G-Bean: an ontology-graph based web tool for biomedical literature retrieval.

PubMed

Wang, James Z; Zhang, Yuanyuan; Dong, Liang; Li, Lin; Srimani, Pradip K; Yu, Philip S

2014-01-01

Currently, most people use NCBI's PubMed to search the MEDLINE database, an important bibliographical information source for life science and biomedical information. However, PubMed has some drawbacks that make it difficult to find relevant publications pertaining to users' individual intentions, especially for non-expert users. To ameliorate the disadvantages of PubMed, we developed G-Bean, a graph based biomedical search engine, to search biomedical articles in MEDLINE database more efficiently. G-Bean addresses PubMed's limitations with three innovations: (1) Parallel document index creation: a multithreaded index creation strategy is employed to generate the document index for G-Bean in parallel; (2) Ontology-graph based query expansion: an ontology graph is constructed by merging four major UMLS (Version 2013AA) vocabularies, MeSH, SNOMEDCT, CSP and AOD, to cover all concepts in National Library of Medicine (NLM) database; a Personalized PageRank algorithm is used to compute concept relevance in this ontology graph and the Term Frequency - Inverse Document Frequency (TF-IDF) weighting scheme is used to re-rank the concepts. The top 500 ranked concepts are selected for expanding the initial query to retrieve more accurate and relevant information; (3) Retrieval and re-ranking of documents based on user's search intention: after the user selects any article from the existing search results, G-Bean analyzes user's selections to determine his/her true search intention and then uses more relevant and more specific terms to retrieve additional related articles. The new articles are presented to the user in the order of their relevance to the already selected articles. Performance evaluation with 106 OHSUMED benchmark queries shows that G-Bean returns more relevant results than PubMed does when using these queries to search the MEDLINE database. PubMed could not even return any search result for some OHSUMED queries because it failed to form the appropriate Boolean query statement automatically from the natural language query strings. G-Bean is available at http://bioinformatics.clemson.edu/G-Bean/index.php. G-Bean addresses PubMed's limitations with ontology-graph based query expansion, automatic document indexing, and user search intention discovery. It shows significant advantages in finding relevant articles from the MEDLINE database to meet the information need of the user.

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

Beyond relevance and recall: testing new user-centred measures of database performance.

PubMed

Stokes, Peter; Foster, Allen; Urquhart, Christine

2009-09-01

Measures of the effectiveness of databases have traditionally focused on recall, precision, with some debate on how relevance can be assessed, and by whom. New measures of database performance are required when users are familiar with search engines, and expect full text availability. This research ascertained which of four bibliographic databases (BNI, CINAHL, MEDLINE and EMBASE) could be considered most useful to nursing and midwifery students searching for information for an undergraduate dissertation. Searches on title were performed for dissertation topics supplied by nursing students (n = 9), who made the relevance judgements. Measures of recall and precision were combined with additional factors to provide measures of effectiveness, while efficiency combined measures of novelty and originality and accessibility combined measures for availability and retrievability, based on obtainability. There were significant differences among the databases in precision, originality and availability, but other differences were not significant (Friedman test). Odds ratio tests indicated that BNI, followed by CINAHL were the most effective, CINAHL the most efficient, and BNI the most accessible. The methodology could help library services in purchase decisions as the measure for accessibility, and odds ratio testing helped to differentiate database performance.

[Systematic literature search in PubMed : A short introduction].

PubMed

Blümle, A; Lagrèze, W A; Motschall, E

2018-03-01

In order to identify current (and relevant) evidence for a specific clinical question within the unmanageable amount of information available, solid skills in performing a systematic literature search are essential. An efficient approach is to search a biomedical database containing relevant literature citations of study reports. The best known database is MEDLINE, which is searchable for free via the PubMed interface. In this article, we explain step by step how to perform a systematic literature search via PubMed by means of an example research question in the field of ophthalmology. First, we demonstrate how to translate the clinical problem into a well-framed and searchable research question, how to identify relevant search terms and how to conduct a text word search and a search with keywords in medical subject headings (MeSH) terms. We then show how to limit the number of search results if the search yields too many irrelevant hits and how to increase the number in the case of too few citations. Finally, we summarize all essential principles that guide a literature search via PubMed.

Information Retrieval in Telemedicine: a Comparative Study on Bibliographic Databases

PubMed Central

Ahmadi, Maryam; Sarabi, Roghayeh Ershad; Orak, Roohangiz Jamshidi; Bahaadinbeigy, Kambiz

2015-01-01

Background and Aims: The first step in each systematic review is selection of the most valid database that can provide the highest number of relevant references. This study was carried out to determine the most suitable database for information retrieval in telemedicine field. Methods: Cinhal, PubMed, Web of Science and Scopus databases were searched for telemedicine matched with Education, cost benefit and patient satisfaction. After analysis of the obtained results, the accuracy coefficient, sensitivity, uniqueness and overlap of databases were calculated. Results: The studied databases differed in the number of retrieved articles. PubMed was identified as the most suitable database for retrieving information on the selected topics with the accuracy and sensitivity ratios of 50.7% and 61.4% respectively. The uniqueness percent of retrieved articles ranged from 38% for Pubmed to 3.0% for Cinhal. The highest overlap rate (18.6%) was found between PubMed and Web of Science. Less than 1% of articles have been indexed in all searched databases. Conclusion: PubMed is suggested as the most suitable database for starting search in telemedicine and after PubMed, Scopus and Web of Science can retrieve about 90% of the relevant articles. PMID:26236086

Information Retrieval in Telemedicine: a Comparative Study on Bibliographic Databases.

PubMed

Ahmadi, Maryam; Sarabi, Roghayeh Ershad; Orak, Roohangiz Jamshidi; Bahaadinbeigy, Kambiz

2015-06-01

The first step in each systematic review is selection of the most valid database that can provide the highest number of relevant references. This study was carried out to determine the most suitable database for information retrieval in telemedicine field. Cinhal, PubMed, Web of Science and Scopus databases were searched for telemedicine matched with Education, cost benefit and patient satisfaction. After analysis of the obtained results, the accuracy coefficient, sensitivity, uniqueness and overlap of databases were calculated. The studied databases differed in the number of retrieved articles. PubMed was identified as the most suitable database for retrieving information on the selected topics with the accuracy and sensitivity ratios of 50.7% and 61.4% respectively. The uniqueness percent of retrieved articles ranged from 38% for Pubmed to 3.0% for Cinhal. The highest overlap rate (18.6%) was found between PubMed and Web of Science. Less than 1% of articles have been indexed in all searched databases. PubMed is suggested as the most suitable database for starting search in telemedicine and after PubMed, Scopus and Web of Science can retrieve about 90% of the relevant articles.

Systematic literature searching in policy relevant, inter-disciplinary reviews: an example from culture and sport.

PubMed

Schucan Bird, Karen; Tripney, Janice

2011-09-01

Within the systematic review process, the searching phase is critical to the final synthesis product, its use and value. Yet, relatively little is known about the utility of different search strategies for reviews of complex, inter-disciplinary evidence. This article used a recently completed programme of work on cultural and sporting engagement to conduct an empirical evaluation of a comprehensive search strategy. Ten different types of search source were evaluated, according to three dimensions: (i) effectiveness in identifying relevant studies; (ii) efficiency in identifying studies; and (iii) adding value by locating studies that were not identified by any other sources. The study found that general bibliographic databases and specialist databases ranked the highest on all three dimensions. Overall, websites and journals were the next most valuable types of source. For reviewers, these findings highlight that general and specialist databases should remain a core component of the comprehensive search strategy, supplemented with other types of sources that can efficiently identify unique or grey literature. For policy makers and other research commissioners, this study highlights the value of methodological analysis for improving the understanding of, and practice in, policy relevant, inter-disciplinary systematic reviews. Copyright © 2011 John Wiley & Sons, Ltd. Copyright © 2011 John Wiley & Sons, Ltd.

High-performance information search filters for acute kidney injury content in PubMed, Ovid Medline and Embase.

PubMed

Hildebrand, Ainslie M; Iansavichus, Arthur V; Haynes, R Brian; Wilczynski, Nancy L; Mehta, Ravindra L; Parikh, Chirag R; Garg, Amit X

2014-04-01

We frequently fail to identify articles relevant to the subject of acute kidney injury (AKI) when searching the large bibliographic databases such as PubMed, Ovid Medline or Embase. To address this issue, we used computer automation to create information search filters to better identify articles relevant to AKI in these databases. We first manually reviewed a sample of 22 992 full-text articles and used prespecified criteria to determine whether each article contained AKI content or not. In the development phase (two-thirds of the sample), we developed and tested the performance of >1.3-million unique filters. Filters with high sensitivity and high specificity for the identification of AKI articles were then retested in the validation phase (remaining third of the sample). We succeeded in developing and validating high-performance AKI search filters for each bibliographic database with sensitivities and specificities in excess of 90%. Filters optimized for sensitivity reached at least 97.2% sensitivity, and filters optimized for specificity reached at least 99.5% specificity. The filters were complex; for example one PubMed filter included >140 terms used in combination, including 'acute kidney injury', 'tubular necrosis', 'azotemia' and 'ischemic injury'. In proof-of-concept searches, physicians found more articles relevant to topics in AKI with the use of the filters. PubMed, Ovid Medline and Embase can be filtered for articles relevant to AKI in a reliable manner. These high-performance information filters are now available online and can be used to better identify AKI content in large bibliographic databases.

Development and Validation of Search Filters to Identify Articles on Family Medicine in Online Medical Databases

PubMed Central

Pols, David H.J.; Bramer, Wichor M.; Bindels, Patrick J.E.; van de Laar, Floris A.; Bohnen, Arthur M.

2015-01-01

Physicians and researchers in the field of family medicine often need to find relevant articles in online medical databases for a variety of reasons. Because a search filter may help improve the efficiency and quality of such searches, we aimed to develop and validate search filters to identify research studies of relevance to family medicine. Using a new and objective method for search filter development, we developed and validated 2 search filters for family medicine. The sensitive filter had a sensitivity of 96.8% and a specificity of 74.9%. The specific filter had a specificity of 97.4% and a sensitivity of 90.3%. Our new filters should aid literature searches in the family medicine field. The sensitive filter may help researchers conducting systematic reviews, whereas the specific filter may help family physicians find answers to clinical questions at the point of care when time is limited. PMID:26195683

What Searches Do Users Run on PEDro? An Analysis of 893,971 Search Commands Over a 6-Month Period.

PubMed

Stevens, Matthew L; Moseley, Anne; Elkins, Mark R; Lin, Christine C-W; Maher, Chris G

2016-08-05

Clinicians must be able to search effectively for relevant research if they are to provide evidence-based healthcare. It is therefore relevant to consider how users search databases of evidence in healthcare, including what information users look for and what search strategies they employ. To date such analyses have been restricted to the PubMed database. Although the Physiotherapy Evidence Database (PEDro) is searched millions of times each year, no studies have investigated how users search PEDro. To assess the content and quality of searches conducted on PEDro. Searches conducted on the PEDro website over 6 months were downloaded and the 'get' commands and page-views extracted. The following data were tabulated: the 25 most common searches; the number of search terms used; the frequency of use of simple and advanced searches, including the use of each advanced search field; and the frequency of use of various search strategies. Between August 2014 and January 2015, 893,971 search commands were entered on PEDro. Fewer than 18 % of these searches used the advanced search features of PEDro. 'Musculoskeletal' was the most common subdiscipline searched, while 'low back pain' was the most common individual search. Around 20 % of all searches contained errors. PEDro is a commonly used evidence resource, but searching appears to be sub-optimal in many cases. The effectiveness of searches conducted by users needs to improve, which could be facilitated by methods such as targeted training and amending the search interface.

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).

Performance appraisal of online MEDLINE access routes.

PubMed Central

Walker, C. J.; McKibbon, K. A.; Haynes, R. B.; Johnston, M. E.

1992-01-01

OBJECTIVE: To compare the performance and cost of 11 online MEDLINE systems with MEDLINE at Elhill. DESIGN: Comparative study. SYSTEMS: Eleven online daytime systems commercially available in North America offering the MEDLINE database. MEASURES: Number of relevant citations, number of irrelevant citations, proportion of searches producing no relevant citations and cost per relevant citation were analyzed for each system. Relevance and cost for each system were compared with direct searching of MEDLINE through NLM for librarian and clinician search strategies for 18 clinical questions. The citations retrieved by both strategies were pooled and rated for relevance on a 7-point scale. RESULTS: Numbers of relevant and irrelevant citations and cost per relevant citation were higher for clinician searches than librarian searches, reflecting the higher total number of citations retrieved by the clinician approaches. A lower proportion of clinician searches produced no relevant citations than librarian searches. CONCLUSIONS: Eleven daytime MEDLINE systems performed similarly in terms of retrieval and cost within similar searching groups. Clinicians, however, tended to capture larger overall retrievals resulting in higher numbers of relevant and irrelevant citations than librarians. PMID:1482922

Citation searching: a systematic review case study of multiple risk behaviour interventions

PubMed Central

2014-01-01

Background The value of citation searches as part of the systematic review process is currently unknown. While the major guides to conducting systematic reviews state that citation searching should be carried out in addition to searching bibliographic databases there are still few studies in the literature that support this view. Rather than using a predefined search strategy to retrieve studies, citation searching uses known relevant papers to identify further papers. Methods We describe a case study about the effectiveness of using the citation sources Google Scholar, Scopus, Web of Science and OVIDSP MEDLINE to identify records for inclusion in a systematic review. We used the 40 included studies identified by traditional database searches from one systematic review of interventions for multiple risk behaviours. We searched for each of the included studies in the four citation sources to retrieve the details of all papers that have cited these studies. We carried out two analyses; the first was to examine the overlap between the four citation sources to identify which citation tool was the most useful; the second was to investigate whether the citation searches identified any relevant records in addition to those retrieved by the original database searches. Results The highest number of citations was retrieved from Google Scholar (1680), followed by Scopus (1173), then Web of Science (1095) and lastly OVIDSP (213). To retrieve all the records identified by the citation tracking searching all four resources was required. Google Scholar identified the highest number of unique citations. The citation tracking identified 9 studies that met the review’s inclusion criteria. Eight of these had already been identified by the traditional databases searches and identified in the screening process while the ninth was not available in any of the databases when the original searches were carried out. It would, however, have been identified by two of the database search strategies if searches had been carried out later. Conclusions Based on the results from this investigation, citation searching as a supplementary search method for systematic reviews may not be the best use of valuable time and resources. It would be useful to verify these findings in other reviews. PMID:24893958

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.

How to prepare a systematic review of economic evaluations for clinical practice guidelines: database selection and search strategy development (part 2/3).

PubMed

Thielen, F W; Van Mastrigt, Gapg; Burgers, L T; Bramer, W M; Majoie, Hjm; Evers, Smaa; Kleijnen, J

2016-12-01

This article is part of the series "How to prepare a systematic review of economic evaluations (EES) for informing evidence-based healthcare decisions", in which a five-step approach is proposed. Areas covered: This paper focuses on the selection of relevant databases and developing a search strategy for detecting EEs, as well as on how to perform the search and how to extract relevant data from retrieved records. Expert commentary: Thus far, little has been published on how to conduct systematic review EEs. Moreover, reliable sources of information, such as the Health Economic Evaluation Database, have ceased to publish updates. Researchers are thus left without authoritative guidance on how to conduct SR-EEs. Together with van Mastrigt et al. we seek to fill this gap.

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.

Full-Text Databases in Medicine.

ERIC Educational Resources Information Center

Sievert, MaryEllen C.; And Others

1995-01-01

Describes types of full-text databases in medicine; discusses features for searching full-text journal databases available through online vendors; reviews research on full-text databases in medicine; and describes the MEDLINE/Full-Text Research Project at the University of Missouri (Columbia) which investigated precision, recall, and relevancy.…

Systematically Identifying Relevant Research: Case Study on Child Protection Social Workers' Resilience

ERIC Educational Resources Information Center

McFadden, Paula; Taylor, Brian J.; Campbell, Anne; McQuilkin, Janice

2012-01-01

Context: The development of a consolidated knowledge base for social work requires rigorous approaches to identifying relevant research. Method: The quality of 10 databases and a web search engine were appraised by systematically searching for research articles on resilience and burnout in child protection social workers. Results: Applied Social…

Standardization of search methods for guideline development: an international survey of evidence-based guideline development groups.

PubMed

Deurenberg, Rikie; Vlayen, Joan; Guillo, Sylvie; Oliver, Thomas K; Fervers, Beatrice; Burgers, Jako

2008-03-01

Effective literature searching is particularly important for clinical practice guideline development. Sophisticated searching and filtering mechanisms are needed to help ensure that all relevant research is reviewed. To assess the methods used for the selection of evidence for guideline development by evidence-based guideline development organizations. A semistructured questionnaire assessing the databases, search filters and evaluation methods used for literature retrieval was distributed to eight major organizations involved in evidence-based guideline development. All of the organizations used search filters as part of guideline development. The medline database was the primary source accessed for literature retrieval. The OVID or SilverPlatter interfaces were used in preference to the freely accessed PubMed interface. The Cochrane Library, embase, cinahl and psycinfo databases were also frequently used by the organizations. All organizations reported the intention to improve and validate their filters for finding literature specifically relevant for guidelines. In the first international survey of its kind, eight major guideline development organizations indicated a strong interest in identifying, improving and standardizing search filters to improve guideline development. It is to be hoped that this will result in the standardization of, and open access to, search filters, an improvement in literature searching outcomes and greater collaboration among guideline development organizations.

Development and Validation of Search Filters to Identify Articles on Family Medicine in Online Medical Databases.

PubMed

Pols, David H J; Bramer, Wichor M; Bindels, Patrick J E; van de Laar, Floris A; Bohnen, Arthur M

2015-01-01

Physicians and researchers in the field of family medicine often need to find relevant articles in online medical databases for a variety of reasons. Because a search filter may help improve the efficiency and quality of such searches, we aimed to develop and validate search filters to identify research studies of relevance to family medicine. Using a new and objective method for search filter development, we developed and validated 2 search filters for family medicine. The sensitive filter had a sensitivity of 96.8% and a specificity of 74.9%. The specific filter had a specificity of 97.4% and a sensitivity of 90.3%. Our new filters should aid literature searches in the family medicine field. The sensitive filter may help researchers conducting systematic reviews, whereas the specific filter may help family physicians find answers to clinical questions at the point of care when time is limited. © 2015 Annals of Family Medicine, Inc.

PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more.

PubMed

Liu, Yifeng; Liang, Yongjie; Wishart, David

2015-07-01

PolySearch2 (http://polysearch.ca) is an online text-mining system for identifying relationships between biomedical entities such as human diseases, genes, SNPs, proteins, drugs, metabolites, toxins, metabolic pathways, organs, tissues, subcellular organelles, positive health effects, negative health effects, drug actions, Gene Ontology terms, MeSH terms, ICD-10 medical codes, biological taxonomies and chemical taxonomies. PolySearch2 supports a generalized 'Given X, find all associated Ys' query, where X and Y can be selected from the aforementioned biomedical entities. An example query might be: 'Find all diseases associated with Bisphenol A'. To find its answers, PolySearch2 searches for associations against comprehensive collections of free-text collections, including local versions of MEDLINE abstracts, PubMed Central full-text articles, Wikipedia full-text articles and US Patent application abstracts. PolySearch2 also searches 14 widely used, text-rich biological databases such as UniProt, DrugBank and Human Metabolome Database to improve its accuracy and coverage. PolySearch2 maintains an extensive thesaurus of biological terms and exploits the latest search engine technology to rapidly retrieve relevant articles and databases records. PolySearch2 also generates, ranks and annotates associative candidates and present results with relevancy statistics and highlighted key sentences to facilitate user interpretation. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more

PubMed Central

Liu, Yifeng; Liang, Yongjie; Wishart, David

2015-01-01

PolySearch2 (http://polysearch.ca) is an online text-mining system for identifying relationships between biomedical entities such as human diseases, genes, SNPs, proteins, drugs, metabolites, toxins, metabolic pathways, organs, tissues, subcellular organelles, positive health effects, negative health effects, drug actions, Gene Ontology terms, MeSH terms, ICD-10 medical codes, biological taxonomies and chemical taxonomies. PolySearch2 supports a generalized ‘Given X, find all associated Ys’ query, where X and Y can be selected from the aforementioned biomedical entities. An example query might be: ‘Find all diseases associated with Bisphenol A’. To find its answers, PolySearch2 searches for associations against comprehensive collections of free-text collections, including local versions of MEDLINE abstracts, PubMed Central full-text articles, Wikipedia full-text articles and US Patent application abstracts. PolySearch2 also searches 14 widely used, text-rich biological databases such as UniProt, DrugBank and Human Metabolome Database to improve its accuracy and coverage. PolySearch2 maintains an extensive thesaurus of biological terms and exploits the latest search engine technology to rapidly retrieve relevant articles and databases records. PolySearch2 also generates, ranks and annotates associative candidates and present results with relevancy statistics and highlighted key sentences to facilitate user interpretation. PMID:25925572

GenderMedDB: an interactive database of sex and gender-specific medical literature.

PubMed

Oertelt-Prigione, Sabine; Gohlke, Björn-Oliver; Dunkel, Mathias; Preissner, Robert; Regitz-Zagrosek, Vera

2014-01-01

Searches for sex and gender-specific publications are complicated by the absence of a specific algorithm within search engines and by the lack of adequate archives to collect the retrieved results. We previously addressed this issue by initiating the first systematic archive of medical literature containing sex and/or gender-specific analyses. This initial collection has now been greatly enlarged and re-organized as a free user-friendly database with multiple functions: GenderMedDB (http://gendermeddb.charite.de). GenderMedDB retrieves the included publications from the PubMed database. Manuscripts containing sex and/or gender-specific analysis are continuously screened and the relevant findings organized systematically into disciplines and diseases. Publications are furthermore classified by research type, subject and participant numbers. More than 11,000 abstracts are currently included in the database, after screening more than 40,000 publications. The main functions of the database include searches by publication data or content analysis based on pre-defined classifications. In addition, registrants are enabled to upload relevant publications, access descriptive publication statistics and interact in an open user forum. Overall, GenderMedDB offers the advantages of a discipline-specific search engine as well as the functions of a participative tool for the gender medicine community.

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

Demystifying the Search Button

PubMed Central

McKeever, Liam; Nguyen, Van; Peterson, Sarah J.; Gomez-Perez, Sandra

2015-01-01

A thorough review of the literature is the basis of all research and evidence-based practice. A gold-standard efficient and exhaustive search strategy is needed to ensure all relevant citations have been captured and that the search performed is reproducible. The PubMed database comprises both the MEDLINE and non-MEDLINE databases. MEDLINE-based search strategies are robust but capture only 89% of the total available citations in PubMed. The remaining 11% include the most recent and possibly relevant citations but are only searchable through less efficient techniques. An effective search strategy must employ both the MEDLINE and the non-MEDLINE portion of PubMed to ensure all studies have been identified. The robust MEDLINE search strategies are used for the MEDLINE portion of the search. Usage of the less robust strategies is then efficiently confined to search only the remaining 11% of PubMed citations that have not been indexed for MEDLINE. The current article offers step-by-step instructions for building such a search exploring methods for the discovery of medical subject heading (MeSH) terms to search MEDLINE, text-based methods for exploring the non-MEDLINE database, information on the limitations of convenience algorithms such as the “related citations feature,” the strengths and pitfalls associated with commonly used filters, the proper usage of Boolean operators to organize a master search strategy, and instructions for automating that search through “MyNCBI” to receive search query updates by email as new citations become available. PMID:26129895

Towards computational improvement of DNA database indexing and short DNA query searching.

PubMed

Stojanov, Done; Koceski, Sašo; Mileva, Aleksandra; Koceska, Nataša; Bande, Cveta Martinovska

2014-09-03

In order to facilitate and speed up the search of massive DNA databases, the database is indexed at the beginning, employing a mapping function. By searching through the indexed data structure, exact query hits can be identified. If the database is searched against an annotated DNA query, such as a known promoter consensus sequence, then the starting locations and the number of potential genes can be determined. This is particularly relevant if unannotated DNA sequences have to be functionally annotated. However, indexing a massive DNA database and searching an indexed data structure with millions of entries is a time-demanding process. In this paper, we propose a fast DNA database indexing and searching approach, identifying all query hits in the database, without having to examine all entries in the indexed data structure, limiting the maximum length of a query that can be searched against the database. By applying the proposed indexing equation, the whole human genome could be indexed in 10 hours on a personal computer, under the assumption that there is enough RAM to store the indexed data structure. Analysing the methodology proposed by Reneker, we observed that hits at starting positions [Formula: see text] are not reported, if the database is searched against a query shorter than [Formula: see text] nucleotides, such that [Formula: see text] is the length of the DNA database words being mapped and [Formula: see text] is the length of the query. A solution of this drawback is also presented.

