids (i.e., proteins that propagate like prions between individual cells), and other prion-related phenomena. There are eight PrionHome classifications for sequences. The first four classifications are derived from experimental observations: prionogenic sequences, prionoids, other prion-related phenomena, and prion interactors. The second four classifications are derived from sequence analysis: orthologs, paralogs, pseudogenes, and candidate-prionogenic sequences. Database entries list: supporting information for PrionHome classifications, prion-determinant areas (where relevant), and disordered and compositionally-biased regions. Also included are literature references for the PrionHome classifications, transcripts and genomic coordinates, and structural data (including comparative models made for the PrionHome from manually curated alignments). We provide database usage examples for both vertebrate and fungal prion contexts. Using the database data, we have performed a detailed analysis of the compositional biases in known budding-yeast prionogenic sequences, showing that the only abundant bias pattern is for asparagine bias with subsidiary serine bias. We anticipate that this database will be a useful experimental aid and reference resource. It is freely available at: http://libaio.biol.mcgill.ca/prion.

PrionHome: A Database of Prions and Other Sequences Relevant to Prion Phenomena

PubMed Central

Harbi, Djamel; Parthiban, Marimuthu; Gendoo, Deena M. A.; Ehsani, Sepehr; Kumar, Manish; Schmitt-Ulms, Gerold; Sowdhamini, Ramanathan; Harrison, Paul M.

2012-01-01

Prions are units of propagation of an altered state of a protein or proteins; prions can propagate from organism to organism, through cooption of other protein copies. Prions contain no necessary nucleic acids, and are important both as both pathogenic agents, and as a potential force in epigenetic phenomena. The original prions were derived from a misfolded form of the mammalian Prion Protein PrP. Infection by these prions causes neurodegenerative diseases. Other prions cause non-Mendelian inheritance in budding yeast, and sometimes act as diseases of yeast. We report the bioinformatic construction of the PrionHome, a database of >2000 prion-related sequences. The data was collated from various public and private resources and filtered for redundancy. The data was then processed according to a transparent classification system of prionogenic sequences (i.e., sequences that can make prions), prionoids (i.e., proteins that propagate like prions between individual cells), and other prion-related phenomena. There are eight PrionHome classifications for sequences. The first four classifications are derived from experimental observations: prionogenic sequences, prionoids, other prion-related phenomena, and prion interactors. The second four classifications are derived from sequence analysis: orthologs, paralogs, pseudogenes, and candidate-prionogenic sequences. Database entries list: supporting information for PrionHome classifications, prion-determinant areas (where relevant), and disordered and compositionally-biased regions. Also included are literature references for the PrionHome classifications, transcripts and genomic coordinates, and structural data (including comparative models made for the PrionHome from manually curated alignments). We provide database usage examples for both vertebrate and fungal prion contexts. Using the database data, we have performed a detailed analysis of the compositional biases in known budding-yeast prionogenic sequences, showing that the only abundant bias pattern is for asparagine bias with subsidiary serine bias. We anticipate that this database will be a useful experimental aid and reference resource. It is freely available at: http://libaio.biol.mcgill.ca/prion. PMID:22363733

Ricin poisoning: a comprehensive review.

PubMed

Audi, Jennifer; Belson, Martin; Patel, Manish; Schier, Joshua; Osterloh, John

2005-11-09

The recent discoveries of ricin, a deadly biologic toxin, at a South Carolina postal facility, a White House mail facility, and a US senator's office has raised concerns among public health officials, physicians, and citizens. Ricin is one of the most potent and lethal substances known, particularly when inhaled. The ease with which the native plant (Ricinus communis) can be obtained and the toxin extracted makes ricin an attractive weapon. To summarize the literature on ricin poisoning and provide recommendations based on our best professional judgment for clinicians and public health officials that are faced with deliberate release of ricin into the environment. LITERATURE ACQUISITION: Using PubMed, we searched MEDLINE and OLDMEDLINE databases (January 1950-August 2005). The Chemical and Biological Information Analysis Center database was searched for historical and military literature related to ricin toxicity. Book chapters, unpublished reports, monographs, relevant news reports, and Web material were also reviewed to find nonindexed articles. Most literature on ricin poisoning involves castor bean ingestion and experimental animal research. Aerosol release of ricin into the environment or adulteration of food and beverages are pathways to exposure likely to be exploited. Symptoms after ingestion (onset within 12 hours) are nonspecific and may include nausea, vomiting, diarrhea, and abdominal pain and may progress to hypotension, liver failure, renal dysfunction, and death due to multiorgan failure or cardiovascular collapse. Inhalation (onset of symptoms is likely within 8 hours) of ricin is expected to produce cough, dyspnea, arthralgias, and fever and may progress to respiratory distress and death, with few other organ system manifestations. Biological analytic methods for detecting ricin exposure are undergoing investigation and may soon be available through reference laboratories. Testing of environmental samples is available through federal reference laboratories. Currently, no antidote, vaccine, or other specific effective therapy is available for ricin poisoning or prevention. Prompt treatment with supportive care is necessary to limit morbidity and mortality. Health care workers and public health officials should consider ricin poisoning in patients with gastrointestinal or respiratory tract illness in the setting a credible threat. Poison control centers and public health authorities should be notified of any known illness associated with ricin exposure.

[Bibliometric analysis of scientific articles on evidence-based nursing of burn in the mainland of China].

PubMed

Yue, L Q; Pi, X Q; Fan, X G

2016-07-20

To analyze the current research status of evidence-based nursing of burn in the mainland of China, in order to provide basis for the improvement of scientificity of burn nursing practice. Chinese scientific articles on evidence-based nursing of burn in the mainland of China published from January 1997 to December 2015 were retrieved from Chinese Biology Medicine disc, Chinese Journals Full-text Database, Wanfang Database, and VIP Database. From the results retrieved, date with regard to publication year, region of affiliation of the first author, journal distribution, literature type, literature quality assessment, topic of evidence-based research, fund program support, implementation of evidence-based practice steps, and language and quantity of reference. Data were processed with Microsoft Excel software. A total of 50 articles conforming to the criteria were retrieved. (1) Articles about evidence-based nursing of burn arose in 2004. Compared with that in the previous year, there was no obvious increase in the number of relevant articles in each year from 2004 to 2011. The number of literature in 2012 was obviously increased than that in each year from 2004 to 2011, while the number of literature in each year from 2012 to 2015 was not obviously increased compared with that in the previous year. (2) The regions of affiliation of the first author were distributed in 13 provinces, 3 minority autonomous regions, and 3 municipalities, with the largest distribution in East China, and Northwest China and Southwest China in the follow. (3) The articles were published in 32 domestic journals, with 9 (28.12%) nursing journals, 5 (15.62%) burn medical related journals, and 18 (56.25%) other journals. Twenty (40%) articles were published in Source Journal for Chinese Scientific and Technical Papers. (4) Regarding the literature type, 31 (62%) articles dealt with clinical experiences, 17 (34%) articles dealt with scientific research, and 2 (4%) articles dealt with case report. (5) There were 21 quantitative study articles and 29 narrative study articles, all with low quality. (6) The topics of evidence-based research in these articles were mainly burn rehabilitation, burn nursing technology, pediatric burn, inhalation injury and airway management, and complications of burn injury. Only one study was supported by fund program. (7) Only one article described complete evidence-based practice steps. (8) The literature cited 57 English articles as references, with an average of 1.14, and 316 Chinese articles, with an average of 6.32. The concept of evidence-based nursing of burn has been initially formed in the mainland of China. The number of relevant articles is on the rise, but the quality needs to be further improved. There is an urgent need to improve nurses' understanding of evidence-based nursing and their command of the method of evidence-based practice through on-job training, so as to improve the scientificity and effectiveness of burn nursing.

Pediatric thymomas: report of two cases and comprehensive review of the literature.

PubMed

Fonseca, Annabelle L; Ozgediz, Doruk E; Christison-Lagay, Emily R; Detterbeck, Frank C; Caty, Michael G

2014-03-01

Thymomas are rare pediatric malignancies with indolent behavior. There are fewer than 50 reported cases and no comprehensive review. We sought to evaluate our recent experience with pediatric thymomas, and comprehensively review the extant literature. A systematic search of the PubMed database was performed using keywords: "thymoma", "pediatric", "juvenile", "childhood", and "child". Additional studies were identified by a manual search of the reference list. We report two patients with thymomas. We identified 22 case reports or series that described 48 patients; 62 % were male, 15 % presented with myasthenia gravis. Fifty percent were Masaoka Stage I, 15 % were Stage II, 13 % were Stage III, and 23 % were Stage IV. Four patients with early stage (I or II) disease were treated with adjuvant therapies in addition to surgical excision, while five patients with late stage (III or IV) disease treated with surgical excision alone. Of studies reporting at least 2-year follow-up, survival was 71 %. Pediatric thymomas are rare tumors with a slight male predominance. Wide variations were observed in the treatment of thymomas across all stages. Our review indicates a need for large database and multi-institutional studies to clearly elucidate clinical course, prognostic factors and outcome.

The care pathway: concepts and theories: an introduction.

PubMed

Schrijvers, Guus; van Hoorn, Arjan; Huiskes, Nicolette

2012-01-01

This article addresses first the definition of a (care) pathway, and then follows a description of theories since the 1950s. It ends with a discussion of theoretical advantages and disadvantages of care pathways for patients and professionals. The objective of this paper is to provide a theoretical base for empirical studies on care pathways. The knowledge for this chapter is based on several books on pathways, which we found by searching in the digital encyclopedia Wikipedia. Although this is not usual in scientific publications, this method was used because books are not searchable by databases as Pubmed. From 2005, we performed a literature search on Pubmed and other literature databases, and with the keywords integrated care pathway, clinical pathway, critical pathway, theory, research, and evaluation. One of the inspirational sources was the website of the European Pathway Association (EPA) and its journal International Journal of Care Pathways. The authors visited several sites for this paper. These are mentioned as illustration of a concept or theory. Most of them have English websites with more information. The URLs of these websites are not mentioned in this paper as a reference, because the content of them changes fast, sometimes every day.

The care pathway: concepts and theories: an introduction

PubMed Central

Schrijvers, Guus; van Hoorn, Arjan; Huiskes, Nicolette

2012-01-01

This article addresses first the definition of a (care) pathway, and then follows a description of theories since the 1950s. It ends with a discussion of theoretical advantages and disadvantages of care pathways for patients and professionals. The objective of this paper is to provide a theoretical base for empirical studies on care pathways. The knowledge for this chapter is based on several books on pathways, which we found by searching in the digital encyclopedia Wikipedia. Although this is not usual in scientific publications, this method was used because books are not searchable by databases as Pubmed. From 2005, we performed a literature search on Pubmed and other literature databases, and with the keywords integrated care pathway, clinical pathway, critical pathway, theory, research, and evaluation. One of the inspirational sources was the website of the European Pathway Association (EPA) and its journal International Journal of Care Pathways. The authors visited several sites for this paper. These are mentioned as illustration of a concept or theory. Most of them have English websites with more information. The URLs of these websites are not mentioned in this paper as a reference, because the content of them changes fast, sometimes every day. PMID:23593066

Sensory overload: A concept analysis.

PubMed

Scheydt, Stefan; Müller Staub, Maria; Frauenfelder, Fritz; Nielsen, Gunnar H; Behrens, Johann; Needham, Ian

2017-04-01

In the context of mental disorders sensory overload is a widely described phenomenon used in conjunction with psychiatric interventions such as removal from stimuli. However, the theoretical foundation of sensory overload as addressed in the literature can be described as insufficient and fragmentary. To date, the concept of sensory overload has not yet been sufficiently specified or analyzed. The aim of the study was to analyze the concept of sensory overload in mental health care. A literature search was undertaken using specific electronic databases, specific journals and websites, hand searches, specific library catalogues, and electronic publishing databases. Walker and Avant's method of concept analysis was used to analyze the sources included in the analysis. All aspects of the method of Walker and Avant were covered in this concept analysis. The conceptual understanding has become more focused, the defining attributes, influencing factors and consequences are described and empirical referents identified. The concept analysis is a first step in the development of a middle-range descriptive theory of sensory overload based on social scientific and stress-theoretical approaches. This specification may serve as a fundament for further research, for the development of a nursing diagnosis or for guidelines. © 2017 Australian College of Mental Health Nurses Inc.

Recommended dietary reference intakes, nutritional goals and dietary guidelines for fat and fatty acids: a systematic review.

PubMed

Aranceta, Javier; Pérez-Rodrigo, Carmen

2012-06-01

Dietary fat and its effects on health and disease has attracted interest for research and Public Health. Since the 1980s many bodies and organizations have published recommendations regarding fat intake. In this paper different sets of recommendations are analyzed following a systematic review process to examine dietary reference intakes, nutritional goals and dietary guidelines for fat and fatty acids. A literature search was conducted in relevant literature databases along a search for suitable grey literature reports. Documents were included if they reported information on either recommended intake levels or dietary reference values or nutritional objectives or dietary guidelines regarding fat and/or fatty acids and/or cholesterol intake or if reported background information on the process followed to produce the recommendations. There is no standard approach for deriving nutrient recommendations. Recommendations vary between countries regarding the levels of intake advised, the process followed to set the recommendations. Recommendations on fat intake share similar figures regarding total fat intake, saturated fats and trans fats. Many sets do not include a recommendation about cholesterol intake. Most recent documents provide advice regarding specific n-3 fatty acids. Despite efforts to develop evidence based nutrient recommendations and dietary guidelines that may contribute to enhance health, there are still many gaps in research. It would be desirable that all bodies concerned remain transparent about the development of dietary recommendations. In order to achieve this, the type of evidence selected to base the recommendations should be specified and ranked. Regular updates of such recommendations should be planned.

Biosecurity-Based Interventions and Strategies To Reduce Campylobacter spp. on Poultry Farms▿

PubMed Central

Newell, D. G.; Elvers, K. T.; Dopfer, D.; Hansson, I.; Jones, P.; James, S.; Gittins, J.; Stern, N. J.; Davies, R.; Connerton, I.; Pearson, D.; Salvat, G.; Allen, V. M.

2011-01-01

The prevention and control of Campylobacter colonization of poultry flocks are important public health strategies for the control of human campylobacteriosis. A critical review of the literature on interventions to control Campylobacter in poultry on farms was undertaken using a systematic approach. Although the focus of the review was on aspects appropriate to the United Kingdom poultry industry, the research reviewed was gathered from worldwide literature. Multiple electronic databases were employed to search the literature, in any language, from 1980 to September 2008. A primary set of 4,316 references was identified and scanned, using specific agreed-upon criteria, to select relevant references related to biosecurity-based interventions. The final library comprised 173 references. Identification of the sources of Campylobacter in poultry flocks was required to inform the development of targeted interventions to disrupt transmission routes. The approach used generally involved risk factor-based surveys related to culture-positive or -negative flocks, usually combined with a structured questionnaire. In addition, some studies, either in combination or independently, undertook intervention trials. Many of these studies were compromised by poor design, sampling, and statistical analysis. The evidence for each potential source and route of transmission on the poultry farm was reviewed critically, and the options for intervention were considered. The review concluded that, in most instances, biosecurity on conventional broiler farms can be enhanced and this should contribute to the reduction of flock colonization. However, complementary, non-biosecurity-based approaches will also be required in the future to maximize the reduction of Campylobacter-positive flocks at the farm level. PMID:21984249

Food composition database development for between country comparisons.

PubMed

Merchant, Anwar T; Dehghan, Mahshid

2006-01-19

Nutritional assessment by diet analysis is a two-stepped process consisting of evaluation of food consumption, and conversion of food into nutrient intake by using a food composition database, which lists the mean nutritional values for a given food portion. Most reports in the literature focus on minimizing errors in estimation of food consumption but the selection of a specific food composition table used in nutrient estimation is also a source of errors. We are conducting a large prospective study internationally and need to compare diet, assessed by food frequency questionnaires, in a comparable manner between different countries. We have prepared a multi-country food composition database for nutrient estimation in all the countries participating in our study. The nutrient database is primarily based on the USDA food composition database, modified appropriately with reference to local food composition tables, and supplemented with recipes of locally eaten mixed dishes. By doing so we have ensured that the units of measurement, method of selection of foods for testing, and assays used for nutrient estimation are consistent and as current as possible, and yet have taken into account some local variations. Using this common metric for nutrient assessment will reduce differential errors in nutrient estimation and improve the validity of between-country comparisons.

dbPAF: an integrative database of protein phosphorylation in animals and fungi.

PubMed

Ullah, Shahid; Lin, Shaofeng; Xu, Yang; Deng, Wankun; Ma, Lili; Zhang, Ying; Liu, Zexian; Xue, Yu

2016-03-24

Protein phosphorylation is one of the most important post-translational modifications (PTMs) and regulates a broad spectrum of biological processes. Recent progresses in phosphoproteomic identifications have generated a flood of phosphorylation sites, while the integration of these sites is an urgent need. In this work, we developed a curated database of dbPAF, containing known phosphorylation sites in H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. pombe and S. cerevisiae. From the scientific literature and public databases, we totally collected and integrated 54,148 phosphoproteins with 483,001 phosphorylation sites. Multiple options were provided for accessing the data, while original references and other annotations were also present for each phosphoprotein. Based on the new data set, we computationally detected significantly over-represented sequence motifs around phosphorylation sites, predicted potential kinases that are responsible for the modification of collected phospho-sites, and evolutionarily analyzed phosphorylation conservation states across different species. Besides to be largely consistent with previous reports, our results also proposed new features of phospho-regulation. Taken together, our database can be useful for further analyses of protein phosphorylation in human and other model organisms. The dbPAF database was implemented in PHP + MySQL and freely available at http://dbpaf.biocuckoo.org.

Ophthalmology and vision science research: part 5: surfing or sieving--using literature databases wisely.

PubMed

Sherwin, Trevor; Gilhotra, Amardeep K

2006-02-01

Literature databases are an ever-expanding resource available to the field of medical sciences. Understanding how to use such databases efficiently is critical for those involved in research. However, for the uninitiated, getting started is a major hurdle to overcome and for the occasional user, the finer points of database searching remain an unacquired skill. In the fifth and final article in this series aimed at those embarking on ophthalmology and vision science research, we look at how the beginning researcher can start to use literature databases and, by using a stepwise approach, how they can optimize their use. This instructional paper gives a hypothetical example of a researcher writing a review article and how he or she acquires the necessary scientific literature for the article. A prototype search of the Medline database is used to illustrate how even a novice might swiftly acquire the skills required for a medium-level search. It provides examples and key tips that can increase the proficiency of the occasional user. Pitfalls of database searching are discussed, as are the limitations of which the user should be aware.

Functional lesional neurosurgery for tremor-a protocol for a systematic review and meta-analysis.

PubMed

Schreglmann, Sebastian R; Krauss, Joachim K; Chang, Jin Woo; Bhatia, Kailash P; Kägi, Georg

2017-05-09

The recent introduction of incision-less lesional neurosurgery using Gamma Knife and MRI-guided focused ultrasound has revived interest in lesional treatment options for tremor disorders. Preliminary literature researches reveal that the consistency of treatment effects after lesional neurosurgery for tremor has not formally been assessed yet. Similarly, the efficacy of different targets for lesional treatment and incidence of persistent side effects of lesional neurosurgical interventions has not been comprehensively assessed. This work therefore aims to describe a suitable process how to review the existing literature on efficacy and persistent side effects of lesional neurosurgical treatment for tremor due to Parkinson's disease, essential tremor, multiple sclerosis and midbrain/rubral tremor. We will search electronic databases (Medline, Cochrane) and reference lists of included articles for studies reporting lesional interventions for tremor in cohorts homogeneous for tremor aetiology and intervention (technique and target). We will include cohorts with a minimum number of five subjects and follow-up of 2 months. One investigator will perform the initial literature search and two investigators then independently decide which references to include for final efficacy and safety analysis. After settling of disagreement, data will be extracted from articles using a standardised template. We will perform a random-effect meta-analysis calculating standardised mean differences (Hedge's g) for comparison in Forest plots and subgroup analysis after assessment of heterogeneity using I 2 statistics. This study will summarise the available evidence on the efficacy of lesional interventions for the most frequent tremor disorders, as well as for the incidence rate of persisting side effects after unilateral lesional treatment. This data will be useful to guide future work on incision-less lesional interventions for tremor. This study has been registered with the PROSPERO database (no. CRD42016048049). © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

A bibliography of literature pertaining to plague (Yersinia pestis)

USGS Publications Warehouse

Ellison, Laura E.; Frank, Megan K. Eberhardt

2011-01-01

Plague is an acute and often fatal zoonotic disease caused by the bacterium Yersinia pestis. Y. pestis mainly cycles between small mammals and their fleas; however, it has the potential to infect humans and frequently causes fatalities if left untreated. It is often considered a disease of the past; however, since the late 1800s, plagueis geographic range has expanded greatly, posing new threats in previously unaffected regions of the world, including the Western United States. A literature search was conducted using Internet resources and databases. The keywords chosen for the searches included plague, Yersinia pestis, management, control, wildlife, prairie dogs, fleas, North America, and mammals. Keywords were used alone or in combination with the other terms. Although this search pertains mostly to North America, citations were included from the international research community, as well. Databases and search engines used included Google (http://www.google.com), Google Scholar (http://scholar.google.com), SciVerse Scopus (http://www.scopus.com), ISI Web of Knowledge (http://apps.isiknowledge.com), and the USGS Library's Digital Desktop (http://library.usgs.gov). The literature-cited sections of manuscripts obtained from keyword searches were cross-referenced to identify additional citations or gray literature that was missed by the Internet search engines. This Open-File Report, published as an Internet-accessible bibliography, is intended to be periodically updated with new citations or older references that may have been missed during this compilation. Hence, the authors would be grateful to receive notice of any new or old papers that the audience (users) think need to be included.

Mapping the literature of dental assisting.

PubMed Central

Hook, S A; Wagner, C F

1999-01-01

The purpose of this study was to identify core journals and the databases that provide access to these journals for the field of dental assisting. This study was completed as a part of the Medical Library Association (MLA) Nursing and Allied Health Resources Section's project to map the literature of allied health. There were three original journals selected for analysis using the prescribed methodology, Dental Assistant, the journal of the American Dental Assistants Association; Journal of the CDAA, the journal of the Canadian Dental Assistants' Association; and Dental Teamwork, published by the American Dental Association. Dental Teamwork ceased publication in December 1996; however, it was considered a necessary part of the analysis due to its extensive coverage of dental assisting as well as its numerous scientific articles with references. In Dental Assistant, there were 16 source articles, containing 206 citations. In Dental Teamwork, there were 31 source articles with 308 citations. In Journal of the CDAA, there were only 3 source articles with 14 citations. Bradford's Law of Scattering was applied to the journal citations. Four databases, MEDLINE, the Cumulative Index to Nursing and Allied Health Literature, EMBASE/Excerpta Medica, and HEALTH were analyzed for their coverage of these cited journals. This study may encourage the dental assisting profession to take a close look at its existing journals and to consider enhancing the content of these journals or the publication of additional journals in the field. Dental assistants of today need substantive literature that deals with all aspects of their chosen profession in order to meet the challenges of providing dental health care in the future. PMID:10427427

MultitaskProtDB: a database of multitasking proteins

PubMed Central

Hernández, Sergio; Ferragut, Gabriela; Amela, Isaac; Perez-Pons, JosepAntoni; Piñol, Jaume; Mozo-Villarias, Angel; Cedano, Juan; Querol, Enrique

2014-01-01

We have compiled MultitaskProtDB, available online at http://wallace.uab.es/multitask, to provide a repository where the many multitasking proteins found in the literature can be stored. Multitasking or moonlighting is the capability of some proteins to execute two or more biological functions. Usually, multitasking proteins are experimentally revealed by serendipity. This ability of proteins to perform multitasking functions helps us to understand one of the ways used by cells to perform many complex functions with a limited number of genes. Even so, the study of this phenomenon is complex because, among other things, there is no database of moonlighting proteins. The existence of such a tool facilitates the collection and dissemination of these important data. This work reports the database, MultitaskProtDB, which is designed as a friendly user web page containing >288 multitasking proteins with their NCBI and UniProt accession numbers, canonical and additional biological functions, monomeric/oligomeric states, PDB codes when available and bibliographic references. This database also serves to gain insight into some characteristics of multitasking proteins such as frequencies of the different pairs of functions, phylogenetic conservation and so forth. PMID:24253302

Identification of contaminant trends and data gaps for terrestrial vertebrates residing in northeastern estuaries of the United States

USGS Publications Warehouse

Rattner, B.A.; Pearson, J.L.; Golden, N.H.; Erwin, R.M.; Ottinger, M.A.

1998-01-01

The Biomonitoring of Environmental Status and Trends (BEST) program of the Department of the Interior is focused to identify and understand effects of contaminant stressors on biological resources under their stewardship. One BEST program activity involves evaluation of retrospective data to assess and predict the condition of biota in Atlantic coast estuaries. A 'Contaminant Exposure and Effects--Terrestrial Vertebrates' database (CEE-TV) has been compiled through computerized literature searches of Fish and Wildlife Reviews, BIOSIS, AGRICOLA, and TOXLINE, review of existing databases (e.g., US EPA Ecological Incident Information System, USGS Diagnostic and Epizootic Databases), and solicitation of unpublished reports from conservation agencies, private groups, and universities. Summary information has been entered into the CEE-TV database, including species, collection date (1965-present), site coordinates, sample matrix, contaminant concentrations, biomarker and bioindicator responses, and reference source, utilizing a 96-field dBase format. Currently, the CEE-TV database contains 3500 georeferenced records representing >200 vertebrate species and > 100,000 individuals residing in estuaries from Maine through Florida. This relational database can be directly queried, imported into the ARC/INFO geographic information system (GIS) to examine spatial tendencies, and used to identify 'hot-spots', generate hypotheses, and focus ecotoxicological assessments. An overview of temporal, phylogenetic, and geographic contaminant exposure and effects information, trends, and data gaps will be presented for terrestrial vertebrates residing in estuaries in the northeast United States.

Development of a reference database for assessing dietary nitrate in vegetables.

PubMed

Blekkenhorst, Lauren C; Prince, Richard L; Ward, Natalie C; Croft, Kevin D; Lewis, Joshua R; Devine, Amanda; Shinde, Sujata; Woodman, Richard J; Hodgson, Jonathan M; Bondonno, Catherine P

2017-08-01

Nitrate from vegetables improves vascular health with short-term intake. Whether this translates into improved long-term health outcomes has yet to be investigated. To enable reliable analysis of nitrate intake from food records, there is a strong need for a comprehensive nitrate content of vegetables database. A systematic literature search (1980-2016) was performed using Medline, Agricola and Commonwealth Agricultural Bureaux abstracts databases. The nitrate content of vegetables database contains 4237 records from 255 publications with data on 178 vegetables and 22 herbs and spices. The nitrate content of individual vegetables ranged from Chinese flat cabbage (median; range: 4240; 3004-6310 mg/kg FW) to corn (median; range: 12; 5-1091 mg/kg FW). The database was applied to estimate vegetable nitrate intake using 24-h dietary recalls (24-HDRs) and food frequency questionnaires (FFQs). Significant correlations were observed between urinary nitrate excretion and 24-HDR (r = 0.4, P = 0.013), between 24-HDR and 12 month FFQs (r = 0.5, P < 0.001) as well as two 4 week FFQs administered 8 weeks apart (r = 0.86, P < 0.001). This comprehensive nitrate database allows quantification of dietary nitrate from a large variety of vegetables. It can be applied to dietary records to explore the associations between nitrate intake and health outcomes in human studies. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

VizieR Online Data Catalog: Partition functions for molecules and atoms (Barklem+, 2016)

NASA Astrophysics Data System (ADS)

Barklem, P. S.; Collet, R.

2016-02-01

The results and input data are presented in the following files. Table 1 contains dissociation energies from the literature, and final adopted values, for 291 molecules. The literature values are from the compilations of Huber & Herzberg (1979, Constants of Diatomic Molecules (Van Nostrand Reinhold), Luo (2007, Comprehensive Handbook of Chemical Bond Energies (CRC Press)) and G2 theory calculations of Curtiss et al. (1991, J. Chem. Phys., 94, 7221). Table 2 contains the input data for the molecular calculations including adopted dissociation energy, nuclear spins, molecular spectroscopic constants and their sources. There are 291 files, one for each molecule, labelled by the molecule name. The various molecular spectroscopic constants are as defined in the paper. Table 4 contains the first, second and third ionisation energies for all chemical elements from H to U. The data comes from the CRC Handbook of Chemistry and Physics (Haynes, W.M. 2010, CRC Handbook of Chemistry and Physics, 91st edn. (CRC Press, Taylor and Francis Group)). Table 5a contains a list of keys to bibliographic references for the atomic energy level data that was extracted from NIST Atomic Spectra Database and used in the present work to compute atomic partition functions. The citation keys are abbreviations of the full bibliographic references which are made available in Table 5b in BibTeX format. Table 5b contains the full bibliographic references for the atomic energy level data that was extracted from the NIST Atomic Spectra Database. Table 6 contains tabulated partition function data as a function of temperature for 291 molecules. Table 7 contains tabulated equilibrium constant data as a function of temperature for 291 molecules. Table 8 contains tabulated partition function data as a function of temperature for 284 atoms and ions. The paper should be consulted for further details. (10 data files).

Literature and information related to the natural resources of the North Aleutian Basin of Alaska.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stull, E.A.; Hlohowskyj, I.; LaGory, K. E.

The North Aleutian Basin Planning Area of the Minerals Management Service (MMS) is a large geographic area with significant natural resources. The Basin includes most of the southeastern part of the Bering Sea Outer Continental Shelf, including all of Bristol Bay. The area supports important habitat for a wide variety of species and globally significant habitat for birds and marine mammals, including several federally listed species. Villages and communities of the Alaska Peninsula and other areas bordering or near the Basin rely on its natural resources (especially commercial and subsistence fishing) for much of their sustenance and livelihood. The offshoremore » area of the North Aleutian Basin is considered to have important hydrocarbon reserves, especially natural gas. In 2006, the MMS released a draft proposed program, 'Outer Continental Shelf Oil and Gas Leasing Program, 2007-2012' and an accompanying draft programmatic environmental impact statement (EIS). The draft proposed program identified two lease sales proposed in the North Aleutian Basin in 2010 and 2012, subject to restrictions. The area proposed for leasing in the Basin was restricted to the Sale 92 Area in the southwestern portion. Additional EISs will be needed to evaluate the potential effects of specific lease actions, exploration activities, and development and production plans in the Basin. A full range of updated multidisciplinary scientific information will be needed to address oceanography, fate and effects of oil spills, marine ecosystems, fish, fisheries, birds, marine mammals, socioeconomics, and subsistence in the Basin. Scientific staff at Argonne National Laboratory were contracted to assist MMS with identifying and prioritizing information needs related to potential future oil and gas leasing and development activities in the North Aleutian Basin. Argonne focused on three related tasks: (1) identify and gather relevant literature published since 1996, (2) synthesize and summarize the literature, and (3) identify and prioritize remaining information needs. To assist in the latter task, MMS convened the North Aleutian Basin Information Status and Research Planning Meeting (the Planning Meeting) in Anchorage, Alaska, from November 28 through December 1, 2006. That meeting and its results are described in 'Proceedings of the North Aleutian Basin Information Status and Research Planning Meeting' (the Planning Meeting report)1. Citations for recent literature (1996-2006) to support an assessment of the impacts of oil and gas development on natural, cultural, and socioeconomic resources in the North Aleutian Basin were entered in a database. The database, a series of Microsoft Excel spreadsheets with links to many of the reference materials, was provided to MMS prior to the Planning Meeting and was made available for participants to use during the meeting. Many types of references were identified and collected from the literature, such as workshop and symposium proceedings, personal web pages, web pages of government and nongovernmental organizations, EISs, books and articles reporting research results, regulatory documents, technical reports, newspaper and newsletter articles, and theses and dissertations. The current report provides (1) a brief overview of the literature; (2) descriptions (in tabular form) of the databased references, including geographic area covered, topic, and species (where relevant); (3) synopses of the contents of the referenced documents and web pages; and (4) a full citation for each reference. At the Planning Meeting, subject matter experts with research experience in the North Aleutian Basin presented overviews of the area's resources, including oceanography, fish and shellfish populations, federal fisheries, commercial fishery economics, community socioeconomics, subsistence, seabirds and shorebirds, waterfowl, seals and sea lions, cetaceans, sea otters, and walruses. These presentations characterized the status of the resource, the current state of knowledge on the topic, and information needs related to an assessment of the effects of oil and gas development. An overview of each presentation and the presentation materials used at the meeting are provided in the Planning Meeting report. The reader should refer to that report as well as to the information presented in the current report for a more complete understanding of each resource.« less

The use of intelligent database systems in acute pancreatitis--a systematic review.

PubMed

van den Heever, Marc; Mittal, Anubhav; Haydock, Matthew; Windsor, John

2014-01-01

Acute pancreatitis (AP) is a complex disease with multiple aetiological factors, wide ranging severity, and multiple challenges to effective triage and management. Databases, data mining and machine learning algorithms (MLAs), including artificial neural networks (ANNs), may assist by storing and interpreting data from multiple sources, potentially improving clinical decision-making. 1) Identify database technologies used to store AP data, 2) collate and categorise variables stored in AP databases, 3) identify the MLA technologies, including ANNs, used to analyse AP data, and 4) identify clinical and non-clinical benefits and obstacles in establishing a national or international AP database. Comprehensive systematic search of online reference databases. The predetermined inclusion criteria were all papers discussing 1) databases, 2) data mining or 3) MLAs, pertaining to AP, independently assessed by two reviewers with conflicts resolved by a third author. Forty-three papers were included. Three data mining technologies and five ANN methodologies were reported in the literature. There were 187 collected variables identified. ANNs increase accuracy of severity prediction, one study showed ANNs had a sensitivity of 0.89 and specificity of 0.96 six hours after admission--compare APACHE II (cutoff score ≥8) with 0.80 and 0.85 respectively. Problems with databases were incomplete data, lack of clinical data, diagnostic reliability and missing clinical data. This is the first systematic review examining the use of databases, MLAs and ANNs in the management of AP. The clinical benefits these technologies have over current systems and other advantages to adopting them are identified. Copyright © 2013 IAP and EPC. Published by Elsevier B.V. All rights reserved.

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

ERIC Educational Resources Information Center

Nemeth, Erik

2010-01-01

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

Cholesterol Point-of-Care Testing for Community Pharmacies: A Review of the Current Literature.

PubMed

Haggerty, Lauren; Tran, Deanna

2017-08-01

To summarize the literature on cholesterol point-of-care tests (POCTs). This article would serve as a resource to assist community pharmacists in developing cholesterol point-of-care (POC) pharmacy services. A literature search was performed in MEDLINE Ovid, PubMed, EMBASE, and Cochrane database using the following medical subject headings (MeSH) terms: point-of-care test, cholesterol, blood chemical analysis, rapid testing, collaborative practice, community pharmacy, and ambulatory care. Additional resources including device manufacturer web sites were summarized to supplement the current literature. All human research articles, review articles, meta-analyses, and abstracts published in English through September 1, 2014, were considered. A total of 36 articles were applicable for review. Information was divided into the following categories to be summarized: devices, pharmacists' impact, and operational cost for the pharmacy. The current literature suggests that POCTs in community pharmacies assist with patient outcomes by providing screenings and referring patients with dyslipidemia for further evaluation. The majority of studies on cholesterol POC devices focused on accuracy, revealing the need for further studies to develop best practices and practice models with successful reimbursement. Accuracy, device specifications, required supplies, and patient preference should be considered when selecting a POC device for purchase.

Participation and environmental aspects in education and the ICF and the ICF-CY: findings from a systematic literature review.

PubMed

Maxwell, Gregor; Alves, Ines; Granlund, Mats

2012-01-01

This paper presents findings from a systematic review of the literature related to participation and the ICF/ICF-CY in educational research. To analyse how and investigate the application of participation in educational research. Specifically, how participation is related to the environmental dimensions availability, accessibility, affordability, accommodability and acceptability. A systematic literature review using database keyword searches and refinement protocols using inclusion and exclusion criteria at abstract, full-text and extraction. Four hundred and twenty-one initial works were found. Twenty-three met the inclusion criteria. Availability and accommodations are the most investigated dimensions. Operationalization of participation is not always consistent with definitions used. Research is developing a holistic approach to investigating participation as, although all papers reference at least one environmental dimension, only four of the 11 empirical works reviewed present a fully balanced approach when theorizing and operationalizing participation; hopefully this balanced approach will continue and influence educational policy and school practice.

[A statistical analysis and perspective of headache-related papers covered in 2011 PubMed].

PubMed

Zhang, Ming-jie; Yu, Sheng-yuan; Chu, Bing-qian; Dai, Wei

2013-01-01

To investigate the distribution and hot spots of literatures on headache by bibliometric analysis in order to provide reference for further study. Literatures that contained headache or migraine in text words published in 2011 in PubMed databases (www.ncbi.nlm.nih.gov/Pubmed) were searched. Journals, countries and subjects were bibliometrically analysed. There were 3683 papers involved to headache published in PubMed in 2011, of which 1527 papers were on headache research. The number of papers on headache research published by USA was the most followed by Italy and Germany (USA 23.25%, Italy 10.74%, Germany 5.83%). The mainly studied subjects were therapy (29.60%), pathophysiology (18.66%) and etiology (16.31%). 14.86% papers published in Cephalalgia, which is one of the most important journals, reported negative results. The emphasis of headache research was on migraine. Therapy, pathophysiology and etiology were the hot spot. Literatures with negative result attracted authors to give the more attention.

Academic dishonesty today, unethical practices tomorrow?

PubMed

LaDuke, Rebekah D

2013-01-01

The purpose of this article was to review the most current published literature on the topics of academic dishonesty, unethical professional practices, and research that studied the correlation between these 2 areas of interest. Literature was retrieved by utilizing key words such as academic dishonesty, cheating, workplace dishonesty, and unethical behavior. Multiple research databases were used and a reference librarian in locating relevant research studies resulting in 16 research articles reviewed and 7 articles referenced within the literature review. Upon completion, it became apparent that nursing educators should be concerned that nursing students found to be academically dishonest today may have a higher incidence of displaying unethical practices as a registered nurse tomorrow. It also became clear that the nursing profession needs to conduct its own research in this field to verify findings discovered by other professions such as engineering, business, and psychology. Finally, recommendations were given on how nursing educators should handle the topic of ethics in nursing programs. Copyright © 2013 Elsevier Inc. All rights reserved.

User`s and reference guide to the INEL RML/analytical radiochemistry sample tracking database version 1.00

DOE Office of Scientific and Technical Information (OSTI.GOV)

Femec, D.A.

This report discusses the sample tracking database in use at the Idaho National Engineering Laboratory (INEL) by the Radiation Measurements Laboratory (RML) and Analytical Radiochemistry. The database was designed in-house to meet the specific needs of the RML and Analytical Radiochemistry. The report consists of two parts, a user`s guide and a reference guide. The user`s guide presents some of the fundamentals needed by anyone who will be using the database via its user interface. The reference guide describes the design of both the database and the user interface. Briefly mentioned in the reference guide are the code-generating tools, CREATE-SCHEMAmore » and BUILD-SCREEN, written to automatically generate code for the database and its user interface. The appendices contain the input files used by the these tools to create code for the sample tracking database. The output files generated by these tools are also included in the appendices.« less

[Profile of a systematic search. Search areas, databases and reports].

PubMed

Korsbek, Lisa; Bendix, Ane Friis; Kidholm, Kristian

2006-04-03

Systematic literature search is a fundamental in evidence-based medicine. But systematic literature search is not yet a very well used way of retrieving evidence-based information. This article profiles a systematic literature search for evidence-based literature. It goes through the most central databases and gives an example of how to document the literature search. The article also sums up the literature search in all reviews in Ugeskrift for Laeger in the year 2004.

Bibliography on CO2 Effects on Vegetation and Ecosystems: 1990-1999 Literature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, Michael H.; Curtis, Peter S.; Institute for Scientific Information

This database provides complete bibliographic citations (plus abstracts and keywords, when available) for more than 2700 references published between 1990 and 1999 on the direct effects of elevated atmospheric concentrations of carbon dioxide (CO2) on vegetation, ecosystems, their components and interactions. This bibliography is an update to Direct Effects of Atmospheric CO2 Enrichment on Plants and Ecosystems: An Updated Bibliographic Data Base (ORNL/CDIAC-70), edited by Boyd R. Strain and Jennifer D. Cure, which covered literature from 1980 to 1994. This bibliography was developed to support the Carbon Dioxide Meta-Analysis Project (CO2MAP) at The Ohio State University, but was designed tomore » be useful for a wide variety of purposes related to the effects of elevated CO2 on vegetation and ecosystems.« less

Conceptualizing belonging.

PubMed

Mahar, Alyson L; Cobigo, Virginie; Stuart, Heather

2013-06-01

To develop a transdisciplinary conceptualization of social belonging that could be used to guide measurement approaches aimed at evaluating the effectiveness of community-based programs for people with disabilities. We conducted a narrative, scoping review of peer reviewed English language literature published between 1990 and July 2011 using multiple databases, with "sense of belonging" as a key search term. The search engine ranked articles for relevance to the search strategy. Articles were searched in order until theoretical saturation was reached. We augmented this search strategy by reviewing reference lists of relevant papers. Theoretical saturation was reached after 40 articles; 22 of which were qualitative accounts. We identified five intersecting themes: subjectivity; groundedness to an external referent; reciprocity; dynamism and self-determination. We define a sense of belonging as a subjective feeling of value and respect derived from a reciprocal relationship to an external referent that is built on a foundation of shared experiences, beliefs or personal characteristics. These feelings of external connectedness are grounded to the context or referent group, to whom one chooses, wants and feels permission to belong. This dynamic phenomenon may be either hindered or promoted by complex interactions between environmental and personal factors.

Photosynthesis-related quantities for education and modeling.

PubMed

Antal, Taras K; Kovalenko, Ilya B; Rubin, Andrew B; Tyystjärvi, Esa

2013-11-01

A quantitative understanding of the photosynthetic machinery depends largely on quantities, such as concentrations, sizes, absorption wavelengths, redox potentials, and rate constants. The present contribution is a collection of numbers and quantities related mainly to photosynthesis in higher plants. All numbers are taken directly from a literature or database source and the corresponding reference is provided. The numerical values, presented in this paper, provide ranges of values, obtained in specific experiments for specific organisms. However, the presented numbers can be useful for understanding the principles of structure and function of photosynthetic machinery and for guidance of future research.

Standardising the descriptive epidemiology of osteoporosis: recommendations from the Epidemiology and Quality of Life Working Group of IOF.

PubMed

Kanis, J A; Adachi, J D; Cooper, C; Clark, P; Cummings, S R; Diaz-Curiel, M; Harvey, N; Hiligsmann, M; Papaioannou, A; Pierroz, D D; Silverman, S L; Szulc, P

2013-11-01

The Committee of Scientific Advisors of International Osteoporosis Foundation (IOF) recommends that papers describing the descriptive epidemiology of osteoporosis using bone mineral density (BMD) at the femoral neck include T-scores derived from an international reference standard. The prevalence of osteoporosis as defined by the T-score is inconsistently reported in the literature which makes comparisons between studies problematic. The Epidemiology and Quality of Life Working Group of IOF convened to make its recommendations and endorsement sought thereafter from the Committee of Scientific Advisors of IOF. The Committee of Scientific Advisors of IOF recommends that papers describing the descriptive epidemiology of osteoporosis using BMD at the femoral neck include T-scores derived from the National Health and Nutrition Examination Survey III reference database for femoral neck measurements in Caucasian women aged 20-29 years. It is expected that the use of the reference standard will help resolve difficulties in the comparison of results between studies and the comparative assessment of new technologies.

Stopping cross section of vanadium for H+ and He+ ions in a large energy interval deduced from backscattering spectra

NASA Astrophysics Data System (ADS)

Moro, M. V.; Bruckner, B.; Grande, P. L.; Tabacniks, M. H.; Bauer, P.; Primetzhofer, D.

2018-06-01

We have experimentally determined electronic stopping cross sections of vanadium for 50-2750 keV protons and for 250-6000 keV He ions by relative measurements in backscattering geometry. To check the consistency of the employed procedure we investigate how to define adequate reference stopping cross section data and chose different reference materials. To proof consistency of different reference data sets, an intercomparison is performed to test the reliability of the evaluation procedure for a wide range of energies. This process yielded consistent results. The resulting stopping cross section data for V are compared to values from the IAEA database, to the most commonly employed semi-empirical program SRIM, and to calculations according to CasP. For helium, our results show a significant deviation of up to 10% with respect to literature and to SRIM, but are in very good agreement with the CasP predictions, in particular when charge-exchange processes are included in the model.

An overview and categorization of dynamic arm supports for people with decreased arm function.

PubMed

Van der Heide, Loek A; van Ninhuijs, Bob; Bergsma, Arjen; Gelderblom, Gert Jan; van der Pijl, Dick J; de Witte, Luc P

2014-08-01

Assistive devices that augment arm function were already introduced during the polio era. Devices are still being developed, but a review has not been performed thus far. To create an overview and categorize assistive devices facilitating arm function in activities of daily living for people with decreased arm function. Literature review. A systematic review in three scientific literature databases. Conference proceedings, assistive technology databases, and references were searched and experts consulted. This resulted in a database of dynamic arm supports. Product information was added, and the devices were categorized. A total of 104 dynamic arm supports were found. These could be categorized as nonactuated devices (N = 39), passively actuated devices (N = 24), actively actuated devices (N = 34), or devices using the functional electrical stimulation principle (N = 7). Functionality analysis resulted in second-level categorization: tremor suppression, facilitation of anti-gravity movement, and assistance of specific joint motion. All devices could be ordered in a categorization of low complexity. Many have been developed; most have disappeared and have been succeeded by similar devices. Limitations of the devices found mainly concern interfacing and the range of motion facilitated. Future devices could make use of whatever residual strength is available in the users' arm for control. The provided overview of devices in this article and the classification developed is relevant for practitioners seeking assistive solutions for their clients as it makes the range of developed solutions both accessible and comprehensible. © The International Society for Prosthetics and Orthotics 2013.

PaperBLAST: Text Mining Papers for Information about Homologs

DOE PAGES

Price, Morgan N.; Arkin, Adam P.

2017-08-15

Large-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources (Swiss-Prot, GeneRIF, and EcoCyc) that link protein sequences to scientific articles. PaperBLAST’s database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quicklymore » finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. With the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about similar proteins, PaperBLAST searches the full text of scientific articles for protein identifiers or gene identifiers, and it links these articles to protein sequences. Then, given a protein of interest, it can quickly find similar proteins in its database by using standard software (BLAST), and it can show snippets of text from relevant papers. We hope that PaperBLAST will make it easier for biologists to predict proteins’ functions.« less

PaperBLAST: Text Mining Papers for Information about Homologs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Price, Morgan N.; Arkin, Adam P.

Large-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources (Swiss-Prot, GeneRIF, and EcoCyc) that link protein sequences to scientific articles. PaperBLAST’s database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quicklymore » finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. With the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about similar proteins, PaperBLAST searches the full text of scientific articles for protein identifiers or gene identifiers, and it links these articles to protein sequences. Then, given a protein of interest, it can quickly find similar proteins in its database by using standard software (BLAST), and it can show snippets of text from relevant papers. We hope that PaperBLAST will make it easier for biologists to predict proteins’ functions.« less

PaperBLAST: Text Mining Papers for Information about Homologs

PubMed Central

Arkin, Adam P.

2017-01-01

ABSTRACT Large-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources (Swiss-Prot, GeneRIF, and EcoCyc) that link protein sequences to scientific articles. PaperBLAST’s database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quickly finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. PaperBLAST is available at http://papers.genomics.lbl.gov/. IMPORTANCE With the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about similar proteins, PaperBLAST searches the full text of scientific articles for protein identifiers or gene identifiers, and it links these articles to protein sequences. Then, given a protein of interest, it can quickly find similar proteins in its database by using standard software (BLAST), and it can show snippets of text from relevant papers. We hope that PaperBLAST will make it easier for biologists to predict proteins’ functions. PMID:28845458

PaperBLAST: Text Mining Papers for Information about Homologs.

PubMed

Price, Morgan N; Arkin, Adam P

2017-01-01

Large-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources (Swiss-Prot, GeneRIF, and EcoCyc) that link protein sequences to scientific articles. PaperBLAST's database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quickly finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. PaperBLAST is available at http://papers.genomics.lbl.gov/. IMPORTANCE With the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about similar proteins, PaperBLAST searches the full text of scientific articles for protein identifiers or gene identifiers, and it links these articles to protein sequences. Then, given a protein of interest, it can quickly find similar proteins in its database by using standard software (BLAST), and it can show snippets of text from relevant papers. We hope that PaperBLAST will make it easier for biologists to predict proteins' functions.

[Bibliometrics and visualization analysis of land use regression models in ambient air pollution research].

PubMed

Zhang, Y J; Zhou, D H; Bai, Z P; Xue, F X

2018-02-10

Objective: To quantitatively analyze the current status and development trends regarding the land use regression (LUR) models on ambient air pollution studies. Methods: Relevant literature from the PubMed database before June 30, 2017 was analyzed, using the Bibliographic Items Co-occurrence Matrix Builder (BICOMB 2.0). Keywords co-occurrence networks, cluster mapping and timeline mapping were generated, using the CiteSpace 5.1.R5 software. Relevant literature identified in three Chinese databases was also reviewed. Results: Four hundred sixty four relevant papers were retrieved from the PubMed database. The number of papers published showed an annual increase, in line with the growing trend of the index. Most papers were published in the journal of Environmental Health Perspectives . Results from the Co-word cluster analysis identified five clusters: cluster#0 consisted of birth cohort studies related to the health effects of prenatal exposure to air pollution; cluster#1 referred to land use regression modeling and exposure assessment; cluster#2 was related to the epidemiology on traffic exposure; cluster#3 dealt with the exposure to ultrafine particles and related health effects; cluster#4 described the exposure to black carbon and related health effects. Data from Timeline mapping indicated that cluster#0 and#1 were the main research areas while cluster#3 and#4 were the up-coming hot areas of research. Ninety four relevant papers were retrieved from the Chinese databases with most of them related to studies on modeling. Conclusion: In order to better assess the health-related risks of ambient air pollution, and to best inform preventative public health intervention policies, application of LUR models to environmental epidemiology studies in China should be encouraged.

BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature.

PubMed

Sen Sarma, Moushumi; Arcoleo, David; Khetani, Radhika S; Chee, Brant; Ling, Xu; He, Xin; Jiang, Jing; Mei, Qiaozhu; Zhai, ChengXiang; Schatz, Bruce

2011-07-01

With the rapid decrease in cost of genome sequencing, the classification of gene function is becoming a primary problem. Such classification has been performed by human curators who read biological literature to extract evidence. BeeSpace Navigator is a prototype software for exploratory analysis of gene function using biological literature. The software supports an automatic analogue of the curator process to extract functions, with a simple interface intended for all biologists. Since extraction is done on selected collections that are semantically indexed into conceptual spaces, the curation can be task specific. Biological literature containing references to gene lists from expression experiments can be analyzed to extract concepts that are computational equivalents of a classification such as Gene Ontology, yielding discriminating concepts that differentiate gene mentions from other mentions. The functions of individual genes can be summarized from sentences in biological literature, to produce results resembling a model organism database entry that is automatically computed. Statistical frequency analysis based on literature phrase extraction generates offline semantic indexes to support these gene function services. The website with BeeSpace Navigator is free and open to all; there is no login requirement at www.beespace.illinois.edu for version 4. Materials from the 2010 BeeSpace Software Training Workshop are available at www.beespace.illinois.edu/bstwmaterials.php.

Young adults with intellectual disability transitioning from school to post-school: a literature review framed within the ICF.

PubMed

Foley, K-R; Dyke, P; Girdler, S; Bourke, J; Leonard, H

2012-01-01

The purpose of this review was to describe literature relating to transition for young people with an intellectual disability and identify gaps within the current knowledge base. A narrative literature review was undertaken. Searches of databases Medline, CINAHL, PsycINFO, ERIC, ISI Web of Science and ProQuest 500 International provided relevant research articles. The search terms used were intellectual disability, transition, employment, and ICF as well as other terms derived from the ICF. Manual searches of reference lists identified additional studies. Furthermore, government websites were searched for relevant reports and policies. Transition literature was explored by ICF domains; body functions and structures, activity and participation and contextual factors. Studies were identified in some but not all areas and included literature describing self-determination and participation in leisure activities for those with mild intellectual disability. However, significant gaps were found particularly for those with severe intellectual disability. The ICF is a useful tool in framing a review of transition literature for young people with intellectual disability due to the complexity and multi-faceted nature of transition. The important influence of environmental factors including family systems, post-school services and access to transport were highlighted as having considerable impacts on transition outcomes.

Diagnostic accuracy of scapular physical examination tests for shoulder disorders: a systematic review.

PubMed

Wright, Alexis A; Wassinger, Craig A; Frank, Mason; Michener, Lori A; Hegedus, Eric J

2013-09-01

To systematically review and critique the evidence regarding the diagnostic accuracy of physical examination tests for the scapula in patients with shoulder disorders. A systematic, computerised literature search of PubMED, EMBASE, CINAHL and the Cochrane Library databases (from database inception through January 2012) using keywords related to diagnostic accuracy of physical examination tests of the scapula. The Quality Assessment of Diagnostic Accuracy Studies tool was used to critique the quality of each paper. Eight articles met the inclusion criteria; three were considered to be of high quality. Of the three high-quality studies, two were in reference to a 'diagnosis' of shoulder pain. Only one high-quality article referenced specific shoulder pathology of acromioclavicular dislocation with reported sensitivity of 71% and 41% for the scapular dyskinesis and SICK scapula test, respectively. Overall, no physical examination test of the scapula was found to be useful in differentially diagnosing pathologies of the shoulder.

Complementary and Alternative Therapies for Autism Spectrum Disorder

PubMed Central

Fusar-Poli, Laura; Rocchetti, Matteo; Provenzani, Umberto; Barale, Francesco

2015-01-01

Background. Complementary and alternative medicine (CAM) represents a popular therapeutic option for patients with autism spectrum disorder (ASD). Unfortunately, there is a paucity of data regarding the efficacy of CAM in ASD. The aim of the present systematic review is to investigate trials of CAM in ASD. Material and Methods. We searched the following databases: MEDLINE, EMBASE, Cochrane Database of Systematic Reviews, CINAHL, Psychology and Behavioral Sciences Collection, Agricola, and Food Science Source. Results. Our literature search identified 2687 clinical publications. After the title/abstract screening, 139 publications were obtained for detailed evaluation. After detailed evaluation 67 studies were included, from hand search of references we retrieved 13 additional studies for a total of 80. Conclusion. There is no conclusive evidence supporting the efficacy of CAM therapies in ASD. Promising results are reported for music therapy, sensory integration therapy, acupuncture, and massage. PMID:26064157

Acupuncture for patients with Alzheimer's disease: a systematic review protocol

PubMed Central

Zhou, Jing; Peng, Weina; Li, Wang; Liu, Zhishun

2014-01-01

Introduction The aim of this protocol is to provide the methods used to assess the effectiveness and safety of acupuncture for the treatment of patients with Alzheimer's disease. Methods and analysis We will search the following electronic databases: The Cochrane Library, PubMed, Medline, Embase, PsycINFO, Chinese Biomedical Literature Database, Chinese Medical Current Contents and China National Knowledge Infrastructure without restriction of language and publication status. Other sources such as Chinese acupuncture journals and the reference list of selected studies will also be searched. After screening the studies, a meta-analysis of randomised controlled trials will be conducted, if possible. Results expressed as risk ratios for dichotomous data and standardised or weighted mean differences for continuous data, will be used for data synthesis. Dissemination The protocol of this systematic review will be disseminated in a peer-reviewed journal and presented at a relevant conference. Trial registration number PROSPERO CRD42014009619 PMID:25142265

Reference Fluid Thermodynamic and Transport Properties Database (REFPROP)

National Institute of Standards and Technology Data Gateway

SRD 23 NIST Reference Fluid Thermodynamic and Transport Properties Database (REFPROP) (PC database for purchase)   NIST 23 contains revised data in a Windows version of the database, including 105 pure fluids and allowing mixtures of up to 20 components. The fluids include the environmentally acceptable HFCs, traditional HFCs and CFCs and 'natural' refrigerants like ammonia

Literature searches on Ayurveda: An update.

PubMed

Aggithaya, Madhur G; Narahari, Saravu R

2015-01-01

The journals that publish on Ayurveda are increasingly indexed by popular medical databases in recent years. However, many Eastern journals are not indexed biomedical journal databases such as PubMed. Literature searches for Ayurveda continue to be challenging due to the nonavailability of active, unbiased dedicated databases for Ayurvedic literature. In 2010, authors identified 46 databases that can be used for systematic search of Ayurvedic papers and theses. This update reviewed our previous recommendation and identified current and relevant databases. To update on Ayurveda literature search and strategy to retrieve maximum publications. Author used psoriasis as an example to search previously listed databases and identify new. The population, intervention, control, and outcome table included keywords related to psoriasis and Ayurvedic terminologies for skin diseases. Current citation update status, search results, and search options of previous databases were assessed. Eight search strategies were developed. Hundred and five journals, both biomedical and Ayurveda, which publish on Ayurveda, were identified. Variability in databases was explored to identify bias in journal citation. Five among 46 databases are now relevant - AYUSH research portal, Annotated Bibliography of Indian Medicine, Digital Helpline for Ayurveda Research Articles (DHARA), PubMed, and Directory of Open Access Journals. Search options in these databases are not uniform, and only PubMed allows complex search strategy. "The Researches in Ayurveda" and "Ayurvedic Research Database" (ARD) are important grey resources for hand searching. About 44/105 (41.5%) journals publishing Ayurvedic studies are not indexed in any database. Only 11/105 (10.4%) exclusive Ayurveda journals are indexed in PubMed. AYUSH research portal and DHARA are two major portals after 2010. It is mandatory to search PubMed and four other databases because all five carry citations from different groups of journals. The hand searching is important to identify Ayurveda publications that are not indexed elsewhere. Availability information of citations in Ayurveda libraries from National Union Catalogue of Scientific Serials in India if regularly updated will improve the efficacy of hand searching. A grey database (ARD) contains unpublished PG/Ph.D. theses. The AYUSH portal, DHARA (funded by Ministry of AYUSH), and ARD should be merged to form single larger database to limit Ayurveda literature searches.

Needs assessment for next generation computer-aided mammography reference image databases and evaluation studies.

PubMed

Horsch, Alexander; Hapfelmeier, Alexander; Elter, Matthias

2011-11-01

Breast cancer is globally a major threat for women's health. Screening and adequate follow-up can significantly reduce the mortality from breast cancer. Human second reading of screening mammograms can increase breast cancer detection rates, whereas this has not been proven for current computer-aided detection systems as "second reader". Critical factors include the detection accuracy of the systems and the screening experience and training of the radiologist with the system. When assessing the performance of systems and system components, the choice of evaluation methods is particularly critical. Core assets herein are reference image databases and statistical methods. We have analyzed characteristics and usage of the currently largest publicly available mammography database, the Digital Database for Screening Mammography (DDSM) from the University of South Florida, in literature indexed in Medline, IEEE Xplore, SpringerLink, and SPIE, with respect to type of computer-aided diagnosis (CAD) (detection, CADe, or diagnostics, CADx), selection of database subsets, choice of evaluation method, and quality of descriptions. 59 publications presenting 106 evaluation studies met our selection criteria. In 54 studies (50.9%), the selection of test items (cases, images, regions of interest) extracted from the DDSM was not reproducible. Only 2 CADx studies, not any CADe studies, used the entire DDSM. The number of test items varies from 100 to 6000. Different statistical evaluation methods are chosen. Most common are train/test (34.9% of the studies), leave-one-out (23.6%), and N-fold cross-validation (18.9%). Database-related terminology tends to be imprecise or ambiguous, especially regarding the term "case". Overall, both the use of the DDSM as data source for evaluation of mammography CAD systems, and the application of statistical evaluation methods were found highly diverse. Results reported from different studies are therefore hardly comparable. Drawbacks of the DDSM (e.g. varying quality of lesion annotations) may contribute to the reasons. But larger bias seems to be caused by authors' own decisions upon study design. RECOMMENDATIONS/CONCLUSION: For future evaluation studies, we derive a set of 13 recommendations concerning the construction and usage of a test database, as well as the application of statistical evaluation methods.

Emerging modalities in dysphagia rehabilitation: neuromuscular electrical stimulation.

PubMed

Huckabee, Maggie-Lee; Doeltgen, Sebastian

2007-10-12

The aim of this review article is to advise the New Zealand medical community about the application of neuromuscular electrical stimulation (NMES) as a treatment for pharyngeal swallowing impairment (dysphagia). NMES in this field of rehabilitation medicine has quickly emerged as a widely used method overseas but has been accompanied by significant controversy. Basic information is provided about the physiologic background of electrical stimulation. The literature reviewed in this manuscript was derived through a computer-assisted search using the biomedical database Medline to identify all relevant articles published until from the initiation of the databases up to January 2007. The reviewers used the following search strategy: [(deglutition disorders OR dysphagia) AND (neuromuscular electrical stimulation OR NMES)]. In addition, the technique of reference tracing was used and very recently published studies known to the authors but not yet included in the database systems were included. This review elucidates not only the substantive potential benefit of this treatment, but also potential key concerns for patient safety and long term outcome. The discussion within the clinical and research communities, especially around the commercially available VitalStim stimulator, is objectively explained.

Contaminant exposure and effects--terrestrial vertebrates database: Trends and data gaps for Atlantic Coast estuaries

USGS Publications Warehouse

Rattner, B.A.; Pearson, J.L.; Golden, N.H.; Cohen, J.B.; Erwin, R.M.; Ottinger, M.A.

2000-01-01

In order to examine the condition of biota in Atlantic coast estuaries, a ?Contaminant Exposure and Effects--Terrestrial Vertebrates? database (CEE-TV) has been compiled through computerized search of published literature, review of existing databases, and solicitation of unpublished reports from conservation agencies, private groups, and universities. Summary information has been entered into the database, including species, collection date (1965-present), site coordinates, estuary name, hydrologic unit catalogue code, sample matrix, contaminant concentrations, biomarker and bioindicator responses, and reference source, utilizing a 98-field character and numeric format. Currently, the CEE-TV database contains 3699 georeferenced records representing 190 vertebrate species and >145,000 individuals residing in estuaries from Maine through Florida. This relational database can be directly queried, imported into a Geographic Information System to examine spatial patterns, identify data gaps and areas of concern, generate hypotheses, and focus ecotoxicological field assessments. Information on birds made up the vast majority (83%) of the database, with only a modicum of data on amphibians (75,000 chemical compounds in commerce, only 118 commonly measured environmental contaminants were quantified in tissues of terrestrial vertebrates. There were no CEE-TV data records in 15 of the 67 estuaries located along the Atlantic coast and Florida Gulf coast. The CEE-TV database has a number of potential applications including focusing biomonitoring efforts to generate critically needed ecotoxicological data in the numerous ?gaps? along the coast, reducing uncertainty about contaminant risk, identifying areas for mitigation, restoration or special management, and ranking ecological conditions of estuaries.

Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine.

PubMed

Singhal, Ayush; Simmons, Michael; Lu, Zhiyong

2016-11-01

The practice of precision medicine will ultimately require databases of genes and mutations for healthcare providers to reference in order to understand the clinical implications of each patient's genetic makeup. Although the highest quality databases require manual curation, text mining tools can facilitate the curation process, increasing accuracy, coverage, and productivity. However, to date there are no available text mining tools that offer high-accuracy performance for extracting such triplets from biomedical literature. In this paper we propose a high-performance machine learning approach to automate the extraction of disease-gene-variant triplets from biomedical literature. Our approach is unique because we identify the genes and protein products associated with each mutation from not just the local text content, but from a global context as well (from the Internet and from all literature in PubMed). Our approach also incorporates protein sequence validation and disease association using a novel text-mining-based machine learning approach. We extract disease-gene-variant triplets from all abstracts in PubMed related to a set of ten important diseases (breast cancer, prostate cancer, pancreatic cancer, lung cancer, acute myeloid leukemia, Alzheimer's disease, hemochromatosis, age-related macular degeneration (AMD), diabetes mellitus, and cystic fibrosis). We then evaluate our approach in two ways: (1) a direct comparison with the state of the art using benchmark datasets; (2) a validation study comparing the results of our approach with entries in a popular human-curated database (UniProt) for each of the previously mentioned diseases. In the benchmark comparison, our full approach achieves a 28% improvement in F1-measure (from 0.62 to 0.79) over the state-of-the-art results. For the validation study with UniProt Knowledgebase (KB), we present a thorough analysis of the results and errors. Across all diseases, our approach returned 272 triplets (disease-gene-variant) that overlapped with entries in UniProt and 5,384 triplets without overlap in UniProt. Analysis of the overlapping triplets and of a stratified sample of the non-overlapping triplets revealed accuracies of 93% and 80% for the respective categories (cumulative accuracy, 77%). We conclude that our process represents an important and broadly applicable improvement to the state of the art for curation of disease-gene-variant relationships.

Trace metal ions release from fixed orthodontic appliances and DNA damage in oral mucosa cells by in vivo studies: A literature review.

PubMed

Downarowicz, Patrycja; Mikulewicz, Marcin

2017-10-01

An overview of professional literature referring to the release of metal ions from fixed orthodontic appliances and their influence on oral mucosa in conditions of in vivo are presented, along with a detailed analysis of the exposure of the cells of cheek mucosa epithelium to metal ions. Electronic databases (PubMed, Elsevier, Ebsco) were searched with no language restrictions. The relevant orthodontic journals and reference lists were checked for all eligible studies. A total of 38 scientific articles were retrieved in the initial search. However, only 7 articles met the inclusion criteria. Statistically significant differences in the levels of the amount of nickel ions, cobalt ions and chromium ions were observed in cells of cheek mucosa. The most biocompatible material used in the production of fixed orthodontic appliances is titanium, and the least biocompatible material is steel, which releases the largest amount of nickel and chromium. Metal ions are released from fixed orthodontic appliances only in the first phase of treatment. It is recommended to conduct further, long-term research on a larger number of patients to define the influence of using fixed orthodontic appliances and biological effect they might have on tissues.

Analysis of context factors in compulsory and incentive strategies for improving attraction and retention of health workers in rural and remote areas: a systematic review.

PubMed

Liu, Xiaoyun; Dou, Lixia; Zhang, Huan; Sun, Yang; Yuan, Beibei

2015-07-21

Current literature systematically reports that interventions to attract and retain health workers in underserved areas need to be context specific but rarely defines what that means. In this systematic review, we try to summarize and analyse context factors influencing the implementation of interventions to attract and retain rural health workers. We searched online databases, relevant websites and reference lists of selected literature to identify studies on compulsory rural service programmes and financial incentives. Forty studies were selected. Information regarding context factors at macro, meso and micro levels was extracted and synthesized. Macro-level context factors include political, economic and social factors. Meso-level factors include health system factors such as maldistribution of health workers, growing private sector, decentralization and health financing. Micro-level factors refer to the policy implementation process including funding sources, administrative agency, legislation process, monitoring and evaluation. Macro-, meso- and micro-level context factors can play different roles in agenda setting, policy formulation and implementation of health interventions to attract and retain rural health workers. These factors should be systematically considered in the different stages of policy process and evaluation.

Community hospitals--the place of local service provision in a modernising NHS: an integrative thematic literature review.

PubMed

Heaney, David; Black, Corri; O'donnell, Catherine A; Stark, Cameron; van Teijlingen, Edwin

2006-12-21

Recent developments within the United Kingdom's (UK) health care system have re-awakened interest in community hospitals (CHs) and their role in the provision of health care. This integrative literature review sought to identify and assess the current evidence base for CHs. A range of electronic reference databases were searched from January 1984 to either December 2004 or February 2005: Medline, Embase, Web of Knowledge, BNI, CINAHL, HMIC, ASSIA, PsychInfo, SIGLE, Dissertation Abstracts, Cochrane Library, Kings Fund website, using both keywords and text words. Thematic analysis identified recurrent themes across the literature; narrative analyses were written for each theme, identifying unifying concepts and discrepant issues. The search strategy identified over 16,000 international references. We included papers of any study design focussing on hospitals in which care was led principally by general practitioners or nurses. Papers from developing countries were excluded. A review of titles revealed 641 potentially relevant references; abstract appraisal identified 161 references for review. During data extraction, a further 48 papers were excluded, leaving 113 papers in the final review. The most common methodological approaches were cross-sectional/descriptive studies, commentaries and expert opinion. There were few experimental studies, systematic reviews, economic studies or studies that reported on longer-term outcomes. The key themes identified were origin and location of CHs; their place in the continuum of care; services provided; effectiveness, efficiency and equity of CHs; and views of patients and staff. In general, there was a lack of robust evidence for the role of CHs, which is partly due to the ad hoc nature of their development and lack of clear strategic vision for their future. Evidence for the effectiveness and efficiency of the services provided was limited. Most people admitted to CHs appeared to be older, suggesting that admittance to CHs was age-related rather than condition-related. Overall the literature surveyed was long on opinion and short of robust studies on CHs. While lack of evidence on CHs does not imply lack of effect, there is an urgent need to develop a research agenda that addresses the key issues of health care delivery in the CH setting.

A Sediment Testing Reference Area Database for the San Francisco Deep Ocean Disposal Site (SF-DODS)

EPA Pesticide Factsheets

EPA established and maintains a SF-DODS reference area database of previously-collected sediment test data. Several sets of sediment test data have been successfully collected from the SF-DODS reference area.

Mapping evidence on the distribution of human papillomavirus-related cancers in sub-Saharan Africa: scoping review protocol.

PubMed

Lekoane, Bridget K M; Mashamba-Thompson, Tivani P; Ginindza, Themba G

2017-11-17

Despite the introduction of HPV vaccines, the incidence of HPV-related cancers (cervical, penile, anal, vulvar, vagina, head, and neck) in sub-Saharan Africa has been rising. The increasing incidence of these HPV-related cancers has been attributed to changes in lifestyle-related risk factors, most notably sexual behavior. The main objective of this study is to map evidence on the distribution of HIV-related cancers in sub-Saharan Africa (SSA). We will conduct a scoping review to explore, describe, and map literature on the distribution of HPV-related cancers in sub-Saharan Africa. The primary search will include peer-reviewed and review articles. The list of references from included studies will also be searched. The search will be performed using EBSCOhost platform by searching the following databases within the platform: Academic search complete, health source: nursing/academic edition, CINAHL with full text, PubMed, Science Direct, Google scholar and World Health Organization (WHO) library databases, and gray literature. The researcher will search the articles using keywords, from the included studies; abstract and full articles will be screened by two independent reviewers. The screening will be guided by the inclusion and exclusion criteria. A thematic content analysis will be used to present the narrative account of the reviews, using NVivo version 10. We anticipate finding relevant literature on the distribution of HPV-related cancers in sub-Saharan Africa. The study findings will help reveal research gaps to guide future research. PROSPERO CRD42017062403.

[The evolution of the concept of self-care in the healthcare system: a narrative literature review].

PubMed

Lommi, Marzia; Matarese, Maria; Alvaro, Rosaria; Piredda, Michela; De Marinis, Maria Grazia

2015-01-01

To identify and analyze the definitions of self-care in the healthcare system in the evolution over time as well as to identify the key actors of self-care. We conducted a narrative review of the literature on the definition of self-care in the CINAHL, PubMed and ILISI databases. The searches ranged from the first year included in each database until May 2013. In addition, a secondary analysis was performed on the references of articles selected to identify additional data sources. The self-care definitions were grouped according to decades and examined in their evolution. The first self-care definitions date back to the seventies, but only in the eighties self-care has been seen as a key resource for healthcare systems. In the nineties, care activities previously considered the exclusive domain of the health professions were included in this concept; and finally over the 2000s the role of health professionals in self-care is highlighted, extending the self-care activities to the psychological, social and spiritual dimensions. Self-care activities can be carried out directly by the person upon himself, delegated to others, or performed on others. The review has showed the large body of literature published in different disciplinary and cultural fields, which has led to the proliferation of definitions and interpretations of self-care. Italy has taken part in a marginal way to the international debate. It would be useful that also Italian nurses did research to describe and understand.

Ethical issues with colorectal cancer screening-a systematic review.

PubMed

Hofmann, Bjørn

2017-06-01

Colorectal cancer (CRC) screening is widely recommended and implemented. However, sometimes CRC screening is not implemented despite good evidence, and some types of CRC screening are implemented despite lack of evidence. The objective of this article is to expose and elucidate relevant ethical issues in the literature on CRC screening that are important for open and transparent deliberation on CRC screening. An axiological question-based method is used for exposing and elucidating ethical issues relevant in HTA. A literature search in MEDLINE, Embase, PsycINFO, PubMed Bioethics subset, ISI Web of Knowledge, Bioethics Literature Database (BELIT), Ethics in Medicine (ETHMED), SIBIL Base dati di bioetica, LEWI Bibliographic Database on Ethics in the Sciences and Humanities, and EUROETHICS identified 870 references of which 114 were found relevant according to title and abstract. The content of the included papers were subject to ethical analysis to highlight the ethical issues, concerns, and arguments. A wide range of important ethical issues were identified. The main benefits are reduced relative CRC mortality rate, and potentially incidence rate, but there is no evidence of reduced absolute mortality rate. Potential harms are bleeding, perforation, false test results, overdetection, overdiagnosis, overtreatment (including unnecessary removal of polyps), and (rarely) death. Other important issues are related to autonomy and informed choice equity, justice, medicalization, and expanding disease. A series of important ethical issues have been identified and need to be addressed in open and transparent deliberation on CRC screening. © 2016 John Wiley & Sons, Ltd.