BioCarian: search engine for exploratory searches in heterogeneous biological databases.

PubMed

Zaki, Nazar; Tennakoon, Chandana

2017-10-02

There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web. Heterogeneous databases can be converted into Resource Description Format (RDF) and queried using SPARQL language. Searching for exact queries in these databases is trivial. However, exploratory searches need customized solutions, especially when multiple databases are involved. This process is cumbersome and time consuming for those without a sufficient background in computer science. In this context, a search engine facilitating exploratory searches of databases would be of great help to the scientific community. We present BioCarian, an efficient and user-friendly search engine for performing exploratory searches on biological databases. The search engine is an interface for SPARQL queries over RDF databases. We note that many of the databases can be converted to tabular form. We first convert the tabular databases to RDF. The search engine provides a graphical interface based on facets to explore the converted databases. The facet interface is more advanced than conventional facets. It allows complex queries to be constructed, and have additional features like ranking of facet values based on several criteria, visually indicating the relevance of a facet value and presenting the most important facet values when a large number of choices are available. For the advanced users, SPARQL queries can be run directly on the databases. Using this feature, users will be able to incorporate federated searches of SPARQL endpoints. We used the search engine to do an exploratory search on previously published viral integration data and were able to deduce the main conclusions of the original publication. BioCarian is accessible via http://www.biocarian.com . We have developed a search engine to explore RDF databases that can be used by both novice and advanced users.

A comparison of the performance of seven key bibliographic databases in identifying all relevant systematic reviews of interventions for hypertension.

PubMed

Rathbone, John; Carter, Matt; Hoffmann, Tammy; Glasziou, Paul

2016-02-09

Bibliographic databases are the primary resource for identifying systematic reviews of health care interventions. Reliable retrieval of systematic reviews depends on the scope of indexing used by database providers. Therefore, searching one database may be insufficient, but it is unclear how many need to be searched. We sought to evaluate the performance of seven major bibliographic databases for the identification of systematic reviews for hypertension. We searched seven databases (Cochrane library, Database of Abstracts of Reviews of Effects (DARE), Excerpta Medica Database (EMBASE), Epistemonikos, Medical Literature Analysis and Retrieval System Online (MEDLINE), PubMed Health and Turning Research Into Practice (TRIP)) from 2003 to 2015 for systematic reviews of any intervention for hypertension. Citations retrieved were screened for relevance, coded and checked for screening consistency using a fuzzy text matching query. The performance of each database was assessed by calculating its sensitivity, precision, the number of missed reviews and the number of unique records retrieved. Four hundred systematic reviews were identified for inclusion from 11,381 citations retrieved from seven databases. No single database identified all the retrieved systematic reviews for hypertension. EMBASE identified the most reviews (sensitivity 69 %) but also retrieved the most irrelevant citations with 7.2 % precision (Pr). The sensitivity of the Cochrane library was 60 %, DARE 57 %, MEDLINE 57 %, PubMed Health 53 %, Epistemonikos 49 % and TRIP 33 %. EMBASE contained the highest number of unique records (n = 43). The Cochrane library identified seven unique records and had the highest precision (Pr = 30 %), followed by Epistemonikos (n = 2, Pr = 19 %). No unique records were found in PubMed Health (Pr = 24 %) DARE (Pr = 21 %), TRIP (Pr = 10 %) or MEDLINE (Pr = 10 %). Searching EMBASE and the Cochrane library identified 88 % of all systematic reviews in the reference set, and searching the freely available databases (Cochrane, Epistemonikos, MEDLINE) identified 83 % of all the reviews. The databases were re-analysed after systematic reviews of non-conventional interventions (e.g. yoga, acupuncture) were removed. Similarly, no database identified all the retrieved systematic reviews. EMBASE identified the most relevant systematic reviews (sensitivity 73 %) but also retrieved the most irrelevant citations with Pr = 5 %. The sensitivity of the Cochrane database was 62 %, followed by MEDLINE (60 %), DARE (55 %), PubMed Health (54 %), Epistemonikos (50 %) and TRIP (31 %). The precision of the Cochrane library was the highest (20 %), followed by PubMed Health (Pr = 16 %), DARE (Pr = 13 %), Epistemonikos (Pr = 12 %), MEDLINE (Pr = 6 %), TRIP (Pr = 6 %) and EMBASE (Pr = 5 %). EMBASE contained the most unique records (n = 34). The Cochrane library identified seven unique records. The other databases held no unique records. The coverage of bibliographic databases varies considerably due to differences in their scope and content. Researchers wishing to identify systematic reviews should not rely on one database but search multiple databases.

The Cystic Fibrosis Database: Content and Research Opportunities.

ERIC Educational Resources Information Center

Shaw, William M., Jr.; And Others

1991-01-01

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

Comparison of CINAHL, EMBASE, and MEDLINE databases for the nurse researcher.

PubMed

Burnham, J; Shearer, B

1993-01-01

The purpose of this research was to determine which of three databases, CINAHL, EMBASE or MEDLINE, should be accessed when researching nursing topics. The three databases were searched for citations on topics selected by three nurse researchers and the results were compared. For the search of nursing care literature on a medical condition, it was helpful to search both CINAHL and MEDLINE. CINAHL provided the majority of relevant articles for the second search, on computers and privacy, but inclusion of MEDLINE and EMBASE enhanced retrieval somewhat. The search on substance abuse in pregnancy, not restricted to nursing literature, retrieved better results when searching both MEDLINE and EMBASE. Due to the nature and distribution of the nursing literature, it is especially important for the searcher to understand and respond to the focus of the researcher.

A nursing qualitative systematic review required MEDLINE and CINAHL for study identification.

PubMed

Subirana, Mireia; Solá, Ivan; Garcia, Josep M; Gich, Ignasi; Urrútia, Gerard

2005-01-01

Analyze the number and the relevance of references retrieved from CINAHL, MEDLINE, and EMBASE to perform a nursing systematic review. A search strategy for the review topic was designed according to thesaurus terms. The study analyzes (1) references with abstract, (2) overlap between databases, (3) reference relevance, (4) relevance agreement between experts, and (5) reference accessibility. Bibliographic search retrieved 232 references: 16% (37) in CINAHL, 68% (157) in MEDLINE, and 16% (38) in EMBASE. Of these, 72% (164) were references retrieved with an abstract: 14% (23) in CINAHL, 70% (115) in MEDLINE, and 16% (26) in EMBASE. Overlap was observed in 2% (5) of the references. Relevance assessment reduced the number of references to 43 (19%): 12 (34.3%) in CINAHL, 31 (19.7%) in MEDLINE, and none in EMBASE (Z=-1.97; P=.048). Agreement between experts achieved a maximum Cohen's kappa of 0.76 (P < .005). References identified in CINAHL were the most difficult to obtain (chi(2)=3.9; df=1; P=.048). To perform a quality bibliographic search for a systematic review on nursing topics, CINAHL and MEDLINE are essential databases for consultation to maximize the accuracy of the search.

Methods and pitfalls in searching drug safety databases utilising the Medical Dictionary for Regulatory Activities (MedDRA).

PubMed

Brown, Elliot G

2003-01-01

The Medical Dictionary for Regulatory Activities (MedDRA) is a unified standard terminology for recording and reporting adverse drug event data. Its introduction is widely seen as a significant improvement on the previous situation, where a multitude of terminologies of widely varying scope and quality were in use. However, there are some complexities that may cause difficulties, and these will form the focus for this paper. Two methods of searching MedDRA-coded databases are described: searching based on term selection from all of MedDRA and searching based on terms in the safety database. There are several potential traps for the unwary in safety searches. There may be multiple locations of relevant terms within a system organ class (SOC) and lack of recognition of appropriate group terms; the user may think that group terms are more inclusive than is the case. MedDRA may distribute terms relevant to one medical condition across several primary SOCs. If the database supports the MedDRA model, it is possible to perform multiaxial searching: while this may help find terms that might have been missed, it is still necessary to consider the entire contents of the SOCs to find all relevant terms and there are many instances of incomplete secondary linkages. It is important to adjust for multiaxiality if data are presented using primary and secondary locations. Other sources for errors in searching are non-intuitive placement and the selection of terms as preferred terms (PTs) that may not be widely recognised. Some MedDRA rules could also result in errors in data retrieval if the individual is unaware of these: in particular, the lack of multiaxial linkages for the Investigations SOC, Social circumstances SOC and Surgical and medical procedures SOC and the requirement that a PT may only be present under one High Level Term (HLT) and one High Level Group Term (HLGT) within any single SOC. Special Search Categories (collections of PTs assembled from various SOCs by searching all of MedDRA) are limited by the small number available and by lack of clarity about criteria applied in their construction. Difficulties in database searching may be addressed by suitable user training and experience, and by central reporting of detected deficiencies in MedDRA. Other remedies may include regulatory guidance on implementation and use of MedDRA. Further systematic review of MedDRA is needed and generation of standardised searches that may be used 'off the shelf' will help, particularly where the same search is performed repeatedly on multiple data sets. Until these enhancements are widely available, MedDRA users should take great care when searching a safety database to ensure that cases are not inadvertently missed.

A scoping review of appropriateness of care research activity in Canada from a health system-level perspective.

PubMed

Brien, Susan; Gheihman, Galina; Tse, Yi Ki Yvonne; Byrnes, Mary; Harrison, Sophia; Dobrow, Mark J

2014-05-01

Jurisdictions are increasingly focusing on appropriate use of healthcare services and interventions as a means to improve health system performance. Our objectives were to conduct a scoping review to (a) map Canadian research and related activity on system-level appropriateness of care and (b) create a resource database that could be used to inform evidence-based decision-making and future research priorities in this area. We searched Medline, EMBASE and CINAHL databases between 2003-2013 using terms including "appropriate," "inappropriate," "health technology assessment" and "cost-effectiveness." Articles were included if they were Canadian-based and relevant to our definition. The database search was complemented by a website search of relevant Canadian organizations. 4,979 articles were identified through the literature search, and 103 articles relevant to system-level appropriateness of care across Canada were charted. Of these, 64 contained an evaluation of appropriateness, 30 used a method of cost-effectiveness or total cost impact analysis and 9 involved another methodology. The most common health service categories included drug therapy (n=40) and health service utilization (n=33). Fifty-eight websites were summarized containing material relevant to system-level appropriateness of care. Our review identifies Canadian research and related activity pertaining to appropriateness of healthcare from a system-level perspective and provides a useful resource both to support evidence-based decision-making and to guide future appropriateness research. Copyright © 2014 Longwoods Publishing.

Semi-Automatic Determination of Citation Relevancy: User Evaluation.

ERIC Educational Resources Information Center

Huffman, G. David

1990-01-01

Discussion of online bibliographic database searches focuses on a software system, SORT-AID/SABRE, that ranks retrieved citations in terms of relevance. Results of a comprehensive user evaluation of the relevance ranking procedure to determine its effectiveness are presented, and implications for future work are suggested. (10 references) (LRW)

Definitions of Quality in Higher Education: A Synthesis of the Literature

ERIC Educational Resources Information Center

Schindler, Laura; Puls-Elvidge, Sarah; Welzant, Heather; Crawford, Linda

2015-01-01

The aim of this paper is to provide a synthesis of the literature on defining quality in the context of higher education. During a search for relevant literature, the authors intentionally cast a wide net, beginning with a broad search in Google Scholar and followed by a narrower search in educational databases, including Academic Search Complete,…

Active browsing using similarity pyramids

NASA Astrophysics Data System (ADS)

Chen, Jau-Yuen; Bouman, Charles A.; Dalton, John C.

1998-12-01

In this paper, we describe a new approach to managing large image databases, which we call active browsing. Active browsing integrates relevance feedback into the browsing environment, so that users can modify the database's organization to suit the desired task. Our method is based on a similarity pyramid data structure, which hierarchically organizes the database, so that it can be efficiently browsed. At coarse levels, the similarity pyramid allows users to view the database as large clusters of similar images. Alternatively, users can 'zoom into' finer levels to view individual images. We discuss relevance feedback for the browsing process, and argue that it is fundamentally different from relevance feedback for more traditional search-by-query tasks. We propose two fundamental operations for active browsing: pruning and reorganization. Both of these operations depend on a user-defined relevance set, which represents the image or set of images desired by the user. We present statistical methods for accurately pruning the database, and we propose a new 'worm hole' distance metric for reorganizing the database, so that members of the relevance set are grouped together.

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

41. DISCOVERY, SEARCH, AND COMMUNICATION OF TEXTUAL KNOWLEDGE RESOURCES IN DISTRIBUTED SYSTEMS a. Discovering and Utilizing Knowledge Sources for Metasearch Knowledge Systems

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

Zamora, Antonio

Advanced Natural Language Processing Tools for Web Information Retrieval, Content Analysis, and Synthesis. The goal of this SBIR was to implement and evaluate several advanced Natural Language Processing (NLP) tools and techniques to enhance the precision and relevance of search results by analyzing and augmenting search queries and by helping to organize the search output obtained from heterogeneous databases and web pages containing textual information of interest to DOE and the scientific-technical user communities in general. The SBIR investigated 1) the incorporation of spelling checkers in search applications, 2) identification of significant phrases and concepts using a combination of linguisticmore » and statistical techniques, and 3) enhancement of the query interface and search retrieval results through the use of semantic resources, such as thesauri. A search program with a flexible query interface was developed to search reference databases with the objective of enhancing search results from web queries or queries of specialized search systems such as DOE's Information Bridge. The DOE ETDE/INIS Joint Thesaurus was processed to create a searchable database. Term frequencies and term co-occurrences were used to enhance the web information retrieval by providing algorithmically-derived objective criteria to organize relevant documents into clusters containing significant terms. A thesaurus provides an authoritative overview and classification of a field of knowledge. By organizing the results of a search using the thesaurus terminology, the output is more meaningful than when the results are just organized based on the terms that co-occur in the retrieved documents, some of which may not be significant. An attempt was made to take advantage of the hierarchy provided by broader and narrower terms, as well as other field-specific information in the thesauri. The search program uses linguistic morphological routines to find relevant entries regardless of whether terms are stored in singular or plural form. Implementation of additional inflectional morphology processes for verbs can enhance retrieval further, but this has to be balanced by the possibility of broadening the results too much. In addition to the DOE energy thesaurus, other sources of specialized organized knowledge such as the Medical Subject Headings (MeSH), the Unified Medical Language System (UMLS), and Wikipedia were investigated. The supporting role of the NLP thesaurus search program was enhanced by incorporating spelling aid and a part-of-speech tagger to cope with misspellings in the queries and to determine the grammatical roles of the query words and identify nouns for special processing. To improve precision, multiple modes of searching were implemented including Boolean operators, and field-specific searches. Programs to convert a thesaurus or reference file into searchable support files can be deployed easily, and the resulting files are immediately searchable to produce relevance-ranked results with builtin spelling aid, morphological processing, and advanced search logic. Demonstration systems were built for several databases, including the DOE energy thesaurus.« less

Network meta-analyses could be improved by searching more sources and by involving a librarian.

PubMed

Li, Lun; Tian, Jinhui; Tian, Hongliang; Moher, David; Liang, Fuxiang; Jiang, Tongxiao; Yao, Liang; Yang, Kehu

2014-09-01

Network meta-analyses (NMAs) aim to rank the benefits (or harms) of interventions, based on all available randomized controlled trials. Thus, the identification of relevant data is critical. We assessed the conduct of the literature searches in NMAs. Published NMAs were retrieved by searching electronic bibliographic databases and other sources. Two independent reviewers selected studies and five trained reviewers abstracted data regarding literature searches, in duplicate. Search method details were examined using descriptive statistics. Two hundred forty-nine NMAs were included. Eight used previous systematic reviews to identify primary studies without further searching, and five did not report any literature searches. In the 236 studies that used electronic databases to identify primary studies, the median number of databases was 3 (interquartile range: 3-5). MEDLINE, EMBASE, and Cochrane Central Register of Controlled Trials were the most commonly used databases. The most common supplemental search methods included reference lists of included studies (48%), reference lists of previous systematic reviews (40%), and clinical trial registries (32%). None of these supplemental methods was conducted in more than 50% of the NMAs. Literature searches in NMAs could be improved by searching more sources, and by involving a librarian or information specialist. Copyright © 2014 Elsevier Inc. All rights reserved.

Review and Comparison of the Search Effectiveness and User Interface of Three Major Online Chemical Databases

ERIC Educational Resources Information Center

Bharti, Neelam; Leonard, Michelle; Singh, Shailendra

2016-01-01

Online chemical databases are the largest source of chemical information and, therefore, the main resource for retrieving results from published journals, books, patents, conference abstracts, and other relevant sources. Various commercial, as well as free, chemical databases are available. SciFinder, Reaxys, and Web of Science are three major…

Search strategies to identify information on adverse effects: a systematic review

PubMed Central

Golder, Su; Loke, Yoon

2009-01-01

Objectives: The review evaluated studies of electronic database search strategies designed to retrieve adverse effects data for systematic reviews. Methods: Studies of adverse effects were located in ten databases as well as by checking references, hand-searching, searching citations, and contacting experts. Two reviewers screened the retrieved records for potentially relevant papers. Results: Five thousand three hundred thirteen citations were retrieved, yielding 19 studies designed to develop or evaluate adverse effect filters, of which 3 met the inclusion criteria. All 3 studies identified highly sensitive search strategies capable of retrieving over 95% of relevant records. However, 1 study did not evaluate precision, while the level of precision in the other 2 studies ranged from 0.8% to 2.8%. Methodological issues in these papers included the relatively small number of records, absence of a validation set of records for testing, and limited evaluation of precision. Conclusions: The results indicate the difficulty of achieving highly sensitive searches for information on adverse effects with a reasonable level of precision. Researchers who intend to locate studies on adverse effects should allow for the amount of resources and time required to conduct a highly sensitive search. PMID:19404498

Clinical effectiveness of garlic (Allium sativum).

PubMed

Pittler, Max H; Ernst, Edzard

2007-11-01

The objective of this review is to update and assess the clinical evidence based on rigorous trials of the effectiveness of garlic (A. sativum). Systematic searches were carried out in Medline, Embase, Amed, the Cochrane Database of Systematic Reviews, Natural Standard, and the Natural Medicines Comprehensive Database (search date December 2006). Our own files, the bibliographies of relevant papers and the contents pages of all issues of the review journal FACT were searched for further studies. No language restrictions were imposed. To be included, trials were required to state that they were randomized and double blind. Systematic reviews and meta-analyses of garlic were included if based on the results of randomized, double-blind trials. The literature searches identified six relevant systematic reviews and meta-analysis and double-blind randomized trials (RCT) that were published subsequently. These relate to cancer, common cold, hypercholesterolemia, hypertension, peripheral arterial disease and pre-eclampsia. The evidence based on rigorous clinical trials of garlic is not convincing. For hypercholesterolemia, the reported effects are small and may therefore not be of clinical relevance. For reducing blood pressure, few studies are available and the reported effects are too small to be clinically meaningful. For all other conditions not enough data are available for clinical recommendations.

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

Online bibliographic sources in hydrology

USGS Publications Warehouse

Wild, Emily C.; Havener, W. Michael

2001-01-01

Traditional commercial bibliographic databases and indexes provide some access to hydrology materials produced by the government; however, these sources do not provide comprehensive coverage of relevant hydrologic publications. This paper discusses bibliographic information available from the federal government and state geological surveys, water resources agencies, and depositories. In addition to information in these databases, the paper describes the scope, styles of citing, subject terminology, and the ways these information sources are currently being searched, formally and informally, by hydrologists. Information available from the federal and state agencies and from the state depositories might be missed by limiting searches to commercially distributed databases.

Should we search Chinese biomedical databases when performing systematic reviews?

PubMed

Cohen, Jérémie F; Korevaar, Daniël A; Wang, Junfeng; Spijker, René; Bossuyt, Patrick M

2015-03-06

Chinese biomedical databases contain a large number of publications available to systematic reviewers, but it is unclear whether they are used for synthesizing the available evidence. We report a case of two systematic reviews on the accuracy of anti-cyclic citrullinated peptide for diagnosing rheumatoid arthritis. In one of these, the authors did not search Chinese databases; in the other, they did. We additionally assessed the extent to which Cochrane reviewers have searched Chinese databases in a systematic overview of the Cochrane Library (inception to 2014). The two diagnostic reviews included a total of 269 unique studies, but only 4 studies were included in both reviews. The first review included five studies published in the Chinese language (out of 151) while the second included 114 (out of 118). The summary accuracy estimates from the two reviews were comparable. Only 243 of the published 8,680 Cochrane reviews (less than 3%) searched one or more of the five major Chinese databases. These Chinese databases index about 2,500 journals, of which less than 6% are also indexed in MEDLINE. All 243 Cochrane reviews evaluated an intervention, 179 (74%) had at least one author with a Chinese affiliation; 118 (49%) addressed a topic in complementary or alternative medicine. Although searching Chinese databases may lead to the identification of a large amount of additional clinical evidence, Cochrane reviewers have rarely included them in their search strategy. We encourage future initiatives to evaluate more systematically the relevance of searching Chinese databases, as well as collaborative efforts to allow better incorporation of Chinese resources in systematic reviews.

Searching the scientific literature: implications for quantitative and qualitative reviews.

PubMed

Wu, Yelena P; Aylward, Brandon S; Roberts, Michael C; Evans, Spencer C

2012-08-01

Literature reviews are an essential step in the research process and are included in all empirical and review articles. Electronic databases are commonly used to gather this literature. However, several factors can affect the extent to which relevant articles are retrieved, influencing future research and conclusions drawn. The current project examined articles obtained by comparable search strategies in two electronic archives using an exemplar search to illustrate factors that authors should consider when designing their own search strategies. Specifically, literature searches were conducted in PsycINFO and PubMed targeting review articles on two exemplar disorders (bipolar disorder and attention deficit/hyperactivity disorder) and issues of classification and/or differential diagnosis. Articles were coded for relevance and characteristics of article content. The two search engines yielded significantly different proportions of relevant articles overall and by disorder. Keywords differed across search engines for the relevant articles identified. Based on these results, it is recommended that when gathering literature for review papers, multiple search engines should be used, and search syntax and strategies be tailored to the unique capabilities of particular engines. For meta-analyses and systematic reviews, authors may consider reporting the extent to which different archives or sources yielded relevant articles for their particular review. Copyright © 2012 Elsevier Ltd. All rights reserved.

The mandible and its foramen: anatomy, anthropology, embryology and resulting clinical implications.

PubMed

Lipski, M; Tomaszewska, I M; Lipska, W; Lis, G J; Tomaszewski, K A

2013-11-01

The aim of this paper is to summarise the knowledge about the anatomy, embryology and anthropology of the mandible and the mandibular foramen and also to highlight the most important clinical implications of the current studies regarding anaesthesia performed in the region of the mandible. An electronic journal search was undertaken to identify all the relevant studies published in English. The search included MEDLINE and EMBASE databases and years from 1950 to 2012. The subject search used a combination of controlled vocabulary and free text based on the search strategy for MEDLINE using key words: 'mandible', 'mandibular', 'foramen', 'anatomy', 'embryology', 'anthropology', and 'mental'. The reference lists of all the relevant studies and existing reviews were screened for additional relevant publications. Basing on relevant manuscripts, this short review about the anatomy, embryology and anthropology of the mandible and the mandibular foramen was written.

High-speed data search

NASA Technical Reports Server (NTRS)

Driscoll, James N.

1994-01-01

The high-speed data search system developed for KSC incorporates existing and emerging information retrieval technology to help a user intelligently and rapidly locate information found in large textual databases. This technology includes: natural language input; statistical ranking of retrieved information; an artificial intelligence concept called semantics, where 'surface level' knowledge found in text is used to improve the ranking of retrieved information; and relevance feedback, where user judgements about viewed information are used to automatically modify the search for further information. Semantics and relevance feedback are features of the system which are not available commercially. The system further demonstrates focus on paragraphs of information to decide relevance; and it can be used (without modification) to intelligently search all kinds of document collections, such as collections of legal documents medical documents, news stories, patents, and so forth. The purpose of this paper is to demonstrate the usefulness of statistical ranking, our semantic improvement, and relevance feedback.