Environmental health impacts of tobacco farming: a review of the literature.

PubMed

Lecours, Natacha; Almeida, Guilherme E G; Abdallah, Jumanne M; Novotny, Thomas E

2012-03-01

To review the literature on environmental health impacts of tobacco farming and to summarise the findings and research gaps in this field. A standard literature search was performed using multiple electronic databases for identification of peer-reviewed articles. The internet and organisational databases were also used to find other types of documents (eg, books and reports). The reference lists of identified relevant documents were reviewed to find additional sources. The selected studies documented many negative environmental impacts of tobacco production at the local level, often linking them with associated social and health problems. The common agricultural practices related to tobacco farming, especially in low-income and middle-income countries, lead to deforestation and soil degradation. Agrochemical pollution and deforestation in turn lead to ecological disruptions that cause a loss of ecosystem services, including land resources, biodiversity and food sources, which negatively impact human health. Multinational tobacco companies' policies and practices contribute to environmental problems related to tobacco leaf production. Development and implementation of interventions against the negative environmental impacts of tobacco production worldwide are necessary to protect the health of farmers, particularly in low-income and middle-income countries. Transitioning these farmers out of tobacco production is ultimately the resolution to this environmental health problem. In order to inform policy, however, further research is needed to better quantify the health impacts of tobacco farming and evaluate the potential alternative livelihoods that may be possible for tobacco farmers globally.

Reference set for performance testing of pediatric vaccine safety signal detection methods and systems.

PubMed

Brauchli Pernus, Yolanda; Nan, Cassandra; Verstraeten, Thomas; Pedenko, Mariia; Osokogu, Osemeke U; Weibel, Daniel; Sturkenboom, Miriam; Bonhoeffer, Jan

2016-12-12

Safety signal detection in spontaneous reporting system databases and electronic healthcare records is key to detection of previously unknown adverse events following immunization. Various statistical methods for signal detection in these different datasources have been developed, however none are geared to the pediatric population and none specifically to vaccines. A reference set comprising pediatric vaccine-adverse event pairs is required for reliable performance testing of statistical methods within and across data sources. The study was conducted within the context of the Global Research in Paediatrics (GRiP) project, as part of the seventh framework programme (FP7) of the European Commission. Criteria for the selection of vaccines considered in the reference set were routine and global use in the pediatric population. Adverse events were primarily selected based on importance. Outcome based systematic literature searches were performed for all identified vaccine-adverse event pairs and complemented by expert committee reports, evidence based decision support systems (e.g. Micromedex), and summaries of product characteristics. Classification into positive (PC) and negative control (NC) pairs was performed by two independent reviewers according to a pre-defined algorithm and discussed for consensus in case of disagreement. We selected 13 vaccines and 14 adverse events to be included in the reference set. From a total of 182 vaccine-adverse event pairs, we classified 18 as PC, 113 as NC and 51 as unclassifiable. Most classifications (91) were based on literature review, 45 were based on expert committee reports, and for 46 vaccine-adverse event pairs, an underlying pathomechanism was not plausible classifying the association as NC. A reference set of vaccine-adverse event pairs was developed. We propose its use for comparing signal detection methods and systems in the pediatric population. Published by Elsevier Ltd.

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

PubMed Central

Pruitt, Kim D.; Tatusova, Tatiana; Maglott, Donna R.

2005-01-01

The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) provides a non-redundant collection of sequences representing genomic data, transcripts and proteins. Although the goal is to provide a comprehensive dataset representing the complete sequence information for any given species, the database pragmatically includes sequence data that are currently publicly available in the archival databases. The database incorporates data from over 2400 organisms and includes over one million proteins representing significant taxonomic diversity spanning prokaryotes, eukaryotes and viruses. Nucleotide and protein sequences are explicitly linked, and the sequences are linked to other resources including the NCBI Map Viewer and Gene. Sequences are annotated to include coding regions, conserved domains, variation, references, names, database cross-references, and other features using a combined approach of collaboration and other input from the scientific community, automated annotation, propagation from GenBank and curation by NCBI staff. PMID:15608248

Personal digital assistant applications for the healthcare provider.

PubMed

Keplar, Kristine E; Urbanski, Christopher J

2003-02-01

To review some common medical applications available for personal digital assistants (PDAs), with brief discussion of the different PDA operating systems and memory requirements. Key search terms included handheld, PDA, personal digital assistants, and medical applications. The literature was accessed through MEDLINE (1999-August 2002). Other information was obtained through secondary sources such as Web sites describing common PDAs. Medical applications available on PDAs are numerous and include general drug references, specialized drug references (e.g., pediatrics, geriatrics, cardiology, infectious disease), diagnostic guides, medical calculators, herbal medication references, nursing references, toxicology references, and patient tracking databases. Costs and memory requirements for these programs can vary; consequently, the healthcare provider must limit the medication applications that are placed on the handheld computer. This article attempts to systematically describe the common medical applications available for the handheld computer along with cost, memory and download requirements, and Web site information. This review found many excellent PDA drug information applications offering many features which will aid the healthcare provider. Very likely, after using these PDA applications, the healthcare provider will find them indispensable, as their multifunctional capabilities can save time, improve accuracy, and allow for general business procedures as well as being a quick reference tool. To avoid the benefits of this technology might be a step backward.

Productivity Loss Related to Neglected Tropical Diseases Eligible for Preventive Chemotherapy: A Systematic Literature Review

PubMed Central

Rijnsburger, Adriana J.; Severens, Johan L.

2016-01-01

Background Neglected Tropical Diseases (NTDs) not only cause health and life expectancy loss, but can also lead to economic consequences including reduced ability to work. This article describes a systematic literature review of the effect on the economic productivity of individuals affected by one of the five worldwide most prevalent NTDs: lymphatic filariasis, onchocerciasis, schistosomiasis, soil-transmitted helminths (ascariasis, trichuriasis, and hookworm infection) and trachoma. These diseases are eligible to preventive chemotherapy (PCT). Methodology/Principal Findings Eleven bibliographic databases were searched using different names of all NTDs and various keywords relating to productivity. Additional references were identified through reference lists from relevant papers. Of the 5316 unique publications found in the database searches, thirteen papers were identified for lymphatic filariasis, ten for onchocerciasis, eleven for schistosomiasis, six for soil-transmitted helminths and three for trachoma. Besides the scarcity in publications reporting the degree of productivity loss, this review revealed large variation in the estimated productivity loss related to these NTDs. Conclusions It is clear that productivity is affected by NTDs, although the actual impact depends on the type and severity of the NTD as well as on the context where the disease occurs. The largest impact on productivity loss of individuals affected by one of these diseases seems to be due to blindness from onchocerciasis and severe schistosomiasis manifestations; productivity loss due to trachoma-related blindness has never been studied directly. However, productivity loss at an individual level might differ from productivity loss at a population level because of differences in the prevalence of NTDs. Variation in estimated productivity loss between and within diseases is caused by differences in research methods and setting. Publications should provide enough information to enable readers to assess the quality and relevance of the study for their purposes. PMID:26890487

Medicinal properties of ‘true’ cinnamon (Cinnamomum zeylanicum): a systematic review

PubMed Central

2013-01-01

Background In traditional medicine Cinnamon is considered a remedy for respiratory, digestive and gynaecological ailments. In-vitro and in-vivo studies from different parts of the world have demonstrated numerous beneficial medicinal effects of Cinnamomum zeylanicum (CZ). This paper aims to systematically review the scientific literature and provide a comprehensive summary on the potential medicinal benefits of CZ. Methods A comprehensive systematic review was conducted in the following databases; PubMed, Web of Science, SciVerse Scopus for studies published before 31st December 2012. The following keywords were used: “Cinnamomum zeylanicum”, “Ceylon cinnamon”, “True cinnamon” and “Sri Lankan cinnamon”. To obtain additional data a manual search was performed using the reference lists of included articles. Results The literature search identified the following number of articles in the respective databases; PubMed=54, Web of Science=76 and SciVerse Scopus=591. Thirteen additional articles were identified by searching reference lists. After removing duplicates the total number of articles included in the present review is 70. The beneficial health effects of CZ identified were; a) anti-microbial and anti-parasitic activity, b) lowering of blood glucose, blood pressure and serum cholesterol, c) anti-oxidant and free-radical scavenging properties, d) inhibition of tau aggregation and filament formation (hallmarks of Alzheimer’s disease), e) inhibitory effects on osteoclastogenesis, f) anti-secretagogue and anti-gastric ulcer effects, g) anti-nociceptive and anti-inflammatory activity, h) wound healing properties and i) hepato-protective effects. The studies reported minimal toxic and adverse effects. Conclusions The available in-vitro and in-vivo evidence suggests that CZ has many beneficial health effects. However, since data on humans are sparse, randomized controlled trials in humans will be necessary to determine whether these effects have public health implications. PMID:24148965

The Magnetics Information Consortium (MagIC)

NASA Astrophysics Data System (ADS)

Johnson, C.; Constable, C.; Tauxe, L.; Koppers, A.; Banerjee, S.; Jackson, M.; Solheid, P.

2003-12-01

The Magnetics Information Consortium (MagIC) is a multi-user facility to establish and maintain a state-of-the-art relational database and digital archive for rock and paleomagnetic data. The goal of MagIC is to make such data generally available and to provide an information technology infrastructure for these and other research-oriented databases run by the international community. As its name implies, MagIC will not be restricted to paleomagnetic or rock magnetic data only, although MagIC will focus on these kinds of information during its setup phase. MagIC will be hosted under EarthRef.org at http://earthref.org/MAGIC/ where two "integrated" web portals will be developed, one for paleomagnetism (currently functional as a prototype that can be explored via the http://earthref.org/databases/PMAG/ link) and one for rock magnetism. The MagIC database will store all measurements and their derived properties for studies of paleomagnetic directions (inclination, declination) and their intensities, and for rock magnetic experiments (hysteresis, remanence, susceptibility, anisotropy). Ultimately, this database will allow researchers to study "on the internet" and to download important data sets that display paleo-secular variations in the intensity of the Earth's magnetic field over geological time, or that display magnetic data in typical Zijderveld, hysteresis/FORC and various magnetization/remanence diagrams. The MagIC database is completely integrated in the EarthRef.org relational database structure and thus benefits significantly from already-existing common database components, such as the EarthRef Reference Database (ERR) and Address Book (ERAB). The ERR allows researchers to find complete sets of literature resources as used in GERM (Geochemical Earth Reference Model), REM (Reference Earth Model) and MagIC. The ERAB contains addresses for all contributors to the EarthRef.org databases, and also for those who participated in data collection, archiving and analysis in the magnetic studies. Integration with these existing components will guarantee direct traceability to the original sources of the MagIC data and metadata. The MagIC database design focuses around the general workflow that results in the determination of typical paleomagnetic and rock magnetic analyses. This ensures that individual data points can be traced between the actual measurements and their associated specimen, sample, site, rock formation and locality. This permits a distinction between original and derived data, where the actual measurements are performed at the specimen level, and data at the sample level and higher are then derived products in the database. These relations will also allow recalculation of derived properties, such as site means, when new data becomes available for a specific locality. Data contribution to the MagIC database is critical in achieving a useful research tool. We have developed a standard data and metadata template that can be used to provide all data at the same time as publication. Software tools are provided to facilitate easy population of these templates. The tools allow for the import/export of data files in a delimited text format, and they provide some advanced functionality to validate data and to check internal coherence of the data in the template. During and after publication these standardized MagIC templates will be stored in the ERR database of EarthRef.org from where they can be downloaded at all times. Finally, the contents of these template files will be automatically parsed into the online relational database.

Treatment of Sjögren's syndrome-associated dry eye an evidence-based review.

PubMed

Akpek, Esen Karamursel; Lindsley, Kristina B; Adyanthaya, Rohit S; Swamy, Ramya; Baer, Alan N; McDonnell, Peter J

2011-07-01

Outcomes-based review of reported treatment options for patients with dry eye secondary to Sjögren's syndrome (SS). Dry eye affects many individuals worldwide. Significant proportion of patients with dry eye has underlying SS, a progressive autoimmune condition. The few suggested guidelines for the treatment of dry eye are mostly based on severity of symptoms and/or clinical findings rather than on outcomes analysis, and do not differentiate SS from other causes of dry eye. METHODS AND LITERATURE REVIEW: A search strategy was developed to identify prospective, interventional studies of treatments for SS-associated dry eye from electronic databases. Eligible references were restricted to English-language articles published after 1975. These sources were augmented by hand searches of reference lists from accessed articles. Study selection, data extraction, and grading of evidence were completed independently by ≥4 review authors. The searches identified 3559 references as of August 10, 2010. After duplicate review of the titles and abstracts, 245 full-text papers were assessed, 62 of which were relevant for inclusion in the review. In the current literature on SS-associated dry eye, there is a paucity of rigorous clinical trials to support therapy recommendations. Nonetheless, the recommended treatments include topical lubricants, topical anti-inflammatory therapy, and tear-conserving strategies. The efficacy of oral secretagogues seems greater in the treatment of oral dryness than ocular dryness. Although oral hydroxychloroquine is commonly prescribed to patients with SS to alleviate fatigue and arthralgias, the literature lacks strong evidence for the efficacy of this treatment for dry eye. Copyright © 2011 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Learning disabilities, dyslexia, and vision: a subject review--a rebuttal, literature review, and commentary.

PubMed

Bowan, Merrill D

2002-09-01

In 1998, the American Academy of Pediatrics, the American Academy of Ophthalmology, and the American Association of Pediatric Ophthalmology and Strabismus (AAP/AAO/AAPOS) published a position paper entitled "Learning Disabilities, Dyslexia And Vision: A Subject Review," intended to support their assertion that there is no relationship between learning disabilities, dyslexia, and vision. The paper presents an unsupported opinion that optometrists (by implication) have said that vision problems cause learning disabilities and/or dyslexia and that visual therapy cures the conditions. The 1998 position paper follows two very similar and discredited papers published in 1972 and 1981. This article critically reviews and comments on the many problems of scholarship, the inconsistencies, and the false allegations the position paper presents. Perhaps the foremost problem is that the authoring committee has ignored a veritable mountain of relevant literature that strongly argues against their assertion that vision does not relate to academic performance. It is for this reason that an overview, drawn from more than 1,400 identified references from Medline and other database sources and pertinent texts that were reviewed, is incorporated into this current article. The AAP/AAO/AAPOS paper is also examined for the Levels of Evidence that their references offer in support of their position. The AAP/AAO/AAPOS paper contains errors and internal inconsistencies. Through highly selective reference choices, it misrepresents the great body of evidence from the literature that supports a relationship between visual and perceptual problems as they contribute to classroom difficulties. The 1998 paper should be retracted because of the errors, bias, and disinformation it presents. The public assigns great trust to authorities for accurate, intellectually honest guidance, which is lacking in this AAP/AAO/AAPOS position paper.

PDS, DOIs, and the Literature

NASA Astrophysics Data System (ADS)

Raugh, Anne; Henneken, Edwin

The Planetary Data System (PDS) is actively involved in designing both metadata and interfaces to make the assignment of Digital Object Identifiers (DOIs) to archival data a part of the archiving process for all data creators. These DOIs will be registered through DataCite, a non-profit organization whose members are all deeply concerned with archival research data, provenance tracking through the literature, and proper acknowledgement of the various types of efforts that contribute to the creation of an archival reference data set. Making the collection of citation metadata and its ingestion into the DataCite DOI database easy - and easy to do correctly - is in the best interests of all stakeholders: the data creators; the curators; the indexing organizations like the Astrophysics Data System (ADS); and the data users. But in order to realize the promise of DOIs, there are three key issues to address: 1) How do we incorporate the metadata collection process simply and naturally into the PDS archive creation process; 2) How do we encourage journal editors to require references to previously published data with the same rigor with which they require references to previously published research and analysis; and finally, 3) How can we change the culture of academic and research employers to recognize that the effort required to prepare a PDS archival data set is a career achievement on par with contributing to a refereed article in the professional literature. Data archives and scholarly publications are the long-term return on investment that funding agencies and the science community expect in exchange for research spending. The traceability and reproducibility ensured by the integration of DOIs and their related metadata into indexing and search services is an essential part of providing and optimizing that return.

A reference system for animal biometrics: application to the northern leopard frog

USGS Publications Warehouse

Petrovska-Delacretaz, D.; Edwards, A.; Chiasson, J.; Chollet, G.; Pilliod, D.S.

2014-01-01

Reference systems and public databases are available for human biometrics, but to our knowledge nothing is available for animal biometrics. This is surprising because animals are not required to give their agreement to be in a database. This paper proposes a reference system and database for the northern leopard frog (Lithobates pipiens). Both are available for reproducible experiments. Results of both open set and closed set experiments are given.

PHYTOTOX: DATABASE DEALING WITH THE EFFECT OF ORGANIC CHEMICALS ON TERRESTRIAL VASCULAR PLANTS

EPA Science Inventory

A new database, PHYTOTOX, dealing with the direct effects of exogenously supplied organic chemicals on terrestrial vascular plants is described. The database consists of two files, a Reference File and Effects File. The Reference File is a bibliographic file of published research...

Performing arts medicine-a bibliographic retrospective of the early literature: an historical examination of bibliographic references pre-1975.

PubMed

Dawson, William J

2013-03-01

Performing arts medicine (PAM) emerged as a medical specialty around 1985. Prior to this time, relatively few publications addressed the identification and concerns of musicians' and dancers' medical problems. To determine what number and types of publications occurred prior to the actual beginnings of PAM as a discipline, and to determine how these original topics compared with present-day publications, a retrospective review of the current bibliographic database of the Performing Arts Medicine Association (PAMA) was undertaken. Out of a total of 12,600 entries to date, 489 references were found published from 1798 through 1974, which represent only 3.9% of the current database listings. One-sixth of the references were originally written in a language other than English. Journal articles were by far the most numerous type of publication. Topics with the highest number of entries included the neurobiology of music (n=77), dental/orofacial matters (71), and biographical accounts of composers or musicians and their illnesses (59). Other frequently published topics included hearing loss, physiology of playing instruments, and instrumental technique and teaching. Early topics with multiple publications included composers' biographies, dystonias, and surgery to improve finger independence for playing piano. Subjects whose publications occurred principally in the last two decades of this review included dermatological disorders, hearing loss, and ballet physiology, teaching, and technique. Those which remain popular to the present day include hearing loss, performance anxiety, focal dystonia, and dental/orofacial problems.

The landscape of research on smartphone medical apps: Coherent taxonomy, motivations, open challenges and recommendations.

PubMed

Hussain, Muzammil; Al-Haiqi, Ahmed; Zaidan, A A; Zaidan, B B; Kiah, M L M; Anuar, Nor Badrul; Abdulnabi, Mohamed

2015-12-01

To survey researchers' efforts in response to the new and disruptive technology of smartphone medical apps, mapping the research landscape form the literature into a coherent taxonomy, and finding out basic characteristics of this emerging field represented on: motivation of using smartphone apps in medicine and healthcare, open challenges that hinder the utility, and the recommendations to improve the acceptance and use of medical apps in the literature. We performed a focused search for every article on (1) smartphone (2) medical or health-related (3) app, in four major databases: MEDLINE, Web of Science, ScienceDirect, and IEEE Xplore. Those databases are deemed broad enough to cover both medical and technical literature. The final set included 133 articles. Most articles (68/133) are reviews and surveys that refer to actual apps or the literature to describe medical apps for a specific specialty, disease, or purpose; or to provide a general overview of the technology. Another group (43/133) carried various studies, from evaluation of apps to exploration of desired features when developing them. Few researchers (17/133) presented actual attempts to develop medical apps, or shared their experiences in doing so. The smallest portion (5/133) proposed general frameworks addressing the production or operation of apps. Since 2010, researchers followed the trend of medical apps in several ways, though leaving areas or aspect for further attention. Regardless of their category, articles focus on the challenges that hinder the full utility of medical apps and do recommend mitigations to them. Research on smartphone medical apps is active and various. We hope that this survey contribute to the understanding of the available options and gaps for other researchers to join this line of research. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Adverse-drug-event data provided by pharmaceutical companies.

PubMed

Cudny, Magdalena E; Graham, Angie S

2008-06-01

Pharmaceutical company drug information center (PCDIC) responses to queries about adverse drug events (ADEs) were studied to determine whether PCDICs search sources other than the prescribing information on the package insert (PI) and whether the PCDICs' approach differs according to whether an ADE is listed in the PI (labeled) or not (unlabeled). Companies were selected from a list of PCDICs in the Physicians' Desk Reference. One oral or injectable prescription drug from each company was selected. For each drug, a labeled ADE and an unlabeled ADE about which to query the PCDICs were randomly selected from the index of an annual publication on ADEs. The investigators telephoned the PCDICs with an open-ended inquiry about the incidence, timing, and management of the ADE as reported in the literature and the company's internal data; they clarified that the request did not concern a specific patient. Whether or not information was provided, the source searched was recorded (PI, literature, internal database), and the percentages of PCDICs that used each source for labeled and for unlabeled ADEs were analyzed. Results were obtained from 100 companies to questions about 100 drugs (200 ADEs). For ADEs overall, 80% used the PI, 50% the medical literature, and 38% internal data. For labeled versus unlabeled ADEs, respectively, the PI was used by 84% and 76%; literature, both 50%; and internal data, 35% and 41%. The PCDIC specialists referencing the PI did not always provide accurate or up-to-date information. Some specialists, when asked to query internal databases, said that was not an option. For both labeled and unlabeled ADEs, the PI was the primary source used by PCDICs to answer safety questions about their products, and internal data were the least-used source. Most resources used by PCDICs are readily available to practicing pharmacists.

Tools for knowledge acquisition within the NeuroScholar system and their application to anatomical tract-tracing data

PubMed Central

Burns, Gully APC; Cheng, Wei-Cheng

2006-01-01

Background Knowledge bases that summarize the published literature provide useful online references for specific areas of systems-level biology that are not otherwise supported by large-scale databases. In the field of neuroanatomy, groups of small focused teams have constructed medium size knowledge bases to summarize the literature describing tract-tracing experiments in several species. Despite years of collation and curation, these databases only provide partial coverage of the available published literature. Given that the scientists reading these papers must all generate the interpretations that would normally be entered into such a system, we attempt here to provide general-purpose annotation tools to make it easy for members of the community to contribute to the task of data collation. Results In this paper, we describe an open-source, freely available knowledge management system called 'NeuroScholar' that allows straightforward structured markup of the PDF files according to a well-designed schema to capture the essential details of this class of experiment. Although, the example worked through in this paper is quite specific to neuroanatomical connectivity, the design is freely extensible and could conceivably be used to construct local knowledge bases for other experiment types. Knowledge representations of the experiment are also directly linked to the contributing textual fragments from the original research article. Through the use of this system, not only could members of the community contribute to the collation task, but input data can be gathered for automated approaches to permit knowledge acquisition through the use of Natural Language Processing (NLP). Conclusion We present a functional, working tool to permit users to populate knowledge bases for neuroanatomical connectivity data from the literature through the use of structured questionnaires. This system is open-source, fully functional and available for download from [1]. PMID:16895608

Consolidation of proteomics data in the Cancer Proteomics database.

PubMed

Arntzen, Magnus Ø; Boddie, Paul; Frick, Rahel; Koehler, Christian J; Thiede, Bernd

2015-11-01

Cancer is a class of diseases characterized by abnormal cell growth and one of the major reasons for human deaths. Proteins are involved in the molecular mechanisms leading to cancer, furthermore they are affected by anti-cancer drugs, and protein biomarkers can be used to diagnose certain cancer types. Therefore, it is important to explore the proteomics background of cancer. In this report, we developed the Cancer Proteomics database to re-interrogate published proteome studies investigating cancer. The database is divided in three sections related to cancer processes, cancer types, and anti-cancer drugs. Currently, the Cancer Proteomics database contains 9778 entries of 4118 proteins extracted from 143 scientific articles covering all three sections: cell death (cancer process), prostate cancer (cancer type) and platinum-based anti-cancer drugs including carboplatin, cisplatin, and oxaliplatin (anti-cancer drugs). The detailed information extracted from the literature includes basic information about the articles (e.g., PubMed ID, authors, journal name, publication year), information about the samples (type, study/reference, prognosis factor), and the proteomics workflow (Subcellular fractionation, protein, and peptide separation, mass spectrometry, quantification). Useful annotations such as hyperlinks to UniProt and PubMed were included. In addition, many filtering options were established as well as export functions. The database is freely available at http://cancerproteomics.uio.no. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DB-PABP: a database of polyanion-binding proteins

PubMed Central

Fang, Jianwen; Dong, Yinghua; Salamat-Miller, Nazila; Russell Middaugh, C.

2008-01-01

The interactions between polyanions (PAs) and polyanion-binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding. Furthermore, many neurodegenerative disease-related proteins are PABPs. Thus, a better understanding of PA/PABP interactions may not only enhance our understandings of biological systems but also provide new clues to these deadly diseases. The literature in this field is widely scattered, suggesting the need for a comprehensive and searchable database of PABPs. The DB-PABP is a comprehensive, manually curated and searchable database of experimentally characterized PABPs. It is freely available and can be accessed online at http://pabp.bcf.ku.edu/DB_PABP/. The DB-PABP was implemented as a MySQL relational database. An interactive web interface was created using Java Server Pages (JSP). The search page of the database is organized into a main search form and a section for utilities. The main search form enables custom searches via four menus: protein names, polyanion names, the source species of the proteins and the methods used to discover the interactions. Available utilities include a commonality matrix, a function of listing PABPs by the number of interacting polyanions and a string search for author surnames. The DB-PABP is maintained at the University of Kansas. We encourage users to provide feedback and submit new data and references. PMID:17916573

DB-PABP: a database of polyanion-binding proteins.

PubMed

Fang, Jianwen; Dong, Yinghua; Salamat-Miller, Nazila; Middaugh, C Russell

2008-01-01

The interactions between polyanions (PAs) and polyanion-binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding. Furthermore, many neurodegenerative disease-related proteins are PABPs. Thus, a better understanding of PA/PABP interactions may not only enhance our understandings of biological systems but also provide new clues to these deadly diseases. The literature in this field is widely scattered, suggesting the need for a comprehensive and searchable database of PABPs. The DB-PABP is a comprehensive, manually curated and searchable database of experimentally characterized PABPs. It is freely available and can be accessed online at http://pabp.bcf.ku.edu/DB_PABP/. The DB-PABP was implemented as a MySQL relational database. An interactive web interface was created using Java Server Pages (JSP). The search page of the database is organized into a main search form and a section for utilities. The main search form enables custom searches via four menus: protein names, polyanion names, the source species of the proteins and the methods used to discover the interactions. Available utilities include a commonality matrix, a function of listing PABPs by the number of interacting polyanions and a string search for author surnames. The DB-PABP is maintained at the University of Kansas. We encourage users to provide feedback and submit new data and references.

CoReCG: a comprehensive database of genes associated with colon-rectal cancer

PubMed Central

Agarwal, Rahul; Kumar, Binayak; Jayadev, Msk; Raghav, Dhwani; Singh, Ashutosh

2016-01-01

Cancer of large intestine is commonly referred as colorectal cancer, which is also the third most frequently prevailing neoplasm across the globe. Though, much of work is being carried out to understand the mechanism of carcinogenesis and advancement of this disease but, fewer studies has been performed to collate the scattered information of alterations in tumorigenic cells like genes, mutations, expression changes, epigenetic alteration or post translation modification, genetic heterogeneity. Earlier findings were mostly focused on understanding etiology of colorectal carcinogenesis but less emphasis were given for the comprehensive review of the existing findings of individual studies which can provide better diagnostics based on the suggested markers in discrete studies. Colon Rectal Cancer Gene Database (CoReCG), contains 2056 colon-rectal cancer genes information involved in distinct colorectal cancer stages sourced from published literature with an effective knowledge based information retrieval system. Additionally, interactive web interface enriched with various browsing sections, augmented with advance search facility for querying the database is provided for user friendly browsing, online tools for sequence similarity searches and knowledge based schema ensures a researcher friendly information retrieval mechanism. Colorectal cancer gene database (CoReCG) is expected to be a single point source for identification of colorectal cancer-related genes, thereby helping with the improvement of classification, diagnosis and treatment of human cancers. Database URL: lms.snu.edu.in/corecg PMID:27114494

MAGA, a new database of gas natural emissions: a collaborative web environment for collecting data.

NASA Astrophysics Data System (ADS)

Cardellini, Carlo; Chiodini, Giovanni; Frigeri, Alessandro; Bagnato, Emanuela; Frondini, Francesco; Aiuppa, Alessandro

2014-05-01

The data on volcanic and non-volcanic gas emissions available online are, as today, are incomplete and most importantly, fragmentary. Hence, there is need for common frameworks to aggregate available data, in order to characterize and quantify the phenomena at various scales. A new and detailed web database (MAGA: MApping GAs emissions) has been developed, and recently improved, to collect data on carbon degassing form volcanic and non-volcanic environments. MAGA database allows researchers to insert data interactively and dynamically into a spatially referred relational database management system, as well as to extract data. MAGA kicked-off with the database set up and with the ingestion in to the database of the data from: i) a literature survey on publications on volcanic gas fluxes including data on active craters degassing, diffuse soil degassing and fumaroles both from dormant closed-conduit volcanoes (e.g., Vulcano, Phlegrean Fields, Santorini, Nysiros, Teide, etc.) and open-vent volcanoes (e.g., Etna, Stromboli, etc.) in the Mediterranean area and Azores, and ii) the revision and update of Googas database on non-volcanic emission of the Italian territory (Chiodini et al., 2008), in the framework of the Deep Earth Carbon Degassing (DECADE) research initiative of the Deep Carbon Observatory (DCO). For each geo-located gas emission site, the database holds images and description of the site and of the emission type (e.g., diffuse emission, plume, fumarole, etc.), gas chemical-isotopic composition (when available), gas temperature and gases fluxes magnitude. Gas sampling, analysis and flux measurement methods are also reported together with references and contacts to researchers expert of each site. In this phase data can be accessed on the network from a web interface, and data-driven web service, where software clients can request data directly from the database, are planned to be implemented shortly. This way Geographical Information Systems (GIS) and Virtual Globes (e.g., Google Earth) could easily access the database, and data could be exchanged with other database. At the moment the database includes: i) more than 1000 flux data about volcanic plume degassing from Etna and Stromboli volcanoes, ii) data from ~ 30 sites of diffuse soil degassing from Napoletan volcanoes, Azores, Canary, Etna, Stromboli, and Vulcano Island, several data on fumarolic emissions (~ 7 sites) with CO2 fluxes; iii) data from ~ 270 non volcanic gas emission site in Italy. We believe MAGA data-base is an important starting point to develop a large scale, expandable data-base aimed to excite, inspire, and encourage participation among researchers. In addition, the possibility to archive location and qualitative information for gas emission/sites not yet investigated, could stimulate the scientific community for future researches and will provide an indication on the current uncertainty on deep carbon fluxes global estimates

Online Reference Service--How to Begin: A Selected Bibliography.

ERIC Educational Resources Information Center

Shroder, Emelie J., Ed.

1982-01-01

Materials in this bibliography were selected and recommended by members of the Use of Machine-Assisted Reference in Public Libraries Committee, Reference and Adult Services Division, American Library Association. Topics include: financial aspects, equipment and communications considerations, comparing databases and database systems, advertising…

Evidence-based librarianship: searching for the needed EBL evidence.

PubMed

Eldredge, J D

2000-01-01

This paper discusses the challenges of finding evidence needed to implement Evidence-Based Librarianship (EBL). Focusing first on database coverage for three health sciences librarianship journals, the article examines the information contents of different databases. Strategies are needed to search for relevant evidence in the library literature via these databases, and the problems associated with searching the grey literature of librarianship. Database coverage, plausible search strategies, and the grey literature of library science all pose challenges to finding the needed research evidence for practicing EBL. Health sciences librarians need to ensure that systems are designed that can track and provide access to needed research evidence to support Evidence-Based Librarianship (EBL).

Electronic Reference Library: Silverplatter's Database Networking Solution.

ERIC Educational Resources Information Center

Millea, Megan

Silverplatter's Electronic Reference Library (ERL) provides wide area network access to its databases using TCP/IP communications and client-server architecture. ERL has two main components: The ERL clients (retrieval interface) and the ERL server (search engines). ERL clients provide patrons with seamless access to multiple databases on multiple…

What is the role of procedural justice in civil commitment?

PubMed

McKenna, B G; Simpson, A I; Coverdale, J H

2000-08-01

To determine best practice management strategies in the clinical application of civil commitment. All relevant literature on the topics of 'civil commitment', 'coercion' and 'procedural justice' were located on MEDLINE and PsychLIT databases and reviewed. Literature on the use of Ulysses contracts and advance directives in mental health treatment was integrated into the findings. Best practice evidence that guides management strategies is limited to the time of enactment of civil commitment. Management strategies involve enhancing the principles of procedural justice as a means of limiting negative patient perception of commitment. In the absence of evidence-based research beyond this point of enactment, grounds for the application of the principles of procedural justice are supported by reference to ethical considerations. Ulysses contracts provide an additional method for strengthening procedural justice. Procedural justice principles should be routinely applied throughout the processes of civil commitment in order to enhance longer term therapeutic outcomes and to blunt paternalism.

The Immigrant and Hispanic Paradoxes: A Systematic Review of Their Predictions and Effects

PubMed Central

Teruya, Stacey A.; Bazargan-Hejazi, Shahrzad

2015-01-01

A survey of the literature indicates that reported advantages of the Immigrant and Hispanic Paradox are inconsistent and equivocal. The healthy migrant hypothesis also suggests that current research approaches consider only “healthy” groups. Other methodological concerns include the simple underreporting of deaths, and that commonly used databases may not include all significant attributes and characteristics. We conducted a systematic review, synthesizing and identifying themes not explicitly found in the current literature. We also employ a simple quantitative index to assess the scholarly strength of references. Paradox protection appears uneven and is not generalizable across races, ethnicities, age groups and genders. In addition, acculturation, health behaviors and diet, ethnicity, acculturative stress, adolescence, undocumented and uninsured status, age of arrival in the United States and length of exposure, gender and age appear to be significant in predicting any beneficial effects. PMID:26120244

Protection motivation theory and physical activity in the general population: a systematic literature review.

PubMed

Bui, Linh; Mullan, Barbara; McCaffery, Kirsten

2013-01-01

An appropriate theoretical framework may be useful for guiding the development of physical activity interventions. This review investigates the effectiveness of the protection motivation theory (PMT), a model based on the cognitive mediation processes of behavioral change, in the prediction and promotion of physical activity participation. A literature search was conducted using the databases MEDLINE, PsycINFO, PubMed, and Web of Science, and a manual search was conducted on relevant reference lists. Studies were included if they tested or applied the PMT, measured physical activity, and sampled from healthy populations. A total of 20 studies were reviewed, grouped into four design categories: prediction, stage discrimination, experimental manipulation, and intervention. The results indicated that the PMT's coping appraisal construct of self-efficacy generally appears to be the most effective in predicting and promoting physical activity participation. In conclusion, the PMT shows some promise, however, there are still substantial gaps in the evidence.

A Circular Dichroism Reference Database for Membrane Proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wallace,B.; Wien, F.; Stone, T.

2006-01-01

Membrane proteins are a major product of most genomes and the target of a large number of current pharmaceuticals, yet little information exists on their structures because of the difficulty of crystallising them; hence for the most part they have been excluded from structural genomics programme targets. Furthermore, even methods such as circular dichroism (CD) spectroscopy which seek to define secondary structure have not been fully exploited because of technical limitations to their interpretation for membrane embedded proteins. Empirical analyses of circular dichroism (CD) spectra are valuable for providing information on secondary structures of proteins. However, the accuracy of themore » results depends on the appropriateness of the reference databases used in the analyses. Membrane proteins have different spectral characteristics than do soluble proteins as a result of the low dielectric constants of membrane bilayers relative to those of aqueous solutions (Chen & Wallace (1997) Biophys. Chem. 65:65-74). To date, no CD reference database exists exclusively for the analysis of membrane proteins, and hence empirical analyses based on current reference databases derived from soluble proteins are not adequate for accurate analyses of membrane protein secondary structures (Wallace et al (2003) Prot. Sci. 12:875-884). We have therefore created a new reference database of CD spectra of integral membrane proteins whose crystal structures have been determined. To date it contains more than 20 proteins, and spans the range of secondary structures from mostly helical to mostly sheet proteins. This reference database should enable more accurate secondary structure determinations of membrane embedded proteins and will become one of the reference database options in the CD calculation server DICHROWEB (Whitmore & Wallace (2004) NAR 32:W668-673).« less

Tuberculosis treatment outcome monitoring in European Union countries: systematic review

PubMed Central

van Hest, Rob; Ködmön, Csaba; Verver, Suzanne; Erkens, Connie G.M.; Straetemans, Masja; Manissero, Davide; de Vries, Gerard

2013-01-01

Treatment success measured by treatment outcome monitoring (TOM) is a key programmatic output of tuberculosis (TB) control programmes. We performed a systematic literature review on national-level TOM in the 30 European Union (EU)/European Economic Areas (EEA) countries to summarise methods used to collect and report data on TOM. Online reference bibliographic databases PubMed/MEDLINE and EMBASE were searched to identify relevant indexed and non-indexed literature published between January 2000 and August 2010. The search strategy resulted in 615 potentially relevant indexed citations, of which 27 full-text national studies (79 data sets) were included for final analysis. The selected studies were performed in 10 EU/EEA countries and gave a fragmented impression of TOM in the EU/EEA. Publication year, study period, sample size, databases, definitions, variables, patient and outcome categories, and population subgroups varied widely, portraying a very heterogeneous picture. This review confirmed previous reports of considerable heterogeneity in publications of TOM results across EU/EEA countries. PubMed/MEDLINE and EMBASE indexed studies are not a suitable instrument to measure representative TOM results for the 30 EU/EEA countries. Uniform and complete reporting to the centralised European Surveillance System will produce the most timely and reliable results of TB treatment outcomes in the EU/EEA. PMID:22790913

Search strategies in systematic reviews in periodontology and implant dentistry.

PubMed

Faggion, Clovis M; Atieh, Momen A; Park, Stephanie

2013-09-01

To perform an overview of literature search strategies in systematic reviews (SRs) published in periodontology and implant dentistry. Two electronic databases (PubMed and Cochrane Database of SRs) were searched, independently and in duplicate, for SRs with meta-analyses on interventions, with the last search performed on 11 November 2012. Manual searches of the reference lists of included SRs and 10 specialty dental journals were conducted. Methodological issues of the search strategies of included SRs were assessed with Cochrane collaboration guidelines and AMSTAR recommendations. The search strategies employed in Cochrane and paper-based SRs were compared. A total of 146 SRs with meta-analyses were included, including 19 Cochrane and 127 paper-based SRs. Some issues, such as "the use of keywords," were reported in most of the SRs (86%). Other issues, such as "search of grey literature" and "language restriction," were not fully reported (34% and 50% respectively). The quality of search strategy reporting in Cochrane SRs was better than that of paper-based SRs for seven of the eight criteria assessed. There is room for improving the quality of reporting of search strategies in SRs in periodontology and implant dentistry, particularly in SRs published in paper-based journals. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Alaska harbor seal (Phoca vitulina) contaminants: A review with annotated bibliography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Papa, R.S.; Becker, P.R.

1998-10-01

The numbers of harbor seals (Phoca vitulina) have declined steadily and substantially over the last two decades in the Central and Western Gulf of Alaska, including Prince William Sound. Although the reasons for this decline have not been identified, hypotheses have included fishery interactions, changes in availability of food resources, human harvests, disease, increase in predation, increase in disturbance, and pollution. Although the presence of contaminants has been suggested as one possible causative factor in the decline of both the harbor seal and Steller sea lion, very little information is readily available on contaminant concentrations in these animals. As anmore » initial step in the development of a database that can be used to define the types of studies needed to address the possible role of anthropogenic contaminants in the decline of this species, existing data and information on levels of contaminants in the harbor seals of Alaska, the contiguous U.S., and other areas of the world were reviewed. This report provides references and current scientific literature, as well as gray literature and unpublished databases. This report is divided into three sections: (1) a synthesis of information based on the review, (2) tables that summarize the published data, and (3) an annotated bibliography.« less

The Arabidopsis Information Resource: Making and Mining the ‘Gold Standard’ Annotated Reference Plant Genome

PubMed Central

Berardini, Tanya Z.; Reiser, Leonore; Li, Donghui; Mezheritsky, Yarik; Muller, Robert; Strait, Emily; Huala, Eva

2015-01-01

The Arabidopsis Information Resource (TAIR) is a continuously updated, online database of genetic and molecular biology data for the model plant Arabidopsis thaliana that provides a global research community with centralized access to data for over 30,000 Arabidopsis genes. TAIR’s biocurators systematically extract, organize, and interconnect experimental data from the literature along with computational predictions, community submissions, and high throughput datasets to present a high quality and comprehensive picture of Arabidopsis gene function. TAIR provides tools for data visualization and analysis, and enables ordering of seed and DNA stocks, protein chips and other experimental resources. TAIR actively engages with its users who contribute expertise and data that augments the work of the curatorial staff. TAIR’s focus in an extensive and evolving ecosystem of online resources for plant biology is on the critically important role of extracting experimentally-based research findings from the literature and making that information computationally accessible. In response to the loss of government grant funding, the TAIR team founded a nonprofit entity, Phoenix Bioinformatics, with the aim of developing sustainable funding models for biological databases, using TAIR as a test case. Phoenix has successfully transitioned TAIR to subscription-based funding while still keeping its data relatively open and accessible. PMID:26201819

[Analysis of relation between the development of study and literatures about benign positional paroxysmal vertigo published international and domestic].

PubMed

Jia, Jianping; Sun, Xiaohui; Dai, Song; Sang, Yuehong

2016-01-01

Benign paroxysmal positional vertigo (BPPV) is a common vestibular disorder that causes vertigo. Study of BPPV has dramatically rapid progress in recent years. We analyze the BPPV growth We searched the international data quantity year by year in database of PubMed, ScienceDirect and WILEY before 2014 respectively, then we searched the domestic data quantity year by year in database of CNKI, VIP and Wanfang Data before 2015 by selecting "Benign paroxysmal positional vertigo" as the keywords. Then we carried out regression analysis with the gathered results in above databases to determine data growth regularity and main factors that affect future development of BPPV. Also, we analyzes published BPPV papers in domestic and international journals. PubMed database contains 808 literatures, ScienceDirect contains 177 database and WILEY contains 46 literatures, All together we collected 1 038 international articles. CNKI contains 440 literatures, VIP contains 580 literatures and WanFang data contains 449 literatures. All together we collected 1 469 domestic literatures. It shows the rising trend of the literature accumulation amount of BPPV. The scattered point diagram of BPPV shows an exponential growing trend, which was growing slowly in the early time but rapidly in recent years. It shows that the development of BPPV has three stages from international arical: exploration period (before 1985), breakthrough period (1986-1998). The deepening stage (after 1998), Chinese literature also has three stages from domestic BPPV precess. Blank period (before the year of 1982), the enlightenment period (1982-2004), the deepening stage (after the year of 2004). In the pregress of BPPV, many outsantding sccholars played an important role in domestic scitifction of researching, which has produced a certain influence in the worldwide.

Using "Reader's Guide to Periodical Literature" on CD-Rom To Teach Database Searching to High School Students.

ERIC Educational Resources Information Center

Kern, Joanne F.

The lack of opportunity for high school sophomores to learn database searching was addressed by the implementation of a computerized magazine article search program. "Reader's Guide to Periodical Literature" on CD-ROM was used to train students in database searching during the time they were assigned to the library to do research papers…

CrossCheck: an open-source web tool for high-throughput screen data analysis.

PubMed

Najafov, Jamil; Najafov, Ayaz

2017-07-19

Modern high-throughput screening methods allow researchers to generate large datasets that potentially contain important biological information. However, oftentimes, picking relevant hits from such screens and generating testable hypotheses requires training in bioinformatics and the skills to efficiently perform database mining. There are currently no tools available to general public that allow users to cross-reference their screen datasets with published screen datasets. To this end, we developed CrossCheck, an online platform for high-throughput screen data analysis. CrossCheck is a centralized database that allows effortless comparison of the user-entered list of gene symbols with 16,231 published datasets. These datasets include published data from genome-wide RNAi and CRISPR screens, interactome proteomics and phosphoproteomics screens, cancer mutation databases, low-throughput studies of major cell signaling mediators, such as kinases, E3 ubiquitin ligases and phosphatases, and gene ontological information. Moreover, CrossCheck includes a novel database of predicted protein kinase substrates, which was developed using proteome-wide consensus motif searches. CrossCheck dramatically simplifies high-throughput screen data analysis and enables researchers to dig deep into the published literature and streamline data-driven hypothesis generation. CrossCheck is freely accessible as a web-based application at http://proteinguru.com/crosscheck.

A novel database of bio-effects from non-ionizing radiation.

PubMed

Leach, Victor; Weller, Steven; Redmayne, Mary

2018-06-06

A significant amount of electromagnetic field/electromagnetic radiation (EMF/EMR) research is available that examines biological and disease associated endpoints. The quantity, variety and changing parameters in the available research can be challenging when undertaking a literature review, meta-analysis, preparing a study design, building reference lists or comparing findings between relevant scientific papers. The Oceania Radiofrequency Scientific Advisory Association (ORSAA) has created a comprehensive, non-biased, multi-categorized, searchable database of papers on non-ionizing EMF/EMR to help address these challenges. It is regularly added to, freely accessible online and designed to allow data to be easily retrieved, sorted and analyzed. This paper demonstrates the content and search flexibility of the ORSAA database. Demonstration searches are presented by Effect/No Effect; frequency-band/s; in vitro; in vivo; biological effects; study type; and funding source. As of the 15th September 2017, the clear majority of 2653 papers captured in the database examine outcomes in the 300 MHz-3 GHz range. There are 3 times more biological "Effect" than "No Effect" papers; nearly a third of papers provide no funding statement; industry-funded studies more often than not find "No Effect", while institutional funding commonly reveal "Effects". Country of origin where the study is conducted/funded also appears to have a dramatic influence on the likely result outcome.

Image: changing how women nurses think about themselves. Literature review.

PubMed

Fletcher, Karen

2007-05-01

This paper presents a review of the public and professional images of nursing in the literature and explores nurse image in the context of Strasen's self-image model. Nurses have struggled since the 1800s with the problem of image. What is known about nurses' image is from the perspective of others: the media, public or other healthcare professionals. Some hints of how nurses see themselves can be found in the literature that suggests how this image could be improved. A literature review for all dates up to 2006 was undertaken using PubMed, Medline and CINAHL databases. Additional references were identified from this literature. Sentinel articles and books were manually searched to identify key concepts. Search words used were nurse, nursing, image and self-image. The findings were examined using the framework of Strasen's self-image model. Public image appears to be intimately intertwined with nurse image. This creates the boundaries that confine and construct the image of nursing. As a profession, nurses do not have a very positive self-image nor do they think highly of themselves. Individually, each nurse has the power to shape the image of nursing. However, nurses must also work together to change the systems that perpetuate negative stereotypes of nurses' image.

Laryngeal complications by orotracheal intubation: Literature review.

PubMed

Mota, Luiz Alberto Alves; de Cavalho, Glauber Barbosa; Brito, Valeska Almeida

2012-04-01

 The injuries caused for the orotracheal intubation are common in our way and widely told by literature. Generally the pipe rank of or consequence of its permanence in the aerial ways of the patient is caused by accidents in. It has diverse types of larynx injuries, caused for multiple mechanisms.  To verify, in literature, the main causes of laryngeal complications after- orotracheal intubation and its mechanisms of injury. Revision of Literature: The searched databases had been LILACS, BIREME and SCIELO. Were updated, books and theses had been used, delimiting itself the period enters 1953 the 2009. The keywords used for the search of articles had been: complications, injuries, larynx, intubation, endotracheal, orotracheal, granulomas, stenosis. 59 references had been selected. The used criteria of inclusion for the choice of articles had been the ones that had shown to the diverse types of injuries caused for the orotracheal intubation and its pathophysiology.  This revision of literature was motivated by the comment in the practical clinic of a great number of laryngeal sequels in patients submitted to the orotracheal intubation. Of that is ahead important the knowledge, for the professionals of the area of health, the types of complications and its causes, with intention to prevent them, adopting measured of prevention of these injuries.

Evaluating the efficacy of Tui Na in treatment of childhood anorexia: a meta-analysis.

PubMed

Xia, Qiao Cui; Feng, Zhang Xin; Ping, Cai Xiao

2014-01-01

Medical practitioners are now seeing more children younger than 15 y who are developing childhood anorexia. Hua Tuo chiropractic treatments are an ancient and practical massage therapy and are a type of Tui Na therapy, which has been used for curing childhood anorexia for thousands of years in China. Research literature suggests that chiropractic care produces outcomes at least comparable with alternative treatments. The research team intended to perform a systematic review to identify and synthesize evidence on the efficacy of Tui Na for treatment of childhood anorexia. Systematic searches were conducted for studies evaluating Tui Na therapy in electronic databases MEDLINE, EMBASE, PsychINFO, the Cochrane Library, the Cumulative Index to Nursing and Allied Health Literature, the Midwives Information and Resource Service, the Health Management Information Consortium, the Health Management and Information Service, PubMed, the Chinese National Knowledge Infrastructure (CNKI), the Chinese Biomedical Literature Database (CBM), the Chinese Scientific Journal Database VIP, the Cumulative Index to Nursing and Allied Health Literature (CINAHL), and the Chinese Clinical Trial Register-from inception to November 2011. The research team hand-searched reference lists and journals, extracted data from the papers, and assessed the quality of the research. Participants of the reviewed studies were infants and children younger than 15 y. Of the 109 papers identified, 3 papers reported on randomized, controlled trials (RCTs) involving 332 patients; 45 covered cohort or quasi-experimental studies; and 61 discussed nonintervention studies. Meta-analysis results from the 3 RCTs showed that Tui Na can improve the curative effect compared with oral medicine that is used for infants and young children with anorexia and can also increase a child's weight. The level of evidence reported was mixed, but given the available evidence, the research team concluded that Tui Na therapy was a viable intervention that could benefit infants and young children with anorexia. No serious adverse events were reported. Larger randomized, controlled trials are required to explore the effects of Tui Na therapy for treatment of childhood anorexia further.

The Pathogen-Host Interactions database (PHI-base): additions and future developments

PubMed Central

Urban, Martin; Pant, Rashmi; Raghunath, Arathi; Irvine, Alistair G.; Pedro, Helder; Hammond-Kosack, Kim E.

2015-01-01

Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and ecosystem health. To combat infection greater comparative knowledge is required on the pathogenic process in multiple species. The Pathogen-Host Interactions database (PHI-base) catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and protist pathogens. Mutant phenotypes are associated with gene information. The included pathogens infect a wide range of hosts including humans, animals, plants, insects, fish and other fungi. The current version, PHI-base 3.6, available at http://www.phi-base.org, stores information on 2875 genes, 4102 interactions, 110 host species, 160 pathogenic species (103 plant, 3 fungal and 54 animal infecting species) and 181 diseases drawn from 1243 references. Phenotypic and gene function information has been obtained by manual curation of the peer-reviewed literature. A controlled vocabulary consisting of nine high-level phenotype terms permits comparisons and data analysis across the taxonomic space. PHI-base phenotypes were mapped via their associated gene information to reference genomes available in Ensembl Genomes. Virulence genes and hotspots can be visualized directly in genome browsers. Future plans for PHI-base include development of tools facilitating community-led curation and inclusion of the corresponding host target(s). PMID:25414340

Orientation and mobility training for partially-sighted older adults using an identification cane: a systematic review

PubMed Central

Ballemans, Judith; Kempen, Gertrudis IJM; Zijlstra, GA Rixt

2011-01-01

Objective: This study aimed to provide an overview of the development, content, feasibility, and effectiveness of existing orientation and mobility training programmes in the use of the identification cane. Data sources: A systematic bibliographic database search in PubMed, PsychInfo, ERIC, CINAHL and the Cochrane Library was performed, in combination with the expert consultation (n = 42; orientation and mobility experts), and hand-searching of reference lists. Review methods: Selection criteria included a description of the development, the content, the feasibility, or the effectiveness of orientation and mobility training in the use of the identification cane. Two reviewers independently agreed on eligibility and methodological quality. A narrative/qualitative data analysis method was applied to extract data from obtained documents. Results: The sensitive database search and hand-searching of reference lists revealed 248 potentially relevant abstracts. None met the eligibility criteria. Expert consultation resulted in the inclusion of six documents in which the information presented on the orientation and mobility training in the use of the identification cane was incomplete and of low methodological quality. Conclusion: Our review of the literature showed a lack of well-described protocols and studies on orientation and mobility training in identification cane use. PMID:21795405

Evaluation of three point-of-care healthcare databases: BMJ Point-of-Care, Clin-eguide and Nursing Reference Centre.

PubMed

Chan, Rachel; Stieda, Vivian

2011-03-01

  Point of care resources make it easier for clinicians to find answers to questions that arise during a clinical encounter. In order to make informed purchase decisions in times of tight budgets, librarians need to have a better understanding of which resources will meet their patrons' clinical information needs.   The goal of this study was to assess the content, interface and usability of three point-of-care tools: BMJ Point-of-Care, Clin-eguide and Nursing Reference Centre.   A questionnaire designed to gather quantitative and qualitative data was created using Survey Monkey. The survey was distributed to healthcare practitioners in Alberta's two largest health regions, and the data were analysed for emergent themes.   The themes that arose--ease of use, validated content, relevancy to practice--generally echoed those stated in the literature. No one database fared significantly better, due to differing features, content and client preference.   Despite the limitations of the survey, the themes that emerged provide a springboard for future research on the efficacy of information resources used at the point of care, and the need for deeper analysis of these recent additions to the medical information market. © 2010 The authors. Health Information and Libraries Journal © 2010 Health Libraries Group.

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.

Perception: a concept analysis.

PubMed

McDonald, Susan M

2012-02-01

Concept analysis methodology by Walker and Avant (2005) was used to define, describe, and delimit the concept of perception. Nursing literature in the Medline database was searched for definitions of "perception." Definitions, uses, and defining attributes of perception were identified; model and contrary cases were developed; and antecedents, consequences, and empirical referents were determined. An operational definition for the concept was developed. Nurses need to be cognizant of how perceptual differences impact the delivery of nursing care. In research, a mixed methodology approach may yield a richer description of the phenomenon and provide useful information for clinical practice. © 2011, The Author. International Journal of Nursing Knowledge © 2011, NANDA International.

Chinese students studying at Australian universities with specific reference to nursing students: a narrative literature review.

PubMed

Wang, Carol Chunfeng; Andre, Kate; Greenwood, Kenneth Mark

2015-04-01

To report the current knowledge on the Chinese nursing students' learning at Australian universities. The intent is to provide educators and researchers with a background to the contexts, the methodologies, the emphases of various relevant studies, and to provide recommendations for future research. Attracting international students has become an important part of Australian universities' business and contributes to their cultural diversity. Teaching international students has received considerable attention in the educational research literature. Experiences of international students can vary greatly depending on their country of origin. This paper critically reviews current literature relating to issues for Chinese students and in particular, Chinese nursing students, the biggest single group of international nursing students at Australian universities Narrative literature review. A comprehensive search of seven electronic databases for literature between 2003 and 2014 helped to identify qualitative and quantitative studies that addressed issues of Asian international students with English as a second language (ESL) (included nursing students) studying in Australia, New Zealand, the UK, the United States and China. Pertinent websites were also searched. The reference lists and bibliographies of retrieved articles were hand- searched to identify other relevant studies. Fifteen studies met the inclusion criteria for the review. The majority of existing literature claimed that there is a range of challenges confronting international students including Chinese nursing students, in assimilation into their host country. These include issues with English language proficiency, cultural barriers, social problems, different learning styles, academic demands, perceived racism, homesickness, lack of assertiveness and financial problems. There is limited research about the Chinese students' study in Australia. In particular, the learning experience of Chinese nursing students has not been fully explored nor understood. This paper highlights the need for further research into the lived learning experience of Chinese nursing students studying at Australian universities. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

Microcomputer-Based Access to Machine-Readable Numeric Databases.

ERIC Educational Resources Information Center

Wenzel, Patrick

1988-01-01

Describes the use of microcomputers and relational database management systems to improve access to numeric databases by the Data and Program Library Service at the University of Wisconsin. The internal records management system, in-house reference tools, and plans to extend these tools to the entire campus are discussed. (3 references) (CLB)

PubSearch and PubFetch: a simple management system for semiautomated retrieval and annotation of biological information from the literature.

PubMed

Yoo, Danny; Xu, Iris; Berardini, Tanya Z; Rhee, Seung Yon; Narayanasamy, Vijay; Twigger, Simon

2006-03-01

For most systems in biology, a large body of literature exists that describes the complexity of the system based on experimental results. Manual review of this literature to extract targeted information into biological databases is difficult and time consuming. To address this problem, we developed PubSearch and PubFetch, which store literature, keyword, and gene information in a relational database, index the literature with keywords and gene names, and provide a Web user interface for annotating the genes from experimental data found in the associated literature. A set of protocols is provided in this unit for installing, populating, running, and using PubSearch and PubFetch. In addition, we provide support protocols for performing controlled vocabulary annotations. Intended users of PubSearch and PubFetch are database curators and biology researchers interested in tracking the literature and capturing information about genes of interest in a more effective way than with conventional spreadsheets and lab notebooks.

Automated processing of shoeprint images based on the Fourier transform for use in forensic science.

PubMed

de Chazal, Philip; Flynn, John; Reilly, Richard B

2005-03-01

The development of a system for automatically sorting a database of shoeprint images based on the outsole pattern in response to a reference shoeprint image is presented. The database images are sorted so that those from the same pattern group as the reference shoeprint are likely to be at the start of the list. A database of 476 complete shoeprint images belonging to 140 pattern groups was established with each group containing two or more examples. A panel of human observers performed the grouping of the images into pattern categories. Tests of the system using the database showed that the first-ranked database image belongs to the same pattern category as the reference image 65 percent of the time and that a correct match appears within the first 5 percent of the sorted images 87 percent of the time. The system has translational and rotational invariance so that the spatial positioning of the reference shoeprint images does not have to correspond with the spatial positioning of the shoeprint images of the database. The performance of the system for matching partial-prints was also determined.

Database Access Systems.

ERIC Educational Resources Information Center

Dalrymple, Prudence W.; Roderer, Nancy K.

1994-01-01

Highlights the changes that have occurred from 1987-93 in database access systems. Topics addressed include types of databases, including CD-ROMs; enduser interface; database selection; database access management, including library instruction and use of primary literature; economic issues; database users; the search process; and improving…

Literature searches on Ayurveda: An update

PubMed Central

Aggithaya, Madhur G.; Narahari, Saravu R.

2015-01-01

Introduction: The journals that publish on Ayurveda are increasingly indexed by popular medical databases in recent years. However, many Eastern journals are not indexed biomedical journal databases such as PubMed. Literature searches for Ayurveda continue to be challenging due to the nonavailability of active, unbiased dedicated databases for Ayurvedic literature. In 2010, authors identified 46 databases that can be used for systematic search of Ayurvedic papers and theses. This update reviewed our previous recommendation and identified current and relevant databases. Aims: To update on Ayurveda literature search and strategy to retrieve maximum publications. Methods: Author used psoriasis as an example to search previously listed databases and identify new. The population, intervention, control, and outcome table included keywords related to psoriasis and Ayurvedic terminologies for skin diseases. Current citation update status, search results, and search options of previous databases were assessed. Eight search strategies were developed. Hundred and five journals, both biomedical and Ayurveda, which publish on Ayurveda, were identified. Variability in databases was explored to identify bias in journal citation. Results: Five among 46 databases are now relevant – AYUSH research portal, Annotated Bibliography of Indian Medicine, Digital Helpline for Ayurveda Research Articles (DHARA), PubMed, and Directory of Open Access Journals. Search options in these databases are not uniform, and only PubMed allows complex search strategy. “The Researches in Ayurveda” and “Ayurvedic Research Database” (ARD) are important grey resources for hand searching. About 44/105 (41.5%) journals publishing Ayurvedic studies are not indexed in any database. Only 11/105 (10.4%) exclusive Ayurveda journals are indexed in PubMed. Conclusion: AYUSH research portal and DHARA are two major portals after 2010. It is mandatory to search PubMed and four other databases because all five carry citations from different groups of journals. The hand searching is important to identify Ayurveda publications that are not indexed elsewhere. Availability information of citations in Ayurveda libraries from National Union Catalogue of Scientific Serials in India if regularly updated will improve the efficacy of hand searching. A grey database (ARD) contains unpublished PG/Ph.D. theses. The AYUSH portal, DHARA (funded by Ministry of AYUSH), and ARD should be merged to form single larger database to limit Ayurveda literature searches. PMID:27313409

An Interactive Iterative Method for Electronic Searching of Large Literature Databases

ERIC Educational Resources Information Center

Hernandez, Marco A.

2013-01-01

PubMed® is an on-line literature database hosted by the U.S. National Library of Medicine. Containing over 21 million citations for biomedical literature--both abstracts and full text--in the areas of the life sciences, behavioral studies, chemistry, and bioengineering, PubMed® represents an important tool for researchers. PubMed® searches return…

[The methods within the evaluation of disease management programmes in control-group designs using the example of diabetes mellitus - a systematic literature review].

PubMed

Drabik, A; Sawicki, P T; Müller, D; Passon, A; Stock, S

2012-08-01

Disease management programmes (DMPs) were implemented in Germany in 2002. Their evaluation is required by law. Beyond the mandatory evaluation, a growing number of published studies evaluate the DMP for diabetes mellitus type 2 in a control-group design. As patients opt into the programme on a voluntary basis it is necessary to adjust the inherent selection bias between groups. The aim of this study is to review published studies which evaluate the diabetes DMP using a control-group design with respect to the methods used. A systematic literature review of electronic databases (PUBMED, Cochrane Library, EMBASE, MEDPILOT) and a hand search of reference lists of the relevant publications was conducted to identify studies evaluating the DMP diabetes mellitus in a control-group design. 8 studies were included in the systematic literature review. 4 studies gathered retrospective claims data from sickness funds, one from physician's records, one study used prospective data from ambulatory care, and 2 studies were based on one patient survey. Methods used for adjustment of selection bias included exact matching, matching using propensity score methods, age-adjusted and sex-separated analysis, and adjustment in a regression model/analysis of covariance. One study did not apply adjustment methods. The intervention period ranged from 1 day to 4 years. Considered outcomes of studies (surrogate parameter, diabetes complications, mortality, quality of life, and claim data) depended on the database. In the evaluation of the DMP diabetes mellitus based on a control-group design neither the database nor the methods used for selection bias adjustment were consistent in the available studies. Effectiveness of DMPs cannot be judged based on this review due to heterogeneity of study designs. To allow for a comprehensive programme evaluation standardised minimum requirements for the evaluation of DMPs in the control group design are required. © Georg Thieme Verlag KG Stuttgart · New York.

Best practices in ranking communicable disease threats: a literature review, 2015.

PubMed

O'Brien, Eleanor Charlotte; Taft, Rachel; Geary, Katie; Ciotti, Massimo; Suk, Jonathan E

2016-04-28

The threat of serious, cross-border communicable disease outbreaks in Europe poses a significant challenge to public health and emergency preparedness because the relative likelihood of these threats and the pathogens involved are constantly shifting in response to a range of changing disease drivers. To inform strategic planning by enabling effective resource allocation to manage the consequences of communicable disease outbreaks, it is useful to be able to rank and prioritise pathogens. This paper reports on a literature review which identifies and evaluates the range of methods used for risk ranking. Searches were performed across biomedical and grey literature databases, supplemented by reference harvesting and citation tracking. Studies were selected using transparent inclusion criteria and underwent quality appraisal using a bespoke checklist based on the AGREE II criteria. Seventeen studies were included in the review, covering five methodologies. A narrative analysis of the selected studies suggests that no single methodology was superior. However, many of the methods shared common components, around which a 'best-practice' framework was formulated. This approach is intended to help inform decision makers' choice of an appropriate risk-ranking study design.

Orthodontic treatment in periodontitis‐susceptible subjects: a systematic literature review

PubMed Central

Lindsten, Rune; Slotte, Christer; Bjerklin, Krister

2016-01-01

Abstract The aim is to evaluate the literature for clinical scientific data on possible effects of orthodontic treatment on periodontal status in periodontitis‐susceptible subjects. A systematic literature review was performed on studies in English using PubMed, MEDLINE, and Cochrane Library central databases (1965‐2014). By manually searching reference lists of selected studies, we identified additional articles; then we searched these publications: Journal of Periodontology, Periodontology 2000, Journal of Clinical Periodontology, American Journal of Orthodontics and Dentofacial Orthopedics, Angle Orthodontist, International Journal of Periodontics & Restorative Dentistry, and European Journal of Orthodontics. Search terms included randomized clinical trials, controlled clinical trials, prospective and retrospective clinical studies, case series >5 patients, periodontitis, orthodontics, alveolar bone loss, tooth migration, tooth movement, orthodontic extrusion, and orthodontic intrusion. Only studies on orthodontic treatment in periodontally compromised dentitions were included. One randomized controlled clinical trial, one controlled clinical trial, and 12 clinical studies were included. No evidence currently exists from controlled studies and randomized controlled clinical trials, which shows that orthodontic treatment improves or aggravates the status of periodontally compromised dentitions. PMID:29744163

Anatomy and histology of apical support: a literature review concerning cardinal and uterosacral ligaments.

PubMed

Ramanah, Rajeev; Berger, Mitchell B; Parratte, Bernard M; DeLancey, John O L

2012-11-01

The objective of this work was to collect and summarize relevant literature on the anatomy, histology, and imaging of apical support of the upper vagina and the uterus provided by the cardinal (CL) and uterosacral (USL) ligaments. A literature search in English, French, and German languages was carried out with the keywords apical support, cardinal ligament, transverse cervical ligament, Mackenrodt ligament, parametrium, paracervix, retinaculum uteri, web, uterosacral ligament, and sacrouterine ligament in the PubMed database. Other relevant journal and textbook articles were sought by retrieving references cited in previous PubMed articles. Fifty references were examined in peer-reviewed journals and textbooks. The USL extends from the S2 to the S4 vertebra region to the dorsal margin of the uterine cervix and/or to the upper third of the posterior vaginal wall. It has a superficial and deep component. Autonomous nerve fibers are a major constituent of the deep USL. CL is defined as a perivascular sheath with a proximal insertion around the origin of the internal iliac artery and a distal insertion on the cervix and/or vagina. It is divided into a cranial (vascular) and a caudal (neural) portions. Histologically, it contains mainly vessels, with no distinct band of connective tissue. Both the deep USL and the caudal CL are closely related to the inferior hypogastric plexus. USL and CL are visceral ligaments, with mesentery-like structures containing vessels, nerves, connective tissue, and adipose tissue.

Prosthetic rehabilitation of oral submucous fibrosis patients: A systematic review of published case reports and case series

PubMed Central

Patil, Shankargouda; Sarode, Gargi S.; Bhandi, Shilpa; Awan, Kamran Habib; Ferrari, Marco

2017-01-01

Background Oral submucous fibrosis (OSF) is an insidious chronic condition characterized by restricted mouth opening. Prosthetic rehabilitation is challenging for OSF patients as obtaining a good impression requires adequate mouth opening. The aim of the present review is to systematically present the data from case reports published in the English-language literature. Method A comprehensive search of the literature databases (PubMed, Medline, SCOPUS, Web of Science and Google Scholar) along with the references of published articles on prosthetic rehabilitation in OSF patients published to date was conducted. Keywords included a combination of ‘Oral submucous fibrosis’, ‘prosthesis’, ‘dentures’ and/or ‘restricted mouth opening’. Citations from selected references and bibliographic linkages taken from similar cases were included in this review. The inclusion criteria selected for case reports on prosthetic rehabilitation in OSF patients, and cases of restricted mouth opening due to causes other than OSF were excluded from the study. Results A total of 21 cases were identified and analysed from 17 papers published in the English-language literature. Of these, 9 cases employed the sectional denture technique, 4 cases emphasized the need-based treatment approach in which conventional methods were modified, and 4 cases used mouth exercising devices. Finally, 1 case each involved, flexible denture, oral screen prosthesis, oral stents, surgery in conjunction with dentures. Conclusion Prosthetic rehabilitation in OSF patients is a multifaceted approach and should be patient specific, although sectional dentures have achieved the best results. PMID:28877246

Gynecomastia and drugs: a critical evaluation of the literature.

PubMed

Nuttall, Frank Q; Warrier, Rohit S; Gannon, Mary C

2015-05-01

A large number of medications have been implicated in the genesis of gynecomastia. However, gynecomastia is common in men, asymptomatic, increases with age, and is considered to be due to an increased estradiol/testosterone ratio. This complicates the interpretation of medication-related gynecomastia. Therefore, we have reviewed the literature in order to assess the data relating gynecomastia onset with utilization of specific medications. The literature was searched in PubMed and the Ovid/Medline databases from the 1946 to January 2015 with the search terminology of "gynecomastia, drugs/medications." A few other articles were found and included. One hundred ten publications were reviewed. Sixty-three were single case reports. There were 24 population-based studies of which 8 were HIV-infected patients treated with antiretroviral agents. Among the case reports, 49 were for individual medications, and 2 were reports of antineoplastic or antiretroviral drug regimens. In the great majority, mastodynia with or without breast enlargement was present and referred to as gynecomastia. Generally, hormonal profiles could not explain the breast enlargement. The pain/tenderness and breast enlargement resolved spontaneously over time. Many different medications have been associated with the presence of "gynecomastia." Generally, it presents as a syndrome characterized by a single painful/tender breast (mastodynia) associated with breast enlargement and is transient. We suggest that these cases be referred to as an acute gynecomastia syndrome. This syndrome also occurs independent of medication use. Thus, in an individual patient, whether it is medication induced often remains uncertain. The pathogenesis remains unknown.

Anatomy and histology of apical support: a literature review concerning cardinal and uterosacral ligaments

PubMed Central

Ramanah, Rajeev; Berger, Mitchell B.; Parratte, Bernard M.

2014-01-01

The objective of this work was to collect and summarize relevant literature on the anatomy, histology, and imaging of apical support of the upper vagina and the uterus provided by the cardinal (CL) and uterosacral (USL) ligaments. A literature search in English, French, and German languages was carried out with the keywords apical support, cardinal ligament, transverse cervical ligament, Mackenrodt ligament, parametrium, paracervix, retinaculum uteri, web, uterosacral ligament, and sacrouterine ligament in the PubMed database. Other relevant journal and textbook articles were sought by retrieving references cited in previous PubMed articles. Fifty references were examined in peer-reviewed journals and textbooks. The USL extends from the S2 to the S4 vertebra region to the dorsal margin of the uterine cervix and/or to the upper third of the posterior vaginal wall. It has a superficial and deep component. Autonomous nerve fibers are a major constituent of the deep USL. CL is defined as a perivascular sheath with a proximal insertion around the origin of the internal iliac artery and a distal insertion on the cervix and/or vagina. It is divided into a cranial (vascular) and a caudal (neural) portions. Histologically, it contains mainly vessels, with no distinct band of connective tissue. Both the deep USL and the caudal CL are closely related to the inferior hypogastric plexus. USL and CL are visceral ligaments, with mesentery-like structures containing vessels, nerves, connective tissue, and adipose tissue. PMID:22618209

Prosthetic rehabilitation of oral submucous fibrosis patients: A systematic review of published case reports and case series.

PubMed

Patil, Shankargouda; Sarode, Sachin Chakradhar; Sarode, Gargi S; Bhandi, Shilpa; Awan, Kamran Habib; Ferrari, Marco

2017-01-01

Oral submucous fibrosis (OSF) is an insidious chronic condition characterized by restricted mouth opening. Prosthetic rehabilitation is challenging for OSF patients as obtaining a good impression requires adequate mouth opening. The aim of the present review is to systematically present the data from case reports published in the English-language literature. A comprehensive search of the literature databases (PubMed, Medline, SCOPUS, Web of Science and Google Scholar) along with the references of published articles on prosthetic rehabilitation in OSF patients published to date was conducted. Keywords included a combination of 'Oral submucous fibrosis', 'prosthesis', 'dentures' and/or 'restricted mouth opening'. Citations from selected references and bibliographic linkages taken from similar cases were included in this review. The inclusion criteria selected for case reports on prosthetic rehabilitation in OSF patients, and cases of restricted mouth opening due to causes other than OSF were excluded from the study. A total of 21 cases were identified and analysed from 17 papers published in the English-language literature. Of these, 9 cases employed the sectional denture technique, 4 cases emphasized the need-based treatment approach in which conventional methods were modified, and 4 cases used mouth exercising devices. Finally, 1 case each involved, flexible denture, oral screen prosthesis, oral stents, surgery in conjunction with dentures. Prosthetic rehabilitation in OSF patients is a multifaceted approach and should be patient specific, although sectional dentures have achieved the best results.

Sodium content of foods contributing to sodium intake: A comparison between selected foods from the CDC Packaged Food Database and the USDA National Nutrient Database for Standard Reference

USDA-ARS?s Scientific Manuscript database

The sodium concentration (mg/100g) for 23 of 125 Sentinel Foods were identified in the 2009 CDC Packaged Food Database (PFD) and compared with data in the USDA’s 2013 Standard Reference 26 (SR 26) database. Sentinel Foods are foods and beverages identified by USDA to be monitored as primary indicat...