Competitive Intelligence: Finding the Clues Online.

ERIC Educational Resources Information Center

Combs, Richard; Moorhead, John

1990-01-01

Defines and discusses competitive intelligence for business decision making and suggests the use of online databases to start looking for relevant information. The best databases to use are described, designing the search strategy is explained, reviewing and editing results are discussed, and the presentation of results is considered. (LRW)

The immune response to anesthesia: part 2 sedatives, opioids, and injectable anesthetic agents.

PubMed

Anderson, Stacy L; Duke-Novakovski, Tanya; Singh, Baljit

2014-11-01

To review the immune response to injectable anesthetics and sedatives and to compare the immunomodulatory properties between inhalation and injectable anesthetic protocols. Review. Multiple literature searches were performed using PubMed and Google Scholar from March 2012 through November 2013. Relevant anesthetic and immune terms were used to search databases without year published or species constraints. The online database for Veterinary Anaesthesia and Analgesia and the Journal of Veterinary Emergency and Critical Care were searched by issue starting in 2000 for relevant articles. Sedatives, injectable anesthetics, opioids, and local anesthetics have immunomodulatory effects that may have positive or negative consequences on disease processes such as endotoxemia, generalized sepsis, tumor growth and metastasis, and ischemia-reperfusion injury. Therefore, anesthetists should consider the immunomodulatory effects of anesthetic drugs when designing anesthetic protocols for their patients. © 2014 Association of Veterinary Anaesthetists and the American College of Veterinary Anesthesia and Analgesia.

An Improved Forensic Science Information Search.

PubMed

Teitelbaum, J

2015-01-01

Although thousands of search engines and databases are available online, finding answers to specific forensic science questions can be a challenge even to experienced Internet users. Because there is no central repository for forensic science information, and because of the sheer number of disciplines under the forensic science umbrella, forensic scientists are often unable to locate material that is relevant to their needs. The author contends that using six publicly accessible search engines and databases can produce high-quality search results. The six resources are Google, PubMed, Google Scholar, Google Books, WorldCat, and the National Criminal Justice Reference Service. Carefully selected keywords and keyword combinations, designating a keyword phrase so that the search engine will search on the phrase and not individual keywords, and prompting search engines to retrieve PDF files are among the techniques discussed. Copyright © 2015 Central Police University.

A Full-Text-Based Search Engine for Finding Highly Matched Documents Across Multiple Categories

NASA Technical Reports Server (NTRS)

Nguyen, Hung D.; Steele, Gynelle C.

2016-01-01

This report demonstrates the full-text-based search engine that works on any Web-based mobile application. The engine has the capability to search databases across multiple categories based on a user's queries and identify the most relevant or similar. The search results presented here were found using an Android (Google Co.) mobile device; however, it is also compatible with other mobile phones.

A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.

PubMed

Mobilio, Dominick; Walker, Gary; Brooijmans, Natasja; Nilakantan, Ramaswamy; Denny, R Aldrin; Dejoannis, Jason; Feyfant, Eric; Kowticwar, Rupesh K; Mankala, Jyoti; Palli, Satish; Punyamantula, Sairam; Tatipally, Maneesh; John, Reji K; Humblet, Christine

2010-08-01

The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.

PubMedReco: A Real-Time Recommender System for PubMed Citations.

PubMed

Samuel, Hamman W; Zaïane, Osmar R

2017-01-01

We present a recommender system, PubMedReco, for real-time suggestions of medical articles from PubMed, a database of over 23 million medical citations. PubMedReco can recommend medical article citations while users are conversing in a synchronous communication environment such as a chat room. Normally, users would have to leave their chat interface to open a new web browser window, and formulate an appropriate search query to retrieve relevant results. PubMedReco automatically generates the search query and shows relevant citations within the same integrated user interface. PubMedReco analyzes relevant keywords associated with the conversation and uses them to search for relevant citations using the PubMed E-utilities programming interface. Our contributions include improvements to the user experience for searching PubMed from within health forums and chat rooms, and a machine learning model for identifying relevant keywords. We demonstrate the feasibility of PubMedReco using BMJ's Doc2Doc forum discussions.

Mapping Systematic Reviews on Atopic Eczema—An Essential Resource for Dermatology Professionals and Researchers

PubMed Central

Futamura, Masaki; Thomas, Kim S.; Grindlay, Douglas J. C.; Doney, Elizabeth J.; Torley, Donna; Williams, Hywel C.

2013-01-01

Background Many research studies have been published on atopic eczema and these are often summarised in systematic reviews (SRs). Identifying SRs can be time-consuming for health professionals, and researchers. In order to facilitate the identification of important research, we have compiled an on-line resource that includes all relevant eczema reviews published since 2000. Methods SRs were searched for in MEDLINE (Ovid), EMBASE (Ovid), PubMed, the Cochrane Database of Systematic Reviews, DARE and NHS Evidence. Selected SRs were assessed against the pre-defined eligibility criteria and relevant articles were grouped by treatment category for the included interventions. All identified systematic reviews are included in the Global Resource of EczemA Trials (GREAT) database (www.greatdatabase.org.uk) and key clinical messages are summarised here. Results A total of 128 SRs reviews were identified, including three clinical guidelines. Of these, 46 (36%) were found in the Cochrane Library. No single database contained all of the SRs found. The number of SRs published per year has increased substantially over the last thirteen years, and reviews were published in a variety of clinical journals. Of the 128 SRs, 1 (1%) was on mechanism, 37 (29%) were on epidemiology, 40 (31%) were on eczema prevention, 29 (23%) were on topical treatments, 31 (24%) were on systemic treatments, and 24 (19%) were on other treatments. All SRs included searches of MEDLINE in their search methods. One hundred six SRs (83%) searched more than one electronic database. There were no language restrictions reported in the search methods of 52 of the SRs (41%). Conclusions This mapping of atopic eczema reviews is a valuable resource. It will help healthcare practitioners, guideline writers, information specialists, and researchers to quickly identify relevant up-to-date evidence in the field for improving patient care. PMID:23505516

Invisible Authorship: Women's Names, Databases, and Technology.

ERIC Educational Resources Information Center

Tescione, Susan M.

Bibliographic databases act as search tools to locate relevant literature and information, but they also disseminate information about the works indexed in the records. Articles and authors that cannot be found cannot be cited, and the ability to disseminate data for that particular work is diminished. This study found no significant differences…

IMPROVED SEARCH OF PRINCIPAL COMPONENT ANALYSIS DATABASES FOR SPECTRO-POLARIMETRIC INVERSION

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

Casini, R.; Lites, B. W.; Ramos, A. Asensio

2013-08-20

We describe a simple technique for the acceleration of spectro-polarimetric inversions based on principal component analysis (PCA) of Stokes profiles. This technique involves the indexing of the database models based on the sign of the projections (PCA coefficients) of the first few relevant orders of principal components of the four Stokes parameters. In this way, each model in the database can be attributed a distinctive binary number of 2{sup 4n} bits, where n is the number of PCA orders used for the indexing. Each of these binary numbers (indices) identifies a group of ''compatible'' models for the inversion of amore » given set of observed Stokes profiles sharing the same index. The complete set of the binary numbers so constructed evidently determines a partition of the database. The search of the database for the PCA inversion of spectro-polarimetric data can profit greatly from this indexing. In practical cases it becomes possible to approach the ideal acceleration factor of 2{sup 4n} as compared to the systematic search of a non-indexed database for a traditional PCA inversion. This indexing method relies on the existence of a physical meaning in the sign of the PCA coefficients of a model. For this reason, the presence of model ambiguities and of spectro-polarimetric noise in the observations limits in practice the number n of relevant PCA orders that can be used for the indexing.« less

Specialist Bibliographic Databases

PubMed Central

2016-01-01

Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls. PMID:27134485

Specialist Bibliographic Databases.

PubMed

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

2016-05-01

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

Adaptive Functioning in Williams Syndrome: A Systematic Review

ERIC Educational Resources Information Center

Brawn, Gabrielle; Porter, Melanie

2018-01-01

Literature on the level of adaptive functioning and relative strengths and weaknesses in functioning of individuals with Williams syndrome (WS) was reviewed. The electronic databases PsycINFO, PubMed, Expanded Academic, Web of Science, Scopus and ProQuest were searched electronically for relevant articles and dissertations using the search terms…

Advanced Image Search: A Strategy for Creating Presentation Boards

ERIC Educational Resources Information Center

Frey, Diane K.; Hines, Jean D.; Swinker, Mary E.

2008-01-01

Finding relevant digital images to create presentation boards requires advanced search skills. This article describes a course assignment involving a technique designed to develop students' literacy skills with respect to locating images of desired quality and content from Internet databases. The assignment was applied in a collegiate apparel…

Another Fine MeSH: Clinical Medicine Meets Information Science.

ERIC Educational Resources Information Center

O'Rourke, Alan; Booth, Andrew; Ford, Nigel

1999-01-01

Discusses evidence-based medicine (EBM) and the need for systematic use of databases like MEDLINE with more sophisticated search strategies to optimize the retrieval of relevant papers. Describes an empirical study of hospital libraries that examined requests for information and search strategies using both structured and unstructured forms.…

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.

A knowledge base for tracking the impact of genomics on population health.

PubMed

Yu, Wei; Gwinn, Marta; Dotson, W David; Green, Ridgely Fisk; Clyne, Mindy; Wulf, Anja; Bowen, Scott; Kolor, Katherine; Khoury, Muin J

2016-12-01

We created an online knowledge base (the Public Health Genomics Knowledge Base (PHGKB)) to provide systematically curated and updated information that bridges population-based research on genomics with clinical and public health applications. Weekly horizon scanning of a wide variety of online resources is used to retrieve relevant scientific publications, guidelines, and commentaries. After curation by domain experts, links are deposited into Web-based databases. PHGKB currently consists of nine component databases. Users can search the entire knowledge base or search one or more component databases directly and choose options for customizing the display of their search results. PHGKB offers researchers, policy makers, practitioners, and the general public a way to find information they need to understand the complicated landscape of genomics and population health.Genet Med 18 12, 1312-1314.

Integrating unified medical language system and association mining techniques into relevance feedback for biomedical literature search.

PubMed

Ji, Yanqing; Ying, Hao; Tran, John; Dews, Peter; Massanari, R Michael

2016-07-19

Finding highly relevant articles from biomedical databases is challenging not only because it is often difficult to accurately express a user's underlying intention through keywords but also because a keyword-based query normally returns a long list of hits with many citations being unwanted by the user. This paper proposes a novel biomedical literature search system, called BiomedSearch, which supports complex queries and relevance feedback. The system employed association mining techniques to build a k-profile representing a user's relevance feedback. More specifically, we developed a weighted interest measure and an association mining algorithm to find the strength of association between a query and each concept in the article(s) selected by the user as feedback. The top concepts were utilized to form a k-profile used for the next-round search. BiomedSearch relies on Unified Medical Language System (UMLS) knowledge sources to map text files to standard biomedical concepts. It was designed to support queries with any levels of complexity. A prototype of BiomedSearch software was made and it was preliminarily evaluated using the Genomics data from TREC (Text Retrieval Conference) 2006 Genomics Track. Initial experiment results indicated that BiomedSearch increased the mean average precision (MAP) for a set of queries. With UMLS and association mining techniques, BiomedSearch can effectively utilize users' relevance feedback to improve the performance of biomedical literature search.

Open, Cross Platform Chemistry Application Unifying Structure Manipulation, External Tools, Databases and Visualization

DTIC Science & Technology

2012-11-27

with powerful analysis tools and an informatics approach leveraging best-of-breed NoSQL databases, in order to store, search and retrieve relevant...dictionaries, and JavaScript also has good support. The MongoDB project[15] was chosen as a scalable NoSQL data store for the cheminfor- matics components

Methods for conducting systematic reviews of risk factors in low- and middle-income countries.

PubMed

Shenderovich, Yulia; Eisner, Manuel; Mikton, Christopher; Gardner, Frances; Liu, Jianghong; Murray, Joseph

2016-03-15

Rates of youth violence are disproportionately high in many low- and middle-income countries [LMICs] but existing reviews of risk factors focus almost exclusively on high-income countries. Different search strategies, including non-English language searches, might be required to identify relevant evidence in LMICs. This paper discusses methodological issues in systematic reviews aiming to include evidence from LMICs, using the example of a recent review of risk factors for child conduct problems and youth violence in LMICs. We searched the main international databases, such as PsycINFO, Medline and EMBASE in English, as well as 12 regional databases in Arabic, Chinese, English, French, Spanish, Portuguese and Russian. In addition, we used internet search engines and Google Scholar, and contacted over 200 researchers and organizations to identify potentially eligible studies in LMICs. The majority of relevant studies were identified in the mainstream databases, but additional studies were also found through regional databases, such as CNKI, Wangfang, LILACS and SciELO. Overall, 85% of eligible studies were in English, and 15% were reported in Chinese, Spanish, Portuguese, Russian or French. Among eligible studies in languages other than English, two-thirds were identified only by regional databases and one-third was also indexed in the main international databases. There are many studies on child conduct problems and youth violence in LMICs which have not been included in prior reviews. Most research on these subjects in LMICs has been produced in the last two-three decades and mostly in middle-income countries, such as China, Brazil, Turkey, South Africa and Russia. Based on our findings, it appears that many studies of child conduct problems and youth violence in LMICs are reported in English, Chinese, Spanish and Portuguese, but few such studies are published in French, Arabic or Russian. If non-English language searches and screening had not been conducted in the current review, 15% of eligible studies would have been missed. Although there are benefits to non-English language searches and the inclusion of non-English studies in meta-analyses, systematic reviewers also need to consider the resources required to incorporate multi-lingual research.

FindIt@Flinders: User Experiences of the Primo Discovery Search Solution

ERIC Educational Resources Information Center

Jarrett, Kylie

2012-01-01

In September 2011, Flinders University Library launched FindIt@Flinders, the Primo discovery layer search to provide simultaneous results from the Library's collections and subscription databases. This research project was an exploratory case study which aimed to show whether students were finding relevant information for their course learning and…

Predicting the performance of fingerprint similarity searching.

PubMed

Vogt, Martin; Bajorath, Jürgen

2011-01-01

Fingerprints are bit string representations of molecular structure that typically encode structural fragments, topological features, or pharmacophore patterns. Various fingerprint designs are utilized in virtual screening and their search performance essentially depends on three parameters: the nature of the fingerprint, the active compounds serving as reference molecules, and the composition of the screening database. It is of considerable interest and practical relevance to predict the performance of fingerprint similarity searching. A quantitative assessment of the potential that a fingerprint search might successfully retrieve active compounds, if available in the screening database, would substantially help to select the type of fingerprint most suitable for a given search problem. The method presented herein utilizes concepts from information theory to relate the fingerprint feature distributions of reference compounds to screening libraries. If these feature distributions do not sufficiently differ, active database compounds that are similar to reference molecules cannot be retrieved because they disappear in the "background." By quantifying the difference in feature distribution using the Kullback-Leibler divergence and relating the divergence to compound recovery rates obtained for different benchmark classes, fingerprint search performance can be quantitatively predicted.

LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC.

PubMed

Allot, Alexis; Peng, Yifan; Wei, Chih-Hsuan; Lee, Kyubum; Phan, Lon; Lu, Zhiyong

2018-05-14

The identification and interpretation of genomic variants play a key role in the diagnosis of genetic diseases and related research. These tasks increasingly rely on accessing relevant manually curated information from domain databases (e.g. SwissProt or ClinVar). However, due to the sheer volume of medical literature and high cost of expert curation, curated variant information in existing databases are often incomplete and out-of-date. In addition, the same genetic variant can be mentioned in publications with various names (e.g. 'A146T' versus 'c.436G>A' versus 'rs121913527'). A search in PubMed using only one name usually cannot retrieve all relevant articles for the variant of interest. Hence, to help scientists, healthcare professionals, and database curators find the most up-to-date published variant research, we have developed LitVar for the search and retrieval of standardized variant information. In addition, LitVar uses advanced text mining techniques to compute and extract relationships between variants and other associated entities such as diseases and chemicals/drugs. LitVar is publicly available at https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/LitVar.

How to locate and appraise qualitative research in complementary and alternative medicine

PubMed Central

2013-01-01

Background The aim of this publication is to present a case study of how to locate and appraise qualitative studies for the conduct of a meta-ethnography in the field of complementary and alternative medicine (CAM). CAM is commonly associated with individualized medicine. However, one established scientific approach to the individual, qualitative research, thus far has been explicitly used very rarely. This article demonstrates a case example of how qualitative research in the field of CAM studies was identified and critically appraised. Methods Several search terms and techniques were tested for the identification and appraisal of qualitative CAM research in the conduct of a meta-ethnography. Sixty-seven electronic databases were searched for the identification of qualitative CAM trials, including CAM databases, nursing, nutrition, psychological, social, medical databases, the Cochrane Library and DIMDI. Results 9578 citations were screened, 223 articles met the pre-specified inclusion criteria, 63 full text publications were reviewed, 38 articles were appraised qualitatively and 30 articles were included. The search began with PubMed, yielding 87% of the included publications of all databases with few additional relevant findings in the specific databases. CINHAL and DIMDI also revealed a high number of precise hits. Although CAMbase and CAM-QUEST® focus on CAM research only, almost no hits of qualitative trials were found there. Searching with broad text terms was the most effective search strategy in all databases. Conclusions This publication presents a case study on how to locate and appraise qualitative studies in the field of CAM. The example shows that the literature search for qualitative studies in the field of CAM is most effective when the search is begun in PubMed followed by CINHAL or DIMDI using broad text terms. Exclusive CAM databases delivered no additional findings to locate qualitative CAM studies. PMID:23731997

How to locate and appraise qualitative research in complementary and alternative medicine.

PubMed

Franzel, Brigitte; Schwiegershausen, Martina; Heusser, Peter; Berger, Bettina

2013-06-03

The aim of this publication is to present a case study of how to locate and appraise qualitative studies for the conduct of a meta-ethnography in the field of complementary and alternative medicine (CAM). CAM is commonly associated with individualized medicine. However, one established scientific approach to the individual, qualitative research, thus far has been explicitly used very rarely. This article demonstrates a case example of how qualitative research in the field of CAM studies was identified and critically appraised. Several search terms and techniques were tested for the identification and appraisal of qualitative CAM research in the conduct of a meta-ethnography. Sixty-seven electronic databases were searched for the identification of qualitative CAM trials, including CAM databases, nursing, nutrition, psychological, social, medical databases, the Cochrane Library and DIMDI. 9578 citations were screened, 223 articles met the pre-specified inclusion criteria, 63 full text publications were reviewed, 38 articles were appraised qualitatively and 30 articles were included. The search began with PubMed, yielding 87% of the included publications of all databases with few additional relevant findings in the specific databases. CINHAL and DIMDI also revealed a high number of precise hits. Although CAMbase and CAM-QUEST® focus on CAM research only, almost no hits of qualitative trials were found there. Searching with broad text terms was the most effective search strategy in all databases. This publication presents a case study on how to locate and appraise qualitative studies in the field of CAM. The example shows that the literature search for qualitative studies in the field of CAM is most effective when the search is begun in PubMed followed by CINHAL or DIMDI using broad text terms. Exclusive CAM databases delivered no additional findings to locate qualitative CAM studies.

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.

The Auroral Planetary Imaging and Spectroscopy (APIS) service

NASA Astrophysics Data System (ADS)

Lamy, L.; Prangé, R.; Henry, F.; Le Sidaner, P.

2015-06-01

The Auroral Planetary Imaging and Spectroscopy (APIS) service, accessible online, provides an open and interactive access to processed auroral observations of the outer planets and their satellites. Such observations are of interest for a wide community at the interface between planetology, magnetospheric and heliospheric physics. APIS consists of (i) a high level database, built from planetary auroral observations acquired by the Hubble Space Telescope (HST) since 1997 with its mostly used Far-Ultraviolet spectro-imagers, (ii) a dedicated search interface aimed at browsing efficiently this database through relevant conditional search criteria and (iii) the ability to interactively work with the data online through plotting tools developed by the Virtual Observatory (VO) community, such as Aladin and Specview. This service is VO compliant and can therefore also been queried by external search tools of the VO community. The diversity of available data and the capability to sort them out by relevant physical criteria shall in particular facilitate statistical studies, on long-term scales and/or multi-instrumental multi-spectral combined analysis.

Methodological developments in searching for studies for systematic reviews: past, present and future?

PubMed

Lefebvre, Carol; Glanville, Julie; Wieland, L Susan; Coles, Bernadette; Weightman, Alison L

2013-09-25

The Cochrane Collaboration was established in 1993, following the opening of the UK Cochrane Centre in 1992, at a time when searching for studies for inclusion in systematic reviews was not well-developed. Review authors largely conducted their own searches or depended on medical librarians, who often possessed limited awareness and experience of systematic reviews. Guidance on the conduct and reporting of searches was limited. When work began to identify reports of randomized controlled trials (RCTs) for inclusion in Cochrane Reviews in 1992, there were only approximately 20,000 reports indexed as RCTs in MEDLINE and none indexed as RCTs in Embase. No search filters had been developed with the aim of identifying all RCTs in MEDLINE or other major databases. This presented The Cochrane Collaboration with a considerable challenge in identifying relevant studies.Over time, the number of studies indexed as RCTs in the major databases has grown considerably and the Cochrane Central Register of Controlled Trials (CENTRAL) has become the best single source of published controlled trials, with approximately 700,000 records, including records identified by the Collaboration from Embase and MEDLINE. Search filters for various study types, including systematic reviews and the Cochrane Highly Sensitive Search Strategies for RCTs, have been developed. There have been considerable advances in the evidence base for methodological aspects of information retrieval. The Cochrane Handbook for Systematic Reviews of Interventions now provides detailed guidance on the conduct and reporting of searches. Initiatives across The Cochrane Collaboration to improve the quality inter alia of information retrieval include: the recently introduced Methodological Expectations for Cochrane Intervention Reviews (MECIR) programme, which stipulates 'mandatory' and 'highly desirable' standards for various aspects of review conduct and reporting including searching, the development of Standard Training Materials for Cochrane Reviews and work on peer review of electronic search strategies. Almost all Cochrane Review Groups and some Cochrane Centres and Fields now have a Trials Search Co-ordinator responsible for study identification and medical librarians and other information specialists are increasingly experienced in searching for studies for systematic reviews.Prospective registration of clinical trials is increasing and searching trials registers is now mandatory for Cochrane Reviews, where relevant. Portals such as the WHO International Clinical Trials Registry Platform (ICTRP) are likely to become increasingly attractive, given concerns about the number of trials which may not be registered and/or published. The importance of access to information from regulatory and reimbursement agencies is likely to increase. Cross-database searching, gateways or portals and improved access to full-text databases will impact on how searches are conducted and reported, as will services such as Google Scholar, Scopus and Web of Science. Technologies such as textual analysis, semantic analysis, text mining and data linkage will have a major impact on the search process but efficient and effective updating of reviews may remain a challenge.In twenty years' time, we envisage that the impact of universal social networking, as well as national and international legislation, will mean that all trials involving humans will be registered at inception and detailed trial results will be routinely available to all. Challenges will remain, however, to ensure the discoverability of relevant information in diverse and often complex sources and the availability of metadata to provide the most efficient access to information. We envisage an ongoing role for information professionals as experts in identifying new resources, researching efficient ways to link or mine them for relevant data and managing their content for the efficient production of systematic reviews.

Methodological developments in searching for studies for systematic reviews: past, present and future?