Document creation, linking, and maintenance system

DOEpatents

Claghorn, Ronald [Pasco, WA

2011-02-15

A document creation and citation system designed to maintain a database of reference documents. The content of a selected document may be automatically scanned and indexed by the system. The selected documents may also be manually indexed by a user prior to the upload. The indexed documents may be uploaded and stored within a database for later use. The system allows a user to generate new documents by selecting content within the reference documents stored within the database and inserting the selected content into a new document. The system allows the user to customize and augment the content of the new document. The system also generates citations to the selected content retrieved from the reference documents. The citations may be inserted into the new document in the appropriate location and format, as directed by the user. The new document may be uploaded into the database and included with the other reference documents. The system also maintains the database of reference documents so that when changes are made to a reference document, the author of a document referencing the changed document will be alerted to make appropriate changes to his document. The system also allows visual comparison of documents so that the user may see differences in the text of the documents.

Health care consumers' experiences of information communication technology--a summary of literature.

PubMed

Akesson, Kerstin M; Saveman, Britt-Inger; Nilsson, Gunilla

2007-09-01

There is an increasing interest in reaching consumers directly through the Internet and different telecommunication systems. The most important contacts in health care will always be the face-to-face meetings, but the tools of health informatics can be seen as a means to an end, which is to provide the best possible health care. A variety of applications have been described in different references. To our knowledge there has been no review of a research-based state of the art in the field of consumers' experiences in using different applications in health informatics. According to the benefits in using information communication technology (ICT) as being cost-effective and timesaving it is of great importance to focus on and examine consumers' experiences. It is important that it is user friendly and regarded as valuable and useful. The aim of this study was to describe consumers' subjective experiences of using electronic resources with reference to health and illness. DESIGN AND/OR METHOD: A systematic literature search was performed in databases CINAHL, Medline and Cochrane, as well as a manual search. Retrieved references (n=14) were appraised according to their scientific structure and quality. A broad search was performed in order to find as many different applications as possible. Our primary intention was to identify existing references describing consumers' experiences with ICT. In spite of this broad search few references were found. Twelve references remained and three themes were identified: support and help, education and information, and telecommunication instead of on-site visiting. Consumers felt more confident and empowered, their knowledge increased and their health status improved due to the ICT resources. Lack of face-to-face meetings or privacy did not appear to be a problem. ICT can improve the nurse-patient relationship and augment well-being for consumers. More research is needed to measure consumers' experiences and factors that influence it. 2006 Elsevier Ireland Ltd

A database on the distribution of butterflies (Lepidoptera) in northern Belgium (Flanders and the Brussels Capital Region)

PubMed Central

Maes, Dirk; Vanreusel, Wouter; Herremans, Marc; Vantieghem, Pieter; Brosens, Dimitri; Gielen, Karin; Beck, Olivier; Van Dyck, Hans; Desmet, Peter; Natuurpunt, Vlinderwerkgroep

2016-01-01

Abstract In this data paper, we describe two datasets derived from two sources, which collectively represent the most complete overview of butterflies in Flanders and the Brussels Capital Region (northern Belgium). The first dataset (further referred to as the INBO dataset – http://doi.org/10.15468/njgbmh) contains 761,660 records of 70 species and is compiled by the Research Institute for Nature and Forest (INBO) in cooperation with the Butterfly working group of Natuurpunt (Vlinderwerkgroep). It is derived from the database Vlinderdatabank at the INBO, which consists of (historical) collection and literature data (1830-2001), for which all butterfly specimens in institutional and available personal collections were digitized and all entomological and other relevant publications were checked for butterfly distribution data. It also contains observations and monitoring data for the period 1991-2014. The latter type were collected by a (small) butterfly monitoring network where butterflies were recorded using a standardized protocol. The second dataset (further referred to as the Natuurpunt dataset – http://doi.org/10.15468/ezfbee) contains 612,934 records of 63 species and is derived from the database http://waarnemingen.be, hosted at the nature conservation NGO Natuurpunt in collaboration with Stichting Natuurinformatie. This dataset contains butterfly observations by volunteers (citizen scientists), mainly since 2008. Together, these datasets currently contain a total of 1,374,594 records, which are georeferenced using the centroid of their respective 5 × 5 km² Universal Transverse Mercator (UTM) grid cell. Both datasets are published as open data and are available through the Global Biodiversity Information Facility (GBIF). PMID:27199606

A database on the distribution of butterflies (Lepidoptera) in northern Belgium (Flanders and the Brussels Capital Region).

PubMed

Maes, Dirk; Vanreusel, Wouter; Herremans, Marc; Vantieghem, Pieter; Brosens, Dimitri; Gielen, Karin; Beck, Olivier; Van Dyck, Hans; Desmet, Peter; Natuurpunt, Vlinderwerkgroep

2016-01-01

In this data paper, we describe two datasets derived from two sources, which collectively represent the most complete overview of butterflies in Flanders and the Brussels Capital Region (northern Belgium). The first dataset (further referred to as the INBO dataset - http://doi.org/10.15468/njgbmh) contains 761,660 records of 70 species and is compiled by the Research Institute for Nature and Forest (INBO) in cooperation with the Butterfly working group of Natuurpunt (Vlinderwerkgroep). It is derived from the database Vlinderdatabank at the INBO, which consists of (historical) collection and literature data (1830-2001), for which all butterfly specimens in institutional and available personal collections were digitized and all entomological and other relevant publications were checked for butterfly distribution data. It also contains observations and monitoring data for the period 1991-2014. The latter type were collected by a (small) butterfly monitoring network where butterflies were recorded using a standardized protocol. The second dataset (further referred to as the Natuurpunt dataset - http://doi.org/10.15468/ezfbee) contains 612,934 records of 63 species and is derived from the database http://waarnemingen.be, hosted at the nature conservation NGO Natuurpunt in collaboration with Stichting Natuurinformatie. This dataset contains butterfly observations by volunteers (citizen scientists), mainly since 2008. Together, these datasets currently contain a total of 1,374,594 records, which are georeferenced using the centroid of their respective 5 × 5 km² Universal Transverse Mercator (UTM) grid cell. Both datasets are published as open data and are available through the Global Biodiversity Information Facility (GBIF).

Google Scholar versus PubMed in locating primary literature to answer drug-related questions.

PubMed

Freeman, Maisha Kelly; Lauderdale, Stacy A; Kendrach, Michael G; Woolley, Thomas W

2009-03-01

Google Scholar linked more visitors to biomedical journal Web sites than did PubMed after the database's initial release; however, its usefulness in locating primary literature articles is unknown. To assess in both databases the availability of primary literature target articles; total number of citations; availability of free, full-text journal articles; and number of primary literature target articles retrieved by year within the first 100 citations of the search results. Drug information question reviews published in The Annals of Pharmacotherapy Drug Information Rounds column served as targets to determine the retrieval ability of Google Scholar and PubMed searches. Reviews printed in this column from January 2006 to June 2007 were eligible for study inclusion. Articles were chosen if at least 2 key words of the printed article were included in the PubMed Medical Subject Heading (MeSH) database, and these terms were searched in both databases. Twenty-two of 33 (67%) eligible Drug Information Rounds articles met the inclusion criteria. The median number of primary literature articles used in each of these articles was 6.5 (IQR 4.8, 8.3; mean +/- SD 8 +/- 5.4). No significant differences were found for the mean number of target primary literature articles located within the first 100 citations in Google Scholar and PubMed searches (5.1 +/- 3.9 vs 5.3 +/- 3.3; p = 0.868). Google Scholar searches located more total results than PubMed (2211.6 +/- 3999.5 vs 44.2 +/- 47.4; p = 0.019). The availability of free, full-text journal articles per Drug Information Rounds article was similar between the databases (1.8 +/- 1.7 vs 2.3 +/- 1.7; p = 0.325). More primary literature articles published prior to 2000 were located with Google Scholar searches compared with PubMed (62.8% vs 34.9%; p = 0.017); however, no statistically significant differences between the databases were observed for articles published after 2000 (66.4 vs 77.1; p = 0.074). No significant differences were identified in the number of target primary literature articles located between databases. PubMed searches yielded fewer total citations than Google Scholar results; however, PubMed appears to be more specific than Google Scholar for locating relevant primary literature articles.

Perceptual quality estimation of H.264/AVC videos using reduced-reference and no-reference models

NASA Astrophysics Data System (ADS)

Shahid, Muhammad; Pandremmenou, Katerina; Kondi, Lisimachos P.; Rossholm, Andreas; Lövström, Benny

2016-09-01

Reduced-reference (RR) and no-reference (NR) models for video quality estimation, using features that account for the impact of coding artifacts, spatio-temporal complexity, and packet losses, are proposed. The purpose of this study is to analyze a number of potentially quality-relevant features in order to select the most suitable set of features for building the desired models. The proposed sets of features have not been used in the literature and some of the features are used for the first time in this study. The features are employed by the least absolute shrinkage and selection operator (LASSO), which selects only the most influential of them toward perceptual quality. For comparison, we apply feature selection in the complete feature sets and ridge regression on the reduced sets. The models are validated using a database of H.264/AVC encoded videos that were subjectively assessed for quality in an ITU-T compliant laboratory. We infer that just two features selected by RR LASSO and two bitstream-based features selected by NR LASSO are able to estimate perceptual quality with high accuracy, higher than that of ridge, which uses more features. The comparisons with competing works and two full-reference metrics also verify the superiority of our models.

A systematic review of the literature of the three related disease entities cheilitis granulomatosa, orofacial granulomatosis and Melkersson - Rosenthal syndrome.

PubMed

Wehl, Goetz; Rauchenzauner, Markus

2018-05-14

Melkersson Rosenthal syndrome (MRS) is a rare disorder of unknown etiology and comprises the triad: orofacial edema, recurrent facial paralysis and lingua plicata. In the current literature confusing heterogeneity exists, mixing together the historically grown terms cheilitis granulomatosa or granulomatous cheilitis, Melkersson Rosenthal syndrome and the umbrella term orofacial granulomatosis (OFG). We provide a systematic review comprising all three disease entities of orofacial granulomatosis using the computerized database "Pubmed Medline" entering the key words "orofacial granulomatosis" (141 references), "Melkersson-Rosenthal syndrome" (207 references), "granulomatous cheilitis" or "cheilitis granulomatosa" (102 references) back to 1956. Full text journals and case studies were included, and data synthesis was performed individually. Etiology remains unclear for all three disease entities. Etiological relatedness to chronic inflammatory bowel disease is under discussion and effectiveness was found for different treatments, e.g. local triamcinolone injections, antibiotics, surgical interventions, TNF alpha blockers or exclusive enteral nutrition. No randomized controlled trial concerning the therapy of orofacial granulomatosis was found. As a consequence, therapeutic conclusions are drawn mainly from small case series, thus limiting the evidence of therapeutic interventions. OFG with the sub-entities MRS and cheilitis granulomatosa is an etiological obscure disease process with various possible therapeutic interventions potentially alleviating the disease course but to broaden treatment knowledge further study in randomized controlled trials are needed. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Structured Forms Reference Set of Binary Images (SFRS)

National Institute of Standards and Technology Data Gateway

NIST Structured Forms Reference Set of Binary Images (SFRS) (Web, free access)   The NIST Structured Forms Database (Special Database 2) consists of 5,590 pages of binary, black-and-white images of synthesized documents. The documents in this database are 12 different tax forms from the IRS 1040 Package X for the year 1988.

STELAR: An experiment in the electronic distribution of astronomical literature

NASA Technical Reports Server (NTRS)

Warnock, A.; Vansteenburg, M. E.; Brotzman, L. E.; Gass, J.; Kovalsky, D.

1992-01-01

STELAR (Study of Electronic Literature for Astronomical Research) is a Goddard-based project designed to test methods of delivering technical literature in machine readable form. To that end, we have scanned a five year span of the ApJ, ApJ Supp, AJ and PASP, and have obtained abstracts for eight leading academic journals from NASA/STI CASI, which also makes these abstracts available through the NASA RECON system. We have also obtained machine readable versions of some journal volumes from the publishers, although in many instances, the final typeset versions are no longer available. The fundamental data object for the STELAR database is the article, a collection of items associated with a scientific paper - abstract, scanned pages (in a variety of formats), figures, OCR extractions, forward and backward references, errata and versions of the paper in various formats (e.g., TEX, SGML, PostScript, DVI). Articles are uniquely referenced in the database by journal name, volume number and page number. The selection and delivery of articles is accomplished through the WAIS (Wide Area Information Server) client/server models requiring only an Internet connection. Modest modifications to the server code have made it capable of delivering the multiple data types required by STELAR. WAIS is a platform independent and fully open multi-disciplinary delivery system, originally developed by Thinking Machines Corp. and made available free of charge. It is based on the ISO Z39.50 standard communications protocol. WAIS servers run under both UNIX and VMS. WAIS clients run on a wide variety of machines, from UNIX-based Xwindows systems to MS-DOS and macintosh microcomputers. The WAIS system includes full-test indexing and searching of documents, network interface and easy access to a variety of document viewers. ASCII versions of the CASI abstracts have been formatted for display and the full test of the abstracts has been indexed. The entire WAIS database of abstracts is now available for use by the astronomical community. Enhancements of the search and retrieval system are under investigation to include specialized searches (by reference, author or keyword, as opposed to full test searches), improved handling of word stems, improvements in relevancy criteria and other retrieval techniques, such as factor spaces. The STELAR project has been assisted by the full cooperation of the AAS, the ASP, the publishers of the academic journals, librarians from GSFC, NRAO and STScI, the Library of Congress, and the University of North Carolina at Chapel Hill.

Users’ guide to the surgical literature: how to perform a high-quality literature search

PubMed Central

Waltho, Daniel; Kaur, Manraj Nirmal; Haynes, R. Brian; Farrokhyar, Forough; Thoma, Achilleas

2015-01-01

Summary The article “Users’ guide to the surgical literature: how to perform a literature search” was published in 2003, but the continuing technological developments in databases and search filters have rendered that guide out of date. The present guide fills an existing gap in this area; it provides the reader with strategies for developing a searchable clinical question, creating an efficient search strategy, accessing appropriate databases, and skillfully retrieving the best evidence to address the research question. PMID:26384150

Classics Online.

ERIC Educational Resources Information Center

Clayman, Dee L.

1995-01-01

Appraises several databases devoted to classical literature. Thesaurus Linguae Graecae (TLG) contains the entire extant corpus of ancient Greek literature, including works on lexicography and historiography, extending into the 15th century. Other works awaiting completion are the Database of Classical Bibliography and a CD-ROM pictorial dictionary…

Methods for the guideline-based development of quality indicators--a systematic review

PubMed Central

2012-01-01

Background Quality indicators (QIs) are used in many healthcare settings to measure, compare, and improve quality of care. For the efficient development of high-quality QIs, rigorous, approved, and evidence-based development methods are needed. Clinical practice guidelines are a suitable source to derive QIs from, but no gold standard for guideline-based QI development exists. This review aims to identify, describe, and compare methodological approaches to guideline-based QI development. Methods We systematically searched medical literature databases (Medline, EMBASE, and CINAHL) and grey literature. Two researchers selected publications reporting methodological approaches to guideline-based QI development. In order to describe and compare methodological approaches used in these publications, we extracted detailed information on common steps of guideline-based QI development (topic selection, guideline selection, extraction of recommendations, QI selection, practice test, and implementation) to predesigned extraction tables. Results From 8,697 hits in the database search and several grey literature documents, we selected 48 relevant references. The studies were of heterogeneous type and quality. We found no randomized controlled trial or other studies comparing the ability of different methodological approaches to guideline-based development to generate high-quality QIs. The relevant publications featured a wide variety of methodological approaches to guideline-based QI development, especially regarding guideline selection and extraction of recommendations. Only a few studies reported patient involvement. Conclusions Further research is needed to determine which elements of the methodological approaches identified, described, and compared in this review are best suited to constitute a gold standard for guideline-based QI development. For this research, we provide a comprehensive groundwork. PMID:22436067

[Comparative analysis of the non-profit, for-profit and public hospital providers: American experiences].

PubMed

Mogyorósy, Zsolt

2004-07-04

The new legislation allowed hospitals and other health care facilities to be converted into for-profit status. The detailed regulatory framework is under development in Hungary. This article reviews the literature of studies comparing hospital financial performance and the quality of care before and after conversion from public or non-profit status to for-profit. Studies were identified through electronic search of Medline (Pubmed), EconLit, Cochrane Library, Economic Evaluation Database (EED), az Health Technology Assessment (HTA) databases, library files and reference lists. The literature search was extended to the Internet, World Bank, International Labor Office (ILO), Organization for Economic Cooperation and Development (OECD), and WHO websites as well as government, academic institutions and large insurance companies web pages for unpublished online information. Time series and before-after studies and systematic literature reviews were included. The conversion from non-profit to for-profit status improved the profitability of the hospitals. However the quality of care (measures in mortality, frequency of side effects, complications) might suffer in the first couple years of the conversion. The conversion may increase the total health care expenditures per capita. Trustful relationship between patients and physicians may also be threatened. The generalisability of the American experiences into the Hungarian single payer system may be limited. From societal point of view, for-profit providers could provide socially beneficial care in areas where it is possible to define, monitor and evaluate the nature and quality characteristics of the services, as well as market competition can be ensured. However most of the healthcare services are too complex to fall into this category.

Vision science literature of Nepal in the database "Web of Science".

PubMed

Risal, S; Prasad, H N

2012-01-01

Vision Science is considered to be a quite developed discipline in Nepal, with much research currently in progress. Though the results of these endeavors are published in scientific journals, formal citation analyses have not been performed on works contributed by Nepalese vision scientists. To study Nepal's contribution to vision science literature in the database "Web of Science". The primary data source of this paper was Web of Science, a citation database of Thomas Reuters. All bibliometric analyses were performed with the help of Web of Science analysis service. In the current database of vision science literature, Nepalese authors contributed 112 publications to Web of Science, 95 of which were original articles. Pokharel GP had the highest number of citations among contributing authors of Nepal. Hennig A contributed the highest number of article as a first author. The Nepal Eye Hospital contributed the highest number of articles as an institution to the field of Vision Science. Currently, only two journals from Nepal including Journal of Nepal Medical Association (JAMA) are indexed in the Web of Science database (Sieving, 2012). To evaluate the total productivity of vision science literature from Nepal, total publication counts from national journals and articles indexed in other databases such as PubMed and Scopus must also be considered. © NEPjOPH.

Efficacy and safety data of subsequent entry biologics pertinent to nephrology practice: a systematic review.

PubMed

Marin, Judith Genevieve; Leung, Marianna; Lo, Clifford; Tsao, Nicole W; Martinusen, Daniel J

2014-01-01

Subsequent entry biologics (SEBs) may soon be a reality in Canadian nephrology practice. Understanding the worldwide experience with these agents will be valuable to Canadian clinicians. To compare the efficacy and safety data between SEBs used in nephrology practice and their reference biologic. Systematic review. Ovid MEDLINE, EMBASE, Cochrane Database of Systematic Reviews, Database of Abstracts of Review of Effects, Cochrane Central Register of Controlled Trials. Adult patients with chronic kidney disease (CKD). Our systematic review follows the process outlined by Cochrane Reviews. For efficacy data, all randomized controlled trials (RCTs), quasi-RCTs and observational trials in nephrology practice were included. For safety data, case series, case reports, review articles in nephrology practice and pharmacovigilance programs were included as well. Only epoetin SEBs trials were published in the literature. Ten studies involving three different epoetin SEBs (epoetin zeta, HX575 and epoetin theta) were included. The mean epoetin dose used did not differ significantly between the SEBs and the reference product. For epoetin zeta and epoetin theta, the mean hemoglobin levels achieved in the studies were similar between the SEBs and the reference epoetin. The HX 575 studies reported a mean absolute change in hemoglobin within the predefined equivalence margin, when compared with the reference biologic. In terms of safety data, 2 cases of pure-red-cell aplasia were linked to the subcutaneous administration of HX 575. Otherwise, the rate of adverse drug reactions was similar when epoetin SEBs were compared with the reference biologic. Our analysis is limited by the paucity of information available on SEB use in nephrology with the exception of epoetin SEBs. Methodological flaw was found in one of the epoetin zeta studies which accounted for 45% of pooled results. Little clinical difference was found between epoetin SEBs and the reference product. Although not deemed clinically important, the financial implication of a possible dose difference between epoetin zeta and reference product should be considered in pharmacoeconomic studies. Ongoing trials are expected to address the risk of pure-red-cell aplasia with HX 575.

Systematic review of the health and social determinants and outcomes of home cooking: protocol.

PubMed

Mills, Susanna; White, Martin; Robalino, Shannon; Wrieden, Wendy; Brown, Heather; Adams, Jean

2015-03-28

The United Kingdom (UK) and wider world are experiencing an obesity epidemic, with lower socio-economic groups disproportionately affected. Dietary quality is also socio-economically patterned, with an estimated quarter of observed inequalities in UK mortality due to inequalities in diet. Food preparation and eating patterns clearly have an impact on dietary intake and hence health. A growing body of evidence indicates that out of home food consumption and eating ready meals may be associated with negative outcomes. However, to date no systematic reviews have assessed the health and social determinants and outcomes of home cooking. Here, home cooking refers to the combination of actions required for preparing hot or cold foods at home, including combining, mixing and often heating ingredients. A systematic review of peer-reviewed literature on home cooking will be undertaken. Studies will be considered for inclusion if they present qualitative or quantitative data on participants from high/very high human development index countries, including all relevant study designs. No language or date of publication restrictions will be applied. Determinants will be considered as factors that influence behaviour and outcomes as potential advantages and disadvantages of engaging in home cooking. Electronic databases of peer-reviewed journal articles covering health, psychology, social sciences and consumer practices will be searched. Published postgraduate theses will also be considered for inclusion. Additional strategies to identify relevant studies will be used, such as citation searches of included articles, evaluation of references from relevant reviews and included articles and the 'related/similar to' function found in certain databases. Two independent researchers will be involved in literature screening (10% at first screen and 100% at second screen), data extraction and quality appraisal. Studies included in the review will be analysed by thematic synthesis and narrative synthesis, as appropriate for the nature of the data retrieved. This review will provide key empirical evidence to inform the development of recommendations for public health policy makers and practitioners to encourage healthier home food preparation, thereby impacting on dietary-related health. This protocol has been registered with the PROSPERO international prospective register of systematic reviews, reference CRD42014013984 .

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins.

PubMed

van Heel, Auke J; de Jong, Anne; Song, Chunxu; Viel, Jakob H; Kok, Jan; Kuipers, Oscar P

2018-05-21

Interest in secondary metabolites such as RiPPs (ribosomally synthesized and posttranslationally modified peptides) is increasing worldwide. To facilitate the research in this field we have updated our mining web server. BAGEL4 is faster than its predecessor and is now fully independent from ORF-calling. Gene clusters of interest are discovered using the core-peptide database and/or through HMM motifs that are present in associated context genes. The databases used for mining have been updated and extended with literature references and links to UniProt and NCBI. Additionally, we have included automated promoter and terminator prediction and the option to upload RNA expression data, which can be displayed along with the identified clusters. Further improvements include the annotation of the context genes, which is now based on a fast blast against the prokaryote part of the UniRef90 database, and the improved web-BLAST feature that dynamically loads structural data such as internal cross-linking from UniProt. Overall BAGEL4 provides the user with more information through a user-friendly web-interface which simplifies data evaluation. BAGEL4 is freely accessible at http://bagel4.molgenrug.nl.

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases

PubMed Central

Foerster, Hartmut; Bombarely, Aureliano; Battey, James N D; Sierro, Nicolas; Ivanov, Nikolai V; Mueller, Lukas A

2018-01-01

Abstract SolCyc is the entry portal to pathway/genome databases (PGDBs) for major species of the Solanaceae family hosted at the Sol Genomics Network. Currently, SolCyc comprises six organism-specific PGDBs for tomato, potato, pepper, petunia, tobacco and one Rubiaceae, coffee. The metabolic networks of those PGDBs have been computationally predicted by the pathologic component of the pathway tools software using the manually curated multi-domain database MetaCyc (http://www.metacyc.org/) as reference. SolCyc has been recently extended by taxon-specific databases, i.e. the family-specific SolanaCyc database, containing only curated data pertinent to species of the nightshade family, and NicotianaCyc, a genus-specific database that stores all relevant metabolic data of the Nicotiana genus. Through manual curation of the published literature, new metabolic pathways have been created in those databases, which are complemented by the continuously updated, relevant species-specific pathways from MetaCyc. At present, SolanaCyc comprises 199 pathways and 29 superpathways and NicotianaCyc accounts for 72 pathways and 13 superpathways. Curator-maintained, taxon-specific databases such as SolanaCyc and NicotianaCyc are characterized by an enrichment of data specific to these taxa and free of falsely predicted pathways. Both databases have been used to update recently created Nicotiana-specific databases for Nicotiana tabacum, Nicotiana benthamiana, Nicotiana sylvestris and Nicotiana tomentosiformis by propagating verifiable data into those PGDBs. In addition, in-depth curation of the pathways in N.tabacum has been carried out which resulted in the elimination of 156 pathways from the 569 pathways predicted by pathway tools. Together, in-depth curation of the predicted pathway network and the supplementation with curated data from taxon-specific databases has substantially improved the curation status of the species–specific N.tabacum PGDB. The implementation of this strategy will significantly advance the curation status of all organism-specific databases in SolCyc resulting in the improvement on database accuracy, data analysis and visualization of biochemical networks in those species. Database URL https://solgenomics.net/tools/solcyc/ PMID:29762652

[Scientific output on nutrition in the scope of Primary Health Care in Brazil: a review of the literature].

PubMed

Canella, Daniela Silva; Silva, Ana Carolina Feldenheimer da; Jaime, Patrícia Constante

2013-02-01

Nutrition campaigns in Primary Health Care (PHC) play an important role in health promotion and the prevention and treatment of injuries. The scope of this paper is to chart and evaluate the scientific output of nutrition in Brazilian PHC. A search and review of the literature and papers was conducted on the PubMed and Lilacs databases, using key words related to PHC and nutrition. The studies were restricted to Brazil with the professionals or population assisted by PHC in the Brazilian Unified Health System and published prior to March 2011. The references in the selected articles were also consulted in order to identify additional studies. From the total of papers located, 68 were eligible and a further 49 were identified in the references lists, such that a total of 117 papers were analyzed. The studies reviewed were mostly original articles, using quantitative methodology, carried out by São Paulo University in that state and published from 2002 to 2011. The main issues were diagnosis seeking the evaluation of nutritional status involving children. The output in this field is growing, although there is a need to redirect the scope of future studies to a focus on intervention models and program evaluation.

Drug sales data analysis for outbreak detection of infectious diseases: a systematic literature review.

PubMed

Pivette, Mathilde; Mueller, Judith E; Crépey, Pascal; Bar-Hen, Avner

2014-11-18

This systematic literature review aimed to summarize evidence for the added value of drug sales data analysis for the surveillance of infectious diseases. A search for relevant publications was conducted in Pubmed, Embase, Scopus, Cochrane Library, African Index Medicus and Lilacs databases. Retrieved studies were evaluated in terms of objectives, diseases studied, data sources, methodologies and performance for real-time surveillance. Most studies compared drug sales data to reference surveillance data using correlation measurements or indicators of outbreak detection performance (sensitivity, specificity, timeliness of the detection). We screened 3266 articles and included 27 in the review. Most studies focused on acute respiratory and gastroenteritis infections. Nineteen studies retrospectively compared drug sales data to reference clinical data, and significant correlations were observed in 17 of them. Four studies found that over-the-counter drug sales preceded clinical data in terms of incidence increase. Five studies developed and evaluated statistical algorithms for selecting drug groups to monitor specific diseases. Another three studies developed models to predict incidence increase from drug sales. Drug sales data analyses appear to be a useful tool for surveillance of gastrointestinal and respiratory disease, and OTC drugs have the potential for early outbreak detection. Their utility remains to be investigated for other diseases, in particular those poorly surveyed.

MimoSA: a system for minimotif annotation

PubMed Central

2010-01-01

Background Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many minimotifs in the primary literature, which have yet to be annotated, while entirely novel minimotifs continue to be published on a weekly basis. Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature. Results We have built the MimoSA application for minimotif annotation. The application supports management of the Minimotif Miner database, literature tracking, and annotation of new minimotifs. MimoSA enables the visualization, organization, selection and editing functions of minimotifs and their attributes in the MnM database. For the literature components, Mimosa provides paper status tracking and scoring of papers for annotation through a freely available machine learning approach, which is based on word correlation. The paper scoring algorithm is also available as a separate program, TextMine. Form-driven annotation of minimotif attributes enables entry of new minimotifs into the MnM database. Several supporting features increase the efficiency of annotation. The layered architecture of MimoSA allows for extensibility by separating the functions of paper scoring, minimotif visualization, and database management. MimoSA is readily adaptable to other annotation efforts that manually curate literature into a MySQL database. Conclusions MimoSA is an extensible application that facilitates minimotif annotation and integrates with the Minimotif Miner database. We have built MimoSA as an application that integrates dynamic abstract scoring with a high performance relational model of minimotif syntax. MimoSA's TextMine, an efficient paper-scoring algorithm, can be used to dynamically rank papers with respect to context. PMID:20565705

DNA Sequences over the Internet Provide Greater Speed and Accuracy for Health Sciences Reference Librarians.

ERIC Educational Resources Information Center

Harzbecker, Joseph, Jr.

1993-01-01

Describes the National Institute of Health's GenBank DNA sequence database and how it can be accessed through the Internet. A real reference question, which was answered successfully using the database, is reproduced to illustrate and elaborate on the potential of the Internet for information retrieval. (10 references) (KRN)

Horse Racing at the Library: How One Library System Increased the Usage of Some of Its Online Databases

ERIC Educational Resources Information Center

Kurhan, Scott H.; Griffing, Elizabeth A.

2011-01-01

Reference services in public libraries are changing dramatically. The Internet, online databases, and shrinking budgets are all making it necessary for non-traditional reference staff to become familiar with online reference tools. Recognizing the need for cross-training, Chesapeake Public Library (CPL) developed a program called the Database…

FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca

PubMed Central

Naithani, Sushma; Partipilo, Christina M.; Raja, Rajani; Elser, Justin L.; Jaiswal, Pankaj

2016-01-01

FragariaCyc is a strawberry-specific cellular metabolic network based on the annotated genome sequence of Fragaria vesca L. ssp. vesca, accession Hawaii 4. It was built on the Pathway-Tools platform using MetaCyc as the reference. The experimental evidences from published literature were used for supporting/editing existing entities and for the addition of new pathways, enzymes, reactions, compounds, and small molecules in the database. To date, FragariaCyc comprises 66 super-pathways, 488 unique pathways, 2348 metabolic reactions, 3507 enzymes, and 2134 compounds. In addition to searching and browsing FragariaCyc, researchers can compare pathways across various plant metabolic networks and analyze their data using Omics Viewer tool. We view FragariaCyc as a resource for the community of researchers working with strawberry and related fruit crops. It can help understanding the regulation of overall metabolism of strawberry plant during development and in response to diseases and abiotic stresses. FragariaCyc is available online at http://pathways.cgrb.oregonstate.edu. PMID:26973684

How Documentalists Update SIMBAD

NASA Astrophysics Data System (ADS)

Buga, M.; Bot, C.; Brouty, M.; Bruneau, C.; Brunet, C.; Cambresy, L.; Eisele, A.; Genova, F.; Lesteven, S.; Loup, C.; Neuville, M.; Oberto, A.; Ochsenbein, F.; Perret, E.; Siebert, A.; Son, E.; Vannier, P.; Vollmer, B.; Vonflie, P.; Wenger, M.; Woelfel, F.

2015-04-01

The Strasbourg astronomical Data Center (CDS) was created in 1972 and has had a major role in astronomy for more than forty years. CDS develops a service called SIMBAD that provides basic data, cross-identifications, bibliography, and measurements for astronomical objects outside the solar system. It brings to the scientific community an added value to content which is updated daily by a team of documentalists working together in close collaboration with astronomers and IT specialists. We explain how the CDS staff updates SIMBAD with object citations in the main astronomical journals, as well as with astronomical data and measurements. We also explain how the identification is made between the objects found in the literature and those already existing in SIMBAD. We show the steps followed by the documentalist team to update the database using different tools developed at CDS, like the sky visualizer Aladin, and the large catalogues and survey database VizieR. As a direct result of this teamwork, SIMBAD integrates almost 10.000 bibliographic references per year. The service receives more than 400.000 queries per day.

A Global Survey of Deep Underground Facilities; Examples of Geotechnical and Engineering Capabilities, Achievements, Challenges (Mines, Shafts, Tunnels, Boreholes, Sites and Underground Facilities for Nuclear Waste and Physics R&D): A Guide to Interactive Global Map Layers, Table Database, References and Notes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tynan, Mark C.; Russell, Glenn P.; Perry, Frank V.

These associated tables, references, notes, and report present a synthesis of some notable geotechnical and engineering information used to create four interactive layer maps for selected: 1) deep mines and shafts; 2) existing, considered or planned radioactive waste management deep underground studies or disposal facilities 3) deep large diameter boreholes, and 4) physics underground laboratories and facilities from around the world. These data are intended to facilitate user access to basic information and references regarding “deep underground” facilities, history, activities, and plans. In general, the interactive maps and database provide each facility’s approximate site location, geology, and engineered features (e.g.:more » access, geometry, depth, diameter, year of operations, groundwater, lithology, host unit name and age, basin; operator, management organization, geographic data, nearby cultural features, other). Although the survey is not comprehensive, it is representative of many of the significant existing and historical underground facilities discussed in the literature addressing radioactive waste management and deep mined geologic disposal safety systems. The global survey is intended to support and to inform: 1) interested parties and decision makers; 2) radioactive waste disposal and siting option evaluations, and 3) safety case development applicable to any mined geologic disposal facility as a demonstration of historical and current engineering and geotechnical capabilities available for use in deep underground facility siting, planning, construction, operations and monitoring.« less

Algorithms for database-dependent search of MS/MS data.

PubMed

Matthiesen, Rune

2013-01-01

The frequent used bottom-up strategy for identification of proteins and their associated modifications generate nowadays typically thousands of MS/MS spectra that normally are matched automatically against a protein sequence database. Search engines that take as input MS/MS spectra and a protein sequence database are referred as database-dependent search engines. Many programs both commercial and freely available exist for database-dependent search of MS/MS spectra and most of the programs have excellent user documentation. The aim here is therefore to outline the algorithm strategy behind different search engines rather than providing software user manuals. The process of database-dependent search can be divided into search strategy, peptide scoring, protein scoring, and finally protein inference. Most efforts in the literature have been put in to comparing results from different software rather than discussing the underlining algorithms. Such practical comparisons can be cluttered by suboptimal implementation and the observed differences are frequently caused by software parameters settings which have not been set proper to allow even comparison. In other words an algorithmic idea can still be worth considering even if the software implementation has been demonstrated to be suboptimal. The aim in this chapter is therefore to split the algorithms for database-dependent searching of MS/MS data into the above steps so that the different algorithmic ideas become more transparent and comparable. Most search engines provide good implementations of the first three data analysis steps mentioned above, whereas the final step of protein inference are much less developed for most search engines and is in many cases performed by an external software. The final part of this chapter illustrates how protein inference is built into the VEMS search engine and discusses a stand-alone program SIR for protein inference that can import a Mascot search result.

Intra- and Inter-database Study for Arabic, English, and German Databases: Do Conventional Speech Features Detect Voice Pathology?

PubMed

Ali, Zulfiqar; Alsulaiman, Mansour; Muhammad, Ghulam; Elamvazuthi, Irraivan; Al-Nasheri, Ahmed; Mesallam, Tamer A; Farahat, Mohamed; Malki, Khalid H

2017-05-01

A large population around the world has voice complications. Various approaches for subjective and objective evaluations have been suggested in the literature. The subjective approach strongly depends on the experience and area of expertise of a clinician, and human error cannot be neglected. On the other hand, the objective or automatic approach is noninvasive. Automatic developed systems can provide complementary information that may be helpful for a clinician in the early screening of a voice disorder. At the same time, automatic systems can be deployed in remote areas where a general practitioner can use them and may refer the patient to a specialist to avoid complications that may be life threatening. Many automatic systems for disorder detection have been developed by applying different types of conventional speech features such as the linear prediction coefficients, linear prediction cepstral coefficients, and Mel-frequency cepstral coefficients (MFCCs). This study aims to ascertain whether conventional speech features detect voice pathology reliably, and whether they can be correlated with voice quality. To investigate this, an automatic detection system based on MFCC was developed, and three different voice disorder databases were used in this study. The experimental results suggest that the accuracy of the MFCC-based system varies from database to database. The detection rate for the intra-database ranges from 72% to 95%, and that for the inter-database is from 47% to 82%. The results conclude that conventional speech features are not correlated with voice, and hence are not reliable in pathology detection. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

A kinetics database and scripts for PHREEQC

NASA Astrophysics Data System (ADS)

Hu, B.; Zhang, Y.; Teng, Y.; Zhu, C.