PubMed Central

2013-01-01

The Cochrane Collaboration was established in 1993, following the opening of the UK Cochrane Centre in 1992, at a time when searching for studies for inclusion in systematic reviews was not well-developed. Review authors largely conducted their own searches or depended on medical librarians, who often possessed limited awareness and experience of systematic reviews. Guidance on the conduct and reporting of searches was limited. When work began to identify reports of randomized controlled trials (RCTs) for inclusion in Cochrane Reviews in 1992, there were only approximately 20,000 reports indexed as RCTs in MEDLINE and none indexed as RCTs in Embase. No search filters had been developed with the aim of identifying all RCTs in MEDLINE or other major databases. This presented The Cochrane Collaboration with a considerable challenge in identifying relevant studies. Over time, the number of studies indexed as RCTs in the major databases has grown considerably and the Cochrane Central Register of Controlled Trials (CENTRAL) has become the best single source of published controlled trials, with approximately 700,000 records, including records identified by the Collaboration from Embase and MEDLINE. Search filters for various study types, including systematic reviews and the Cochrane Highly Sensitive Search Strategies for RCTs, have been developed. There have been considerable advances in the evidence base for methodological aspects of information retrieval. The Cochrane Handbook for Systematic Reviews of Interventions now provides detailed guidance on the conduct and reporting of searches. Initiatives across The Cochrane Collaboration to improve the quality inter alia of information retrieval include: the recently introduced Methodological Expectations for Cochrane Intervention Reviews (MECIR) programme, which stipulates 'mandatory’ and 'highly desirable’ standards for various aspects of review conduct and reporting including searching, the development of Standard Training Materials for Cochrane Reviews and work on peer review of electronic search strategies. Almost all Cochrane Review Groups and some Cochrane Centres and Fields now have a Trials Search Co-ordinator responsible for study identification and medical librarians and other information specialists are increasingly experienced in searching for studies for systematic reviews. Prospective registration of clinical trials is increasing and searching trials registers is now mandatory for Cochrane Reviews, where relevant. Portals such as the WHO International Clinical Trials Registry Platform (ICTRP) are likely to become increasingly attractive, given concerns about the number of trials which may not be registered and/or published. The importance of access to information from regulatory and reimbursement agencies is likely to increase. Cross-database searching, gateways or portals and improved access to full-text databases will impact on how searches are conducted and reported, as will services such as Google Scholar, Scopus and Web of Science. Technologies such as textual analysis, semantic analysis, text mining and data linkage will have a major impact on the search process but efficient and effective updating of reviews may remain a challenge. In twenty years’ time, we envisage that the impact of universal social networking, as well as national and international legislation, will mean that all trials involving humans will be registered at inception and detailed trial results will be routinely available to all. Challenges will remain, however, to ensure the discoverability of relevant information in diverse and often complex sources and the availability of metadata to provide the most efficient access to information. We envisage an ongoing role for information professionals as experts in identifying new resources, researching efficient ways to link or mine them for relevant data and managing their content for the efficient production of systematic reviews. PMID:24066664

The contribution of nurses to incident disclosure: a narrative review.

PubMed

Harrison, Reema; Birks, Yvonne; Hall, Jill; Bosanquet, Kate; Harden, Melissa; Iedema, Rick

2014-02-01

To explore (a) how nurses feel about disclosing patient safety incidents to patients, (b) the current contribution that nurses make to the process of disclosing patient safety incidents to patients and (c) the barriers that nurses report as inhibiting their involvement in disclosure. A systematic search process was used to identify and select all relevant material. Heterogeneity in study design of the included articles prohibited a meta-analysis and findings were therefore synthesised in a narrative review. A range of text words, synonyms and subject headings were developed in conjunction with the York Centre for Reviews and Dissemination and used to undertake a systematic search of electronic databases (MEDLINE; EMBASE; CENTRAL; PsycINFO; Health Management and Information Consortium; CINAHL; ASSIA; Science Citation Index; Social Science Citation Index; Cochrane Database of Systematic Reviews; Database of Abstracts of Reviews of Effects; Health Technology Assessment Database; Health Systems Evidence; PASCAL; LILACS). Retrieval of studies was restricted to those published after 1980. Further data sources were: websites, grey literature, research in progress databases, hand-searching of relevant journals and author contact. The title and abstract of each citation was independently screened by two reviewers and disagreements resolved by consensus or consultation with a third person. Full text articles retrieved were further screened against the inclusion and exclusion criteria then checked by a second reviewer (YB). Relevant data were extracted and findings were synthesised in a narrative empirical synthesis. The systematic search and selection process identified 15 publications which included 11 unique studies that emerged from a range of locations. Findings suggest that nurses currently support both physicians and patients through incident disclosure, but may be ill-prepared to disclose incidents independently. Barriers to nurse involvement included a lack of opportunities for education and training, and the multiple and sometimes conflicting roles within nursing. Numerous potential benefits were identified that may result from nurses having a greater contribution to the disclosure process, but the provision of support and training is essential to overcome the reported barriers faced by nurses internationally. Copyright © 2013 Elsevier Ltd. All rights reserved.

Performances of 27 MEDLINE systems tested by searches with clinical questions.

PubMed Central

Haynes, R B; Walker, C J; McKibbon, K A; Johnston, M E; Willan, A R

1994-01-01

OBJECTIVE: To compare the performances of online and compact-disc (CD-ROM) versions of the National Library of Medicine's (NLM) MEDLINE database. DESIGN: Analytic survey. INTERVENTION: Clinical questions were drawn from 18 searches originally conducted spontaneously by clinicians from wards and clinics who had used Grateful Med Version 4.0. Clinicians' search strategies were translated to meet the specific requirements of 13 online and 14 CD-ROM MEDLINE systems. A senior librarian and vendors' representatives constructed independent searches from the clinicians' questions. The librarian and clinician searches were run through each system, in command mode for the librarian and menu mode for clinicians, when available. Vendor searches were run through the vendors' own systems only. MAIN MEASUREMENTS: Numbers of relevant and irrelevant citations retrieved, cost (for online systems only), and time. RESULTS: Systems varied substantially for all searches, and for librarian and clinician searches separately, with respect to the numbers of relevant and irrelevant citations retrieved (p < 0.001 for both) and the cost per relevant citation (p = 0.012), but not with respect to the time per search. Based on combined rankings for the highest number of relevant and the lowest number of irrelevant citations retrieved, the SilverPlatter CD-ROM MEDLINE clinical journal subset performed best for librarian searches, while the PaperChase online system worked best for clinician searches. For cost per relevant citation retrieved, Dialog's Knowledge Index performed best for both librarian and clinician searches. CONCLUSIONS: There were substantial differences in the performances of competing MEDLINE systems, and performance was affected by search strategy, which was conceived by a librarian or by clinicians. PMID:7719810

An approach to functionally relevant clustering of the protein universe: Active site profile‐based clustering of protein structures and sequences

PubMed Central

Knutson, Stacy T.; Westwood, Brian M.; Leuthaeuser, Janelle B.; Turner, Brandon E.; Nguyendac, Don; Shea, Gabrielle; Kumar, Kiran; Hayden, Julia D.; Harper, Angela F.; Brown, Shoshana D.; Morris, John H.; Ferrin, Thomas E.; Babbitt, Patricia C.

2017-01-01

Abstract Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification—amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two‐Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure‐Function Linkage Database, SFLD) self‐identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self‐identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well‐curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP‐identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F‐measure and performance analysis on the enolase search results and comparison to GEMMA and SCI‐PHY demonstrate that TuLIP avoids the over‐division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results. PMID:28054422

An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences.

PubMed

Knutson, Stacy T; Westwood, Brian M; Leuthaeuser, Janelle B; Turner, Brandon E; Nguyendac, Don; Shea, Gabrielle; Kumar, Kiran; Hayden, Julia D; Harper, Angela F; Brown, Shoshana D; Morris, John H; Ferrin, Thomas E; Babbitt, Patricia C; Fetrow, Jacquelyn S

2017-04-01

Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification-amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two-Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure-Function Linkage Database, SFLD) self-identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self-identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well-curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP-identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F-measure and performance analysis on the enolase search results and comparison to GEMMA and SCI-PHY demonstrate that TuLIP avoids the over-division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

NASA Technology Takes Center Stage

NASA Technical Reports Server (NTRS)

2004-01-01

In today's fast-paced business world, there is often more information available to researchers than there is time to search through it. Data mining has become the answer to finding the proverbial "needle in a haystack," as companies must be able to quickly locate specific pieces of information from large collections of data. Perilog, a suite of data-mining tools, searches for hidden patterns in large databases to determine previously unrecognized relationships. By retrieving and organizing contextually relevant data from any sequence of terms - from genetic data to musical notes - the software can intelligently compile information about desired topics from databases.

A bibliometric analysis of systematic reviews on vaccines and immunisation.

PubMed

Fernandes, Silke; Jit, Mark; Bozzani, Fiammetta; Griffiths, Ulla K; Scott, J Anthony G; Burchett, Helen E D

2018-04-19

SYSVAC is an online bibliographic database of systematic reviews and systematic review protocols on vaccines and immunisation compiled by the London School of Hygiene & Tropical Medicine and hosted by the World Health Organization (WHO) through their National Immunization Technical Advisory Groups (NITAG) resource centre (www.nitag-resource.org). Here the development of the database and a bibliometric review of its content is presented, describing trends in the publication of policy-relevant systematic reviews on vaccines and immunisation from 2008 to 2016. Searches were conducted in seven scientific databases according to a standardized search protocol, initially in 2014 with the most recent update in January 2017. Abstracts and titles were screened according to specific inclusion criteria. All included publications were coded into relevant categories based on a standardized protocol and subsequently analysed to look at trends in time, topic, area of focus, population and geographic location. After screening for inclusion criteria, 1285 systematic reviews were included in the database. While in 2008 there were only 34 systematic reviews on a vaccine-related topic, this increased to 322 in 2016. The most frequent pathogens/diseases studied were influenza, human papillomavirus and pneumococcus. There were several areas of duplication and overlap. As more systematic reviews are published it becomes increasingly time-consuming for decision-makers to identify relevant information among the ever-increasing volume available. The risk of duplication also increases, particularly given the current lack of coordination of systematic reviews on vaccine-related questions, both in terms of their commissioning and their execution. The SYSVAC database offers an accessible catalogue of vaccine-relevant systematic reviews with, where possible access or a link to the full-text. SYSVAC provides a freely searchable platform to identify existing vaccine-policy-relevant systematic reviews. Systematic reviews will need to be assessed adequately for each specific question and quality. Copyright © 2018. Published by Elsevier Ltd.

The Library's New Relevance: Fostering the First-Year Student's Acquisition, Evaluation, and Integration of Print and Electronic Materials

ERIC Educational Resources Information Center

Hlavaty, Greg; Townsend, Murphy

2010-01-01

Modern composition instructors often use and teach research methods for Internet search engines and electronic databases. It is not their intent to turn back the clock. However, if they can help students connect the world of Internet searches and the university library, they can promote information literacy in its broadest sense by developing…

The Contemporary Thesaurus of Social Science Terms and Synonyms: A Guide for Natural Language Computer Searching.

ERIC Educational Resources Information Center

Knapp, Sara D., Comp.

This book is designed primarily to help users find meaningful words for natural language, or free-text, computer searching of bibliographic and textual databases in the social and behavioral sciences. Additionally, it covers many socially relevant and technical topics not covered by the usual literary thesaurus, therefore it may also be useful for…

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…

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

IRIS is a search tool plug-in that is used to implement latent topic feedback for enhancing text navigation. It accepts a list of returned documents from an information retrieval wywtem that is generated from keyword search queries. Data is pulled directly from a topic information database and processed by IRIS to determine the most prominent and relevant topics, along with topic-ngrams, associated with the list of returned documents. User selected topics are then used to expand the query and presumabley refine the search results.

Glycan fragment database: a database of PDB-based glycan 3D structures.

PubMed

Jo, Sunhwan; Im, Wonpil

2013-01-01

The glycan fragment database (GFDB), freely available at http://www.glycanstructure.org, is a database of the glycosidic torsion angles derived from the glycan structures in the Protein Data Bank (PDB). Analogous to protein structure, the structure of an oligosaccharide chain in a glycoprotein, referred to as a glycan, can be characterized by the torsion angles of glycosidic linkages between relatively rigid carbohydrate monomeric units. Knowledge of accessible conformations of biologically relevant glycans is essential in understanding their biological roles. The GFDB provides an intuitive glycan sequence search tool that allows the user to search complex glycan structures. After a glycan search is complete, each glycosidic torsion angle distribution is displayed in terms of the exact match and the fragment match. The exact match results are from the PDB entries that contain the glycan sequence identical to the query sequence. The fragment match results are from the entries with the glycan sequence whose substructure (fragment) or entire sequence is matched to the query sequence, such that the fragment results implicitly include the influences from the nearby carbohydrate residues. In addition, clustering analysis based on the torsion angle distribution can be performed to obtain the representative structures among the searched glycan structures.

The CTBTO Link to the database of the International Seismological Centre (ISC)

NASA Astrophysics Data System (ADS)

Bondar, I.; Storchak, D. A.; Dando, B.; Harris, J.; Di Giacomo, D.

2011-12-01

The CTBTO Link to the database of the International Seismological Centre (ISC) is a project to provide access to seismological data sets maintained by the ISC using specially designed interactive tools. The Link is open to National Data Centres and to the CTBTO. By means of graphical interfaces and database queries tailored to the needs of the monitoring community, the users are given access to a multitude of products. These include the ISC and ISS bulletins, covering the seismicity of the Earth since 1904; nuclear and chemical explosions; the EHB bulletin; the IASPEI Reference Event list (ground truth database); and the IDC Reviewed Event Bulletin. The searches are divided into three main categories: The Area Based Search (a spatio-temporal search based on the ISC Bulletin), the REB search (a spatio-temporal search based on specific events in the REB) and the IMS Station Based Search (a search for historical patterns in the reports of seismic stations close to a particular IMS seismic station). The outputs are HTML based web-pages with a simplified version of the ISC Bulletin showing the most relevant parameters with access to ISC, GT, EHB and REB Bulletins in IMS1.0 format for single or multiple events. The CTBTO Link offers a tool to view REB events in context within the historical seismicity, look at observations reported by non-IMS networks, and investigate station histories and residual patterns for stations registered in the International Seismographic Station Registry.

Current knowledge and trends in age-related macular degeneration: genetics, epidemiology, and prevention.

PubMed

Velez-Montoya, Raul; Oliver, Scott C N; Olson, Jeffrey L; Fine, Stuart L; Quiroz-Mercado, Hugo; Mandava, Naresh

2014-03-01

To address the most dynamic and current issues concerning human genetics, risk factors, pharmacoeconomics, and prevention regarding age-related macular degeneration. An online review of the database Pubmed and Ovid was performed, searching for the key words: age-related macular degeneration, AMD, pharmacoeconomics, risk factors, VEGF, prevention, genetics and their compound phrases. The search was limited to articles published since 1985 to date. All returned articles were carefully screened and their references were manually reviewed for additional relevant data. The webpage www.clinicaltrials.gov was also accessed in search of relevant research trials. A total of 366 articles were reviewed, including 64 additional articles extracted from the references and 25 webpages and online databases from different institutions. At the end, only 244 references were included in this review. Age-related macular degeneration is a complex multifactorial disease that has an uneven manifestation around the world but with one common denominator, it is increasing and spreading. The economic burden that this disease poses in developed nations will increase in the coming years. Effective preventive therapies need to be developed in the near future.

Application and Effects of Linguistic Functions on Information Retrieval in a German Language Full-Text Database: Comparison between Retrieval in Abstract and Full Text.

ERIC Educational Resources Information Center

Tauchert, Wolfgang; And Others

1991-01-01

Describes the PADOK-II project in Germany, which was designed to give information on the effects of linguistic algorithms on retrieval in a full-text database, the German Patent Information System (GPI). Relevance assessments are discussed, statistical evaluations are described, and searches are compared for the full-text section versus the…

Family support for reducing morbidity and mortality in people with HIV/AIDS.

PubMed

Mohanan, Padma; Kamath, Asha

2009-07-08

Care and support play a critical role in assisting people who are HIV-positive to understand the need for prevention and to enable them to protect others. As the HIV/AIDS pandemic progresses and HIV-seropositive individuals contend with devastating illness, it seemed timely to inquire if they receive support from family members. It also was important to develop a normative idea of how much family support exists and from whom it emanates. To assess the effect of family support on morbidity, mortality, quality of life, and economics in families with at least one HIV-infected member, in developing countries. The following databases were searched:The Cochrane Central Register for Controlled Trials (CENTRAL), the Cochrane Database of Systematic Reviews, MEDLINE, AIDSLINE, CINAHL, Dissertation Abstracts International (DAI), EMBASE, BIOSIS, SCISEARCH, the Cochrane HIV/AIDS group specialized register, INDMED, Proquest, and various South Asian abstracting databases, will be included in the database list. The publication sites of the World Health Organization, the US Centers for Disease Control and Prevention, and other international research and non-governmental organizations. An extensive search strategy string was developed in consultation with the trial search coordinator of the HIV/AIDS Review Group. Numerous relevant keywords were included in the string to get an exhaustive electronic literature search. The search was not restricted by language. Articles from other languages were translated into English with the help of experts. A hand search was carried out in many journals and abstracts of the conference proceedings of national and international conferences related to AIDS (e.g. the International Conference on HIV/AIDS and STI in Africa [ICASA]). Efforts also were made to contact experts to identify unpublished research and trials still underway. Intervention studies. Randomized control trials (RCTs) and quasi-RCTs involving HIV-infected individuals with family support in developing countries. We independently screened the results of the search to select potentially relevant studies and to retrieve the full articles. We independently applied the inclusion criteria to the potentially relevant studies. No studies were identified that fulfilled the selection criteria. We were unable to find any trials of family support in reducing the morbidity and mortality in HIV-infected persons in developing countries. There is insufficient evidence to bring out the effect of family support in reducing the morbidity and mortality of HIV-infected persons in developing countries. This review has highlighted the dearth of high-quality quantitative research about family support. There is a clear need for rigorous studies of the clinical effects of family support on people with HIV in developing countries.

Development of a One-Stop Data Search and Discovery Engine using Ontologies for Semantic Mappings (HydroSeek)

NASA Astrophysics Data System (ADS)

Piasecki, M.; Beran, B.

2007-12-01

Search engines have changed the way we see the Internet. The ability to find the information by just typing in keywords was a big contribution to the overall web experience. While the conventional search engine methodology worked well for textual documents, locating scientific data remains a problem since they are stored in databases not readily accessible by search engine bots. Considering different temporal, spatial and thematic coverage of different databases, especially for interdisciplinary research it is typically necessary to work with multiple data sources. These sources can be federal agencies which generally offer national coverage or regional sources which cover a smaller area with higher detail. However for a given geographic area of interest there often exists more than one database with relevant data. Thus being able to query multiple databases simultaneously is a desirable feature that would be tremendously useful for scientists. Development of such a search engine requires dealing with various heterogeneity issues. In scientific databases, systems often impose controlled vocabularies which ensure that they are generally homogeneous within themselves but are semantically heterogeneous when moving between different databases. This defines the boundaries of possible semantic related problems making it easier to solve than with the conventional search engines that deal with free text. We have developed a search engine that enables querying multiple data sources simultaneously and returns data in a standardized output despite the aforementioned heterogeneity issues between the underlying systems. This application relies mainly on metadata catalogs or indexing databases, ontologies and webservices with virtual globe and AJAX technologies for the graphical user interface. Users can trigger a search of dozens of different parameters over hundreds of thousands of stations from multiple agencies by providing a keyword, a spatial extent, i.e. a bounding box, and a temporal bracket. As part of this development we have also added an environment that allows users to do some of the semantic tagging, i.e. the linkage of a variable name (which can be anything they desire) to defined concepts in the ontology structure which in turn provides the backbone of the search engine.

Literature search for research planning and identification of research problem

PubMed Central

Grewal, Anju; Kataria, Hanish; Dhawan, Ira

2016-01-01

Literature search is a key step in performing good authentic research. It helps in formulating a research question and planning the study. The available published data are enormous; therefore, choosing the appropriate articles relevant to your study in question is an art. It can be time-consuming, tiring and can lead to disinterest or even abandonment of search in between if not carried out in a step-wise manner. Various databases are available for performing literature search. This article primarily stresses on how to formulate a research question, the various types and sources for literature search, which will help make your search specific and time-saving. PMID:27729689

Literature search for research planning and identification of research problem.

PubMed

Grewal, Anju; Kataria, Hanish; Dhawan, Ira

2016-09-01

Literature search is a key step in performing good authentic research. It helps in formulating a research question and planning the study. The available published data are enormous; therefore, choosing the appropriate articles relevant to your study in question is an art. It can be time-consuming, tiring and can lead to disinterest or even abandonment of search in between if not carried out in a step-wise manner. Various databases are available for performing literature search. This article primarily stresses on how to formulate a research question, the various types and sources for literature search, which will help make your search specific and time-saving.

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

A survey of the neuroscience resource landscape: perspectives from the neuroscience information framework.

PubMed

Cachat, Jonathan; Bandrowski, Anita; Grethe, Jeffery S; Gupta, Amarnath; Astakhov, Vadim; Imam, Fahim; Larson, Stephen D; Martone, Maryann E

2012-01-01

The number of available neuroscience resources (databases, tools, materials, and networks) available via the Web continues to expand, particularly in light of newly implemented data sharing policies required by funding agencies and journals. However, the nature of dense, multifaceted neuroscience data and the design of classic search engine systems make efficient, reliable, and relevant discovery of such resources a significant challenge. This challenge is especially pertinent for online databases, whose dynamic content is largely opaque to contemporary search engines. The Neuroscience Information Framework was initiated to address this problem of finding and utilizing neuroscience-relevant resources. Since its first production release in 2008, NIF has been surveying the resource landscape for the neurosciences, identifying relevant resources and working to make them easily discoverable by the neuroscience community. In this chapter, we provide a survey of the resource landscape for neuroscience: what types of resources are available, how many there are, what they contain, and most importantly, ways in which these resources can be utilized by the research community to advance neuroscience research. Copyright © 2012 Elsevier Inc. All rights reserved.

Patenting of university and non-university public research organisations in Germany: evidence from patent applications for medical research results.

PubMed

Tinnemann, Peter; Ozbay, Jonas; Saint, Victoria A; Willich, Stefan N

2010-11-18

Patents are one of the most important forms of intellectual property. They grant a time-limited exclusivity on the use of an invention allowing the recuperation of research costs. The use of patents is fiercely debated for medical innovation and especially controversial for publicly funded research, where the patent holder is an institution accountable to public interest. Despite this controversy, for the situation in Germany almost no empirical information exists. The purpose of this study is to examine the amount, types and trends of patent applications for health products submitted by German public research organisations. We conducted a systematic search for patent documents using the publicly accessible database search interface of the German Patent and Trademark Office. We defined keywords and search criteria and developed search patterns for the database request. We retrieved documents with application date between 1988 and 2006 and processed the collected data stepwise to compile the most relevant documents in patent families for further analysis. We developed a rationale and present individual steps of a systematic method to request and process patent data from a publicly accessible database. We retrieved and processed 10194 patent documents. Out of these, we identified 1772 relevant patent families, applied for by 193 different universities and non-university public research organisations. 827 (47%) of these patent families contained granted patents. The number of patent applications submitted by universities and university-affiliated institutions more than tripled since the introduction of legal reforms in 2002, constituting almost half of all patent applications and accounting for most of the post-reform increase. Patenting of most non-university public research organisations remained stable. We search, process and analyse patent applications from publicly accessible databases. Internationally mounting evidence questions the viability of policies to increase commercial exploitation of publicly funded research results. To evaluate the outcome of research policies a transparent evidence base for public debate is needed in Germany.

Patenting of University and Non-University Public Research Organisations in Germany: Evidence from Patent Applications for Medical Research Results

PubMed Central

Tinnemann, Peter; Özbay, Jonas; Saint, Victoria A.; Willich, Stefan N.

2010-01-01

Background Patents are one of the most important forms of intellectual property. They grant a time-limited exclusivity on the use of an invention allowing the recuperation of research costs. The use of patents is fiercely debated for medical innovation and especially controversial for publicly funded research, where the patent holder is an institution accountable to public interest. Despite this controversy, for the situation in Germany almost no empirical information exists. The purpose of this study is to examine the amount, types and trends of patent applications for health products submitted by German public research organisations. Methods/Principal Findings We conducted a systematic search for patent documents using the publicly accessible database search interface of the German Patent and Trademark Office. We defined keywords and search criteria and developed search patterns for the database request. We retrieved documents with application date between 1988 and 2006 and processed the collected data stepwise to compile the most relevant documents in patent families for further analysis. We developed a rationale and present individual steps of a systematic method to request and process patent data from a publicly accessible database. We retrieved and processed 10194 patent documents. Out of these, we identified 1772 relevant patent families, applied for by 193 different universities and non-university public research organisations. 827 (47%) of these patent families contained granted patents. The number of patent applications submitted by universities and university-affiliated institutions more than tripled since the introduction of legal reforms in 2002, constituting almost half of all patent applications and accounting for most of the post-reform increase. Patenting of most non-university public research organisations remained stable. Conclusions We search, process and analyse patent applications from publicly accessible databases. Internationally mounting evidence questions the viability of policies to increase commercial exploitation of publicly funded research results. To evaluate the outcome of research policies a transparent evidence base for public debate is needed in Germany. PMID:21124982

Integrating query of relational and textual data in clinical databases: a case study.