2017-12-01

Kinetics of geochemical reactions has been increasingly used in numerical models to simulate coupled flow, mass transport, and chemical reactions. However, the kinetic data are scattered in the literature. To assemble a kinetic dataset for a modeling project is an intimidating task for most. In order to facilitate the application of kinetics in geochemical modeling, we assembled kinetics parameters into a database for the geochemical simulation program, PHREEQC (version 3.0). Kinetics data were collected from the literature. Our database includes kinetic data for over 70 minerals. The rate equations are also programmed into scripts with the Basic language. Using the new kinetic database, we simulated reaction path during the albite dissolution process using various rate equations in the literature. The simulation results with three different rate equations gave difference reaction paths at different time scale. Another application involves a coupled reactive transport model simulating the advancement of an acid plume in an acid mine drainage site associated with Bear Creek Uranium tailings pond. Geochemical reactions including calcite, gypsum, and illite were simulated with PHREEQC using the new kinetic database. The simulation results successfully demonstrated the utility of new kinetic database.

Planning for CD-ROM in the Reference Department.

ERIC Educational Resources Information Center

Graves, Gail T.; And Others

1987-01-01

Outlines the evaluation criteria used by the reference department at the Williams Library at the University of Mississippi in selecting databases and hardware used in CD-ROM workstations. The factors discussed include database coverage, costs, and security. (CLB)

Community hospitals – the place of local service provision in a modernising NHS: an integrative thematic literature review

PubMed Central

Heaney, David; Black, Corri; O'Donnell, Catherine A; Stark, Cameron; van Teijlingen, Edwin

2006-01-01

Background Recent developments within the United Kingdom's (UK) health care system have re-awakened interest in community hospitals (CHs) and their role in the provision of health care. This integrative literature review sought to identify and assess the current evidence base for CHs. Methods A range of electronic reference databases were searched from January 1984 to either December 2004 or February 2005: Medline, Embase, Web of Knowledge, BNI, CINAHL, HMIC, ASSIA, PsychInfo, SIGLE, Dissertation Abstracts, Cochrane Library, Kings Fund website, using both keywords and text words. Thematic analysis identified recurrent themes across the literature; narrative analyses were written for each theme, identifying unifying concepts and discrepant issues. Results The search strategy identified over 16,000 international references. We included papers of any study design focussing on hospitals in which care was led principally by general practitioners or nurses. Papers from developing countries were excluded. A review of titles revealed 641 potentially relevant references; abstract appraisal identified 161 references for review. During data extraction, a further 48 papers were excluded, leaving 113 papers in the final review. The most common methodological approaches were cross-sectional/descriptive studies, commentaries and expert opinion. There were few experimental studies, systematic reviews, economic studies or studies that reported on longer-term outcomes. The key themes identified were origin and location of CHs; their place in the continuum of care; services provided; effectiveness, efficiency and equity of CHs; and views of patients and staff. In general, there was a lack of robust evidence for the role of CHs, which is partly due to the ad hoc nature of their development and lack of clear strategic vision for their future. Evidence for the effectiveness and efficiency of the services provided was limited. Most people admitted to CHs appeared to be older, suggesting that admittance to CHs was age-related rather than condition-related. Conclusion Overall the literature surveyed was long on opinion and short of robust studies on CHs. While lack of evidence on CHs does not imply lack of effect, there is an urgent need to develop a research agenda that addresses the key issues of health care delivery in the CH setting. PMID:17184517

TRENDS: A flight test relational database user's guide and reference manual

NASA Technical Reports Server (NTRS)

Bondi, M. J.; Bjorkman, W. S.; Cross, J. L.

1994-01-01

This report is designed to be a user's guide and reference manual for users intending to access rotocraft test data via TRENDS, the relational database system which was developed as a tool for the aeronautical engineer with no programming background. This report has been written to assist novice and experienced TRENDS users. TRENDS is a complete system for retrieving, searching, and analyzing both numerical and narrative data, and for displaying time history and statistical data in graphical and numerical formats. This manual provides a 'guided tour' and a 'user's guide' for the new and intermediate-skilled users. Examples for the use of each menu item within TRENDS is provided in the Menu Reference section of the manual, including full coverage for TIMEHIST, one of the key tools. This manual is written around the XV-15 Tilt Rotor database, but does include an appendix on the UH-60 Blackhawk database. This user's guide and reference manual establishes a referrable source for the research community and augments NASA TM-101025, TRENDS: The Aeronautical Post-Test, Database Management System, Jan. 1990, written by the same authors.

Analysis of plant gums and saccharide materials in paint samples: comparison of GC-MS analytical procedures and databases

PubMed Central

2012-01-01

Background Saccharide materials have been used for centuries as binding media, to paint, write and illuminate manuscripts and to apply metallic leaf decorations. Although the technical literature often reports on the use of plant gums as binders, actually several other saccharide materials can be encountered in paint samples, not only as major binders, but also as additives. In the literature, there are a variety of analytical procedures that utilize GC-MS to characterize saccharide materials in paint samples, however the chromatographic profiles are often extremely different and it is impossible to compare them and reliably identify the paint binder. Results This paper presents a comparison between two different analytical procedures based on GC-MS for the analysis of saccharide materials in works-of-art. The research presented here evaluates the influence of the analytical procedure used, and how it impacts the sugar profiles obtained from the analysis of paint samples that contain saccharide materials. The procedures have been developed, optimised and systematically used to characterise plant gums at the Getty Conservation Institute in Los Angeles, USA (GCI) and the Department of Chemistry and Industrial Chemistry of the University of Pisa, Italy (DCCI). The main steps of the analytical procedures and their optimisation are discussed. Conclusions The results presented highlight that the two methods give comparable sugar profiles, whether the samples analysed are simple raw materials, pigmented and unpigmented paint replicas, or paint samples collected from hundreds of centuries old polychrome art objects. A common database of sugar profiles of reference materials commonly found in paint samples was thus compiled. The database presents data also from those materials that only contain a minor saccharide fraction. This database highlights how many sources of saccharides can be found in a paint sample, representing an important step forward in the problem of identifying polysaccharide binders in paint samples. PMID:23050842

Analysis of plant gums and saccharide materials in paint samples: comparison of GC-MS analytical procedures and databases.

PubMed

Lluveras-Tenorio, Anna; Mazurek, Joy; Restivo, Annalaura; Colombini, Maria Perla; Bonaduce, Ilaria

2012-10-10

Saccharide materials have been used for centuries as binding media, to paint, write and illuminate manuscripts and to apply metallic leaf decorations. Although the technical literature often reports on the use of plant gums as binders, actually several other saccharide materials can be encountered in paint samples, not only as major binders, but also as additives. In the literature, there are a variety of analytical procedures that utilize GC-MS to characterize saccharide materials in paint samples, however the chromatographic profiles are often extremely different and it is impossible to compare them and reliably identify the paint binder. This paper presents a comparison between two different analytical procedures based on GC-MS for the analysis of saccharide materials in works-of-art. The research presented here evaluates the influence of the analytical procedure used, and how it impacts the sugar profiles obtained from the analysis of paint samples that contain saccharide materials. The procedures have been developed, optimised and systematically used to characterise plant gums at the Getty Conservation Institute in Los Angeles, USA (GCI) and the Department of Chemistry and Industrial Chemistry of the University of Pisa, Italy (DCCI). The main steps of the analytical procedures and their optimisation are discussed. The results presented highlight that the two methods give comparable sugar profiles, whether the samples analysed are simple raw materials, pigmented and unpigmented paint replicas, or paint samples collected from hundreds of centuries old polychrome art objects. A common database of sugar profiles of reference materials commonly found in paint samples was thus compiled. The database presents data also from those materials that only contain a minor saccharide fraction. This database highlights how many sources of saccharides can be found in a paint sample, representing an important step forward in the problem of identifying polysaccharide binders in paint samples.

Structured Forms Reference Set of Binary Images II (SFRS2)

National Institute of Standards and Technology Data Gateway

NIST Structured Forms Reference Set of Binary Images II (SFRS2) (Web, free access)   The second NIST database of structured forms (Special Database 6) consists of 5,595 pages of binary, black-and-white images of synthesized documents containing hand-print. The documents in this database are 12 different tax forms with the IRS 1040 Package X for the year 1988.

Filling Terrorism Gaps: VEOs, Evaluating Databases, and Applying Risk Terrain Modeling to Terrorism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hagan, Ross F.

2016-08-29

This paper aims to address three issues: the lack of literature differentiating terrorism and violent extremist organizations (VEOs), terrorism incident databases, and the applicability of Risk Terrain Modeling (RTM) to terrorism. Current open source literature and publicly available government sources do not differentiate between terrorism and VEOs; furthermore, they fail to define them. Addressing the lack of a comprehensive comparison of existing terrorism data sources, a matrix comparing a dozen terrorism databases is constructed, providing insight toward the array of data available. RTM, a method for spatial risk analysis at a micro level, has some applicability to terrorism research, particularlymore » for studies looking at risk indicators of terrorism. Leveraging attack data from multiple databases, combined with RTM, offers one avenue for closing existing research gaps in terrorism literature.« less

ReprDB and panDB: minimalist databases with maximal microbial representation.

PubMed

Zhou, Wei; Gay, Nicole; Oh, Julia

2018-01-18

Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes. We report pipelines that efficiently traverse all open access microbial genomes and assemble non-redundant genomic information. The pipelines result in two species-resolution microbial reference databases of relatively small sizes: reprDB, which assembles microbial representative or reference genomes, and panDB, for which we developed a novel iterative alignment algorithm to identify and assemble non-redundant genomic regions in multiple sequenced strains. With the databases, we managed to assign taxonomic labels and genome positions to the majority of metagenomic reads from human skin and gut microbiomes, demonstrating a significant improvement over a previous database-guided analysis on the same datasets. reprDB and panDB leverage the rapid increases in the number of open access microbial genomes to more fully profile metagenomic samples. Additionally, the databases exclude redundant sequence information to avoid inflated storage or memory space and indexing or analyzing time. Finally, the novel iterative alignment algorithm significantly increases efficiency in pan-genome identification and can be useful in comparative genomic analyses.

LC-PDA-ESI/MS identification of the phenolic components of three compositae spices: chamomile, tarragon, and Mexican arnica.

PubMed

Lin, Long-Ze; Harnly, James M

2012-06-01

Chamomile (Matricaria chamomilla L.), tarragon (Artemisia dracunculus L.) and Mexican arnica (Heterotheca inuoides) are common compositae spices and herbs found in the US market. They contain flavonoids and hydroxycinnamates that are potentially beneficial to human health. A standardized LC-PDA-ESI/MS profiling method was used to identify 51 flavonoids and 17 hydroxycinnamates. Many of the identifications were confirmed with authentic standards or through references in the literature or the laboratory's database. More than half of the phenol compounds for each spice had not been previously reported. The phenolic profile can be used for plant authentication and to correlate with biological activities.

LC-PDA-ESI/MS Identification of the Phenolic Components of Three Compositae Spices: Chamomile, Tarragon, and Mexican Arnica

PubMed Central

Harnly, James M.

2013-01-01

Chamomile (Matricaria chamomilla L.), tarragon (Artemisia dracunculus L.) and Mexican arnica (Heterotheca inuoides) are common compositae spices and herbs found in the US market. They contain flavonoids and hydroxycinnamates that are potentially beneficial to human health. A standardized LC-PDA-ESI/MS profiling method was used to identify 51 flavonoids and 17 hydroxycinnamates. Many of the identifications were confirmed with authentic standards or through references in the literature or the laboratory’s database. More than half of the phenol compounds for each spice had not been previously reported. The phenolic profile can be used for plant authentication and to correlate with biological activities. PMID:22816299

Constructing a Graph Database for Semantic Literature-Based Discovery.

PubMed

Hristovski, Dimitar; Kastrin, Andrej; Dinevski, Dejan; Rindflesch, Thomas C

2015-01-01

Literature-based discovery (LBD) generates discoveries, or hypotheses, by combining what is already known in the literature. Potential discoveries have the form of relations between biomedical concepts; for example, a drug may be determined to treat a disease other than the one for which it was intended. LBD views the knowledge in a domain as a network; a set of concepts along with the relations between them. As a starting point, we used SemMedDB, a database of semantic relations between biomedical concepts extracted with SemRep from Medline. SemMedDB is distributed as a MySQL relational database, which has some problems when dealing with network data. We transformed and uploaded SemMedDB into the Neo4j graph database, and implemented the basic LBD discovery algorithms with the Cypher query language. We conclude that storing the data needed for semantic LBD is more natural in a graph database. Also, implementing LBD discovery algorithms is conceptually simpler with a graph query language when compared with standard SQL.

DR-GAS: a database of functional genetic variants and their phosphorylation states in human DNA repair systems.

PubMed

Sehgal, Manika; Singh, Tiratha Raj

2014-04-01

We present DR-GAS(1), a unique, consolidated and comprehensive DNA repair genetic association studies database of human DNA repair system. It presents information on repair genes, assorted mechanisms of DNA repair, linkage disequilibrium, haplotype blocks, nsSNPs, phosphorylation sites, associated diseases, and pathways involved in repair systems. DNA repair is an intricate process which plays an essential role in maintaining the integrity of the genome by eradicating the damaging effect of internal and external changes in the genome. Hence, it is crucial to extensively understand the intact process of DNA repair, genes involved, non-synonymous SNPs which perhaps affect the function, phosphorylated residues and other related genetic parameters. All the corresponding entries for DNA repair genes, such as proteins, OMIM IDs, literature references and pathways are cross-referenced to their respective primary databases. DNA repair genes and their associated parameters are either represented in tabular or in graphical form through images elucidated by computational and statistical analyses. It is believed that the database will assist molecular biologists, biotechnologists, therapeutic developers and other scientific community to encounter biologically meaningful information, and meticulous contribution of genetic level information towards treacherous diseases in human DNA repair systems. DR-GAS is freely available for academic and research purposes at: http://www.bioinfoindia.org/drgas. Copyright © 2014 Elsevier B.V. All rights reserved.

Mindfulness in nursing: an evolutionary concept analysis.

PubMed

White, Lacie

2014-02-01

To report an analysis of the concept of mindfulness. Mindfulness is an emerging concept in health care that has significant implications for a variety of clinical populations. Nursing uses this concept in limited ways, and subsequently requires conceptual clarity to further identify its significance, use and applications in nursing. Mindfulness was explored using Rodgers evolutionary method of concept analysis. For this analysis, a sample of 59 English theoretical and research-based articles from the Cumulative Index to Nursing and Allied Health Literature database were obtained. The search was conducted between all-inclusive years of the database, 1981-2012. Data were analysed with particular focus on the attributes, antecedents, consequences, references and related terms that arose in relation to mindfulness in the nursing literature. The analysis found five intricately connected attributes: mindfulness is a transformative process where one develops an increasing ability to 'experience being present', with 'acceptance', 'attention' and 'awareness'. Antecedents, attributes and consequences appeared to inform and strengthen one another over time. Mindfulness is a significant concept for the discipline of nursing with practical applications for nurse well-being, the development and sustainability of therapeutic nursing qualities and holistic health promotion. It is imperative that nurse well-being and self-care become a more prominent focus in nursing research and education. Further development of the concept of mindfulness could support this focus, particularly through rigorous qualitative methodologies. © 2013 John Wiley & Sons Ltd.

Information for physicians and pharmacists about drugs that might cause dry mouth: a study of monographs and published literature.

PubMed

Nguyen, Caroline T; MacEntee, Michael I; Mintzes, Barbara; Perry, Thomas L

2014-01-01

Over three-quarters of the older population take medications that can potentially cause dry mouth. Physicians or pharmacists rarely inform patients about this adverse effect and its potentially severe damage to the teeth, mouth and general health. The objectives of this study were to (1) identify warnings in the literature about dry mouth associated with the most frequently prescribed pharmaceutical products in Canada; and (2) consider how this information might be obtained by physicians, pharmacists and patients. Monographs on the 72 most frequently prescribed medications during 2010 were retrieved from the Compendium of Pharmaceuticals and Specialties (CPS, a standard drug information reference for physicians and pharmacists), the National Library of Medicine's 'DailyMed' database, directly from the manufacturers, and from a systematic search of biomedical journals. The CPS provided monographs for 43% of the medications, and requests to manufacturers produced the remaining monographs. Mentions of dry mouth were identified in 61% of the products (43% amongst CPS monographs; an additional 43% amongst manufacturers' monographs; 7% in the DailyMed database and 7% from biomedical journals); five medications had contradictory reports in different monographs. Nearly two-thirds (61%) of the most commonly prescribed medications can cause dry mouth, yet warnings about this adverse effect and its potentially serious consequences are not readily available to physicians, pharmacists, dentists or patients.

Perspective: Interactive material property databases through aggregation of literature data

NASA Astrophysics Data System (ADS)

Seshadri, Ram; Sparks, Taylor D.

2016-05-01

Searchable, interactive, databases of material properties, particularly those relating to functional materials (magnetics, thermoelectrics, photovoltaics, etc.) are curiously missing from discussions of machine-learning and other data-driven methods for advancing new materials discovery. Here we discuss the manual aggregation of experimental data from the published literature for the creation of interactive databases that allow the original experimental data as well additional metadata to be visualized in an interactive manner. The databases described involve materials for thermoelectric energy conversion, and for the electrodes of Li-ion batteries. The data can be subject to machine-learning, accelerating the discovery of new materials.

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:…

Pedagogical Approaches to Diagnostic Imaging Education: A Narrative Review of the Literature

PubMed Central

Linaker, Kathleen L.

2015-01-01

Objective The purpose of this study was to examine literature on how radiology is taught and learned by both radiology residents and undergraduates in the health professions. Methods A review of the literature was performed using relevant key words. Articles were retrieved through December 2012 using PubMed, ScienceDirect, ERIC, Proquest, and ICL databases along with a manual review of references. Results Of the 4716 unique abstracts reviewed by the author, 91 were found to be relevant to the purpose of this study. The literature retrieved reported pedagogical approaches to teaching radiology including the following: problem solving, technology as teacher, independent learning tools, visiting lectureships, case based teaching, and conferences. There was some exploration of the relative effectiveness of educational formats. Suggestions for future research identify 7 areas of relative consistency. Conclusion Radiology is a clinical skill that requires integration science, clinical information, clinical experiences, and information recorded on diagnostic imaging studies. The research in this area focuses on problem solving, the use of algorithm/scripts, introducing uncertainty in clinical scenarios, incorporating technology in learning environments, active learning techniques, and methods of independent learning. Although the literature in this area is still in its infancy, the research examining the relative effectiveness of these various educational formats is often contradictory, suggesting that this is a complex area of study with numerous factors influencing student learning. PMID:26770173

[Current situation and existing problems of acupuncture for primary hypertension].

PubMed

Zhang, Lili; Wei, Pengfei; Chen, Shaozong

2018-03-12

To analyze the present situation and existing problems of acupuncture for primary hypertension (PH) based on clinical research literature in recent 20 years. The clinical research literature regarding acupuncture for PH were searched from China National Knowledge Infrastructure (CNKI), VIP data network (VIP) and Wanfang database from 1997 through 2016; a total of 218 papers met the inclusive criteria. Microsoft Excel and Apriori algorithm of SPSS Clementine software were applied to analyze the data. The main acupoints of acupuncture for PH were Taichong (LR 3), Quchi (LI 11), Zusanli (ST 36) and Hegu (LI 4), but its support degree was only 12.21%. 127 papers were randomized controlled trials, accounting for 58.26%. 158 papers had clear diagnostic criteria, accounting for 72.48%. 138 papers had clear efficacy evaluation criteria, accounting for 63.30%. Only 5.05% of the papers were classified as high-quality literature by using Jadad scale. In recent 20 years, some rules existed in acupoint selection for PH, but the support degree was low so it could not accurately guide clinical treatment. Although the clinical literature quality of acupuncture for PH was gradually increasing, the proportion of high-quality literature was low, therefore modern medical research model and foreign similar research should be followed to design a more rigorous trial protocol. As a result, the quality of clinical research is increased to provide reference for future clinical treatment.

The land management and operations database (LMOD)

USDA-ARS?s Scientific Manuscript database

This paper presents the design, implementation, deployment, and application of the Land Management and Operations Database (LMOD). LMOD is the single authoritative source for reference land management and operation reference data within the USDA enterprise data warehouse. LMOD supports modeling appl...

Fire-induced water-repellent soils, an annotated bibliography

USGS Publications Warehouse

Kalendovsky, M.A.; Cannon, S.H.

1997-01-01

The development and nature of water-repellent, or hydrophobic, soils are important issues in evaluating hillslope response to fire. The following annotated bibliography was compiled to consolidate existing published research on the topic. Emphasis was placed on the types, causes, effects and measurement techniques of water repellency, particularly with respect to wildfires and prescribed burns. Each annotation includes a general summary of the respective publication, as well as highlights of interest to this focus. Although some references on the development of water repellency without fires, the chemistry of hydrophobic substances, and remediation of water-repellent conditions are included, coverage of these topics is not intended to be comprehensive. To develop this database, the GeoRef, Agricola, and Water Resources Abstracts databases were searched for appropriate references, and the bibliographies of each reference were then reviewed for additional entries. Additional references will be added to this bibliography as they become available. The annotated bibliography can be accessed on the Web at http://geohazards.cr.usgs.gov/html_files/landslides/ofr97-720/biblio.html. A database consisting of the references and keywords is available through a link at the above address. This database was compiled using EndNote2 plus software by Niles and Associates, and is necessary to search the database.

Identifying complications of interventional procedures from UK routine healthcare databases: a systematic search for methods using clinical codes.

PubMed

Keltie, Kim; Cole, Helen; Arber, Mick; Patrick, Hannah; Powell, John; Campbell, Bruce; Sims, Andrew

2014-11-28

Several authors have developed and applied methods to routine data sets to identify the nature and rate of complications following interventional procedures. But, to date, there has been no systematic search for such methods. The objective of this article was to find, classify and appraise published methods, based on analysis of clinical codes, which used routine healthcare databases in a United Kingdom setting to identify complications resulting from interventional procedures. A literature search strategy was developed to identify published studies that referred, in the title or abstract, to the name or acronym of a known routine healthcare database and to complications from procedures or devices. The following data sources were searched in February and March 2013: Cochrane Methods Register, Conference Proceedings Citation Index - Science, Econlit, EMBASE, Health Management Information Consortium, Health Technology Assessment database, MathSciNet, MEDLINE, MEDLINE in-process, OAIster, OpenGrey, Science Citation Index Expanded and ScienceDirect. Of the eligible papers, those which reported methods using clinical coding were classified and summarised in tabular form using the following headings: routine healthcare database; medical speciality; method for identifying complications; length of follow-up; method of recording comorbidity. The benefits and limitations of each approach were assessed. From 3688 papers identified from the literature search, 44 reported the use of clinical codes to identify complications, from which four distinct methods were identified: 1) searching the index admission for specified clinical codes, 2) searching a sequence of admissions for specified clinical codes, 3) searching for specified clinical codes for complications from procedures and devices within the International Classification of Diseases 10th revision (ICD-10) coding scheme which is the methodology recommended by NHS Classification Service, and 4) conducting manual clinical review of diagnostic and procedure codes. The four distinct methods identifying complication from codified data offer great potential in generating new evidence on the quality and safety of new procedures using routine data. However the most robust method, using the methodology recommended by the NHS Classification Service, was the least frequently used, highlighting that much valuable observational data is being ignored.

Job satisfaction evaluation in low back pain: a literature review and tools appraisal.

PubMed

Ratinaud, M C; Chamoux, A; Glace, B; Coudeyre, E

2013-09-01

Among occupational risk factors of recurrence, chronicity and no return to work in low back pain, poor job satisfaction is the only high evidence-based factor. To find out any validated questionnaire usable to assess job satisfaction in low back pain patients, both in clinical practice and research setting. A systematic literature search on Pubmed and Cochrane library databases and un-indexed literature was made. "Job satisfaction" and "low back pain" keywords were used. Only English and French relevant articles were retained. A double assessment was made of listed questionnaires according to psychometric properties and daily practice use. Among the 40 articles retained only four used a validated questionnaire. Among the 12 different questionnaires, only two are validated in their English version (Job Descriptive Index [JDI] and the Work Environment Scale [WES]) and one in its French Version (JDI). Because they are time consuming, use these questionnaires in daily practice seems difficult. Based on literature review and questionnaire heterogeneity, at this time, there is no reference job satisfaction questionnaire. For daily practice, global job satisfaction visual analog scale could be useful. For research and intervention, JDI is more suitable despite its validity is still questionable. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Mapping the literature of home health nursing.

PubMed

Friedman, Yelena

2006-04-01

The purpose of this study was to identify core journals in home health nursing and to determine how well these journals were covered by indexing and abstracting services. The study was part of the project for mapping the nursing literature of the Medical Library Association's Nursing and Allied Health Resource Section. A citation analysis of two core journals was done to determine distribution of references by format types and age of citations and dispersion of the literature, according to Bradford's Law of Scattering. The analysis of indexing coverage for Zone 1 and 2 was also provided. The study showed that 64.2% of citations came from journals, versus 22.9% from books and 12.9% from other publications. PubMed/ MEDLINE rated highest in average indexing coverage of Zone 1 and 2 journals, followed by CINAHL. PsycINFO, SocioAbstracts, and EBSCO Health Business FullTEXT showed practically no coverage for the home health nursing literature. As expected, journal articles were found to be the primary source for referencing and books, the secondary source. In regard to bibliographic control, no databases provided full coverage of the journals in the field of home health nursing. PubMed/MEDLINE and CINAHL gave better results in combination, because CINAHL tended to cover more nursing journals, while PubMed/MEDLINE did better with medical titles.

Enabling medication management through health information technology (Health IT).

PubMed

McKibbon, K Ann; Lokker, Cynthia; Handler, Steve M; Dolovich, Lisa R; Holbrook, Anne M; O'Reilly, Daria; Tamblyn, Robyn; J Hemens, Brian; Basu, Runki; Troyan, Sue; Roshanov, Pavel S; Archer, Norman P; Raina, Parminder

2011-04-01

The objective of the report was to review the evidence on the impact of health information technology (IT) on all phases of the medication management process (prescribing and ordering, order communication, dispensing, administration and monitoring as well as education and reconciliation), to identify the gaps in the literature and to make recommendations for future research. We searched peer-reviewed electronic databases, grey literature, and performed hand searches. Databases searched included MEDLINE®, Embase, CINAHL (Cumulated Index to Nursing and Allied Health Literature), Cochrane Database of Systematic Reviews, International Pharmaceutical Abstracts, Compendex, Inspec (which includes IEEE Xplore), Library and Information Science Abstracts, E-Prints in Library and Information Science, PsycINFO, Sociological Abstracts, and Business Source Complete. Grey literature searching involved Internet searching, reviewing relevant Web sites, and searching electronic databases of grey literatures. AHRQ also provided all references in their e-Prescribing, bar coding, and CPOE knowledge libraries. Paired reviewers looked at citations to identify studies on a range of health IT used to assist in the medication management process (MMIT) during multiple levels of screening (titles and abstracts, full text and final review for assignment of questions and data abstrction). Randomized controlled trials and cohort, case-control, and case series studies were independently assessed for quality. All data were abstracted by one reviewer and examined by one of two different reviewers with content and methods expertise. 40,582 articles were retrieved. After duplicates were removed, 32,785 articles were screened at the title and abstract phase. 4,578 full text articles were assessed and 789 articles were included in the final report. Of these, 361 met only content criteria and were listed without further abstraction. The final report included data from 428 articles across the seven key questions. Study quality varied according to phase of medication management. Substantially more studies, and studies with stronger comparative methods, evaluated prescribing and monitoring. Clinical decision support systems (CDSS) and computerized provider order entry (CPOE) systems were studied more than any other application of MMIT. Physicians were more often the subject of evaluation than other participants. Other health care professionals, patients, and families are important but not studied as thoroughly as physicians. These nonphysicians groups often value different aspects of MMIT, have diverse needs, and use systems differently. Hospitals and ambulatory clinics were well-represented in the literature with less emphasis placed on long-term care facilities, communities, homes, and nonhospital pharmacies. Most studies evaluated changes in process and outcomes of use, usability, and knowledge, skills, and attitudes. Most showed moderate to substantial improvement with implementation of MMIT. Economics studies and those with clinical outcomes were less frequently studied. Those articles that did address economics and clinical outcomes often showed equivocal findings on the effectiveness and cost-effectiveness of MMIT systems. Qualitative studies provided evidence of strong perceptions, both positive and negative, of the effects of MMIT and unintended consequences. We found little data on the effects of forms of medications, conformity, standards, and open source status. Much descriptive literature discusses implementation issues but little strong evidence exists. Interest is strong in MMIT and more groups and institutions will implement systems in the next decades, especially with the Federal Government's push toward more health IT to support better and more cost-effective health care. MMIT is well-studied, although on closer examination of the literature the evidence is not uniform across phases of medication management, groups of people involved, or types of MMIT. MMIT holds the promise of improved processes; clinical and economics studies and the understanding of sustainability issues are lacking.

16 CFR 1102.6 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE (Eff. Jan. 10, 2011) Background and Definitions... Product Safety Information Database. (2) Commission or CPSC means the Consumer Product Safety Commission... Information Database, also referred to as the Database, means the database on the safety of consumer products...

DianaHealth.com, an On-Line Database Containing Appraisals of the Clinical Value and Appropriateness of Healthcare Interventions: Database Development and Retrospective Analysis.

PubMed

Bonfill, Xavier; Osorio, Dimelza; Solà, Ivan; Pijoan, Jose Ignacio; Balasso, Valentina; Quintana, Maria Jesús; Puig, Teresa; Bolibar, Ignasi; Urrútia, Gerard; Zamora, Javier; Emparanza, José Ignacio; Gómez de la Cámara, Agustín; Ferreira-González, Ignacio

2016-01-01

To describe the development of a novel on-line database aimed to serve as a source of information concerning healthcare interventions appraised for their clinical value and appropriateness by several initiatives worldwide, and to present a retrospective analysis of the appraisals already included in the database. Database development and a retrospective analysis. The database DianaHealth.com is already on-line and it is regularly updated, independent, open access and available in English and Spanish. Initiatives are identified in medical news, in article references, and by contacting experts in the field. We include appraisals in the form of clinical recommendations, expert analyses, conclusions from systematic reviews, and original research that label any health care intervention as low-value or inappropriate. We obtain the information necessary to classify the appraisals according to type of intervention, specialties involved, publication year, authoring initiative, and key words. The database is accessible through a search engine which retrieves a list of appraisals and a link to the website where they were published. DianaHealth.com also provides a brief description of the initiatives and a section where users can report new appraisals or suggest new initiatives. From January 2014 to July 2015, the on-line database included 2940 appraisals from 22 initiatives: eleven campaigns gathering clinical recommendations from scientific societies, five sets of conclusions from literature review, three sets of recommendations from guidelines, two collections of articles on low clinical value in medical journals, and an initiative of our own. We have developed an open access on-line database of appraisals about healthcare interventions considered of low clinical value or inappropriate. DianaHealth.com could help physicians and other stakeholders make better decisions concerning patient care and healthcare systems sustainability. Future efforts should be focused on assessing the impact of these appraisals in the clinical practice.

DianaHealth.com, an On-Line Database Containing Appraisals of the Clinical Value and Appropriateness of Healthcare Interventions: Database Development and Retrospective Analysis

PubMed Central

Bonfill, Xavier; Osorio, Dimelza; Solà, Ivan; Pijoan, Jose Ignacio; Balasso, Valentina; Quintana, Maria Jesús; Puig, Teresa; Bolibar, Ignasi; Urrútia, Gerard; Zamora, Javier; Emparanza, José Ignacio; Gómez de la Cámara, Agustín; Ferreira-González, Ignacio

2016-01-01

Objective To describe the development of a novel on-line database aimed to serve as a source of information concerning healthcare interventions appraised for their clinical value and appropriateness by several initiatives worldwide, and to present a retrospective analysis of the appraisals already included in the database. Methods and Findings Database development and a retrospective analysis. The database DianaHealth.com is already on-line and it is regularly updated, independent, open access and available in English and Spanish. Initiatives are identified in medical news, in article references, and by contacting experts in the field. We include appraisals in the form of clinical recommendations, expert analyses, conclusions from systematic reviews, and original research that label any health care intervention as low-value or inappropriate. We obtain the information necessary to classify the appraisals according to type of intervention, specialties involved, publication year, authoring initiative, and key words. The database is accessible through a search engine which retrieves a list of appraisals and a link to the website where they were published. DianaHealth.com also provides a brief description of the initiatives and a section where users can report new appraisals or suggest new initiatives. From January 2014 to July 2015, the on-line database included 2940 appraisals from 22 initiatives: eleven campaigns gathering clinical recommendations from scientific societies, five sets of conclusions from literature review, three sets of recommendations from guidelines, two collections of articles on low clinical value in medical journals, and an initiative of our own. Conclusions We have developed an open access on-line database of appraisals about healthcare interventions considered of low clinical value or inappropriate. DianaHealth.com could help physicians and other stakeholders make better decisions concerning patient care and healthcare systems sustainability. Future efforts should be focused on assessing the impact of these appraisals in the clinical practice. PMID:26840451

The Pathogen-Host Interactions database (PHI-base): additions and future developments.

PubMed

Urban, Martin; Pant, Rashmi; Raghunath, Arathi; Irvine, Alistair G; Pedro, Helder; Hammond-Kosack, Kim E

2015-01-01

Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and ecosystem health. To combat infection greater comparative knowledge is required on the pathogenic process in multiple species. The Pathogen-Host Interactions database (PHI-base) catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and protist pathogens. Mutant phenotypes are associated with gene information. The included pathogens infect a wide range of hosts including humans, animals, plants, insects, fish and other fungi. The current version, PHI-base 3.6, available at http://www.phi-base.org, stores information on 2875 genes, 4102 interactions, 110 host species, 160 pathogenic species (103 plant, 3 fungal and 54 animal infecting species) and 181 diseases drawn from 1243 references. Phenotypic and gene function information has been obtained by manual curation of the peer-reviewed literature. A controlled vocabulary consisting of nine high-level phenotype terms permits comparisons and data analysis across the taxonomic space. PHI-base phenotypes were mapped via their associated gene information to reference genomes available in Ensembl Genomes. Virulence genes and hotspots can be visualized directly in genome browsers. Future plans for PHI-base include development of tools facilitating community-led curation and inclusion of the corresponding host target(s). © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Finding European bioethical literature: an evaluation of the leading abstracting and indexing services

PubMed Central

Fangerau, H

2004-01-01

Objectives: In this study the author aimed to provide information for researchers to help them with the selection of suitable databases for finding medical ethics literature. The quantity of medical ethical literature that is indexed in different existing electronic bibliographies was ascertained. Method: Using the international journal index Ulrich's Periodicals Directory, journals on medical ethics were identified. The electronic bibliographies indexing these journals were analysed. In an additional analysis documentalists indexing bioethical literature were asked to name European journals on medical ethics. The bibliographies indexing these journals were examined. Results: Of 290 journals on medical ethics 173 were indexed in at least one bibliography. Current Contents showed the highest coverage with 66 (22.8%) journals indexed followed by MEDLINE (22.1%). By a combined search in the top ten bibliographies with the highest coverage, a maximum coverage of 45.2% of all journals could be reached. All the bibliographies showed a tendency to index more North American than European literature. This result was verified by the supplementary analysis of a sample of continental European journals. Here EMBASE covered the highest number of journals (20.6%) followed by the Russian Academy of Sciences Bibliographies (19.2%). Conclusion: A medical ethics literature search has to be carried out in several databases in order to reach an adequate collection of literature. The databases one wishes to combine should be carefully chosen. There seems to be a regional bias in the most popular databases, favouring North American periodicals compared with European literature on medical ethics. PMID:15173367

Defining a reference set to support methodological research in drug safety.

PubMed

Ryan, Patrick B; Schuemie, Martijn J; Welebob, Emily; Duke, Jon; Valentine, Sarah; Hartzema, Abraham G

2013-10-01

Methodological research to evaluate the performance of methods requires a benchmark to serve as a referent comparison. In drug safety, the performance of analyses of spontaneous adverse event reporting databases and observational healthcare data, such as administrative claims and electronic health records, has been limited by the lack of such standards. To establish a reference set of test cases that contain both positive and negative controls, which can serve the basis for methodological research in evaluating methods performance in identifying drug safety issues. Systematic literature review and natural language processing of structured product labeling was performed to identify evidence to support the classification of drugs as either positive controls or negative controls for four outcomes: acute liver injury, acute kidney injury, acute myocardial infarction, and upper gastrointestinal bleeding. Three-hundred and ninety-nine test cases comprised of 165 positive controls and 234 negative controls were identified across the four outcomes. The majority of positive controls for acute kidney injury and upper gastrointestinal bleeding were supported by randomized clinical trial evidence, while the majority of positive controls for acute liver injury and acute myocardial infarction were only supported based on published case reports. Literature estimates for the positive controls shows substantial variability that limits the ability to establish a reference set with known effect sizes. A reference set of test cases can be established to facilitate methodological research in drug safety. Creating a sufficient sample of drug-outcome pairs with binary classification of having no effect (negative controls) or having an increased effect (positive controls) is possible and can enable estimation of predictive accuracy through discrimination. Since the magnitude of the positive effects cannot be reliably obtained and the quality of evidence may vary across outcomes, assumptions are required to use the test cases in real data for purposes of measuring bias, mean squared error, or coverage probability.

Health economic analyses in medical nutrition: a systematic literature review.

PubMed

Walzer, Stefan; Droeschel, Daniel; Nuijten, Mark; Chevrou-Séverac, Hélène

2014-01-01

Medical nutrition is a specific nutrition category either covering specific dietary needs and/or nutrient deficiency in patients or feeding patients unable to eat normally. Medical nutrition is regulated by a specific bill in Europe and in the US, with specific legislation and guidelines, and is provided to patients with special nutritional needs and indications for nutrition support. Therefore, medical nutrition products are delivered by medical prescription and supervised by health care professionals. Although these products have existed for more than 2 decades, health economic evidence of medical nutrition interventions is scarce. This research assesses the current published health economic evidence for medical nutrition by performing a systematic literature review related to health economic analysis of medical nutrition. A systematic literature search was done using standard literature databases, including PubMed, the Health Technology Assessment Database, and the National Health Service Economic Evaluation Database. Additionally, a free web-based search was conducted using the same search terms utilized in the systematic database search. The clinical background and basis of the analysis, health economic design, and results were extracted from the papers finally selected. The Drummond checklist was used to validate the quality of health economic modeling studies and the AMSTAR (A Measurement Tool to Assess Systematic Reviews) checklist was used for published systematic reviews. Fifty-three papers were identified and obtained via PubMed, or directly via journal webpages for further assessment. Thirty-two papers were finally included in a thorough data extraction procedure, including those identified by a "gray literature search" utilizing the Google search engine and cross-reference searches. Results regarding content of the studies showed that malnutrition was the underlying clinical condition in most cases (32%). In addition, gastrointestinal disorders (eg, surgery, cancer) were often analyzed. In terms of settings, 56% of papers covered inpatients, whereas 14 papers (44%) captured outpatients, including patients in community centers. Interestingly, in comparison with the papers identified overall, very few health economic models were found. Most of the articles were modeling analyses and economic trials in different design settings. Overall, only eight health economic models were published and were validated applying the Drummond checklist. In summary, most of the models included were carried out to quite a high standard, although some areas were identified for further improvement. Of the two systematic health economic reviews identified, one achieved the highest quality score when applying the AMSTAR checklist. The reasons for finding only a few modeling studies but quite a large number of clinical trials with health economic endpoints, might be different. Until recently, health economics has not been required for reimbursement or coverage decisions concerning medical nutrition interventions. Further, there might be specifics of medical nutrition which might not allow easy modeling and consequently explain the limited uptake so far. The health economic data on medical nutrition generated and published is quite ample. However, it has been primarily based on database analysis and clinical studies. Only a few modeling analyses have been carried out, indicating a need for further research to understand the specifics of medical nutrition and their applicability for health economic modeling.

Development of estimates of dietary nitrates, nitrites, and nitrosamines for use with the Short Willet Food Frequency Questionnaire.

PubMed

Griesenbeck, John S; Steck, Michelle D; Huber, John C; Sharkey, Joseph R; Rene, Antonio A; Brender, Jean D

2009-04-06

Studies have suggested that nitrates, nitrites, and nitrosamines have an etiologic role in adverse pregnancy outcomes and chronic diseases such as cancer. Although an extensive body of literature exists on estimates of these compounds in foods, the extant data varies in quality, quantified estimates, and relevance. We developed estimates of nitrates, nitrites, and nitrosamines for food items listed in the Short Willet Food Frequency Questionnaire (WFFQ) as adapted for use in the National Birth Defects Prevention Study. Multiple reference databases were searched for published literature reflecting nitrate, nitrite, and nitrosamine values in foods. Relevant published literature was reviewed; only publications reporting results for items listed on the WFFQ were selected for inclusion. The references selected were prioritized according to relevance to the U.S. population. Based on our estimates, vegetable products contain the highest levels of nitrate, contributing as much as 189 mg/serving. Meat and bean products contain the highest levels of nitrites with values up to 1.84 mg/serving. Alcohol, meat and dairy products contain the highest values of nitrosamines with a maximum value of 0.531 microg/serving. The estimates of dietary nitrates, nitrites, and nitrosamines generated in this study are based on the published values currently available. To our knowledge, these are the only estimates specifically designed for use with the adapted WFFQ and generated to represent food items available to the U.S. population. The estimates provided may be useful in other research studies, specifically in those exploring the relation between exposure to these compounds in foods and adverse health outcomes.

Bartonella, a Common Cause of Endocarditis: a Report on 106 Cases and Review

PubMed Central

Edouard, Sophie; Nabet, Cecile; Lepidi, Hubert; Fournier, Pierre-Edouard

2014-01-01

Bartonella spp. are fastidious bacteria that cause blood culture-negative endocarditis and have been increasingly reported. In this study, we included all patients retrospectively and prospectively diagnosed with Bartonella endocarditis in our French reference center between 2005 and 2013. Our diagnosis was based on the modified Duke criteria and microbiological findings, including serological and PCR results. To review the published literature, we searched all human Bartonella endocarditis cases published in the PubMed database between January 2005 and October 2013. We report here a large series of 106 cases, which include 59 cases that had not previously been reported or mentioned. Indirect immunofluorescence assays, Western blotting, and real-time PCR from total blood, serum, and valve tissue exhibited sensitivities of 58%, 100%, 33%, 36%, and 91%, respectively. The number of cases reported in the literature between 2005 and 2013 increased to reach a cumulative number of 196 cases. The number of cases reported in the literature by other centers is increasing more rapidly than that reported by our French reference center (P < 10−2). Currently, there is a lack of criteria for the diagnosis of Bartonella endocarditis. We suggest that a positive PCR result from a cardiac valve or blood specimen, an IgG titer of ≥800 using an immunofluorescence assay, or a positive Western blot assay be considered major Duke criteria for Bartonella endocarditis. There is no real increase in the incidence of these infections but rather a better understanding and interest in the disease resulting from the improvement of diagnostic tools. PMID:25540398

Medical devices early assessment methods: systematic literature review.

PubMed

Markiewicz, Katarzyna; van Til, Janine A; IJzerman, Maarten J

2014-04-01

The aim of this study was to get an overview of current theory and practice in early assessments of medical devices, and to identify aims and uses of early assessment methods used in practice. A systematic literature review was conducted in September 2013, using computerized databases (PubMed, Science Direct, and Scopus), and references list search. Selected articles were categorized based on their type, objective, and main target audience. The methods used in the application studies were extracted and mapped throughout the early stages of development and for their particular aims. Of 1,961 articles identified, eighty-three studies passed the inclusion criteria, and thirty were included by searching reference lists. There were thirty-one theoretical papers, and eighty-two application papers included. Most studies investigated potential applications/possible improvement of medical devices, developed early assessment framework or included stakeholder perspective in early development stages. Among multiple qualitative and quantitative methods identified, only few were used more than once. The methods aim to inform strategic considerations (e.g., literature review), economic evaluation (e.g., cost-effectiveness analysis), and clinical effectiveness (e.g., clinical trials). Medical devices were often in the prototype product development stage, and the results were usually aimed at informing manufacturers. This study showed converging aims yet widely diverging methods for early assessment during medical device development. For early assessment to become an integral part of activities in the development of medical devices, methods need to be clarified and standardized, and the aims and value of assessment itself must be demonstrated to the main stakeholders for assuring effective and efficient medical device development.

Authorship Trends in 30 Years of the Journal of Arthroplasty.

PubMed

Lehman, Jason D; Schairer, William W; Gu, Alex; Blevins, Jason L; Sculco, Peter K

2017-05-01

While various studies have investigated trends in characteristics of authors in other medical literature, no study has examined these characteristics in the field of arthroplasty. A database was created of all articles published in The Journal of Arthroplasty in 1986, 1990, 1995, 2000, 2005, 2010, and 2015. Degree(s) of authors, number of authors, number of references, and region of institution were recorded. A total of 1343 original articles were assessed over the study period. There was a significant increase in the number of authors per publication from 3.45 in 1986 to 4.98 in 2015 (P < .001) and number of references per article from 17.36 to 29.76 (P < .001). There was a significant increase in proportion of first authors with a bachelor's degree (P = .001), MD/PhD (P < .001), and MD/MBA (P = .016), with a significant decrease in first authors with an MD degree only (P < .001). There was a significant increase in number of last authors with an MD/PhD (P = .001) and MD/MBA (P = .003). There has been a significant growth in papers from outside North America (P = .007), with a decrease in articles from the UK/Ireland (P = .003) and an increase in contributions from the Far East (P < .001). Trends of authorship characteristics in the arthroplasty literature largely mirror those seen in other medical literature including increased number of authors per article over time, changes in author qualifications, and increased contributions from international author groups. Copyright © 2016 Elsevier Inc. All rights reserved.

Ethical issues in using Twitter for public health surveillance and research: developing a taxonomy of ethical concepts from the research literature.

PubMed

Conway, Mike

2014-12-22

The rise of social media and microblogging platforms in recent years, in conjunction with the development of techniques for the processing and analysis of "big data", has provided significant opportunities for public health surveillance using user-generated content. However, relatively little attention has been focused on developing ethically appropriate approaches to working with these new data sources. Based on a review of the literature, this study seeks to develop a taxonomy of public health surveillance-related ethical concepts that emerge when using Twitter data, with a view to: (1) explicitly identifying a set of potential ethical issues and concerns that may arise when researchers work with Twitter data, and (2) providing a starting point for the formation of a set of best practices for public health surveillance through the development of an empirically derived taxonomy of ethical concepts. We searched Medline, Compendex, PsycINFO, and the Philosopher's Index using a set of keywords selected to identify Twitter-related research papers that reference ethical concepts. Our initial set of queries identified 342 references across the four bibliographic databases. We screened titles and abstracts of these references using our inclusion/exclusion criteria, eliminating duplicates and unavailable papers, until 49 references remained. We then read the full text of these 49 articles and discarded 36, resulting in a final inclusion set of 13 articles. Ethical concepts were then identified in each of these 13 articles. Finally, based on a close reading of the text, a taxonomy of ethical concepts was constructed based on ethical concepts discovered in the papers. From these 13 articles, we iteratively generated a taxonomy of ethical concepts consisting of 10 top level categories: privacy, informed consent, ethical theory, institutional review board (IRB)/regulation, traditional research vs Twitter research, geographical information, researcher lurking, economic value of personal information, medical exceptionalism, and benefit of identifying socially harmful medical conditions. In summary, based on a review of the literature, we present a provisional taxonomy of public health surveillance-related ethical concepts that emerge when using Twitter data.

Ethical Issues in Using Twitter for Public Health Surveillance and Research: Developing a Taxonomy of Ethical Concepts From the Research Literature

PubMed Central

2014-01-01

Background The rise of social media and microblogging platforms in recent years, in conjunction with the development of techniques for the processing and analysis of “big data”, has provided significant opportunities for public health surveillance using user-generated content. However, relatively little attention has been focused on developing ethically appropriate approaches to working with these new data sources. Objective Based on a review of the literature, this study seeks to develop a taxonomy of public health surveillance-related ethical concepts that emerge when using Twitter data, with a view to: (1) explicitly identifying a set of potential ethical issues and concerns that may arise when researchers work with Twitter data, and (2) providing a starting point for the formation of a set of best practices for public health surveillance through the development of an empirically derived taxonomy of ethical concepts. Methods We searched Medline, Compendex, PsycINFO, and the Philosopher’s Index using a set of keywords selected to identify Twitter-related research papers that reference ethical concepts. Our initial set of queries identified 342 references across the four bibliographic databases. We screened titles and abstracts of these references using our inclusion/exclusion criteria, eliminating duplicates and unavailable papers, until 49 references remained. We then read the full text of these 49 articles and discarded 36, resulting in a final inclusion set of 13 articles. Ethical concepts were then identified in each of these 13 articles. Finally, based on a close reading of the text, a taxonomy of ethical concepts was constructed based on ethical concepts discovered in the papers. Results From these 13 articles, we iteratively generated a taxonomy of ethical concepts consisting of 10 top level categories: privacy, informed consent, ethical theory, institutional review board (IRB)/regulation, traditional research vs Twitter research, geographical information, researcher lurking, economic value of personal information, medical exceptionalism, and benefit of identifying socially harmful medical conditions. Conclusions In summary, based on a review of the literature, we present a provisional taxonomy of public health surveillance-related ethical concepts that emerge when using Twitter data. PMID:25533619

Error and Uncertainty in the Accuracy Assessment of Land Cover Maps

NASA Astrophysics Data System (ADS)

Sarmento, Pedro Alexandre Reis

Traditionally the accuracy assessment of land cover maps is performed through the comparison of these maps with a reference database, which is intended to represent the "real" land cover, being this comparison reported with the thematic accuracy measures through confusion matrixes. Although, these reference databases are also a representation of reality, containing errors due to the human uncertainty in the assignment of the land cover class that best characterizes a certain area, causing bias in the thematic accuracy measures that are reported to the end users of these maps. The main goal of this dissertation is to develop a methodology that allows the integration of human uncertainty present in reference databases in the accuracy assessment of land cover maps, and analyse the impacts that uncertainty may have in the thematic accuracy measures reported to the end users of land cover maps. The utility of the inclusion of human uncertainty in the accuracy assessment of land cover maps is investigated. Specifically we studied the utility of fuzzy sets theory, more precisely of fuzzy arithmetic, for a better understanding of human uncertainty associated to the elaboration of reference databases, and their impacts in the thematic accuracy measures that are derived from confusion matrixes. For this purpose linguistic values transformed in fuzzy intervals that address the uncertainty in the elaboration of reference databases were used to compute fuzzy confusion matrixes. The proposed methodology is illustrated using a case study in which the accuracy assessment of a land cover map for Continental Portugal derived from Medium Resolution Imaging Spectrometer (MERIS) is made. The obtained results demonstrate that the inclusion of human uncertainty in reference databases provides much more information about the quality of land cover maps, when compared with the traditional approach of accuracy assessment of land cover maps. None

Psychiatric manifestations of 22q11.2 deletion syndrome: a literature review.

PubMed

Bertrán, M; Tagle, F P; Irarrázaval, M

2018-03-01

The 22q11.2 deletion syndrome is a genetic disorder with variable clinical manifestations. It affects one out of 5950 neonates and has an autosomal dominant inheritance pattern. The aim of this article is to review its psychiatric manifestations and any underlying genetic alterations. We reviewed the scientific literature available as of October 2014 in the LILACS and Medline databases. Sixty per cent of these patients fulfilled diagnostic criteria for a mental disorder at some point in their lives, referring to psychotic disorders, attention deficit hyperactivity disorder, mood disorders, anxiety disorders, and autism spectrum disorders. Specific genes, such as COMT and PRODH, have been linked to these psychiatric manifestations. It is necessary to raise awareness among all health care professionals so that they understand the relevance of these manifestations, are able to anticipate them, and can provide appropriate information to patients and family members. Copyright © 2015 Sociedad Española de Neurología. Publicado por Elsevier España, S.L.U. All rights reserved.

[Tendencies of studies addressing the eldest individuals of aged population in the community: a (inter)national systematic review].

PubMed

Rosset, Idiane; Pedrazzi, Elizandra Cristina; Roriz-Cruz, Matheus; de Morais, Eliane Pinheiro; Rodrigues, Rosalina Aparecida Partezani

2011-03-01

The purpose of this study was to identify and analyze the tendencies and types of studies published in Brazil and abroad, involving elders aged>80 years, living in the community. A systematic review of national literature was performed using the LILACS and SciELO databases, and PUBMED and EMBASE for international literature, covering publications of the last two decades. Twelve national and 162 international references were selected. Biological sciences were the prevalent area both at the national (50%) and international (74.1%) levels. All national studies were observational, 91.7% of which were cross-sectional. Of the international studies, 93.3% were observational, 48.1% of which were cross-sectional and 37.6% were cohort studies. The United States were the country responsible for 41.4% of all international publications. Brazil and China were the only developing countries with international publications. Despite the significant number of international scientific publications as of 2005, this fact has not been observed at the national level.

Direct access to physical therapy for the patient with musculoskeletal disorders, a literature review

PubMed Central

Piano, Leonardo; Maselli, Filippo; Viceconti, Antonello; Gianola, Silvia; Ciuro, Aldo

2017-01-01

[Purpose] To present legislation comparing direct and referred access—or other measures—to physical therapy. The focus is on the management of the most burdensome musculoskeletal disorders in terms of regulations, costs, effectiveness, safety and cost-effectiveness. [Methods] Main biomedical databases and gray literature were searched ranging from a global scenario to the analysis of targeted geographical areas and specifically Italy and the Region Piedmont. [Results] legislation on Direct Access highlights inconsistencies among the countries belonging to World Confederation for Physical Therapy. Direct Access could be an effective, safe and efficient organization model for the management of patients with musculoskeletal diseases and seems to be more effective safer and cost effective. [Conclusion] Direct Access is a virtuous model which can help improve the global quality of physical therapy services. Further studies are required to confirm this approach and determine whether the findings of the present overview can be replicated in different countries and healthcare systems. PMID:28878484

Direct access to physical therapy for the patient with musculoskeletal disorders, a literature review.

PubMed

Piano, Leonardo; Maselli, Filippo; Viceconti, Antonello; Gianola, Silvia; Ciuro, Aldo

2017-08-01

[Purpose] To present legislation comparing direct and referred access-or other measures-to physical therapy. The focus is on the management of the most burdensome musculoskeletal disorders in terms of regulations, costs, effectiveness, safety and cost-effectiveness. [Methods] Main biomedical databases and gray literature were searched ranging from a global scenario to the analysis of targeted geographical areas and specifically Italy and the Region Piedmont. [Results] legislation on Direct Access highlights inconsistencies among the countries belonging to World Confederation for Physical Therapy. Direct Access could be an effective, safe and efficient organization model for the management of patients with musculoskeletal diseases and seems to be more effective safer and cost effective. [Conclusion] Direct Access is a virtuous model which can help improve the global quality of physical therapy services. Further studies are required to confirm this approach and determine whether the findings of the present overview can be replicated in different countries and healthcare systems.

Achieving hemostasis in dermatology – Part 1: Preoperative, intraoperative, and postoperative management

PubMed Central

Kaur, Ravneet Ruby; Glick, Jaimie B.; Siegel, Daniel

2013-01-01

As dermatological procedures continue to become increasingly complex, improved methods and tools to achieve appropriate hemostasis become necessary. The methods for achieving adequate hemostasis are variable and depend greatly on the type of procedure performed and the unique characteristics of the individual patient. In Part 1 of this review, we discuss the preoperative, intraoperative, and postoperative management of patients undergoing dermatologic surgery. We address oral medications and supplements that affect hemostasis, hemostatic anesthesia, and intraoperative interventions such as suture ligation and heat-generating cautery devices. In Part 2 of this review, we will discuss topical hemostats. The authors conducted an extensive literature review using the following keywords: “hemostasis,” “dermatology,” “dermatological surgery,” “dermatologic sutures,” “electrosurgery,” “hemostatic anesthesia,” and “laser surgery.” Sources for this article were identified by searching the English literature in the Pubmed database for the time period from 1940 to March 2012. A thorough bibliography search was also conducted and key references were examined. PMID:23741660

The Proximal Effects of Acute Alcohol Consumption on Male-to-Female Aggression: A Meta-Analytic Review of the Experimental Literature.

PubMed

Crane, Cory A; Godleski, Stephanie A; Przybyla, Sarahmona M; Schlauch, Robert C; Testa, Maria

2016-12-01

The current meta-analytic review examined the experimental literature to quantify the causal effect of acute alcohol consumption on self-reported and observed indicators of male-to-female general, sexual, and intimate partner aggression. Database and reference list searches yielded 22 studies conducted between 1981 and 2014 that met all criteria for inclusion and that were subjected to full text coding for analysis. Results detected a significant overall effect (d = .36), indicating that male participants who consumed alcohol evidenced greater aggressive behavior toward females while completing a subsequent laboratory aggression paradigm than male participants who received no alcohol. We found homogeneity across all categories of potential moderator variables. Results further indicated that alcohol resulted in comparable increases of male-to-female sexual (d = .32) and intimate partner (d = .45) aggression. Further research is required to draw meaningful conclusions about individual and situational factors that may interact with acute alcohol consumption to produce the highest levels of risk. © The Author(s) 2015.

African Americans' Perceptions of Pain and Pain Management: A Systematic Review.

PubMed

Booker, Staja Q

2016-01-01

The purpose of this systematic review is to explore the perceptions of acute, persistent, and disease-specific pain and treatment options held by adult African Americans. Underassessment and undermanagement of pain in African Americans has been well documented; however, the cultural continuum of pain perceptions and their influence on pain assessment and management has not been synthesized. Electronic database searches of the Cumulative Index for Nursing and Allied Health Literature and PubMed, Web-based searches of the pain-specific journals plus a manual search of reference lists identified 41 relevant articles addressing perceptions of pain and/or pain management. Analysis of the literature revealed six themes: (a) meaning of pain, (b) description of pain, (c) coping with pain, (d) impact of pain, (e) patient-provider relationship, and (f) treatment approaches. These findings warrant further research and indicate the need for more precise evaluation of pain in African Americans, highlighting an imperative to incorporate cultural patterns into pain management practice and education. © The Author(s) 2014.

The impact of volunteer mentoring schemes on carers of people with dementia and volunteer mentors: a systematic review.

PubMed

Smith, Raymond; Greenwood, Nan

2014-02-01

This systematic review aims to examine the differences and similarities between the various types of volunteer mentoring (befriending, mentoring and peer support) and to identify the benefits for carers and volunteers. Literature searching was performed using 8 electronic databases, gray literature, and reference list searching of relevant systematic reviews. Searches were carried out in January 2013. Four studies fitted the inclusion criteria, with 3 investigating peer support and 1 befriending for carers. Quantitative findings highlighted a weak but statistically significant (P =.04) reduction in depression after 6 months of befriending. Qualitative findings highlighted the value carers placed on the volunteer mentors' experiential similarity. Matching was not essential for the development of successful volunteer mentoring relationships. In conclusion, the lack of need for matching and the importance of experiential similarity deserve further investigation. However, this review highlights a lack of demonstrated efficacy of volunteer mentoring for carers of people with dementia.

Neuromuscular electric stimulation in patellofemoral dysfunction: literature review

PubMed Central

dos Santos, Ricardo Lucas; Souza, Márcia Leal São Pedro; dos Santos, Fernanda Andrade

2013-01-01

Patellofemoral dysfunction is a fairly common deficiency among young individuals that primarily affects females and may be characterized by pain, swelling and retropatellar crepitation. The purpose of this review of literature from the period between 2005 and 2011 was to systematize knowledge in relation to the increase in quadriceps muscle strength and pain relief in patients with patellofemoral dysfunction, using neuromuscular electrical stimulation and resistance exercises. The inclusion criteria were intervention articles from the past six years, in English, Spanish and Portuguese, which used muscle strengthening and neuromuscular electrical stimulation for rehabilitation obtained through searches in the electronic databases Medline and Lilacs and in the Bireme library. The bibliographic search yielded 28 references, of which nine were excluded in accordance with the aims and inclusion criteria while 16 articles were selected for reading of the abstracts and subsequent analysis. Mediumfrequency Neuromuscular Electrical Stimulation (NMES) can be used in association with resistance exercises as an adjuvant in the treatment of patellofemoral dysfunction (PFD), both to achieve muscle rebalance and for pain relief. PMID:24453645

The Proximal Effects of Acute Alcohol Consumption on Male-to-Female Aggression: A Meta-Analytic Review of the Experimental Literature

PubMed Central

Crane, Cory A.; Godleski, Stephanie A.; Przybyla, Sarahmona M.; Schlauch, Robert C.; Testa, Maria

2015-01-01

The current meta-analytic review examined the experimental literature to quantify the causal effect of acute alcohol consumption on self-reported and observed indicators of male-to-female general, sexual, and intimate partner aggression. Database and reference list searches yielded 22 studies conducted between 1981 and 2014 that met all criteria for inclusion and that were subjected to full text coding for analysis. Results detected a significant overall effect (d = .36), indicating that male participants who consumed alcohol evidenced greater aggressive behavior toward females while completing a subsequent laboratory aggression paradigm than male participants who received no alcohol. We found homogeneity across all categories of potential moderator variables. Results further indicated that alcohol resulted in comparable increases of male-to-female sexual (d = .32) and intimate partner (d = .45) aggression. Further research is required to draw meaningful conclusions about individual and situational factors that may interact with acute alcohol consumption to produce the highest levels of risk. PMID:26009568

[Status of diagnosis and treatment devices of acupuncture based on SooPAT and bibliometrics in China].

PubMed

Bai, Lin; Ren, Yulan; Guo, Taipin; Chen, Lin; Zhou, Yumei; Feng, Shuwei; Li, Ji; Liang, Fanrong

2016-11-12

To perform a bibliometrics analysis on patent literature regarding diagnosis and treatment devices of acupuncture in China, aiming to provide references for the development of diagnosis and treatment devices of acupuncture. Based on SooPAT, a patent database, the patent literature regarding diagnosis and treatment devices of acupuncture in China was collected. With bibliometrics methods, the annual distribution of type, quantity, classification and content of diagnosis and treatment devices of acupuncture were analyzed. The number of acupuncture diagnosis and treatment devices reached its peak in 2012 and 2013 in China. The A61N in patent and utility model patent were the most, which were mainly related to electrotherapy, magnetic therapy, radioactive therapy and ultrasound therapy, etc. The main content was acupuncture treatment devices and meridian treatment devices. The 24-01 in design patent was the most, involving fixation devices used by doctors, hospitals and laboratories, etc. Currently the majority of diagnosis and treatment devices of acupuncture is therapeutic apparatus, while the acupuncture diagnosis devices are needed.

[Economic and epidemiologic aspects of generalized anxiety disorder: a review of the literature].

PubMed

Albarracin, G; Rovira, J; Carreras, L; Rejas, J

2008-01-01

The objective is to assess the prevalence and treatment patterns of generalized anxiety disorder (GAD) in Spain as well as the cost associated to this disorder in different countries. A search in the literature of health and economics databases was conducted. In regards to the 32 references selected, 6 studies had data on the prevalence of GAD and 3 on treatment patterns in Spain and 11 studies on the costs associated to the disease on an international level. The remaining 20 studies were of general interest for methodological or contextual reasons. GAD is a mental disorder with high prevalence. According to some authors, it is probably underdiagnosed. No appropriate long term treatment is available. High health care and social costs are associated to GAD. The frequent presence of comorbidity, different definitions and methodologies used in the studies limits the comparability and synthesis of the results. It also makes it difficult to obtain valid estimations of prevalence and costs.

Language Disorders: A 10-Year Research Update Review

PubMed Central

TOPPELBERG, CLAUDIO O.; SHAPIRO, THEODORE

2012-01-01

Objective To review the past 10 years of research in child language or communication disorders, which are highly prevalent in the general population and comorbid with childhood psychiatric disorders. Method A literature search of 3 major databases was conducted. The child language literature, describing the domains of language development—phonology, grammar, semantics, and pragmatics—is reviewed. Results Disorders of grammar, semantics, and pragmatics, but not phonology, overlap significantly with childhood psychiatric disorders. Receptive language disorders have emerged as high-risk indicators, often undiagnosed. Language disorders and delays are psychiatric risk factors and have implications for evaluation, therapy, and research. However, they are often undiagnosed in child mental health and community settings. The research has focused mostly on monolingual English-speaking children. Conclusion Awareness of basic child language development, delay, and deviance is crucial for the practicing child and adolescent psychiatrist, who must diagnose and refer relevant cases for treatment and remediation. Future research needs to address the growing language diversity of our clinical populations. PMID:10673823

Wind-Wildlife Impacts Literature Database (WILD)(Fact Sheet)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

The Wind-Wildlife Impacts Literature Database (WILD), developed and maintained by the National Wind Technology Center (NWTC) at the National Renewable Energy Laboratory (NREL), is comprised of over 1,000 citations pertaining to the effects of land-based wind, offshore wind, marine and hydrokinetic, power lines, and communication and television towers on wildlife.

Reference Values for Human Posture Measurements Based on Computerized Photogrammetry: A Systematic Review.

PubMed

Macedo Ribeiro, Ana Freire; Bergmann, Anke; Lemos, Thiago; Pacheco, Antônio Guilherme; Mello Russo, Maitê; Santos de Oliveira, Laura Alice; de Carvalho Rodrigues, Erika

The main objective of this study was to review the literature to identify reference values for angles and distances of body segments related to upright posture in healthy adult women with the Postural Assessment Software (PAS/SAPO). Electronic databases (BVS, PubMed, SciELO and Scopus) were assessed using the following descriptors: evaluation, posture, photogrammetry, physical therapy, postural alignment, postural assessment, and physiotherapy. Studies that performed postural evaluation in healthy adult women with PAS/SAPO and were published in English, Portuguese and Spanish, between the years 2005 and 2014 were included. Four studies met the inclusion criteria. Data from the included studies were grouped to establish the statistical descriptors (mean, variance, and standard deviation) of the body angles and distances. A total of 29 variables were assessed (10 in the anterior views, 16 in the lateral right and left views, and 3 in the posterior views), and its respective mean and standard deviation were calculated. Reference values for the anterior and posterior views showed no symmetry between the right and left sides of the body in the frontal plane. There were also small differences in the calculated reference values for the lateral view. The proposed reference values for quantitative evaluation of the upright posture in healthy adult women estimated in the present study using PAS/SAPO could guide future studies and help clinical practice. Copyright © 2017. Published by Elsevier Inc.

Knowledge silos: assessing knowledge sharing between specialties through the vestibular schwannoma literature.

PubMed

Schnurman, Zane; Golfinos, John G; Roland, J Thomas; Kondziolka, Douglas

2017-12-01

OBJECTIVE It is common for a medical disorder to be managed or researched by individuals who work within different specialties. It is known that both neurosurgeons and neurotologists manage vestibular schwannoma (VS) patients. While overlap in specialty focus has the potential to stimulate multidisciplinary collaboration and innovative thinking, there is a risk of specialties forming closed-communication loops, called knowledge silos, which may inhibit knowledge diffusion. This study quantitatively assessed knowledge sharing between neurosurgery and otolaryngology on the subject of VS. METHODS A broad Web of Science search was used to download details for 4439 articles related to VS through 2016. The publishing journal's specialty and the authors' specialties (based on author department) were determined for available articles. All 114,647 of the article references were categorized by journal specialty. The prevalence of several VS topics was assessed using keyword searches of titles. RESULTS For articles written by neurosurgeons, 44.0% of citations were from neurosurgery journal articles and 23.4% were from otolaryngology journals. The citations of otolaryngology authors included 11.6% neurosurgery journals and 56.5% otolaryngology journals. Both author specialty and journal specialty led to more citations of the same specialty, though author specialty had the largest effect. Comparing the specialties' literature, several VS topics had significantly different levels of coverage, including radiosurgery and hearing topics. Despite the availability of the Internet, there has been no change in the proportions of references for either specialty since 1997 (the year PubMed became publicly available). CONCLUSIONS Partial knowledge silos are observed between neurosurgery and otolaryngology on the topic of VS, based on the peer-reviewed literature. The increase in access provided by the Internet and searchable online databases has not decreased specialty reference bias. These findings offer lessons to improve cross-specialty collaboration, physician learning, and consensus building.

Electroacupuncture for women with stress urinary incontinence: Protocol for a systematic review and meta-analysis.

PubMed

Huang, Weixin; Li, Xiaohui; Wang, Yuanping; Yan, Xia; Wu, Siping

2017-12-01

Stress urinary incontinence (SUI) is a widespread complaint in the adult women. Electroacupuncture has been widely applied in the treatment of SUI. But its efficacy has not been evaluated scientifically and systematically. Therefore, we provide a protocol of systematic evaluation to assess the effectiveness and safety of electroacupuncture treatment on women with SUI. The retrieved databases include 3 English literature databases, namely PubMed, Embase, and Cochrane Library, and 3 Chinese literature databases, namely Chinese Biomedical Literature Database (CBM), China National Knowledge Infrastructure (CNKI), and Wanfang Database. The randomized controlled trials (RCTs) of the electroacupuncture treatment on women with SUI will be searched in the above-mentioned databases from the time when the respective databases were established to December 2017. The change from baseline in the amount of urine leakage measured by the 1-hour pad test will be accepted as the primary outcomes. We will use RevMan V.5.3 software as well to compute the data synthesis carefully when a meta-analysis is allowed. This study will provide a high-quality synthesis to assess the effectiveness and safety of electroacupuncture treatment on women with SUI. The conclusion of our systematic review will provide evidence to judge whether electroacupuncture is an effective intervention for women with SUI. PROSPERO CRD42017070947.

DEXTER: Disease-Expression Relation Extraction from Text.

PubMed

Gupta, Samir; Dingerdissen, Hayley; Ross, Karen E; Hu, Yu; Wu, Cathy H; Mazumder, Raja; Vijay-Shanker, K

2018-01-01

Gene expression levels affect biological processes and play a key role in many diseases. Characterizing expression profiles is useful for clinical research, and diagnostics and prognostics of diseases. There are currently several high-quality databases that capture gene expression information, obtained mostly from large-scale studies, such as microarray and next-generation sequencing technologies, in the context of disease. The scientific literature is another rich source of information on gene expression-disease relationships that not only have been captured from large-scale studies but have also been observed in thousands of small-scale studies. Expression information obtained from literature through manual curation can extend expression databases. While many of the existing databases include information from literature, they are limited by the time-consuming nature of manual curation and have difficulty keeping up with the explosion of publications in the biomedical field. In this work, we describe an automated text-mining tool, Disease-Expression Relation Extraction from Text (DEXTER) to extract information from literature on gene and microRNA expression in the context of disease. One of the motivations in developing DEXTER was to extend the BioXpress database, a cancer-focused gene expression database that includes data derived from large-scale experiments and manual curation of publications. The literature-based portion of BioXpress lags behind significantly compared to expression information obtained from large-scale studies and can benefit from our text-mined results. We have conducted two different evaluations to measure the accuracy of our text-mining tool and achieved average F-scores of 88.51 and 81.81% for the two evaluations, respectively. Also, to demonstrate the ability to extract rich expression information in different disease-related scenarios, we used DEXTER to extract information on differential expression information for 2024 genes in lung cancer, 115 glycosyltransferases in 62 cancers and 826 microRNA in 171 cancers. All extractions using DEXTER are integrated in the literature-based portion of BioXpress.Database URL: http://biotm.cis.udel.edu/DEXTER.

Construction and comparative evaluation of different activity detection methods in brain FDG-PET.

PubMed

Buchholz, Hans-Georg; Wenzel, Fabian; Gartenschläger, Martin; Thiele, Frank; Young, Stewart; Reuss, Stefan; Schreckenberger, Mathias

2015-08-18

We constructed and evaluated reference brain FDG-PET databases for usage by three software programs (Computer-aided diagnosis for dementia (CAD4D), Statistical Parametric Mapping (SPM) and NEUROSTAT), which allow a user-independent detection of dementia-related hypometabolism in patients' brain FDG-PET. Thirty-seven healthy volunteers were scanned in order to construct brain FDG reference databases, which reflect the normal, age-dependent glucose consumption in human brain, using either software. Databases were compared to each other to assess the impact of different stereotactic normalization algorithms used by either software package. In addition, performance of the new reference databases in the detection of altered glucose consumption in the brains of patients was evaluated by calculating statistical maps of regional hypometabolism in FDG-PET of 20 patients with confirmed Alzheimer's dementia (AD) and of 10 non-AD patients. Extent (hypometabolic volume referred to as cluster size) and magnitude (peak z-score) of detected hypometabolism was statistically analyzed. Differences between the reference databases built by CAD4D, SPM or NEUROSTAT were observed. Due to the different normalization methods, altered spatial FDG patterns were found. When analyzing patient data with the reference databases created using CAD4D, SPM or NEUROSTAT, similar characteristic clusters of hypometabolism in the same brain regions were found in the AD group with either software. However, larger z-scores were observed with CAD4D and NEUROSTAT than those reported by SPM. Better concordance with CAD4D and NEUROSTAT was achieved using the spatially normalized images of SPM and an independent z-score calculation. The three software packages identified the peak z-scores in the same brain region in 11 of 20 AD cases, and there was concordance between CAD4D and SPM in 16 AD subjects. The clinical evaluation of brain FDG-PET of 20 AD patients with either CAD4D-, SPM- or NEUROSTAT-generated databases from an identical reference dataset showed similar patterns of hypometabolism in the brain regions known to be involved in AD. The extent of hypometabolism and peak z-score appeared to be influenced by the calculation method used in each software package rather than by different spatial normalization parameters.