PubMed

Fisk, John M; Mutalik, Pradeep; Levin, Forrest W; Erdos, Joseph; Taylor, Caroline; Nadkarni, Prakash

2003-01-01

The authors designed and implemented a clinical data mart composed of an integrated information retrieval (IR) and relational database management system (RDBMS). Using commodity software, which supports interactive, attribute-centric text and relational searches, the mart houses 2.8 million documents that span a five-year period and supports basic IR features such as Boolean searches, stemming, and proximity and fuzzy searching. Results are relevance-ranked using either "total documents per patient" or "report type weighting." Non-curated medical text has a significant degree of malformation with respect to spelling and punctuation, which creates difficulties for text indexing and searching. Presently, the IR facilities of RDBMS packages lack the features necessary to handle such malformed text adequately. A robust IR+RDBMS system can be developed, but it requires integrating RDBMSs with third-party IR software. RDBMS vendors need to make their IR offerings more accessible to non-programmers.

Tips and tricks for using the internet for professional purposes.

PubMed

Ceylan, Hasan Huseyin; Güngören, Nurdan; Küçükdurmaz, Fatih

2017-05-01

Online resources provide access to large amounts of information which is expanding every day. Using search engines for reaching the relevant, updated and complete literature that is indexed in various bibliographical databases has already become part of the medical professionals' everyday life.However, most researchers often fail to conduct a efficient literature search on the internet. The right techniques in literature search save time and improve the quality of the retrieved data.Efficient literature search is not a talent but a learnable skill, which should be a formal part of medical education.This review briefly outlines the commonly used bibliographic databases, namely Pubmed, Cochrane Library, Web of Science, Scopus, EMBASE, CINAHL and Google Scholar. Also the definition of grey literature and its features are summarised. Cite this article: EFORT Open Rev 2017;2. DOI: 10.1302/2058-5241.2.160066. Originally published online at www.efortopenreviews.org.

Tips and tricks for using the internet for professional purposes

PubMed Central

Ceylan, Hasan Huseyin; Güngören, Nurdan; Küçükdurmaz, Fatih

2017-01-01

Online resources provide access to large amounts of information which is expanding every day. Using search engines for reaching the relevant, updated and complete literature that is indexed in various bibliographical databases has already become part of the medical professionals’ everyday life. However, most researchers often fail to conduct a efficient literature search on the internet. The right techniques in literature search save time and improve the quality of the retrieved data. Efficient literature search is not a talent but a learnable skill, which should be a formal part of medical education. This review briefly outlines the commonly used bibliographic databases, namely Pubmed, Cochrane Library, Web of Science, Scopus, EMBASE, CINAHL and Google Scholar. Also the definition of grey literature and its features are summarised. Cite this article: EFORT Open Rev 2017;2. DOI: 10.1302/2058-5241.2.160066. Originally published online at www.efortopenreviews.org PMID:28630750

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

Literature searching for clinical and cost-effectiveness studies used in health technology assessment reports carried out for the National Institute for Clinical Excellence appraisal system.

PubMed

Royle, P; Waugh, N

2003-01-01

To contribute to making searching for Technology Assessment Reports (TARs) more cost-effective by suggesting an optimum literature retrieval strategy. A sample of 20 recent TARs. All sources used to search for clinical and cost-effectiveness studies were recorded. In addition, all studies that were included in the clinical and cost-effectiveness sections of the TARs were identified, and their characteristics recorded, including author, journal, year, study design, study size and quality score. Each was also classified by publication type, and then checked to see whether it was indexed in the following databases: MEDLINE, EMBASE, and then either the Cochrane Controlled Trials Register (CCTR) for clinical effectiveness studies or the NHS Economic Evaluation Database (NHS EED) for the cost-effectiveness studies. Any study not found in at least one of these databases was checked to see whether it was indexed in the Science Citation Index (SCI) and BIOSIS, and the American Society of Clinical Oncology (ASCO) Online if a cancer review. Any studies still not found were checked to see whether they were in a number of additional databases. The median number of sources searched per TAR was 20, and the range was from 13 to 33 sources. Six sources (CCTR, DARE, EMBASE, MEDLINE, NHS EED and sponsor/industry submissions to National Institute for Clinical Excellence) were used in all reviews. After searching the MEDLINE, EMBASE and NHS EED databases, 87.3% of the clinical effectiveness studies and 94.8% of the cost-effectiveness studies were found, rising to 98.2% when SCI, BIOSIS and ASCO Online and 97.9% when SCI and ASCO Online, respectively, were added. The median number of sources searched for the 14 TARs that included an economic model was 9.0 per TAR. A sensitive search filter for identifying non-randomised controlled trials (RCT), constructed for MEDLINE and using the search terms from the bibliographic records in the included studies, retrieved only 85% of the known sample. Therefore, it is recommended that when searching for non-RCT studies a search is done for the intervention alone, and records are then scanned manually for those that look relevant. Searching additional databases beyond the Cochrane Library (which includes CCTR, NHS EED and the HTA database), MEDLINE, EMBASE and SCI, plus BIOSIS limited to meeting abstracts only, was seldom found to be effective in retrieving additional studies for inclusion in the clinical and cost-effectiveness sections of TARs (apart from reviews of cancer therapies, where a search of the ASCO database is recommended). A more selective approach to database searching would suffice in most cases and would save resources, thereby making the TAR process more efficient. However, searching non-database sources (including submissions from manufacturers, recent meeting abstracts, contact with experts and checking reference lists) does appear to be a productive way of identifying further studies.

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

EPA Science Inventory

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 li...

A Bayesian network approach to the database search problem in criminal proceedings

PubMed Central

2012-01-01

Background The ‘database search problem’, that is, the strengthening of a case - in terms of probative value - against an individual who is found as a result of a database search, has been approached during the last two decades with substantial mathematical analyses, accompanied by lively debate and centrally opposing conclusions. This represents a challenging obstacle in teaching but also hinders a balanced and coherent discussion of the topic within the wider scientific and legal community. This paper revisits and tracks the associated mathematical analyses in terms of Bayesian networks. Their derivation and discussion for capturing probabilistic arguments that explain the database search problem are outlined in detail. The resulting Bayesian networks offer a distinct view on the main debated issues, along with further clarity. Methods As a general framework for representing and analyzing formal arguments in probabilistic reasoning about uncertain target propositions (that is, whether or not a given individual is the source of a crime stain), this paper relies on graphical probability models, in particular, Bayesian networks. This graphical probability modeling approach is used to capture, within a single model, a series of key variables, such as the number of individuals in a database, the size of the population of potential crime stain sources, and the rarity of the corresponding analytical characteristics in a relevant population. Results This paper demonstrates the feasibility of deriving Bayesian network structures for analyzing, representing, and tracking the database search problem. The output of the proposed models can be shown to agree with existing but exclusively formulaic approaches. Conclusions The proposed Bayesian networks allow one to capture and analyze the currently most well-supported but reputedly counter-intuitive and difficult solution to the database search problem in a way that goes beyond the traditional, purely formulaic expressions. The method’s graphical environment, along with its computational and probabilistic architectures, represents a rich package that offers analysts and discussants with additional modes of interaction, concise representation, and coherent communication. PMID:22849390

Oral oncoprevention by phytochemicals - a systematic review disclosing the therapeutic dilemma.

PubMed

Bhavana, Sujana Mulk; Lakshmi, Chintamaneni Raja

2014-10-01

The aim of this article is to emphasize and focus on the preclinical and clinical update on phytochemicals and their role in prevention of oral carcinogenesis. Accordingly, the literature search was made following database: Embase, Medline, Science Citation index, NIH public access, pubmed and Cochrane Database of systematic reviews. Several internet websites were also searched to access publications from major phytochemical research sites and relevant information was obtained with regards to each plant chemical. The authors also spotted different list servers through wignet.com, Stanford cancer research etc: The data base search was made from the inception to 1988 and updated till 2013. A systematic method was obtained for literature search and data collection was critiqued. 60 articles were searched, among which there were only 6 systematic reviews on phytochemicals regarding oral carcinogenesis. Additional articles were obtained on phytochemicals and their mechanism of action in other cancers, which were regarded as background material. The studies done by various authors on each phytochemical has been briefly emphasized.

NASA's Global Change Master Directory: Discover and Access Earth Science Data Sets, Related Data Services, and Climate Diagnostics

NASA Astrophysics Data System (ADS)

Aleman, A.; Olsen, L. M.; Ritz, S.; Stevens, T.; Morahan, M.; Grebas, S. K.

2011-12-01

NASA's Global Change Master Directory provides the scientific community with the ability to discover, access, and use Earth science data, data-related services, and climate diagnostics worldwide.The GCMD offers descriptions of Earth science data sets using the Directory Interchange Format (DIF) metadata standard; Earth science related data services are described using the Service Entry Resource Format (SERF); and climate visualizations are described using the Climate Diagnostic (CD) standard. The DIF, SERF and CD standards each capture data attributes used to determine whether a data set, service, or climate visualization is relevant to a user's needs.Metadata fields include: title, summary, science keywords, service keywords, data center, data set citation, personnel, instrument, platform, quality, related URL, temporal and spatial coverage, data resolution and distribution information.In addition, nine valuable sets of controlled vocabularies have been developed to assist users in normalizing the search for data descriptions. An update to the GCMD's search functionality is planned to further capitalize on the controlled vocabularies during database queries.By implementing a dynamic keyword "tree", users will have the ability to search for data sets by combining keywords in new ways.This will allow users to conduct more relevant and efficient database searches to support the free exchange and re-use of Earth science data.

Supplementary search methods were more effective and offered better value than bibliographic database searching: A case study from public health and environmental enhancement.

PubMed

Cooper, Chris; Lovell, Rebecca; Husk, Kerryn; Booth, Andrew; Garside, Ruth

2018-06-01

We undertook a systematic review to evaluate the health benefits of environmental enhancement and conservation activities. We were concerned that a conventional process of study identification, focusing on exhaustive searches of bibliographic databases as the primary search method, would be ineffective, offering limited value. The focus of this study is comparing study identification methods. We compare (1) an approach led by searches of bibliographic databases with (2) an approach led by supplementary search methods. We retrospectively assessed the effectiveness and value of both approaches. Effectiveness was determined by comparing (1) the total number of studies identified and screened and (2) the number of includable studies uniquely identified by each approach. Value was determined by comparing included study quality and by using qualitative sensitivity analysis to explore the contribution of studies to the synthesis. The bibliographic databases approach identified 21 409 studies to screen and 2 included qualitative studies were uniquely identified. Study quality was moderate, and contribution to the synthesis was minimal. The supplementary search approach identified 453 studies to screen and 9 included studies were uniquely identified. Four quantitative studies were poor quality but made a substantive contribution to the synthesis; 5 studies were qualitative: 3 studies were good quality, one was moderate quality, and 1 study was excluded from the synthesis due to poor quality. All 4 included qualitative studies made significant contributions to the synthesis. This case study found value in aligning primary methods of study identification to maximise location of relevant evidence. Copyright © 2017 John Wiley & Sons, Ltd.

GEMINI: a computationally-efficient search engine for large gene expression datasets.

PubMed

DeFreitas, Timothy; Saddiki, Hachem; Flaherty, Patrick

2016-02-24

Low-cost DNA sequencing allows organizations to accumulate massive amounts of genomic data and use that data to answer a diverse range of research questions. Presently, users must search for relevant genomic data using a keyword, accession number of meta-data tag. However, in this search paradigm the form of the query - a text-based string - is mismatched with the form of the target - a genomic profile. To improve access to massive genomic data resources, we have developed a fast search engine, GEMINI, that uses a genomic profile as a query to search for similar genomic profiles. GEMINI implements a nearest-neighbor search algorithm using a vantage-point tree to store a database of n profiles and in certain circumstances achieves an [Formula: see text] expected query time in the limit. We tested GEMINI on breast and ovarian cancer gene expression data from The Cancer Genome Atlas project and show that it achieves a query time that scales as the logarithm of the number of records in practice on genomic data. In a database with 10(5) samples, GEMINI identifies the nearest neighbor in 0.05 sec compared to a brute force search time of 0.6 sec. GEMINI is a fast search engine that uses a query genomic profile to search for similar profiles in a very large genomic database. It enables users to identify similar profiles independent of sample label, data origin or other meta-data information.

The database search problem: a question of rational decision making.

PubMed

Gittelson, S; Biedermann, A; Bozza, S; Taroni, F

2012-10-10

This paper applies probability and decision theory in the graphical interface of an influence diagram to study the formal requirements of rationality which justify the individualization of a person found through a database search. The decision-theoretic part of the analysis studies the parameters that a rational decision maker would use to individualize the selected person. The modeling part (in the form of an influence diagram) clarifies the relationships between this decision and the ingredients that make up the database search problem, i.e., the results of the database search and the different pairs of propositions describing whether an individual is at the source of the crime stain. These analyses evaluate the desirability associated with the decision of 'individualizing' (and 'not individualizing'). They point out that this decision is a function of (i) the probability that the individual in question is, in fact, at the source of the crime stain (i.e., the state of nature), and (ii) the decision maker's preferences among the possible consequences of the decision (i.e., the decision maker's loss function). We discuss the relevance and argumentative implications of these insights with respect to recent comments in specialized literature, which suggest points of view that are opposed to the results of our study. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Toward Computational Cumulative Biology by Combining Models of Biological Datasets

PubMed Central

Faisal, Ali; Peltonen, Jaakko; Georgii, Elisabeth; Rung, Johan; Kaski, Samuel

2014-01-01

A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher's experimental dataset to earlier work in the field. The search is (i) data-driven to enable new findings, going beyond the state of the art of keyword searches in annotations, (ii) modeling-driven, to include both biological knowledge and insights learned from data, and (iii) scalable, as it is accomplished without building one unified grand model of all data. Assuming each dataset has been modeled beforehand, by the researchers or automatically by database managers, we apply a rapidly computable and optimizable combination model to decompose a new dataset into contributions from earlier relevant models. By using the data-driven decomposition, we identify a network of interrelated datasets from a large annotated human gene expression atlas. While tissue type and disease were major driving forces for determining relevant datasets, the found relationships were richer, and the model-based search was more accurate than the keyword search; moreover, it recovered biologically meaningful relationships that are not straightforwardly visible from annotations—for instance, between cells in different developmental stages such as thymocytes and T-cells. Data-driven links and citations matched to a large extent; the data-driven links even uncovered corrections to the publication data, as two of the most linked datasets were not highly cited and turned out to have wrong publication entries in the database. PMID:25427176

Toward computational cumulative biology by combining models of biological datasets.

PubMed

Faisal, Ali; Peltonen, Jaakko; Georgii, Elisabeth; Rung, Johan; Kaski, Samuel

2014-01-01

A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher's experimental dataset to earlier work in the field. The search is (i) data-driven to enable new findings, going beyond the state of the art of keyword searches in annotations, (ii) modeling-driven, to include both biological knowledge and insights learned from data, and (iii) scalable, as it is accomplished without building one unified grand model of all data. Assuming each dataset has been modeled beforehand, by the researchers or automatically by database managers, we apply a rapidly computable and optimizable combination model to decompose a new dataset into contributions from earlier relevant models. By using the data-driven decomposition, we identify a network of interrelated datasets from a large annotated human gene expression atlas. While tissue type and disease were major driving forces for determining relevant datasets, the found relationships were richer, and the model-based search was more accurate than the keyword search; moreover, it recovered biologically meaningful relationships that are not straightforwardly visible from annotations-for instance, between cells in different developmental stages such as thymocytes and T-cells. Data-driven links and citations matched to a large extent; the data-driven links even uncovered corrections to the publication data, as two of the most linked datasets were not highly cited and turned out to have wrong publication entries in the database.

Methodologies and Methods for User Behavioral Research.

ERIC Educational Resources Information Center

Wang, Peiling

1999-01-01

Discusses methodological issues in empirical studies of information-related behavior in six specific research areas: information needs and uses; information seeking; relevance judgment; online searching (including online public access catalog, online database, and the Web); human-system interactions; and reference transactions. (Contains 191…

Team X Spacecraft Instrument Database Consolidation

NASA Technical Reports Server (NTRS)

Wallenstein, Kelly A.

2005-01-01

In the past decade, many changes have been made to Team X's process of designing each spacecraft, with the purpose of making the overall procedure more efficient over time. One such improvement is the use of information databases from previous missions, designs, and research. By referring to these databases, members of the design team can locate relevant instrument data and significantly reduce the total time they spend on each design. The files in these databases were stored in several different formats with various levels of accuracy. During the past 2 months, efforts have been made in an attempt to combine and organize these files. The main focus was in the Instruments department, where spacecraft subsystems are designed based on mission measurement requirements. A common database was developed for all instrument parameters using Microsoft Excel to minimize the time and confusion experienced when searching through files stored in several different formats and locations. By making this collection of information more organized, the files within them have become more easily searchable. Additionally, the new Excel database offers the option of importing its contents into a more efficient database management system in the future. This potential for expansion enables the database to grow and acquire more search features as needed.

Validation of SmartRank: A likelihood ratio software for searching national DNA databases with complex DNA profiles.

PubMed

Benschop, Corina C G; van de Merwe, Linda; de Jong, Jeroen; Vanvooren, Vanessa; Kempenaers, Morgane; Kees van der Beek, C P; Barni, Filippo; Reyes, Eusebio López; Moulin, Léa; Pene, Laurent; Haned, Hinda; Sijen, Titia

2017-07-01

Searching a national DNA database with complex and incomplete profiles usually yields very large numbers of possible matches that can present many candidate suspects to be further investigated by the forensic scientist and/or police. Current practice in most forensic laboratories consists of ordering these 'hits' based on the number of matching alleles with the searched profile. Thus, candidate profiles that share the same number of matching alleles are not differentiated and due to the lack of other ranking criteria for the candidate list it may be difficult to discern a true match from the false positives or notice that all candidates are in fact false positives. SmartRank was developed to put forward only relevant candidates and rank them accordingly. The SmartRank software computes a likelihood ratio (LR) for the searched profile and each profile in the DNA database and ranks database entries above a defined LR threshold according to the calculated LR. In this study, we examined for mixed DNA profiles of variable complexity whether the true donors are retrieved, what the number of false positives above an LR threshold is and the ranking position of the true donors. Using 343 mixed DNA profiles over 750 SmartRank searches were performed. In addition, the performance of SmartRank and CODIS were compared regarding DNA database searches and SmartRank was found complementary to CODIS. We also describe the applicable domain of SmartRank and provide guidelines. The SmartRank software is open-source and freely available. Using the best practice guidelines, SmartRank enables obtaining investigative leads in criminal cases lacking a suspect. Copyright © 2017 Elsevier B.V. All rights reserved.

Information extraction for enhanced access to disease outbreak reports.

PubMed

Grishman, Ralph; Huttunen, Silja; Yangarber, Roman

2002-08-01

Document search is generally based on individual terms in the document. However, for collections within limited domains it is possible to provide more powerful access tools. This paper describes a system designed for collections of reports of infectious disease outbreaks. The system, Proteus-BIO, automatically creates a table of outbreaks, with each table entry linked to the document describing that outbreak; this makes it possible to use database operations such as selection and sorting to find relevant documents. Proteus-BIO consists of a Web crawler which gathers relevant documents; an information extraction engine which converts the individual outbreak events to a tabular database; and a database browser which provides access to the events and, through them, to the documents. The information extraction engine uses sets of patterns and word classes to extract the information about each event. Preparing these patterns and word classes has been a time-consuming manual operation in the past, but automated discovery tools now make this task significantly easier. A small study comparing the effectiveness of the tabular index with conventional Web search tools demonstrated that users can find substantially more documents in a given time period with Proteus-BIO.

The APIS service : a tool for accessing value-added HST planetary auroral observations over 1997-2015

NASA Astrophysics Data System (ADS)

Lamy, L.; Henry, F.; Prangé, R.; Le Sidaner, P.

2015-10-01

The Auroral Planetary Imaging and Spectroscopy (APIS) service http://obspm.fr/apis/ provides an open and interactive access to processed auroral observations of the outer planets and their satellites. Such observations are of interest for a wide community at the interface between planetology, magnetospheric and heliospheric physics. APIS consists of (i) a high level database, built from planetary auroral observations acquired by the Hubble Space Telescope (HST) since 1997 with its mostly used Far-Ultraviolet spectro- imagers, (ii) a dedicated search interface aimed at browsing efficiently this database through relevant conditional search criteria (Figure 1) and (iii) the ability to interactively work with the data online through plotting tools developed by the Virtual Observatory (VO) community, such as Aladin and Specview. This service is VO compliant and can therefore also been queried by external search tools of the VO community. The diversity of available data and the capability to sort them out by relevant physical criteria shall in particular facilitate statistical studies, on long-term scales and/or multi-instrumental multispectral combined analysis [1,2]. We will present the updated capabilities of APIS with several examples. Several tutorials are available online.

Kefir and Cancer: A Systematic Review of Literatures.

PubMed

Rafie, Nahid; Golpour Hamedani, Sahar; Ghiasvand, Reza; Miraghajani, Maryam

2015-12-01

Some studies have suggested chemopreventive effects of kefir, a fermented milk product, on carcinogenesis. The aim of this review study was to evaluate the scientific evidence for effects of kefir on cancer prevention and treatment. We systematically searched for all relevant studies published before June 2015, using PubMed, Google scholar, Cochrane and Science Direct, SID, MedLib and Srlst databases. Relevant studies were reviewed based on systematic review (PRISMA) guidelines. From a total of 2208 papers obtained at the initial database search, 11 publications including 7 in vitro and 4 experimental studies were eligible. In vitro studies on breast, colon, skin and gastric cancers and leukemia cell lines and experimental studies on different sarcomas consistently showed beneficial effects of kefir on cancer prevention and treatment. The results of this systematic review suggest that kefir may be associated with cancer prevention and it also has beneficial effects in cancer treatment. This protection may be associated with kefir bioactive components including peptides, polysaccharides and sphingolipids.

Are opioid antagonists effective in reducing self-injury in adults with intellectual disability? A systematic review.

PubMed

Roy, A; Roy, M; Deb, S; Unwin, G; Roy, A

2015-01-01

Self-injury in people with intellectual disability (ID) may be due to variety of factors both environmental and biological. As the drive in UK is to manage people with ID and problem behaviours in the community, it is important to critically examine all treatment options available. As abnormalities in the endogenous opioid system may be a factor in some people with ID, we undertook a systematic review to evaluate the evidence for the effectiveness of opioid antagonists. Four electronic databases were searched for relevant journal articles. In addition, cross-referencing of pertinent reviews and a hand search for articles in major international ID journals between the years 2010 and 2012 was carried out to ensure that all relevant articles were identified. We also searched databases for unpublished clinical trials to overcome publication bias. Each database was searched up to present (February 2013) with no restrictions on the date of publication. The search terms consisted of broad expressions used to describe ID and autistic spectrum disorder as well as terms relating to opioid antagonists and specific drugs. All studies identified by the electronic database search and hand search were examined on the basis of title alone for relevance and duplication. The abstracts of the remaining papers were then scrutinised against the inclusion criteria. Where abstracts failed to provide adequate information, the full texts for these papers were obtained. All the full texts were then evaluated against the inclusion proforma. Two reviewers carried out all the stages of the process independently. The reviewers met to discuss their selections and where disagreements arose, these were settled by discussion with a member of the study group. Data from each study meeting the inclusion criteria was extracted on a pre-piloted data extraction form. The quality of each study was further assessed using the Jadad scale, a tool developed to assess the quality of randomised controlled trials. Out of 10 randomised control trials eight reported a reduction in the frequency of self-injurious behaviour. This meant that 62 participants out of 124 (50%) showed an improvement of which 61 were statistically significant. Forty-nine participants had autism. Eleven (9%) had minor side-effects. The improvement was more marked in people with severe and profound ID and was not affected by the coexistence of autism. This review suggests that some people respond to opioid antagonists with a reduction in self-injury but the trials do not predict who they may be. Future research may identify this sub-group when opioid antagonists may prove to be a useful addition in the pharmacotherapy of self-injury. © 2014 MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.

[Macroeconomic costs of eye diseases].

PubMed

Hirneiß, C; Kampik, A; Neubauer, A S

2014-05-01

Eye diseases that are relevant regarding their macroeconomic costs and their impact on society include cataract, diabetic retinopathy, age-related maculopathy, glaucoma and refractive errors. The aim of this article is to provide a comprehensive overview of direct and indirect costs for major eye disease categories for Germany, based on existing literature and data sources. A semi-structured literature search was performed in the databases Medline and Embase and in the search machine Google for relevant original papers and reviews on costs of eye diseases with relevance for or transferability to Germany (last research date October 2013). In addition, manual searching was performed in important national databases and information sources, such as the Federal Office of Statistics and scientific societies. The direct costs for these diseases add up to approximately 2.6 billion Euros yearly for the Federal Republic of Germany, including out of the pocket payments from patients but excluding optical aids (e.g. glasses). In addition to those direct costs there are also indirect costs which are caused e.g. by loss of employment or productivity or by a reduction in health-related quality of life. These indirect costs can only be roughly estimated. Including the indirect costs for the eye diseases investigated, a total yearly macroeconomic cost ranging between 4 and 12 billion Euros is estimated for Germany. The costs for the eye diseases cataract, diabetic retinopathy, age-related maculopathy, glaucoma and refractive errors have a macroeconomic relevant dimension. Based on the predicted demographic changes with an ageing society an increase of the prevalence and thus also an increase of costs for eye diseases is expected in the future.

The gene expression database for mouse development (GXD): putting developmental expression information at your fingertips.

PubMed

Smith, Constance M; Finger, Jacqueline H; Kadin, James A; Richardson, Joel E; Ringwald, Martin

2014-10-01

Because molecular mechanisms of development are extraordinarily complex, the understanding of these processes requires the integration of pertinent research data. Using the Gene Expression Database for Mouse Development (GXD) as an example, we illustrate the progress made toward this goal, and discuss relevant issues that apply to developmental databases and developmental research in general. Since its first release in 1998, GXD has served the scientific community by integrating multiple types of expression data from publications and electronic submissions and by making these data freely and widely available. Focusing on endogenous gene expression in wild-type and mutant mice and covering data from RNA in situ hybridization, in situ reporter (knock-in), immunohistochemistry, reverse transcriptase-polymerase chain reaction, Northern blot, and Western blot experiments, the database has grown tremendously over the years in terms of data content and search utilities. Currently, GXD includes over 1.4 million annotated expression results and over 260,000 images. All these data and images are readily accessible to many types of database searches. Here we describe the data and search tools of GXD; explain how to use the database most effectively; discuss how we acquire, curate, and integrate developmental expression information; and describe how the research community can help in this process. Copyright © 2014 The Authors Developmental Dynamics published by Wiley Periodicals, Inc. on behalf of American Association of Anatomists.

Measurement tools for the diagnosis of nasal septal deviation: a systematic review

PubMed Central

2014-01-01

Objective To perform a systematic review of measurement tools utilized for the diagnosis of nasal septal deviation (NSD). Methods Electronic database searches were performed using MEDLINE (from 1966 to second week of August 2013), EMBASE (from 1966 to second week of August 2013), Web of Science (from 1945 to second week of August 2013) and all Evidence Based Medicine Reviews Files (EBMR); Cochrane Database of Systematic Review (CDSR), Cochrane Central Register of Controlled Trials (CCTR), Cochrane Methodology Register (CMR), Database of Abstracts of Reviews of Effects (DARE), American College of Physicians Journal Club (ACP Journal Club), Health Technology Assessments (HTA), NHS Economic Evaluation Database (NHSEED) till the second quarter of 2013. The search terms used in database searches were ‘nasal septum’, ‘deviation’, ‘diagnosis’, ‘nose deformities’ and ‘nose malformation’. The studies were reviewed using the updated Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. Results Online searches resulted in 23 abstracts after removal of duplicates that resulted from overlap of studies between the electronic databases. An additional 15 abstracts were excluded due to lack of relevance. A total of 8 studies were systematically reviewed. Conclusions Diagnostic modalities such as acoustic rhinometry, rhinomanometry and nasal spectral sound analysis may be useful in identifying NSD in anterior region of the nasal cavity, but these tests in isolation are of limited utility. Compared to anterior rhinoscopy, nasal endoscopy, and imaging the above mentioned index tests lack sensitivity and specificity in identifying the presence, location, and severity of NSD. PMID:24762010

Evidence-based practice: extending the search to find material for the systematic review

PubMed Central

Helmer, Diane; Savoie, Isabelle; Green, Carolyn; Kazanjian, Arminée

2001-01-01

Background: Cochrane-style systematic reviews increasingly require the participation of librarians. Guidelines on the appropriate search strategy to use for systematic reviews have been proposed. However, research evidence supporting these recommendations is limited. Objective: This study investigates the effectiveness of various systematic search methods used to uncover randomized controlled trials (RCTs) for systematic reviews. Effectiveness is defined as the proportion of relevant material uncovered for the systematic review using extended systematic review search methods. The following extended systematic search methods are evaluated: searching subject-specific or specialized databases (including trial registries), hand searching, scanning reference lists, and communicating personally. Methods: Two systematic review projects were prospectively monitored regarding the method used to identify items as well as the type of items retrieved. The proportion of RCTs identified by each systematic search method was calculated. Results: The extended systematic search methods uncovered 29.2% of all items retrieved for the systematic reviews. The search of specialized databases was the most effective method, followed by scanning of reference lists, communicating personally, and hand searching. Although the number of items identified through hand searching was small, these unique items would otherwise have been missed. Conclusions: Extended systematic search methods are effective tools for uncovering material for the systematic review. The quality of the items uncovered has yet to be assessed and will be key in evaluating the value of the systematic search methods. PMID:11837256

Dynamic taxonomies applied to a web-based relational database for geo-hydrological risk mitigation

NASA Astrophysics Data System (ADS)

Sacco, G. M.; Nigrelli, G.; Bosio, A.; Chiarle, M.; Luino, F.

2012-02-01

In its 40 years of activity, the Research Institute for Geo-hydrological Protection of the Italian National Research Council has amassed a vast and varied collection of historical documentation on landslides, muddy-debris flows, and floods in northern Italy from 1600 to the present. Since 2008, the archive resources have been maintained through a relational database management system. The database is used for routine study and research purposes as well as for providing support during geo-hydrological emergencies, when data need to be quickly and accurately retrieved. Retrieval speed and accuracy are the main objectives of an implementation based on a dynamic taxonomies model. Dynamic taxonomies are a general knowledge management model for configuring complex, heterogeneous information bases that support exploratory searching. At each stage of the process, the user can explore or browse the database in a guided yet unconstrained way by selecting the alternatives suggested for further refining the search. Dynamic taxonomies have been successfully applied to such diverse and apparently unrelated domains as e-commerce and medical diagnosis. Here, we describe the application of dynamic taxonomies to our database and compare it to traditional relational database query methods. The dynamic taxonomy interface, essentially a point-and-click interface, is considerably faster and less error-prone than traditional form-based query interfaces that require the user to remember and type in the "right" search keywords. Finally, dynamic taxonomy users have confirmed that one of the principal benefits of this approach is the confidence of having considered all the relevant information. Dynamic taxonomies and relational databases work in synergy to provide fast and precise searching: one of the most important factors in timely response to emergencies.

CENTRAL, PEDro, PubMed, and EMBASE are the most comprehensive databases indexing randomized controlled trials of physical therapy interventions.

PubMed

Michaleff, Zoe A; Costa, Leonardo O P; Moseley, Anne M; Maher, Christopher G; Elkins, Mark R; Herbert, Robert D; Sherrington, Catherine

2011-02-01

Many bibliographic databases index research studies evaluating the effects of health care interventions. One study has concluded that the Physiotherapy Evidence Database (PEDro) has the most complete indexing of reports of randomized controlled trials of physical therapy interventions, but the design of that study may have exaggerated estimates of the completeness of indexing by PEDro. The purpose of this study was to compare the completeness of indexing of reports of randomized controlled trials of physical therapy interventions by 8 bibliographic databases. This study was an audit of bibliographic databases. Prespecified criteria were used to identify 400 reports of randomized controlled trials from the reference lists of systematic reviews published in 2008 that evaluated physical therapy interventions. Eight databases (AMED, CENTRAL, CINAHL, EMBASE, Hooked on Evidence, PEDro, PsycINFO, and PubMed) were searched for each trial report. The proportion of the 400 trial reports indexed by each database was calculated. The proportions of the 400 trial reports indexed by the databases were as follows: CENTRAL, 95%; PEDro, 92%; PubMed, 89%; EMBASE, 88%; CINAHL, 53%; AMED, 50%; Hooked on Evidence, 45%; and PsycINFO, 6%. Almost all of the trial reports (99%) were found in at least 1 database, and 88% were indexed by 4 or more databases. Four trial reports were uniquely indexed by a single database only (2 in CENTRAL and 1 each in PEDro and PubMed). The results are only applicable to searching for English-language published reports of randomized controlled trials evaluating physical therapy interventions. The 4 most comprehensive databases of trial reports evaluating physical therapy interventions were CENTRAL, PEDro, PubMed, and EMBASE. Clinicians seeking quick answers to clinical questions could search any of these databases knowing that all are reasonably comprehensive. PEDro, unlike the other 3 most complete databases, is specific to physical therapy, so studies not relevant to physical therapy are less likely to be retrieved. Researchers could use CENTRAL, PEDro, PubMed, and EMBASE in combination to conduct exhaustive searches for randomized trials in physical therapy.

MyLibrary: A Web Personalized Digital Library.

ERIC Educational Resources Information Center

Rocha, Catarina; Xexeo, Geraldo; da Rocha, Ana Regina C.

With the increasing availability of information on Internet information providers, like search engines, digital libraries and online databases, it becomes more important to have personalized systems that help users to find relevant information. One type of personalization that is growing in use is recommender systems. This paper presents…

Emotional Intelligence Research within Human Resource Development Scholarship

ERIC Educational Resources Information Center

Farnia, Forouzan; Nafukho, Fredrick Muyia

2016-01-01

Purpose: The purpose of this study is to review and synthesize pertinent emotional intelligence (EI) research within the human resource development (HRD) scholarship. Design/methodology/approach: An integrative review of literature was conducted and multiple electronic databases were searched to find the relevant resources. Using the content…

Critical Assessment of Search Strategies in Systematic Reviews in Endodontics.

PubMed

Yaylali, Ibrahim Ethem; Alaçam, Tayfun

2016-06-01

The aim of this study was to perform an overview of literature search strategies in systematic reviews (SRs) published in 2 endodontic journals, Journal of Endodontics and International Endodontic Journal. A search was done by using the MEDLINE (PubMed interface) database to retrieve the articles published between January 1, 2000 and December 31, 2015. The last search was on January 10, 2016. All the SRs published in the 2 journals were retrieved and screened. Eligible SRs were assessed by using 11 questions about search strategies in the SRs that were adapted from 2 guidelines (ie, AMSTAR checklist and the Cochrane Handbook). A total of 83 SRs were retrieved by electronic search. Of these, 55 were from the Journal of Endodontics, and 28 were from the International Endodontic Journal. After screening, 2 SRs were excluded, and 81 SRs were included in the study. Some issues, such as search of grey literature and contact with study authors, were not fully reported (30% and 25%, respectively). On the other hand, some issues, such as the use of index terms and key words and search in at least 2 databases, were reported in most of the SRs (97% and 95%, respectively). The overall quality of the search strategy in both journals was 61%. No significant difference was found between the 2 journals in terms of evaluation criteria (P > .05). There exist areas for improving the quality of reporting of search strategies in SRs; for example, grey literature should be searched for unpublished studies, no language limitation should be applied to databases, and authors should make an attempt to contact the authors of included studies to obtain further relevant information. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Integrating Query of Relational and Textual Data in Clinical Databases: A Case Study

PubMed Central

Fisk, John M.; Mutalik, Pradeep; Levin, Forrest W.; Erdos, Joseph; Taylor, Caroline; Nadkarni, Prakash

2003-01-01

Objectives: The authors designed and implemented a clinical data mart composed of an integrated information retrieval (IR) and relational database management system (RDBMS). Design: Using commodity software, which supports interactive, attribute-centric text and relational searches, the mart houses 2.8 million documents that span a five-year period and supports basic IR features such as Boolean searches, stemming, and proximity and fuzzy searching. Measurements: Results are relevance-ranked using either “total documents per patient” or “report type weighting.” Results: Non-curated medical text has a significant degree of malformation with respect to spelling and punctuation, which creates difficulties for text indexing and searching. Presently, the IR facilities of RDBMS packages lack the features necessary to handle such malformed text adequately. Conclusion: A robust IR+RDBMS system can be developed, but it requires integrating RDBMSs with third-party IR software. RDBMS vendors need to make their IR offerings more accessible to non-programmers. PMID:12509355

Exploring FlyBase Data Using QuickSearch.

PubMed

Marygold, Steven J; Antonazzo, Giulia; Attrill, Helen; Costa, Marta; Crosby, Madeline A; Dos Santos, Gilberto; Goodman, Joshua L; Gramates, L Sian; Matthews, Beverley B; Rey, Alix J; Thurmond, Jim

2016-12-08

FlyBase (flybase.org) is the primary online database of genetic, genomic, and functional information about Drosophila species, with a major focus on the model organism Drosophila melanogaster. The long and rich history of Drosophila research, combined with recent surges in genomic-scale and high-throughput technologies, mean that FlyBase now houses a huge quantity of data. Researchers need to be able to rapidly and intuitively query these data, and the QuickSearch tool has been designed to meet these needs. This tool is conveniently located on the FlyBase homepage and is organized into a series of simple tabbed interfaces that cover the major data and annotation classes within the database. This unit describes the functionality of all aspects of the QuickSearch tool. With this knowledge, FlyBase users will be equipped to take full advantage of all QuickSearch features and thereby gain improved access to data relevant to their research. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

BioModels Database: a repository of mathematical models of biological processes.

PubMed

Chelliah, Vijayalakshmi; Laibe, Camille; Le Novère, Nicolas

2013-01-01

BioModels Database is a public online resource that allows storing and sharing of published, peer-reviewed quantitative, dynamic models of biological processes. The model components and behaviour are thoroughly checked to correspond the original publication and manually curated to ensure reliability. Furthermore, the model elements are annotated with terms from controlled vocabularies as well as linked to relevant external data resources. This greatly helps in model interpretation and reuse. Models are stored in SBML format, accepted in SBML and CellML formats, and are available for download in various other common formats such as BioPAX, Octave, SciLab, VCML, XPP and PDF, in addition to SBML. The reaction network diagram of the models is also available in several formats. BioModels Database features a search engine, which provides simple and more advanced searches. Features such as online simulation and creation of smaller models (submodels) from the selected model elements of a larger one are provided. BioModels Database can be accessed both via a web interface and programmatically via web services. New models are available in BioModels Database at regular releases, about every 4 months.

NASA's Global Change Master Directory: Discover and Access Earth Science Data Sets, Related Data Services, and Climate Diagnostics

NASA Technical Reports Server (NTRS)

Aleman, Alicia; Olsen, Lola; Ritz, Scott; Morahan, Michael; Cepero, Laurel; Stevens, Tyler

2011-01-01

NASA's Global Change Master Directory provides the scientific community with the ability to discover, access, and use Earth science data, data-related services, and climate diagnostics worldwide. The GCMD offers descriptions of Earth science data sets using the Directory Interchange Format (DIF) metadata standard; Earth science related data services are described using the Service Entry Resource Format (SERF); and climate visualizations are described using the Climate Diagnostic (CD) standard. The DIF, SERF and CD standards each capture data attributes used to determine whether a data set, service, or climate visualization is relevant to a user's needs. Metadata fields include: title, summary, science keywords, service keywords, data center, data set citation, personnel, instrument, platform, quality, related URL, temporal and spatial coverage, data resolution and distribution information. In addition, nine valuable sets of controlled vocabularies have been developed to assist users in normalizing the search for data descriptions. An update to the GCMD's search functionality is planned to further capitalize on the controlled vocabularies during database queries. By implementing a dynamic keyword "tree", users will have the ability to search for data sets by combining keywords in new ways. This will allow users to conduct more relevant and efficient database searches to support the free exchange and re-use of Earth science data. http://gcmd.nasa.gov/

MalaCards: an integrated compendium for diseases and their annotation

PubMed Central

Rappaport, Noa; Nativ, Noam; Stelzer, Gil; Twik, Michal; Guan-Golan, Yaron; Iny Stein, Tsippi; Bahir, Iris; Belinky, Frida; Morrey, C. Paul; Safran, Marilyn; Lancet, Doron

2013-01-01

Comprehensive disease classification, integration and annotation are crucial for biomedical discovery. At present, disease compilation is incomplete, heterogeneous and often lacking systematic inquiry mechanisms. We introduce MalaCards, an integrated database of human maladies and their annotations, modeled on the architecture and strategy of the GeneCards database of human genes. MalaCards mines and merges 44 data sources to generate a computerized card for each of 16 919 human diseases. Each MalaCard contains disease-specific prioritized annotations, as well as inter-disease connections, empowered by the GeneCards relational database, its searches and GeneDecks set analyses. First, we generate a disease list from 15 ranked sources, using disease-name unification heuristics. Next, we use four schemes to populate MalaCards sections: (i) directly interrogating disease resources, to establish integrated disease names, synonyms, summaries, drugs/therapeutics, clinical features, genetic tests and anatomical context; (ii) searching GeneCards for related publications, and for associated genes with corresponding relevance scores; (iii) analyzing disease-associated gene sets in GeneDecks to yield affiliated pathways, phenotypes, compounds and GO terms, sorted by a composite relevance score and presented with GeneCards links; and (iv) searching within MalaCards itself, e.g. for additional related diseases and anatomical context. The latter forms the basis for the construction of a disease network, based on shared MalaCards annotations, embodying associations based on etiology, clinical features and clinical conditions. This broadly disposed network has a power-law degree distribution, suggesting that this might be an inherent property of such networks. Work in progress includes hierarchical malady classification, ontological mapping and disease set analyses, striving to make MalaCards an even more effective tool for biomedical research. Database URL: http://www.malacards.org/ PMID:23584832

SHOP: scaffold HOPping by GRID-based similarity searches.

PubMed

Bergmann, Rikke; Linusson, Anna; Zamora, Ismael

2007-05-31

A new GRID-based method for scaffold hopping (SHOP) is presented. In a fully automatic manner, scaffolds were identified in a database based on three types of 3D-descriptors. SHOP's ability to recover scaffolds was assessed and validated by searching a database spiked with fragments of known ligands of three different protein targets relevant for drug discovery using a rational approach based on statistical experimental design. Five out of eight and seven out of eight thrombin scaffolds and all seven HIV protease scaffolds were recovered within the top 10 and 31 out of 31 neuraminidase scaffolds were in the 31 top-ranked scaffolds. SHOP also identified new scaffolds with substantially different chemotypes from the queries. Docking analysis indicated that the new scaffolds would have similar binding modes to those of the respective query scaffolds observed in X-ray structures. The databases contained scaffolds from published combinatorial libraries to ensure that identified scaffolds could be feasibly synthesized.

[Neuromuscular electric stimulation therapy in otorhinolaryngology].

PubMed

Miller, S; Kühn, D; Jungheim, M; Schwemmle, C; Ptok, M

2014-02-01

Animal experiments have shown that after specific nerve traumatization, neuromuscular electrostimulation (NMES) can promote nerve regeneration and reduce synkinesia without negatively interfering with normal regeneration processes. NMES is used routinely in physical rehabilitation medicine. This systematic literature search in the Cochrane Central Register of Controlled Trials, the Cochrane Database of Systematic Reviews, the DAHTA database, the Health Technology Assessment Database and MEDLINE or PubMed considered studies on the use of NMES in otorhinolaryngology that have been published in German or English. The search identified 180 studies. These were evaluated and relevant studies were included in the further evaluation. In the fields of otorhinolaryngology and phoniatry/paediatric audiology, clinical studies investigating the effects of NMES on facial and laryngeal paresis, as well as dysphonia and dysphagia have been carried out. The evidence collected to date is encouraging; particularly for the treatment of certain forms of dysphagia and laryngeal paresis.

Clinicopathological effects of pepper (oleoresin capsicum) spray.

PubMed

Yeung, M F; Tang, William Y M

2015-12-01

Pepper (oleoresin capsicum) spray is one of the most common riot-control measures used today. Although not lethal, exposure of pepper spray can cause injury to different organ systems. This review aimed to summarise the major clinicopathological effects of pepper spray in humans. MEDLINE, EMBASE database, and Cochrane Database of Systematic Reviews were used to search for terms associated with the clinicopathological effects of pepper spray in humans and those describing the pathophysiology of capsaicin. A phone interview with two individuals recently exposed to pepper spray was also conducted to establish clinical symptoms. Major key words used for the MEDLINE search were "pepper spray", "OC spray", "oleoresin capsicum"; and other key words as "riot control agents", "capsaicin", and "capsaicinoid". We then combined the key words "capsaicin" and "capsaicinoid" with the major key words to narrow down the number of articles. A search with other databases including EMBASE and Cochrane Database of Systematic Reviews was also conducted with the above phrases to identify any additional related articles. All article searches were confined to human study. The bibliography of articles was screened for additional relevant studies including non-indexed reports, and information from these was also recorded. Non-English articles were included in the search. Fifteen articles were considered relevant. Oleoresin capsicum causes almost instantaneous irritative symptoms to the skin, eyes, and respiratory system. Dermatological effects include a burning sensation, erythema, and hyperalgesia. Ophthalmic effects involve blepharospasm, conjunctivitis, peri-orbital oedema, and corneal pathology. Following inhalation, a stinging or burning sensation can be felt in the nose with sore throat, chest tightness, or dyspnoea. The major pathophysiology is neurogenic inflammation caused by capsaicinoid in the pepper spray. There is no antidote for oleoresin capsicum. Treatment consists of thorough decontamination, symptom-directed supportive measures, and early detection and treatment of systemic toxicity. Decontamination should be carefully carried out to avoid contamination of the surrounding skin and clothing. Pepper (oleoresin capsicum) spray is an effective riot-control agent and does not cause life-threatening clinical effects in the majority of exposed individuals. Early decontamination minimises the irritant effects.

Educational games for health professionals.

PubMed

Akl, Elie A; Kairouz, Victor F; Sackett, Kay M; Erdley, William S; Mustafa, Reem A; Fiander, Michelle; Gabriel, Carolynne; Schünemann, Holger

2013-03-28

The use of games as an educational strategy has the potential to improve health professionals' performance (e.g. adherence to standards of care) through improving their knowledge, skills and attitudes. The objective was to assess the effect of educational games on health professionals' performance, knowledge, skills, attitude and satisfaction, and on patient outcomes. We searched the following databases in January 2012: MEDLINE, AMED, CINAHL, Cochrane Central Database of Controlled Trials, EMBASE, EPOC Register, ERIC, Proquest Dissertations & Theses Database, and PsycINFO. Related reviews were sought in DARE and the above named databases. Database searches identified 1546 citations. We also screened the reference lists of included studies in relevant reviews, contacted authors of relevant papers and reviews, and searched ISI Web of Science for papers citing studies included in the review. These search methods identified an additional 62 unique citations for a total of 1608 for this update. We included randomized controlled trials (RCT), controlled clinical trials (CCT), controlled before and after (CBA) and interrupted time-series analysis (ITS). Study participants were qualified health professionals or in postgraduate training. The intervention was an educational game with "a form of competitive activity or sport played according to rules". Using a standardized data form we extracted data on methodological quality, participants, interventions and outcomes of interest that included patient outcomes, professional behavior (process of care outcomes), and professional's knowledge, skills, attitude and satisfaction. The search strategy identified a total of 2079 unique citations. Out of 84 potentially eligible citations, we included two RCTs. The game evaluated in the first study used as a reinforcement technique, was based on the television game show "Family Feud" and focused on infection control. The study did not assess any patient or process of care outcomes. The group that was randomized to the game had statistically higher scores on the knowledge test (P = 0.02). The second study compared game-based learning ("Snakes and Ladders" board game) with traditional case-based learning of stroke prevention and management. The effect on knowledge was not statistically different between the two groups immediately and 3 months after the intervention. The level of reported enjoyment was higher in the game-based group. The findings of this systematic review neither confirm nor refute the utility of games as a teaching strategy for health professionals. There is a need for additional high-quality research to explore the impact of educational games on patient and performance outcomes.