South African Helichrysum species: a review of the traditional uses, biological activity and phytochemistry.

PubMed

Lourens, A C U; Viljoen, A M; van Heerden, F R

2008-10-28

In South Africa, the genus Helichrysum is widely used in traditional medicine. The uses are well documented although renaming of species and the resulting confusing taxonomic nomenclature may cause uncertainty as to which specific species was referred to in some reports. The aim of this paper is to present a collated and coherent overview of the documented traditional uses of Helichrysum species and to update the botanical identity of previously studied species. Databases (Scifinder, ISI Web of Knowledge) and several books were used to collect in information on South African Helichrysum species. The traditional uses, chemistry and biological activity of Helichrysum species have been summarized. It was attempted to give clarity as to exactly which species is refer to in the ethnobotanical literature. Although a large number of ethnopharmacological uses have been documented and the chemistry of the genus has been studied extensively, only a few South African species have been investigated for their biological activity.

Information systems: the key to evidence-based health practice.

PubMed Central

Rodrigues, R. J.

2000-01-01

Increasing prominence is being given to the use of best current evidence in clinical practice and health services and programme management decision-making. The role of information in evidence-based practice (EBP) is discussed, together with questions of how advanced information systems and technology (IS&T) can contribute to the establishment of a broader perspective for EBP. The author examines the development, validation and use of a variety of sources of evidence and knowledge that go beyond the well-established paradigm of research, clinical trials, and systematic literature review. Opportunities and challenges in the implementation and use of IS&T and knowledge management tools are examined for six application areas: reference databases, contextual data, clinical data repositories, administrative data repositories, decision support software, and Internet-based interactive health information and communication. Computerized and telecommunications applications that support EBP follow a hierarchy in which systems, tasks and complexity range from reference retrieval and the processing of relatively routine transactions, to complex "data mining" and rule-driven decision support systems. PMID:11143195

A systematic review of ultrasound-accelerated catheter-directed thrombolysis in the treatment of deep vein thrombosis.

PubMed

Shi, Yadong; Shi, Wanyin; Chen, Liang; Gu, Jianping

2018-04-01

To review the clinical evidence for ultrasound-accelerated catheter-directed thrombolysis (UACDT) using the EKOS system in the treatment of deep vein thrombosis (DVT) in terms of case selection, procedural outcomes, clinical outcomes and safety outcomes. A systematic literature search strategy was used to identify the use of the EKOS system in the treatment of DVT using the following electronic databases: MEDLINE, EMBASE, the Cochrane databases and the Web of Science. The references in the relevant literature were also screened. Our literature search identified a total of 16 unique clinical studies. Twelve of the sixteen studies were retrospective case series studies. To date, only one randomised controlled trial (RCT) is available. Overall, UACDT using the EKOS system was performed 548 times in 512 patients. Among all cases, 77-100% achieved substantial lysis (> 50%) based on the different definitions of the individual studies. This treatment modality appears to be safe, as there were no reported procedure-related pulmonary embolisms (PE) and only one procedure-related death was reported. Bleeding events were reported in 14 of the 16 studies, and 3.9% (20/512) of the cases of bleeding were considered major. During the follow-up, post-thrombotic syndrome was observed in 17.1% (20/117) of cases. UACDT using the EKOS system is an effective, safe and promising treatment modality for DVT, but the existing clinical evidence is inadequate to make UACDT using the EKOS system the first-line choice for DVT. Additional prospective large-sample RCTs with long-term follow-ups are warranted to define the role of UACDT using the EKOS system in the treatment of DVT.

Can nutrition be promoted through agriculture-led food price policies? A systematic review

PubMed Central

Dangour, Alan D; Hawkesworth, Sophie; Shankar, Bhavani; Watson, Louise; Srinivasan, C S; Morgan, Emily H; Haddad, Lawrence; Waage, Jeff

2013-01-01

Objective To systematically review the available evidence on whether national or international agricultural policies that directly affect the price of food influence the prevalence rates of undernutrition or nutrition-related chronic disease in children and adults. Design Systematic review. Setting Global. Search strategy We systematically searched five databases for published literature (MEDLINE, EconLit, Agricola, AgEcon Search, Scopus) and systematically browsed other databases and relevant organisational websites for unpublished literature. Reference lists of included publications were hand-searched for additional relevant studies. We included studies that evaluated or simulated the effects of national or international food-price-related agricultural policies on nutrition outcomes reporting data collected after 1990 and published in English. Primary and secondary outcomes Prevalence rates of undernutrition (measured with anthropometry or clinical deficiencies) and overnutrition (obesity and nutrition-related chronic diseases including cancer, heart disease and diabetes). Results We identified a total of four relevant reports; two ex post evaluations and two ex ante simulations. A study from India reported on the undernutrition rates in children, and the other three studies from Egypt, the Netherlands and the USA reported on the nutrition-related chronic disease outcomes in adults. Two of the studies assessed the impact of policies that subsidised the price of agricultural outputs and two focused on public food distribution policies. The limited evidence base provided some support for the notion that agricultural policies that change the prices of foods at a national level can have an effect on population-level nutrition and health outcomes. Conclusions A systematic review of the available literature suggests that there is a paucity of robust direct evidence on the impact of agricultural price policies on nutrition and health. PMID:23801712

Efficacy of interventions to improve physical activity levels in individuals with stroke: a systematic review protocol.

PubMed

Aguiar, Larissa Tavares; Martins, Júlia Caetano; Nadeau, Sylvie; Britto, Raquel Rodrigues; Teixeira-Salmela, Luci F; Faria, Christina D C M

2017-01-05

Stroke is a leading health problem worldwide and an important cause of disability. Stroke survivors show low levels of physical activity, and increases in physical activity levels may improve function and health status. Therefore, the aims are to identify which interventions that have been employed to increase physical activity levels with stroke survivors, to verify their efficacy and to identify the gaps in the literature. A systematic review of randomised controlled trials that investigated the efficacy of interventions aiming at increasing physical activity levels of stroke survivors will be conducted. Electronic searches will be performed in the MEDLINE, Physiotherapy Evidence Database (PEDro), Excerpta Medica (EMBASE), Literatura Latino-Americana e do Caribe em Ciências da Saúde (LILACS) and Scientific Electronic Library Online (SCIELO) databases. Hand searches of the reference lists of the included studies or relevant reviews will also be employed. Two independent reviewers will screen all the retrieved titles, abstracts and full texts. A third reviewer will be referred to solve any disagreements. The quality of the included studies will be assessed by the PEDro Rating Scale. This systematic review will also include a qualitative synthesis. Meta-analyses will be performed, if the studies are sufficiently homogeneous. This review will follow the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) statement. The quality of the evidence regarding physical activity will be assessed, according to the Grading of Recommendations Assessment, Development and Evaluation (GRADE). This systematic review will provide information on which interventions are effective for increasing physical activity levels of stroke survivors. This evidence may be important for clinical decision-making and will allow the identification of gaps in the literature that may be useful for the definition of future research goals and the planning of new trials. CRD42016037750. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Efficacy of interventions to improve physical activity levels in individuals with stroke: a systematic review protocol

PubMed Central

Aguiar, Larissa Tavares; Martins, Júlia Caetano; Nadeau, Sylvie; Britto, Raquel Rodrigues; Teixeira-Salmela, Luci F; Faria, Christina D C M

2017-01-01

Introduction Stroke is a leading health problem worldwide and an important cause of disability. Stroke survivors show low levels of physical activity, and increases in physical activity levels may improve function and health status. Therefore, the aims are to identify which interventions that have been employed to increase physical activity levels with stroke survivors, to verify their efficacy and to identify the gaps in the literature. Methods and analysis A systematic review of randomised controlled trials that investigated the efficacy of interventions aiming at increasing physical activity levels of stroke survivors will be conducted. Electronic searches will be performed in the MEDLINE, Physiotherapy Evidence Database (PEDro), Excerpta Medica (EMBASE), Literatura Latino-Americana e do Caribe em Ciências da Saúde (LILACS) and Scientific Electronic Library Online (SCIELO) databases. Hand searches of the reference lists of the included studies or relevant reviews will also be employed. Two independent reviewers will screen all the retrieved titles, abstracts and full texts. A third reviewer will be referred to solve any disagreements. The quality of the included studies will be assessed by the PEDro Rating Scale. This systematic review will also include a qualitative synthesis. Meta-analyses will be performed, if the studies are sufficiently homogeneous. This review will follow the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) statement. The quality of the evidence regarding physical activity will be assessed, according to the Grading of Recommendations Assessment, Development and Evaluation (GRADE). Discussion This systematic review will provide information on which interventions are effective for increasing physical activity levels of stroke survivors. This evidence may be important for clinical decision-making and will allow the identification of gaps in the literature that may be useful for the definition of future research goals and the planning of new trials. Trial registration number CRD42016037750. PMID:28057651

Herbal Medicine for Oligomenorrhea and Amenorrhea: A Systematic Review of Ancient and Conventional Medicine

PubMed Central

Tansaz, Mojgan; Nazemiyeh, Hossein; Fazljou, Seyed Mohammad Bagher

2018-01-01

Introduction Menstrual bleeding cessation is one of the most frequent gynecologic disorders among women in reproductive age. The treatment is based on hormone therapy. Due to the increasing request for alternative medicine remedies in the field of women's diseases, in present study, it was tried to overview medicinal plants used to treat oligomenorrhea and amenorrhea according to the pharmaceutical textbooks of traditional Persian medicine (TPM) and review the evidence in the conventional medicine. Methods This systematic review was designed and performed in 2017 in order to gather information regarding herbal medications of oligomenorrhea and amenorrhea in TPM and conventional medicine. This study had several steps as searching Iranian traditional medicine literature and extracting the emmenagogue plants, classifying the plants, searching the electronic databases, and finding evidences. To search traditional Persian medicine references, Noor digital library was used, which includes several ancient traditional medical references. The classification of plants was done based on the repetition and potency of the plants in the ancient literatures. The required data was gathered using databases such as PubMed, Scopus, Google Scholar, Cochrane Library, Science Direct, and web of knowledge. Results In present study of all 198 emmenagogue medicinal plants found in TPM, 87 cases were specified to be more effective in treating oligomenorrhea and amenorrhea. In second part of present study, where a search of conventional medicine was performed, 12 studies were found, which had 8 plants investigated: Vitex agnus-castus, Trigonella foenum-graecum, Foeniculum vulgare, Cinnamomum verum, Paeonia lactiflora, Sesamum indicum, Mentha longifolia, and Urtica dioica. Conclusion. Traditional Persian medicine has proposed many different medicinal plants for treatment of oligomenorrhea and amenorrhea. Although just few plants have been proven to be effective for treatment of menstrual irregularities, the results and the classification in present study can be used as an outline for future studies and treatment. PMID:29744355

Herbal Medicine for Oligomenorrhea and Amenorrhea: A Systematic Review of Ancient and Conventional Medicine.

PubMed

Moini Jazani, Arezoo; Hamdi, Kobra; Tansaz, Mojgan; Nazemiyeh, Hossein; Sadeghi Bazargani, Homayoun; Fazljou, Seyed Mohammad Bagher; Nasimi Doost Azgomi, Ramin

2018-01-01

Menstrual bleeding cessation is one of the most frequent gynecologic disorders among women in reproductive age. The treatment is based on hormone therapy. Due to the increasing request for alternative medicine remedies in the field of women's diseases, in present study, it was tried to overview medicinal plants used to treat oligomenorrhea and amenorrhea according to the pharmaceutical textbooks of traditional Persian medicine (TPM) and review the evidence in the conventional medicine. This systematic review was designed and performed in 2017 in order to gather information regarding herbal medications of oligomenorrhea and amenorrhea in TPM and conventional medicine. This study had several steps as searching Iranian traditional medicine literature and extracting the emmenagogue plants, classifying the plants, searching the electronic databases, and finding evidences. To search traditional Persian medicine references, Noor digital library was used, which includes several ancient traditional medical references. The classification of plants was done based on the repetition and potency of the plants in the ancient literatures. The required data was gathered using databases such as PubMed, Scopus, Google Scholar, Cochrane Library, Science Direct, and web of knowledge. In present study of all 198 emmenagogue medicinal plants found in TPM, 87 cases were specified to be more effective in treating oligomenorrhea and amenorrhea. In second part of present study, where a search of conventional medicine was performed, 12 studies were found, which had 8 plants investigated: Vitex agnus-castus, Trigonella foenum-graecum, Foeniculum vulgare, Cinnamomum verum, Paeonia lactiflora, Sesamum indicum, Mentha longifolia, and Urtica dioica. Conclusion . Traditional Persian medicine has proposed many different medicinal plants for treatment of oligomenorrhea and amenorrhea. Although just few plants have been proven to be effective for treatment of menstrual irregularities, the results and the classification in present study can be used as an outline for future studies and treatment.

Use of dual-energy X-ray absorptiometry (DXA) for diagnosis and fracture risk assessment; WHO-criteria, T- and Z-score, and reference databases.

PubMed

Dimai, Hans P

2017-11-01

Dual-energy X-ray absorptiometry (DXA) is a two-dimensional imaging technology developed to assess bone mineral density (BMD) of the entire human skeleton and also specifically of skeletal sites known to be most vulnerable to fracture. In order to simplify interpretation of BMD measurement results and allow comparability among different DXA-devices, the T-score concept was introduced. This concept involves an individual's BMD which is then compared with the mean value of a young healthy reference population, with the difference expressed as a standard deviation (SD). Since the early nineties of the past century, the diagnostic categories "normal, osteopenia, and osteoporosis", as recommended by a WHO working Group, are based on this concept. Thus, DXA is still the globally accepted "gold-standard" method for the noninvasive diagnosis of osteoporosis. Another score obtained from DXA measurement, termed Z-score, describes the number of SDs by which the BMD in an individual differs from the mean value expected for age and sex. Although not intended for diagnosis of osteoporosis in adults, it nevertheless provides information about an individual's fracture risk compared to peers. DXA measurement can either be used as a "stand-alone" means in the assessment of an individual's fracture risk, or incorporated into one of the available fracture risk assessment tools such as FRAX® or Garvan, thus improving the predictive power of such tools. The issue which reference databases should be used by DXA-device manufacturers for T-score reference standards has been recently addressed by an expert group, who recommended use National Health and Nutrition Examination Survey III (NHANES III) databases for the hip reference standard but own databases for the lumbar spine. Furthermore, in men it is recommended use female reference databases for calculation of the T-score and use male reference databases for calculation of Z-score. Copyright © 2017 Elsevier Inc. All rights reserved.

An Algorithmic Approach to the Management of Infantile Digital Fibromatosis: Review of Literature and a Case Report.

PubMed

Eypper, Elizabeth H; Lee, Johnson C; Tarasen, Ashley J; Weinberg, Maxene H; Adetayo, Oluwaseun A

2018-01-01

Objective: Infantile digital fibromatosis is a rare benign childhood tumor, infrequently cited in the literature. Hallmarks include nodular growths exclusive to fingers and toes and the presence of eosinophilic cytoplasmic inclusions on histology. This article aims to exemplify diagnoses of infantile digital fibromatosis and possible treatment options. Methods: A computerized English literature search was performed in the PubMed/MEDLINE database using MeSH headings "infantile," "juvenile," "digital," and "fibromatosis." Twenty electronic publications were selected and their clinical and histological data recorded and used to compile a treatment algorithm. Results: A 9-month-old male child was referred for a persistent, symptomatic nodule on the third left toe. A direct excision with Brunner-type incisions was performed under general anesthesia. The procedure was successful without complications. The patient has no recurrence at 2 years postsurgery and continues to be followed. Histological examination revealed a proliferation of bland, uniformly plump spindle cells with elongated nuclei and small central nucleoli without paranuclear inclusions consistent with fibromatosis. Conclusions: Asymptomatic nodules should be observed for spontaneous regression or treated with nonsurgical techniques such as chemotherapeutic or steroid injection. Surgical removal should be reserved for cases with structural or functional compromise.

BODY IMAGE IN CHILDHOOD: AN INTEGRATIVE LITERATURE REVIEW.

PubMed

Neves, Clara Mockdece; Cipriani, Flávia Marcelle; Meireles, Juliana Fernandes Filgueiras; Morgado, Fabiane Frota da Rocha; Ferreira, Maria Elisa Caputo

2017-01-01

To analyse the scientific literature regarding the evaluation of body image in children through an integrative literature review. An intersection of the keywords "body image" AND "child" was conducted in Scopus, Medline and Virtual Health Library (BVS - Biblioteca Virtual de Saúde) databases. The electronic search was based on studies published from January 2013 to January 2016, in order to verify the most current investigations on the subject. Exclusion criteria were: articles in duplicate; no available summaries; not empirical; not assessing any component of body image; the sample did not consider the target age of this research (0 to 12 years old) and/or considered clinical populations; besides articles not fully available. 7,681 references were identified, and, after the exclusion criteria were implemented, 33 studies were analysed. Results showed that the perceptual and attitudinal dimensions focusing on body dissatisfaction were explored, mainly evaluated by silhouette scales. Intervention programs were developed internationally to prevent negative body image in children. The studies included in this review evaluated specific aspects of body image in children, especially body perception and body dissatisfaction. The creation of specific tools for children to evaluate body image is recommended to promote the psychosocial well being of individuals throughout human development.

Student Evaluations, Outcomes, and National Licensure Examinations in Radiology Education: A Narrative Review of the Literature.

PubMed

Linaker, Kathleen L

2015-12-01

The purpose of this study was to examine literature on radiological student evaluation and outcome assessments including national board examinations. A review of the literature was performed using relevant key words. Articles were retrieved through December 2012 using PubMed, ScienceDirect, ERIC, Proquest, and ICL databases along with a manual review of references. Of the 4716 unique abstracts reviewed by the author, 54 were found to be relevant to the purpose of this study. Student grade point average correlates with board scores in the nursing, chiropractic, and medical professions. Scores on the chiropractic college admission test and undergraduate grade point average correlate with success in professional college. There is a correlation between board scores and college attended. Board preparation programs do not appear to affect board examination scores. Although evaluations can be effective teaching tools, they are not used by many radiology programs. Some programs have inadequate evaluations and do not allow students to review their evaluations. There are no definitive links between mastery of radiology and specific evaluations, outcomes, or pre-professional/clinical grades. Studies suggest that board examination scores reflect long-term mastery of knowledge rather than short-term memorization of facts.

Phantom eye syndrome: a review of the literature.

PubMed

Andreotti, Agda M; Goiato, Marcelo C; Pellizzer, Eduardo P; Pesqueira, Aldiéris A; Guiotti, Aimée M; Gennari-Filho, Humberto; dos Santos, Daniela M

2014-01-01

The purpose of this literature review was to describe the main features of phantom eye syndrome in relation to their possible causes, symptoms, treatments, and influence of eye amputation on quality of life of anophthalmic patients. For this, a bibliographical research was performed in Pubmed database using the following terms: "eye amputation," "eye trauma," "phantom eye syndrome," "phantom pain," and "quality of life," associated or not. Thirteen studies were selected, besides some relevant references contained in the selected manuscripts and other studies hallowed in the literature. Thus, 56 articles were included in this review. The phantom eye syndrome is defined as any sensation reported by the patient with anophthalmia, originated anophthalmic cavity. In phantom eye syndrome, at least one of these three symptoms has to be present: phantom vision, phantom pain, and phantom sensations. This syndrome has a direct influence on the quality of life of the patients, and psychological support is recommended before and after the amputation of the eyeball as well as aid in the treatment of the syndrome. Therefore, it is suggested that, for more effective treatment of phantom eye syndrome, drug therapy should be associated with psychological approach.

NASA STI Database, Aerospace Database and ARIN coverage of 'space law'

NASA Technical Reports Server (NTRS)

Buchan, Ronald L.

1992-01-01

The space-law coverage provided by the NASA STI Database, the Aerospace Database, and ARIN is briefly described. Particular attention is given to the space law content of the two Databases and of ARIN, the NASA Thesauras space law terminology, space law publication forms, and the availability of the space law literature.

libChEBI: an API for accessing the ChEBI database.

PubMed

Swainston, Neil; Hastings, Janna; Dekker, Adriano; Muthukrishnan, Venkatesh; May, John; Steinbeck, Christoph; Mendes, Pedro

2016-01-01

ChEBI is a database and ontology of chemical entities of biological interest. It is widely used as a source of identifiers to facilitate unambiguous reference to chemical entities within biological models, databases, ontologies and literature. ChEBI contains a wealth of chemical data, covering over 46,500 distinct chemical entities, and related data such as chemical formula, charge, molecular mass, structure, synonyms and links to external databases. Furthermore, ChEBI is an ontology, and thus provides meaningful links between chemical entities. Unlike many other resources, ChEBI is fully human-curated, providing a reliable, non-redundant collection of chemical entities and related data. While ChEBI is supported by a web service for programmatic access and a number of download files, it does not have an API library to facilitate the use of ChEBI and its data in cheminformatics software. To provide this missing functionality, libChEBI, a comprehensive API library for accessing ChEBI data, is introduced. libChEBI is available in Java, Python and MATLAB versions from http://github.com/libChEBI, and provides full programmatic access to all data held within the ChEBI database through a simple and documented API. libChEBI is reliant upon the (automated) download and regular update of flat files that are held locally. As such, libChEBI can be embedded in both on- and off-line software applications. libChEBI allows better support of ChEBI and its data in the development of new cheminformatics software. Covering three key programming languages, it allows for the entirety of the ChEBI database to be accessed easily and quickly through a simple API. All code is open access and freely available.

A taxonomy has been developed for outcomes in medical research to help improve knowledge discovery.

PubMed

Dodd, Susanna; Clarke, Mike; Becker, Lorne; Mavergames, Chris; Fish, Rebecca; Williamson, Paula R

2018-04-01

There is increasing recognition that insufficient attention has been paid to the choice of outcomes measured in clinical trials. The lack of a standardized outcome classification system results in inconsistencies due to ambiguity and variation in how outcomes are described across different studies. Being able to classify by outcome would increase efficiency in searching sources such as clinical trial registries, patient registries, the Cochrane Database of Systematic Reviews, and the Core Outcome Measures in Effectiveness Trials (COMET) database of core outcome sets (COS), thus aiding knowledge discovery. A literature review was carried out to determine existing outcome classification systems, none of which were sufficiently comprehensive or granular for classification of all potential outcomes from clinical trials. A new taxonomy for outcome classification was developed, and as proof of principle, outcomes extracted from all published COS in the COMET database, selected Cochrane reviews, and clinical trial registry entries were classified using this new system. Application of this new taxonomy to COS in the COMET database revealed that 274/299 (92%) COS include at least one physiological outcome, whereas only 177 (59%) include at least one measure of impact (global quality of life or some measure of functioning) and only 105 (35%) made reference to adverse events. This outcome taxonomy will be used to annotate outcomes included in COS within the COMET database and is currently being piloted for use in Cochrane Reviews within the Cochrane Linked Data Project. Wider implementation of this standard taxonomy in trial and systematic review databases and registries will further promote efficient searching, reporting, and classification of trial outcomes. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Automated detection of records in biological sequence databases that are inconsistent with the literature.

PubMed

Bouadjenek, Mohamed Reda; Verspoor, Karin; Zobel, Justin

2017-07-01

We investigate and analyse the data quality of nucleotide sequence databases with the objective of automatic detection of data anomalies and suspicious records. Specifically, we demonstrate that the published literature associated with each data record can be used to automatically evaluate its quality, by cross-checking the consistency of the key content of the database record with the referenced publications. Focusing on GenBank, we describe a set of quality indicators based on the relevance paradigm of information retrieval (IR). Then, we use these quality indicators to train an anomaly detection algorithm to classify records as "confident" or "suspicious". Our experiments on the PubMed Central collection show assessing the coherence between the literature and database records, through our algorithms, is an effective mechanism for assisting curators to perform data cleansing. Although fewer than 0.25% of the records in our data set are known to be faulty, we would expect that there are many more in GenBank that have not yet been identified. By automated comparison with literature they can be identified with a precision of up to 10% and a recall of up to 30%, while strongly outperforming several baselines. While these results leave substantial room for improvement, they reflect both the very imbalanced nature of the data, and the limited explicitly labelled data that is available. Overall, the obtained results show promise for the development of a new kind of approach to detecting low-quality and suspicious sequence records based on literature analysis and consistency. From a practical point of view, this will greatly help curators in identifying inconsistent records in large-scale sequence databases by highlighting records that are likely to be inconsistent with the literature. Copyright © 2017 Elsevier Inc. All rights reserved.

The Impact of Online Bibliographic Databases on Teaching and Research in Political Science.

ERIC Educational Resources Information Center

Reichel, Mary

The availability of online bibliographic databases greatly facilitates literature searching in political science. The advantages to searching databases online include combination of concepts, comprehensiveness, multiple database searching, free-text searching, currency, current awareness services, document delivery service, and convenience.…

Reflecting on the challenges of building a rich interconnected metadata database to describe the experiments of phase six of the coupled climate model intercomparison project (CMIP6) for the Earth System Documentation Project (ES-DOC) and anticipating the opportunities that tooling and services based on rich metadata can provide.

NASA Astrophysics Data System (ADS)

Pascoe, C. L.

2017-12-01

The Coupled Model Intercomparison Project (CMIP) has coordinated climate model experiments involving multiple international modelling teams since 1995. This has led to a better understanding of past, present, and future climate. The 2017 sixth phase of the CMIP process (CMIP6) consists of a suite of common experiments, and 21 separate CMIP-Endorsed Model Intercomparison Projects (MIPs) making a total of 244 separate experiments. Precise descriptions of the suite of CMIP6 experiments have been captured in a Common Information Model (CIM) database by the Earth System Documentation Project (ES-DOC). The database contains descriptions of forcings, model configuration requirements, ensemble information and citation links, as well as text descriptions and information about the rationale for each experiment. The database was built from statements about the experiments found in the academic literature, the MIP submissions to the World Climate Research Programme (WCRP), WCRP summary tables and correspondence with the principle investigators for each MIP. The database was collated using spreadsheets which are archived in the ES-DOC Github repository and then rendered on the ES-DOC website. A diagramatic view of the workflow of building the database of experiment metadata for CMIP6 is shown in the attached figure.The CIM provides the formalism to collect detailed information from diverse sources in a standard way across all the CMIP6 MIPs. The ES-DOC documentation acts as a unified reference for CMIP6 information to be used both by data producers and consumers. This is especially important given the federated nature of the CMIP6 project. Because the CIM allows forcing constraints and other experiment attributes to be referred to by more than one experiment, we can streamline the process of collecting information from modelling groups about how they set up their models for each experiment. End users of the climate model archive will be able to ask questions enabled by the interconnectedness of the metadata such as "Which MIPs make use of experiment A?" and "Which experiments use forcing constraint B?".

AN ASSESSMENT OF GROUND TRUTH VARIABILITY USING A "VIRTUAL FIELD REFERENCE DATABASE"

EPA Science Inventory

A "Virtual Field Reference Database (VFRDB)" was developed from field measurment data that included location and time, physical attributes, flora inventory, and digital imagery (camera) documentation foy 1,01I sites in the Neuse River basin, North Carolina. The sampling f...

Interactome of the hepatitis C virus: Literature mining with ANDSystem.

PubMed

Saik, Olga V; Ivanisenko, Timofey V; Demenkov, Pavel S; Ivanisenko, Vladimir A

2016-06-15

A study of the molecular genetics mechanisms of host-pathogen interactions is of paramount importance in developing drugs against viral diseases. Currently, the literature contains a huge amount of information that describes interactions between HCV and human proteins. In addition, there are many factual databases that contain experimentally verified data on HCV-host interactions. The sources of such data are the original data along with the data manually extracted from the literature. However, the manual analysis of scientific publications is time consuming and, because of this, databases created with such an approach often do not have complete information. One of the most promising methods to provide actualisation and completeness of information is text mining. Here, with the use of a previously developed method by the authors using ANDSystem, an automated extraction of information on the interactions between HCV and human proteins was conducted. As a data source for the text mining approach, PubMed abstracts and full text articles were used. Additionally, external factual databases were analyzed. On the basis of this analysis, a special version of ANDSystem, extended with the HCV interactome, was created. The HCV interactome contains information about the interactions between 969 human and 11 HCV proteins. Among the 969 proteins, 153 'new' proteins were found not previously referred to in any external databases of protein-protein interactions for HCV-host interactions. Thus, the extended ANDSystem possesses a more comprehensive detailing of HCV-host interactions versus other existing databases. It was interesting that HCV proteins more preferably interact with human proteins that were already involved in a large number of protein-protein interactions as well as those associated with many diseases. Among human proteins of the HCV interactome, there were a large number of proteins regulated by microRNAs. It turned out that the results obtained for protein-protein interactions and microRNA-regulation did not depend on how well the proteins were studied, while protein-disease interactions appeared to be dependent on the level of study. In particular, the mean number of diseases linked to well-studied proteins (proteins were considered well-studied if they were mentioned in 50 or more PubMed publications) from the HCV interactome was 20.8, significantly exceeding the mean number of associations with diseases (10.1) for the total set of well-studied human proteins present in ANDSystem. For proteins not highly poorly-studied investigated, proteins from the HCV interactome (each protein was referred to in less than 50 publications) distribution of the number of diseases associated with them had no statistically significant differences from the distribution of the number of diseases associated with poorly-studied proteins based on the total set of human proteins stored in ANDSystem. With this, the average number of associations with diseases for the HCV interactome and the total set of human proteins were 0.3 and 0.2, respectively. Thus, ANDSystem, extended with the HCV interactome, can be helpful in a wide range of issues related to analyzing HCV-host interactions in the search for anti-HCV drug targets. The demo version of the extended ANDSystem covered here containing only interactions between human proteins, genes, metabolites, diseases, miRNAs and molecular-genetic pathways, as well as interactions between human proteins/genes and HCV proteins, is freely available at the following web address: http://www-bionet.sscc.ru/psd/andhcv/. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

RefPrimeCouch—a reference gene primer CouchApp

PubMed Central

Silbermann, Jascha; Wernicke, Catrin; Pospisil, Heike; Frohme, Marcus

2013-01-01

To support a quantitative real-time polymerase chain reaction standardization project, a new reference gene database application was required. The new database application was built with the explicit goal of simplifying not only the development process but also making the user interface more responsive and intuitive. To this end, CouchDB was used as the backend with a lightweight dynamic user interface implemented client-side as a one-page web application. Data entry and curation processes were streamlined using an OpenRefine-based workflow. The new RefPrimeCouch database application provides its data online under an Open Database License. Database URL: http://hpclife.th-wildau.de:5984/rpc/_design/rpc/view.html PMID:24368831

RefPrimeCouch--a reference gene primer CouchApp.

PubMed

Silbermann, Jascha; Wernicke, Catrin; Pospisil, Heike; Frohme, Marcus

2013-01-01

To support a quantitative real-time polymerase chain reaction standardization project, a new reference gene database application was required. The new database application was built with the explicit goal of simplifying not only the development process but also making the user interface more responsive and intuitive. To this end, CouchDB was used as the backend with a lightweight dynamic user interface implemented client-side as a one-page web application. Data entry and curation processes were streamlined using an OpenRefine-based workflow. The new RefPrimeCouch database application provides its data online under an Open Database License. Database URL: http://hpclife.th-wildau.de:5984/rpc/_design/rpc/view.html.

Optics survivability support, volume 2

NASA Astrophysics Data System (ADS)

Wild, N.; Simpson, T.; Busdeker, A.; Doft, F.

1993-01-01

This volume of the Optics Survivability Support Final Report contains plots of all the data contained in the computerized Optical Glasses Database. All of these plots are accessible through the Database, but are included here as a convenient reference. The first three pages summarize the types of glass included with a description of the radiation source, test date, and the original data reference. This information is included in the database as a macro button labeled 'LLNL DATABASE'. Following this summary is an Abbe chart showing which glasses are included and where they lie as a function of nu(sub d) and n(sub d). This chart is also callable through the database as a macro button labeled 'ABBEC'.

Nuclear Science References Database

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pritychenko, B., E-mail: pritychenko@bnl.gov; Běták, E.; Singh, B.

2014-06-15

The Nuclear Science References (NSR) database together with its associated Web interface, is the world's only comprehensive source of easily accessible low- and intermediate-energy nuclear physics bibliographic information for more than 210,000 articles since the beginning of nuclear science. The weekly-updated NSR database provides essential support for nuclear data evaluation, compilation and research activities. The principles of the database and Web application development and maintenance are described. Examples of nuclear structure, reaction and decay applications are specifically included. The complete NSR database is freely available at the websites of the National Nuclear Data Center (http://www.nndc.bnl.gov/nsr) and the International Atomic Energymore » Agency (http://www-nds.iaea.org/nsr)« less

Three Library and Information Science Databases Revisited: Currency, Coverage and Overlap, Interindexing Consistency.

ERIC Educational Resources Information Center

Blackwell, Michael Lind

This study evaluates the "Education Resources Information Center" (ERIC), "Library and Information Science Abstracts" (LISA), and "Library Literature" (LL) databases, determining how long the databases take to enter records (indexing delay), how much duplication of effort exists among the three databases (indexing…

APPLICATION OF A "VITURAL FIELD REFERENCE DATABASE" TO ASSESS LAND-COVER MAP ACCURACIES

EPA Science Inventory

An accuracy assessment was performed for the Neuse River Basin, NC land-cover/use
(LCLU) mapping results using a "Virtual Field Reference Database (VFRDB)". The VFRDB was developed using field measurement and digital imagery (camera) data collected at 1,409 sites over a perio...

USDA National Nutrient Database for Standard Reference, release 28

USDA-ARS?s Scientific Manuscript database

The USDA National Nutrient Database for Standard Reference, Release 28 contains data for nearly 8,800 food items for up to 150 food components. SR28 replaces the previous release, SR27, originally issued in August 2014. Data in SR28 supersede values in the printed handbooks and previous electronic...

Best Practices for Data Publication to Facilitate Integration into NED: A Reference Guide for Authors

NASA Astrophysics Data System (ADS)

Schmitz, Marion; Mazzarella, J. M.; Madore, B. F.; Ogle, P. M.; Ebert, R.; Baker, K.; Chan, H.; Chen, X.; Fadda, D.; Frayer, C.; Jacobson, J. D.; LaGue, C.; Lo, T. M.; Pevunova, O.; Terek, S.; Steer, I.

2014-01-01

At the urging of the NASA/IPAC Extragalactic Database (NED) Users Committee, the NED Team has prepared and published on its website a new document titled "Best Practices for Data Publication to Facilitate Integration into NED: A Reference Guide for Authors" (http://ned.ipac.caltech.edu/docs/BPDP/NED_BPDP.pdf). We hope that journal publishers will incorporate links to this living document in their Instructions to Authors to provide a practical reference for authors, referees, and science editors so as to help avoid various pitfalls that often impede the interpretation of data and metadata, and also delay their integration into NED, SIMBAD, ADS and other systems. In particular, we discuss the importance of using proper naming conventions, providing the epoch and system of coordinates, including units and uncertainties, and giving sufficient metadata for the unambiguous interpretation of tabular, imaging, and spectral data. The biggest impediments to the assimilation of new data from the literature into NED are ambiguous object names and non-unique, coordinate-based identifiers. A Checklist of Recommendations will be presented which includes links to sections of the Best Practices document that provide further examples, explanation, and rationale.

Olson's Major World Ecosystem Complexes Ranked by Carbon in Live Vegetation: An Updated Database Using the GLC2000 Land Cover Product (NDP-017b, a 2006 update of the original 1985 and 2001 data file))

DOE Data Explorer

Gibbs, Holly K. [Center for Sustainability and the Global Environment, University of Wisconsin, Madison, WI (United States)

2006-01-01

In the 1980s, Olson et al. developed a data base and corresponding map following more than 20 years of field investigations, consultations, and analyses of published literature. The original data characterize the use and vegetative cover of the Earth's land surface with a 0.5° by 0.5° grid. The purpose of these world-ecosystem-complex data and the accompanying map were to provide a current reference base for interpreting the role of vegetation in the global cycling of CO2 and other gases and a basis for improved estimates of vegetation and soil carbon, of natural exchanges of CO2, and of net historic shifts of carbon between the biosphere and the atmosphere. These data were widely used and cited in carbon cycle research. This updated database extends the methodology of Olson et al. to more contemporary land cover conditions of the Global Land Cover Database (GLC2000). The GLC2000 data were developed using remotely sensed imagery acquired in 2000. The updated data are presented in a GIS format and include estimates of mean and maximum carbon density values.