Searching bioremediation patents through Cooperative Patent Classification (CPC).

PubMed

Prasad, Rajendra

2016-03-01

Patent classification systems have traditionally evolved independently at each patent jurisdiction to classify patents handled by their examiners to be able to search previous patents while dealing with new patent applications. As patent databases maintained by them went online for free access to public as also for global search of prior art by examiners, the need arose for a common platform and uniform structure of patent databases. The diversity of different classification, however, posed problems of integrating and searching relevant patents across patent jurisdictions. To address this problem of comparability of data from different sources and searching patents, WIPO in the recent past developed what is known as International Patent Classification (IPC) system which most countries readily adopted to code their patents with IPC codes along with their own codes. The Cooperative Patent Classification (CPC) is the latest patent classification system based on IPC/European Classification (ECLA) system, developed by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO) which is likely to become a global standard. This paper discusses this new classification system with reference to patents on bioremediation.

A review on mode-I interlaminar fracture toughness of fibre reinforced composites

NASA Astrophysics Data System (ADS)

Nasuha, N.; Azmi, A. I.; Tan, C. L.

2017-10-01

Composite material has been growing rapidly throughout the year for its unique properties in comparisons with metal. Recently, there has been a growth on studying the way to reduce the delamination failure, which is the primary challenge on laminated fibre composite. This failure can degrade the strength of composite materials, hence loses its function. In this review, database search was performed using the keywords search on “interlaminar fracture toughness”, “double cantilever beam”, “delamination resistance” and “Mode-I GIC”. The searches were performed on Google Scholar, Scopus and Web of Science with further cross-referencing with other databases. Most relevant studies were selected for review and referencing by the author. This review paper gives a brief explanation on Mode-I interlaminar fracture toughness of composite material. This fracture mode is the most common modes on studying the delamination failure.

Review of Recent Literature Relevant to the Environmental Effects of Marine and Hydrokinetic Energy Devices; Task 2.1.3: Effects on Aquatic Organisms - Fiscal Year 2012 Progress Report

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

Kropp, Roy K.

2013-01-01

A literature search was conducted by using the Web of Science® databases component of the ISI Web of KnowledgeSM to identify recent articles that would be useful to help assess the potential environmental effects of renewable energy development in the ocean, with emphasis on seabirds and fish. Several relatively recent general review articles that included possible effects on seabirds and fish were examined to begin the search process. From these articles, several general topics of potential environmental effects on seabirds and fish were derived. These topics were used as the primary search factors. Additional sources were identified by cross-checking themore » Web of Science databases for articles that cited the review articles. It also became clear that the potential effects frequently w« less

Quality of life in maltreated children and adult survivors of child maltreatment: a systematic review.

PubMed

Weber, S; Jud, A; Landolt, M A

2016-02-01

To review data on health-related quality of life (HRQoL) in individuals with childhood trauma, including psychological maltreatment, physical maltreatment, sexual abuse, and neglect. The literature search was conducted with pre-defined keywords using the following electronic bibliographic databases: EMBASE, PubMed, MEDLINE, CINAHL, PsyINFO, PSYNDEX, and Cochrane Database of Systematic Reviews. Further databases were searched for relevant dissertations. Study selection and data extraction were completed by two independent reviewers. The literature search yielded 1568 entries. Nineteen articles met all inclusion criteria and were retained for further analysis. Findings quite consistently showed significant negative associations between child maltreatment and both self- and proxy-rated HRQoL. Effect sizes range from small to large. Number of types of maltreatment and HRQoL were found to be negatively related. Data on HRQoL for maltreated children are still rare. Studies often investigate adult survivors of child maltreatment. Considering HRQoL in children and adolescents who suffered maltreatment would allow the planning of effective interventions and the evaluation of treatments to improve HRQoL of these children.

SABRE--A Novel Software Tool for Bibliographic Post-Processing.

ERIC Educational Resources Information Center

Burge, Cecil D.

1989-01-01

Describes the software architecture and application of SABRE (Semi-Automated Bibliographic Environment), which is one of the first products to provide a semi-automatic environment for relevancy ranking of citations obtained from searches of bibliographic databases. Features designed to meet the review, categorization, culling, and reporting needs…

28 CFR 25.6 - Accessing records in the system.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 28 Judicial Administration 1 2014-07-01 2014-07-01 false Accessing records in the system. 25.6 Section 25.6 Judicial Administration DEPARTMENT OF JUSTICE DEPARTMENT OF JUSTICE INFORMATION SYSTEMS The...) Search the relevant databases (i.e., NICS Index, NCIC, III) for any matching records; and (iv) Provide...

28 CFR 25.6 - Accessing records in the system.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 28 Judicial Administration 1 2011-07-01 2011-07-01 false Accessing records in the system. 25.6 Section 25.6 Judicial Administration DEPARTMENT OF JUSTICE DEPARTMENT OF JUSTICE INFORMATION SYSTEMS The...) Search the relevant databases (i.e., NICS Index, NCIC, III) for any matching records; and (iv) Provide...

28 CFR 25.6 - Accessing records in the system.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 28 Judicial Administration 1 2012-07-01 2012-07-01 false Accessing records in the system. 25.6 Section 25.6 Judicial Administration DEPARTMENT OF JUSTICE DEPARTMENT OF JUSTICE INFORMATION SYSTEMS The...) Search the relevant databases (i.e., NICS Index, NCIC, III) for any matching records; and (iv) Provide...

28 CFR 25.6 - Accessing records in the system.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 28 Judicial Administration 1 2013-07-01 2013-07-01 false Accessing records in the system. 25.6 Section 25.6 Judicial Administration DEPARTMENT OF JUSTICE DEPARTMENT OF JUSTICE INFORMATION SYSTEMS The...) Search the relevant databases (i.e., NICS Index, NCIC, III) for any matching records; and (iv) Provide...

Beliefs, Knowledge, Implementation, and Integration of Evidence-Based Practice Among Primary Health Care Providers: Protocol for a Scoping Review.

PubMed

Pereira, Filipa; Salvi, Mireille; Verloo, Henk

2017-08-01

The adoption of evidence-based practice (EBP) is promoted because it is widely recognized for improving the quality and safety of health care for patients, and reducing avoidable costs. Providers of primary care face numerous challenges to ensuring the effectiveness of their daily practices. Primary health care is defined as: the entry level into a health care services system, providing a first point of contact for all new needs and problems; patient-focused (not disease-oriented) care over time; care for all but the most uncommon or unusual conditions; and coordination or integration of care, regardless of where or by whom that care is delivered. Primary health care is the principal means by which to approach the main goal of any health care services system: optimization of health status. This review aims to scope publications examining beliefs, knowledge, implementation, and integration of EBPs among primary health care providers (HCPs). We will conduct a systematic scoping review of published articles in the following electronic databases, from their start dates until March 31, 2017: Medical Literature Analysis and Retrieval System Online (MEDLINE) via PubMed (from 1946), Embase (from 1947), Cumulative Index to Nursing and Allied Health Literature (CINAHL; from 1937), the Cochrane Central Register of Controlled Trials (CENTRAL; from 1992), PsycINFO (from 1806), Web of Science (from 1900), Joanna Briggs Institute (JBI) database (from 1998), Database of Abstracts of Reviews of Effects (DARE; from 1996), Trip medical database (from 1997), and relevant professional scientific journals (from their start dates). We will use the predefined search terms of, "evidence-based practice" and, "primary health care" combined with other terms, such as, "beliefs", "knowledge", "implementation", and "integration". We will also conduct a hand search of the bibliographies of all relevant articles and a search for unpublished studies using Google Scholar, ProQuest, Mednar, and WorldCat. We will consider publications in English, French, Spanish, and Portuguese. The electronic database searches were completed in April 2017. Retrieved articles are currently being screened, and the entire study is expected to be completed by November 2017. This systematic scoping review will provide a greater understanding of the beliefs, knowledge, implementation, and integration of EBPs among primary HCPs. The findings will inform clinical practice and help to draw a global picture of the EBP research topics that are relevant to primary care providers. ©Filipa Pereira, Mireille Salvi, Henk Verloo. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 01.08.2017.

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/

[Design of computerised database for clinical and basic management of uveal melanoma].

PubMed

Bande Rodríguez, M F; Santiago Varela, M; Blanco Teijeiro, M J; Mera Yañez, P; Pardo Perez, M; Capeans Tome, C; Piñeiro Ces, A

2012-09-01

The uveal melanoma is the most common primary intraocular tumour in adults. The objective of this work is to show how a computerised database has been formed with specific applications, for clinical and research use, to an extensive group of patients diagnosed with uveal melanoma. For the design of the database a selection of categories, attributes and values was created based on the classifications and parameters given by various authors of articles which have had great relevance in the field of uveal melanoma in recent years. The database has over 250 patient entries with specific information on their clinical history, diagnosis, treatment and progress. It enables us to search any parameter of the entry and make quick and simple statistical studies of them. The database models have been transformed into a basic tool for clinical practice, as they are an efficient way of storing, compiling and selective searching of information. When creating a database it is very important to define a common strategy and the use of a standard language. Copyright © 2011 Sociedad Española de Oftalmología. Published by Elsevier Espana. All rights reserved.

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

Lifestyle causes of male infertility.

PubMed

Durairajanayagam, Damayanthi

2018-03-01

To examine the potential effects of lifestyle factors on male reproductive health. Evidence of a global decline in human sperm quality over recent decades has been accumulating. Environmental, occupational, and modifiable lifestyle factors may contribute to this decline. This review focuses on key lifestyle factors that are associated with male infertility such as smoking cigarettes, alcohol intake, use of illicit drugs, obesity, psychological stress, advanced paternal age, dietary practices, and coffee consumption. Other factors such as testicular heat stress, intense cycling training, lack of sleep and exposure to electromagnetic radiation from mobile phone use are briefly discussed. A comprehensive literature search was performed to identify and synthesise all relevant information, mainly from within the last decade, on the major lifestyle factors associated with male infertility and semen quality. Database searches were limited to reports published in English only. A manual search of bibliographies of the reports retrieved was conducted to identify additional relevant articles. In all, 1012 articles were identified from the database search and after reviewing the titles and abstract of the reports, 104 articles met the inclusion criteria. Of these, 30 reports were excluded as the full-text could not be retrieved and the abstract did not have relevant data. The remaining 74 reports were reviewed for data on association between a particular lifestyle factor and male infertility and were included in the present review. The major lifestyle factors discussed in the present review are amongst the multiple potential risk factors that could impair male fertility. However, their negative impact may well be mostly overcome by behaviour modification and better lifestyle choices. Greater awareness and recognition of the possible impact of these lifestyle factors are important amongst couples seeking conception.

Physical activity in advanced cancer patients: a systematic review protocol.

PubMed

Lowe, Sonya S; Tan, Maria; Faily, Joan; Watanabe, Sharon M; Courneya, Kerry S

2016-03-11

Progressive, incurable cancer is associated with increased fatigue, increased muscle weakness, and reduced physical functioning, all of which negatively impact quality of life. Physical activity has demonstrated benefits on cancer-related fatigue and physical functioning in early-stage cancer patients; however, its impact on these outcomes in end-stage cancer has not been established. The aim of this systematic review is to determine the potential benefits, harms, and effects of physical activity interventions on quality of life outcomes in advanced cancer patients. A systematic review of peer-reviewed literature on physical activity in advanced cancer patients will be undertaken. Empirical quantitative studies will be considered for inclusion if they present interventional or observational data on physical activity in advanced cancer patients. Searches will be conducted in the following electronic databases: CINAHL; CIRRIE Database of International Rehabilitation Research; Cochrane Database of Systematic Reviews (CDSR); Database of Abstracts of Reviews of Effects (DARE); Cochrane Central Register of Controlled Trials (CENTRAL); EMBASE; MEDLINE; PEDro: the Physiotherapy Evidence Database; PQDT; PsycInfo; PubMed; REHABDATA; Scopus; SPORTDiscus; and Web of Science, to identify relevant studies of interest. Additional strategies to identify relevant studies will include citation searches and evaluation of reference lists of included articles. Titles, abstracts, and keywords of identified studies from the search strategies will be screened for inclusion criteria. Two independent reviewers will conduct quality appraisal using the Effective Public Health Practice Project Quality Assessment Tool for Quantitative Studies (EPHPP) and the Cochrane risk of bias tool. A descriptive summary of included studies will describe the study designs, participant and activity characteristics, and objective and patient-reported outcomes. This systematic review will summarize the current evidence base on physical activity interventions in advanced cancer patients. The findings from this systematic review will identify gaps to be explored by future research studies and inform future practice guideline development of physical activity interventions in advanced cancer patients. PROSPERO CRD42015026281.

Dialysis search filters for PubMed, Ovid MEDLINE, and Embase databases.

PubMed

Iansavichus, Arthur V; Haynes, R Brian; Lee, Christopher W C; Wilczynski, Nancy L; McKibbon, Ann; Shariff, Salimah Z; Blake, Peter G; Lindsay, Robert M; Garg, Amit X

2012-10-01

Physicians frequently search bibliographic databases, such as MEDLINE via PubMed, for best evidence for patient care. The objective of this study was to develop and test search filters to help physicians efficiently retrieve literature related to dialysis (hemodialysis or peritoneal dialysis) from all other articles indexed in PubMed, Ovid MEDLINE, and Embase. A diagnostic test assessment framework was used to develop and test robust dialysis filters. The reference standard was a manual review of the full texts of 22,992 articles from 39 journals to determine whether each article contained dialysis information. Next, 1,623,728 unique search filters were developed, and their ability to retrieve relevant articles was evaluated. The high-performance dialysis filters consisted of up to 65 search terms in combination. These terms included the words "dialy" (truncated), "uremic," "catheters," and "renal transplant wait list." These filters reached peak sensitivities of 98.6% and specificities of 98.5%. The filters' performance remained robust in an independent validation subset of articles. These empirically derived and validated high-performance search filters should enable physicians to effectively retrieve dialysis information from PubMed, Ovid MEDLINE, and Embase.

HONselect: multilingual assistant search engine operated by a concept-based interface system to decentralized heterogeneous sources.

PubMed

Boyer, C; Baujard, V; Scherrer, J R

2001-01-01

Any new user to the Internet will think that to retrieve the relevant document is an easy task especially with the wealth of sources available on this medium, but this is not the case. Even experienced users have difficulty formulating the right query for making the most of a search tool in order to efficiently obtain an accurate result. The goal of this work is to reduce the time and the energy necessary in searching and locating medical and health information. To reach this goal we have developed HONselect [1]. The aim of HONselect is not only to improve efficiency in retrieving documents but to respond to an increased need for obtaining a selection of relevant and accurate documents from a breadth of various knowledge databases including scientific bibliographical references, clinical trials, daily news, multimedia illustrations, conferences, forum, Web sites, clinical cases, and others. The authors based their approach on the knowledge representation using the National Library of Medicine's Medical Subject Headings (NLM, MeSH) vocabulary and classification [2,3]. The innovation is to propose a multilingual "one-stop searching" (one Web interface to databases currently in English, French and German) with full navigational and connectivity capabilities. The user may choose from a given selection of related terms the one that best suit his search, navigate in the term's hierarchical tree, and access directly to a selection of documents from high quality knowledge suppliers such as the MEDLINE database, the NLM's ClinicalTrials.gov server, the NewsPage's daily news, the HON's media gallery, conference listings and MedHunt's Web sites [4, 5, 6, 7, 8, 9]. HONselect, developed by HON, a non-profit organisation [10], is a free online available multilingual tool based on the MeSH thesaurus to index, select, retrieve and display accurate, up to date, high-level and quality documents.

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

PubstractHelper: A Web-based Text-Mining Tool for Marking Sentences in Abstracts from PubMed Using Multiple User-Defined Keywords.

PubMed

Chen, Chou-Cheng; Ho, Chung-Liang

2014-01-01

While a huge amount of information about biological literature can be obtained by searching the PubMed database, reading through all the titles and abstracts resulting from such a search for useful information is inefficient. Text mining makes it possible to increase this efficiency. Some websites use text mining to gather information from the PubMed database; however, they are database-oriented, using pre-defined search keywords while lacking a query interface for user-defined search inputs. We present the PubMed Abstract Reading Helper (PubstractHelper) website which combines text mining and reading assistance for an efficient PubMed search. PubstractHelper can accept a maximum of ten groups of keywords, within each group containing up to ten keywords. The principle behind the text-mining function of PubstractHelper is that keywords contained in the same sentence are likely to be related. PubstractHelper highlights sentences with co-occurring keywords in different colors. The user can download the PMID and the abstracts with color markings to be reviewed later. The PubstractHelper website can help users to identify relevant publications based on the presence of related keywords, which should be a handy tool for their research. http://bio.yungyun.com.tw/ATM/PubstractHelper.aspx and http://holab.med.ncku.edu.tw/ATM/PubstractHelper.aspx.

OntoMate: a text-mining tool aiding curation at the Rat Genome Database

PubMed Central

Liu, Weisong; Laulederkind, Stanley J. F.; Hayman, G. Thomas; Wang, Shur-Jen; Nigam, Rajni; Smith, Jennifer R.; De Pons, Jeff; Dwinell, Melinda R.; Shimoyama, Mary

2015-01-01

The Rat Genome Database (RGD) is the premier repository of rat genomic, genetic and physiologic data. Converting data from free text in the scientific literature to a structured format is one of the main tasks of all model organism databases. RGD spends considerable effort manually curating gene, Quantitative Trait Locus (QTL) and strain information. The rapidly growing volume of biomedical literature and the active research in the biological natural language processing (bioNLP) community have given RGD the impetus to adopt text-mining tools to improve curation efficiency. Recently, RGD has initiated a project to use OntoMate, an ontology-driven, concept-based literature search engine developed at RGD, as a replacement for the PubMed (http://www.ncbi.nlm.nih.gov/pubmed) search engine in the gene curation workflow. OntoMate tags abstracts with gene names, gene mutations, organism name and most of the 16 ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. All listed terms are linked both to data entry boxes and a term browser in the curation tool. OntoMate also provides user-activated filters for species, date and other parameters relevant to the literature search. Using the system for literature search and import has streamlined the process compared to using PubMed. The system was built with a scalable and open architecture, including features specifically designed to accelerate the RGD gene curation process. With the use of bioNLP tools, RGD has added more automation to its curation workflow. Database URL: http://rgd.mcw.edu PMID:25619558

Locating qualitative studies in dementia on MEDLINE, EMBASE, CINAHL, and PsycINFO: A comparison of search strategies.

PubMed

Rogers, Morwenna; Bethel, Alison; Abbott, Rebecca

2017-10-28

Qualitative research in dementia improves understanding of the experience of people affected by dementia. Searching databases for qualitative studies is problematic. Qualitative-specific search strategies might help with locating studies. To examine the effectiveness (sensitivity and precision) of 5 qualitative strategies on locating qualitative research studies in dementia in 4 major databases (MEDLINE, EMBASE, PsycINFO, and CINAHL). Qualitative dementia studies were checked for inclusion on MEDLINE, EMBASE, PsycINFO, and CINAHL. Five qualitative search strategies (subject headings, simple free-text terms, complex free-text terms, and 2 broad-based strategies) were tested for study retrieval. Specificity, precision and number needed to read were calculated. Two hundred fourteen qualitative studies in dementia were included. PsycINFO and CINAHL held the most qualitative studies out the 4 databases studied (N = 171 and 166, respectively) and both held unique records (N = 14 and 7, respectively). The controlled vocabulary strategy in CINAHL returned 96% (N = 192) of studies held; by contrast, controlled vocabulary in PsycINFO returned 7% (N = 13) of studies held. The broad-based strategies returned more studies (93-99%) than the other free-text strategies (22-82%). Precision ranged from 0.061 to 0.004 resulting in a number needed to read to obtain 1 relevant study ranging from 16 (simple free-text search in CINAHL) to 239 (broad-based search in EMBASE). Qualitative search strategies using 3 broad terms were more sensitive than long complex searches. The controlled vocabulary for qualitative research in CINAHL was particularly effective. Furthermore, results indicate that MEDLINE and EMBASE offer little benefit for locating qualitative dementia research if CINAHL and PSYCINFO are also searched. Copyright © 2017 John Wiley & Sons, Ltd.

LIVIVO - the Vertical Search Engine for Life Sciences.

PubMed

Müller, Bernd; Poley, Christoph; Pössel, Jana; Hagelstein, Alexandra; Gübitz, Thomas

2017-01-01

The explosive growth of literature and data in the life sciences challenges researchers to keep track of current advancements in their disciplines. Novel approaches in the life science like the One Health paradigm require integrated methodologies in order to link and connect heterogeneous information from databases and literature resources. Current publications in the life sciences are increasingly characterized by the employment of trans-disciplinary methodologies comprising molecular and cell biology, genetics, genomic, epigenomic, transcriptional and proteomic high throughput technologies with data from humans, plants, and animals. The literature search engine LIVIVO empowers retrieval functionality by incorporating various literature resources from medicine, health, environment, agriculture and nutrition. LIVIVO is developed in-house by ZB MED - Information Centre for Life Sciences. It provides a user-friendly and usability-tested search interface with a corpus of 55 Million citations derived from 50 databases. Standardized application programming interfaces are available for data export and high throughput retrieval. The search functions allow for semantic retrieval with filtering options based on life science entities. The service oriented architecture of LIVIVO uses four different implementation layers to deliver search services. A Knowledge Environment is developed by ZB MED to deal with the heterogeneity of data as an integrative approach to model, store, and link semantic concepts within literature resources and databases. Future work will focus on the exploitation of life science ontologies and on the employment of NLP technologies in order to improve query expansion, filters in faceted search, and concept based relevancy rankings in LIVIVO.

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.

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.

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.

Impact of Overt and Subclinical Hypothyroidism on Exercise Tolerance: A Systematic Review

ERIC Educational Resources Information Center

Lankhaar, Jeannette A. C.; de Vries, Wouter R.; Jansen, Jaap A. C. G.; Zelissen, Pierre M. J.; Backx, Frank J. G.

2014-01-01

Purpose: This systematic review describes the state of the art of the impact of hypothyroidism on exercise tolerance and physical performance capacity in untreated and treated patients with hypothyroidism. Method: A systematic computer-aided search was conducted using biomedical databases. Relevant studies in English, German, and Dutch, published…

Peer Assisted Learning in Clinical Education: Literature Review

ERIC Educational Resources Information Center

Henning, Jolene M.; Weidner, Thomas G.; Marty, Melissa C.

2008-01-01

Objective: To examine the occurrence, benefits, and preferences for peer assisted learning (PAL) in medical and allied health clinical education, and to identify areas in athletic training which need further research. Data Sources: Using relevant terms, five databases were searched for the period 1980-2006 regarding literature on the use of PAL in…

Is there a difference between child self-ratings and parent proxy-ratings of the quality of life of children with a diagnosis of attention-deficit hyperactivity disorder (ADHD)? A systematic review of the literature.

PubMed

Galloway, Helen; Newman, Emily

2017-03-01

There are contemporary indicators that parent proxy-ratings and child self-ratings of a child's quality of life (QoL) are not interchangeable. This review examines dual informant studies to assess parent-child agreement on the QoL of children with attention-deficit/hyperactivity disorder. A systematic search of four major databases (PsycINFO, MEDLINE, EMBASE and Cochrane databases) was completed, and related peer-reviewed journals were hand-searched. Studies which reported quantitative QoL ratings for matched parent and child dyads were screened in accordance with relevant inclusion and exclusion criteria. Key findings were extracted from thirteen relevant studies, which were rated for conformity to the recommendations of an adapted version of the STROBE statement guidelines for observational studies. In the majority of studies reviewed, children rated their QoL more highly than their parents. There was some evidence for greater agreement on the physical health domain than psychosocial domains.

Visual search asymmetries within color-coded and intensity-coded displays.

PubMed

Yamani, Yusuke; McCarley, Jason S

2010-06-01

Color and intensity coding provide perceptual cues to segregate categories of objects within a visual display, allowing operators to search more efficiently for needed information. Even within a perceptually distinct subset of display elements, however, it may often be useful to prioritize items representing urgent or task-critical information. The design of symbology to produce search asymmetries (Treisman & Souther, 1985) offers a potential technique for doing this, but it is not obvious from existing models of search that an asymmetry observed in the absence of extraneous visual stimuli will persist within a complex color- or intensity-coded display. To address this issue, in the current study we measured the strength of a visual search asymmetry within displays containing color- or intensity-coded extraneous items. The asymmetry persisted strongly in the presence of extraneous items that were drawn in a different color (Experiment 1) or a lower contrast (Experiment 2) than the search-relevant items, with the targets favored by the search asymmetry producing highly efficient search. The asymmetry was attenuated but not eliminated when extraneous items were drawn in a higher contrast than search-relevant items (Experiment 3). Results imply that the coding of symbology to exploit visual search asymmetries can facilitate visual search for high-priority items even within color- or intensity-coded displays. PsycINFO Database Record (c) 2010 APA, all rights reserved.

Occupational injury among migrant workers in China: a systematic review.

PubMed

Fitzgerald, Simon; Chen, Xin; Qu, Hui; Sheff, Mira Grice

2013-10-01

This review considers the state of occupational injury surveillance and prevention among migrant workers in China and suggests areas of focus for future research on the topic. Bibliographic databases were searched for qualitative and quantitative studies on surveillance of and interventions to prevent occupational injury among migrant workers in mainland China. Additional abstracts were identified from the citations of relevant articles from the database search. Studies fitting the inclusion criteria were evaluated, and findings were extracted and summarised. The search uncovered 726 studies in the English-language databases searched, and 3109 in the Chinese database. This article analyses a total of 19 research articles that fit the inclusion criteria with qualitative or quantitative data on occupational injury surveillance and prevention of migrant workers in China. Despite evidence of the vulnerability of migrant workers in the workplace, there is little systematic surveillance of occupational injury and few evaluated interventions. Migrant workers account for a disproportionate burden of occupational injury morbidity and mortality in China. However, data are inconsistent and inadequate to detail injury incidence or to evaluate interventions. The following are suggestions to decrease injury incidence among migrants: strengthen the national system of occupational injury surveillance; focus surveillance and interventions on high-risk occupations employing migrants such as construction, manufacturing and small mining operations; improve occupational safety training and access to appropriate safety equipment; evaluate recent changes in occupational health and safety and evaluate outcome of multi-party interventions to reduce occupational injury among migrant workers.

Occupational injury among migrant workers in China: a systematic review

PubMed Central

Fitzgerald, Simon; Chen, Xin; Qu, Hui; Sheff, Mira Grice

2017-01-01

Objectives This review considers the state of occupational injury surveillance and prevention among migrant workers in China and suggests areas of focus for future research on the topic. Methods Bibliographic databases were searched for qualitative and quantitative studies on surveillance of and interventions to prevent occupational injury among migrant workers in mainland China. Additional abstracts were identified from the citations of relevant articles from the database search. Studies fitting the inclusion criteria were evaluated, and findings were extracted and summarised. Results The search uncovered 726 studies in the English-language databases searched, and 3109 in the Chinese database. This article analyses a total of 19 research articles that fit the inclusion criteria with qualitative or quantitative data on occupational injury surveillance and prevention of migrant workers in China. Despite evidence of the vulnerability of migrant workers in the workplace, there is little systematic surveillance of occupational injury and few evaluated interventions. Conclusions Migrant workers account for a disproportionate burden of occupational injury morbidity and mortality in China. However, data are inconsistent and inadequate to detail injury incidence or to evaluate interventions. The following are suggestions to decrease injury incidence among migrants: strengthen the national system of occupational injury surveillance; focus surveillance and interventions on high-risk occupations employing migrants such as construction, manufacturing and small mining operations; improve occupational safety training and access to appropriate safety equipment; evaluate recent changes in occupational health and safety and evaluate outcome of multi-party interventions to reduce occupational injury among migrant workers. PMID:23710065

Is 'self-medication' a useful term to retrieve related publications in the literature? A systematic exploration of related terms.

PubMed

Mansouri, Ava; Sarayani, Amir; Ashouri, Asieh; Sherafatmand, Mona; Hadjibabaie, Molouk; Gholami, Kheirollah

2015-01-01

Self-Medication (SM), i.e. using medications to treat oneself, is a major concern for health researchers and policy makers. The terms "self medication" or "self-medication" (SM terms) have been used to explain various concepts while several terms have also been employed to define this practice. Hence, retrieving relevant publications would require exhaustive literature screening. So, we assessed the current situation of SM terms in the literature to improve the relevancy of search outcomes. In this Systematic exploration, SM terms were searched in the 6 following databases and publisher's portals till April 2012: Web of Science, Scopus, PubMed, Google scholar, ScienceDirect, and Wiley. A simple search query was used to include only publications with SM terms. We used Relative-Risk (RR) to estimate the probability of SM terms use in related compared to unrelated publications. Sensitivity and specificity of SM terms as keywords in search query were also calculated. Relevant terms to SM practice were extracted and their Likelihood Ratio positive and negative (LR+/-) were calculated to assess their effect on the probability of search outcomes relevancy in addition to previous search queries. We also evaluated the content of unrelated publications. All mentioned steps were performed in title (TI) and title or abstract (TIAB) of publications. 1999 related and 1917 unrelated publications were found. SM terms RR was 4.5 in TI and 2.1 in TIAB. SM terms sensitivity and specificity respectively were 55.4% and 87.7% in TI and 84.0% and 59.5% in TIAB. "OTC" and "Over-The-Counter Medication", with LR+ 16.78 and 16.30 respectively, provided the most conclusive increase in the probability of the relevancy of publications. The most common unrelated SM themes were self-medication hypothesis, drug abuse and Zoopharmacognosy. Due to relatively low specificity or sensitivity of SM terms, relevant terms should be employed in search queries and clear definitions of SM applications should be applied to improve the relevancy of publications.

Is ‘Self-Medication’ a Useful Term to Retrieve Related Publications in the Literature? A Systematic Exploration of Related Terms

PubMed Central

Mansouri, Ava; Sarayani, Amir; Ashouri, Asieh; Sherafatmand, Mona; Hadjibabaie, Molouk; Gholami, Kheirollah

2015-01-01

Background Self-Medication (SM), i.e. using medications to treat oneself, is a major concern for health researchers and policy makers. The terms “self medication” or “self-medication” (SM terms) have been used to explain various concepts while several terms have also been employed to define this practice. Hence, retrieving relevant publications would require exhaustive literature screening. So, we assessed the current situation of SM terms in the literature to improve the relevancy of search outcomes. Methods In this Systematic exploration, SM terms were searched in the 6 following databases and publisher’s portals till April 2012: Web of Science, Scopus, PubMed, Google scholar, ScienceDirect, and Wiley. A simple search query was used to include only publications with SM terms. We used Relative-Risk (RR) to estimate the probability of SM terms use in related compared to unrelated publications. Sensitivity and specificity of SM terms as keywords in search query were also calculated. Relevant terms to SM practice were extracted and their Likelihood Ratio positive and negative (LR+/-) were calculated to assess their effect on the probability of search outcomes relevancy in addition to previous search queries. We also evaluated the content of unrelated publications. All mentioned steps were performed in title (TI) and title or abstract (TIAB) of publications. Results 1999 related and 1917 unrelated publications were found. SM terms RR was 4.5 in TI and 2.1 in TIAB. SM terms sensitivity and specificity respectively were 55.4% and 87.7% in TI and 84.0% and 59.5% in TIAB. “OTC” and “Over-The-Counter Medication”, with LR+ 16.78 and 16.30 respectively, provided the most conclusive increase in the probability of the relevancy of publications. The most common unrelated SM themes were self-medication hypothesis, drug abuse and Zoopharmacognosy. Conclusions Due to relatively low specificity or sensitivity of SM terms, relevant terms should be employed in search queries and clear definitions of SM applications should be applied to improve the relevancy of publications. PMID:25932634

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

NASA Astrophysics Data System (ADS)

Braams, Bastiaan J.; Chung, Hyun-Kyung

2012-05-01

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

The Hawaiian Algal Database: a laboratory LIMS and online resource for biodiversity data

PubMed Central

Wang, Norman; Sherwood, Alison R; Kurihara, Akira; Conklin, Kimberly Y; Sauvage, Thomas; Presting, Gernot G

2009-01-01

Background Organization and presentation of biodiversity data is greatly facilitated by databases that are specially designed to allow easy data entry and organized data display. Such databases also have the capacity to serve as Laboratory Information Management Systems (LIMS). The Hawaiian Algal Database was designed to showcase specimens collected from the Hawaiian Archipelago, enabling users around the world to compare their specimens with our photographs and DNA sequence data, and to provide lab personnel with an organizational tool for storing various biodiversity data types. Description We describe the Hawaiian Algal Database, a comprehensive and searchable database containing photographs and micrographs, geo-referenced collecting information, taxonomic checklists and standardized DNA sequence data. All data for individual samples are linked through unique accession numbers. Users can search online for sample information by accession number, numerous levels of taxonomy, or collection site. At the present time the database contains data representing over 2,000 samples of marine, freshwater and terrestrial algae from the Hawaiian Archipelago. These samples are primarily red algae, although other taxa are being added. Conclusion The Hawaiian Algal Database is a digital repository for Hawaiian algal samples and acts as a LIMS for the laboratory. Users can make use of the online search tool to view and download specimen photographs and micrographs, DNA sequences and relevant habitat data, including georeferenced collecting locations. It is publicly available at . PMID:19728892

Assessment of indexing trends with specific and general terms for herbal medicine.

PubMed

Bartol, Tomaz

2012-12-01

Concepts for medicinal plants are represented by a variety of associated general terms with specific indexing patterns in databases, which may not consistently reflect growth of records. The objectives of this study are to assess the development in databases by identifying general terms that describe herbal medicine with optimal retrieval recall and to identify possible special trends in co-occurrence of specific and general concepts. Different search strategies are tested in cab abstracts, medline and web of science. Specific terms (Origanum and Salvia) are employed. Relevant general terms (e.g. 'Plants, Medicinal', Phytotherapy, Herbal drugs) are identified, along with indexing trends and co-occurrences. Growth trends, in specific (narrower) terms, are similar among databases. General terms, however, exhibit dissimilar trends, sometimes almost opposing one another. Co-occurrence of specific and general terms is changing over time. General terms may not denote definite development of trends as the use of terms differs amongst databases, making it difficult to correctly assess possible numbers of relevant records. Perceived increase can, sometimes, be attributed to an increased occurrence of a more general term alongside the specific one. Thesaurus-controlled databases may yield more hits, because of 'up-posted' (broader) terms. Use of broader terms is helpful as it enhances retrieval of relevant documents. © 2012 The authors. Health Information and Libraries Journal © 2012 Health Libraries Group.

ZINC: A Free Tool to Discover Chemistry for Biology

PubMed Central

2012-01-01

ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site also enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number. Small custom subsets may be created, edited, shared, docked, downloaded, and conveyed to a vendor for purchase. The database is maintained and curated for a high purchasing success rate and is freely available at zinc.docking.org. PMID:22587354

An overview of biomedical literature search on the World Wide Web in the third millennium.

PubMed

Kumar, Prince; Goel, Roshni; Jain, Chandni; Kumar, Ashish; Parashar, Abhishek; Gond, Ajay Ratan

2012-06-01

Complete access to the existing pool of biomedical literature and the ability to "hit" upon the exact information of the relevant specialty are becoming essential elements of academic and clinical expertise. With the rapid expansion of the literature database, it is almost impossible to keep up to date with every innovation. Using the Internet, however, most people can freely access this literature at any time, from almost anywhere. This paper highlights the use of the Internet in obtaining valuable biomedical research information, which is mostly available from journals, databases, textbooks and e-journals in the form of web pages, text materials, images, and so on. The authors present an overview of web-based resources for biomedical researchers, providing information about Internet search engines (e.g., Google), web-based bibliographic databases (e.g., PubMed, IndMed) and how to use them, and other online biomedical resources that can assist clinicians in reaching well-informed clinical decisions.

Interactive and Versatile Navigation of Structural Databases.

PubMed

Korb, Oliver; Kuhn, Bernd; Hert, Jérôme; Taylor, Neil; Cole, Jason; Groom, Colin; Stahl, Martin

2016-05-12

We present CSD-CrossMiner, a novel tool for pharmacophore-based searches in crystal structure databases. Intuitive pharmacophore queries describing, among others, protein-ligand interaction patterns, ligand scaffolds, or protein environments can be built and modified interactively. Matching crystal structures are overlaid onto the query and visualized as soon as they are available, enabling the researcher to quickly modify a hypothesis on the fly. We exemplify the utility of the approach by showing applications relevant to real-world drug discovery projects, including the identification of novel fragments for a specific protein environment or scaffold hopping. The ability to concurrently search protein-ligand binding sites extracted from the Protein Data Bank (PDB) and small organic molecules from the Cambridge Structural Database (CSD) using the same pharmacophore query further emphasizes the flexibility of CSD-CrossMiner. We believe that CSD-CrossMiner closes an important gap in mining structural data and will allow users to extract more value from the growing number of available crystal structures.

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…

Marriage and Family Counseling. Searchlight Plus: Relevant Resources in High Interest Areas. 57+.

ERIC Educational Resources Information Center

Okun, Barbara F.

This information analysis paper is based on a computer search of the ERIC database from November 1966 through March 1984, and on pertinent outside resources related to marriage and family counseling. A brief historical perspective of the field of marriage and family counseling is provided, and the differences and overlaps between family,…

Prevalence of Chronic Health Conditions in Children with Intellectual Disability: A Systematic Literature Review

ERIC Educational Resources Information Center

Oeseburg, Barth; Dijkstra, Geke J.; Groothoff, Johan W.; Reijneveld, Sijmen A.; Jansen, Danielle E. M. C.

2011-01-01

A systematic review of the prevalence rates of chronic health conditions in populations of children with intellectual disability was provided. We identified 2,994 relevant studies by searching Medline, Cinahl, and PsycINFO databases from 1996 to 2008. We included the 31 studies that had sufficient methodological quality. The 6 most prevalent…

Parenting Interventions for Male Young Offenders: A Review of the Evidence on What Works

ERIC Educational Resources Information Center

Buston, K.; Parkes, A.; Thomson, H.; Wight, D.; Fenton, C.

2012-01-01

Approximately one in four incarcerated male young offenders in the UK is an actual or expectant father. This paper reviews evidence on the effectiveness of parenting interventions for male young offenders. We conducted systematic searches across 20 databases and consulted experts. Twelve relevant evaluations were identified: 10 from the UK, of…

The Relationship between Emotional Recognition Ability and Challenging Behaviour in Adults with an Intellectual Disability. A Systematic Review

ERIC Educational Resources Information Center

Davies, Bronwen; Frude, Neil; Jenkins, Rosemary

2015-01-01

This review questions whether a relationship exists between emotional recognition ability and challenging behaviour in people with an intellectual disability. A search was completed of a number of databases to identify relevant articles, and these were then evaluated against defined criteria. Eight articles were reviewed and their aims, study…

Feeding Interventions for Children with Cerebral Palsy: A Review of the Evidence

ERIC Educational Resources Information Center

Snider, Laurie; Majnemer, Annette; Darsaklis, Vasiliki

2011-01-01

Aim: To examine the evidence of the effectiveness of different feeding interventions for children with cerebral palsy. Methods: A search of 12 electronic databases identified all relevant studies. For each study, the quality of the methods was assessed according to the study design. A total of 33 articles were retrieved, and 21 studies were…

Music Interventions for Children with Autism: Narrative Review of the Literature

ERIC Educational Resources Information Center

Simpson, Kate; Keen, Deb

2011-01-01

It is widely reported that music can be beneficial to individuals with autism. This review was undertaken to determine the evidence base for the use of music as an intervention for children with autism. After searching relevant databases, 128 articles were identified of which 20 articles met the study's inclusion criteria. Composed songs and…

Effectiveness of the Practice Style and Reciprocal Style of Teaching: A Meta-Analysis

ERIC Educational Resources Information Center

Chatoupis, Constantine; Vagenas, George

2018-01-01

The purpose of this meta-analysis was to examine the effectiveness of Mosston and Ashworth's (2008) practice and reciprocal styles of teaching on motor skill acquisition of school-age and university students. A systematic search in bibliographical databases led to the identification of 23 relevant studies published in peer-reviewed journals. Using…

A Firefly Algorithm-based Approach for Pseudo-Relevance Feedback: Application to Medical Database.

PubMed

Khennak, Ilyes; Drias, Habiba

2016-11-01

The difficulty of disambiguating the sense of the incomplete and imprecise keywords that are extensively used in the search queries has caused the failure of search systems to retrieve the desired information. One of the most powerful and promising method to overcome this shortcoming and improve the performance of search engines is Query Expansion, whereby the user's original query is augmented by new keywords that best characterize the user's information needs and produce more useful query. In this paper, a new Firefly Algorithm-based approach is proposed to enhance the retrieval effectiveness of query expansion while maintaining low computational complexity. In contrast to the existing literature, the proposed approach uses a Firefly Algorithm to find the best expanded query among a set of expanded query candidates. Moreover, this new approach allows the determination of the length of the expanded query empirically. Experimental results on MEDLINE, the on-line medical information database, show that our proposed approach is more effective and efficient compared to the state-of-the-art.

Finding relevant biomedical datasets: the UC San Diego solution for the bioCADDIE Retrieval Challenge

PubMed Central

Wei, Wei; Ji, Zhanglong; He, Yupeng; Zhang, Kai; Ha, Yuanchi; Li, Qi; Ohno-Machado, Lucila

2018-01-01

Abstract The number and diversity of biomedical datasets grew rapidly in the last decade. A large number of datasets are stored in various repositories, with different formats. Existing dataset retrieval systems lack the capability of cross-repository search. As a result, users spend time searching datasets in known repositories, and they typically do not find new repositories. The biomedical and healthcare data discovery index ecosystem (bioCADDIE) team organized a challenge to solicit new indexing and searching strategies for retrieving biomedical datasets across repositories. We describe the work of one team that built a retrieval pipeline and examined its performance. The pipeline used online resources to supplement dataset metadata, automatically generated queries from users’ free-text questions, produced high-quality retrieval results and achieved the highest inferred Normalized Discounted Cumulative Gain among competitors. The results showed that it is a promising solution for cross-database, cross-domain and cross-repository biomedical dataset retrieval. Database URL: https://github.com/w2wei/dataset_retrieval_pipeline PMID:29688374

Intellectual property analysis of holographic materials business

NASA Astrophysics Data System (ADS)

Reingand, Nadya; Hunt, David

2006-02-01

The paper presents an overview of intellectual property in the field of holographic photosensitive materials and highlights the possibilities offered by patent searching and analysis. Thousands of patent documents relevant to holographic materials have been uncovered by the study. The search was performed in the following databases: U.S. Patent Office, European Patent Office, and Japanese Patent Office for the time frame of 1971 through November 2005. The patent analysis has unveiled trends in patent temporal distribution, leading IP portfolios, companies competition within the holographic materials market and other interesting insights.

Intellectual property (IP) analysis of embossed hologram business

NASA Astrophysics Data System (ADS)

Hunt, David; Reingand, Nadya; Cantrell, Robert

2006-02-01

This paper presents an overview of patents and patent applications on security embossed holograms, and highlights the possibilities offered by patent searching and analysis. Thousands of patent documents relevant to embossed holograms were uncovered by the study. The search was performed in the following databases: U.S. Patent Office, European Patent Office, Japanese Patent Office and Korean Patent Office for the time frame from 1971 through November 2005. The patent analysis unveils trends in patent temporal distribution, patent families formation, significant technological coverage within the embossed holography market and other interesting insights.

Intellectual property in holographic interferometry

NASA Astrophysics Data System (ADS)

Reingand, Nadya; Hunt, David

2006-08-01

This paper presents an overview of patents and patent applications on holographic interferometry, and highlights the possibilities offered by patent searching and analysis. Thousands of patent documents relevant to holographic interferometry were uncovered by the study. The search was performed in the following databases: U.S. Patent Office, European Patent Office, Japanese Patent Office and Korean Patent Office for the time frame from 1971 through May 2006. The patent analysis unveils trends in patent temporal distribution, patent families formation, significant technological coverage within the market of system that employ holographic interferometry and other interesting insights.

Searching ClinicalTrials.gov and the International Clinical Trials Registry Platform to inform systematic reviews: what are the optimal search approaches?

PubMed

Glanville, Julie M; Duffy, Steven; McCool, Rachael; Varley, Danielle

2014-07-01

Since 2005, International Committee of Medical Journal Editors (ICMJE) member journals have required that clinical trials be registered in publicly available trials registers before they are considered for publication. The research explores whether it is adequate, when searching to inform systematic reviews, to search for relevant clinical trials using only public trials registers and to identify the optimal search approaches in trials registers. A search was conducted in ClinicalTrials.gov and the International Clinical Trials Registry Platform (ICTRP) for research studies that had been included in eight systematic reviews. Four search approaches (highly sensitive, sensitive, precise, and highly precise) were performed using the basic and advanced interfaces in both resources. On average, 84% of studies were not listed in either resource. The largest number of included studies was retrieved in ClinicalTrials.gov and ICTRP when a sensitive search approach was used in the basic interface. The use of the advanced interface maintained or improved sensitivity in 16 of 19 strategies for Clinicaltrials.gov and 8 of 18 for ICTRP. No single search approach was sensitive enough to identify all studies included in the 6 reviews. Trials registers cannot yet be relied upon as the sole means to locate trials for systematic reviews. Trials registers lag behind the major bibliographic databases in terms of their search interfaces. For systematic reviews, trials registers and major bibliographic databases should be searched. Trials registers should be searched using sensitive approaches, and both the registers consulted in this study should be searched.

Does Iron Supplementation Improve Performance in Iron-Deficient Nonanemic Athletes?

PubMed

Rubeor, Amity; Goojha, Carmen; Manning, Jeffrey; White, Jordan

2018-05-01

Supplementing iron-deficient nonanemic (IDNA) athletes with iron to improve performance is a trend in endurance sports. To investigate the benefits of iron on performance, identify a ferritin level cutoff in IDNA athletes, and determine which iron supplementation regimens are most effective. A search of the PubMed, CINAHL, Embase, ERIC, and Cochrane databases was performed in 2014 including all articles. Citations of pertinent review articles were also searched. In 2017, the search was repeated. Inclusion criteria comprised studies of level 1 to 3 evidence, written in the English language, that researched iron supplementation in nonanemic athletes and reported performance outcomes. Systematic review. Level 3. The search terms used included athletic performance, resistance training, athletes, physical endurance, iron, iron deficiency, supplement, non-anemic, low ferritin, ferritin, ferritin blood level, athletes, and sports. A total of 1884 studies were identified through the initial database search, and 13 were identified through searching references of relevant review articles. A subsequent database search identified 46 studies. Following exclusions, 12 studies with a total of 283 participants were included. Supplementing IDNA athletes with iron improved performance in 6 studies (146 participants) and did not improve performance in the other 6 studies (137 participants). In the 6 studies that showed improved performance with iron supplementation, all used a ferritin level cutoff of ≤20 μg/L for treatment. Additionally, all studies that showed improved performance used oral iron as a supplement. The evidence is equivocal as to whether iron supplementation in IDNA athletes improves athletic performance. Supplementing athletes with ferritin levels <20 μg/L may be more beneficial than supplementing athletes with higher baseline ferritin levels.

Short dental implants: an emerging concept in implant treatment.

PubMed

Al-Hashedi, Ashwaq Ali; Taiyeb Ali, Tara Bai; Yunus, Norsiah

2014-06-01

Short implants have been advocated as a treatment option in many clinical situations where the use of conventional implants is limited. This review outlines the effectiveness and clinical outcomes of using short implants as a valid treatment option in the rehabilitation of edentulous atrophic alveolar ridges. Initially, an electronic search was performed on the following databases: Medline, PubMed, Embase, Cochrane Database of Systematic Reviews, and DARE using key words from January 1990 until May 2012. An additional hand search was included for the relevant articles in the following journals: International Journal of Oral and Maxillofacial Implants, Clinical Oral Implants Research, Journal of Clinical Periodontology, International Journal of Periodontics, Journal of Periodontology, and Clinical Implant Dentistry and Related Research. Any relevant papers from the journals' references were hand searched. Articles were included if they provided detailed data on implant length, reported survival rates, mentioned measures for implant failure, were in the English language, involved human subjects, and researched implants inserted in healed atrophic ridges with a follow-up period of at least 1 year after implant-prosthesis loading. Short implants demonstrated a high rate of success in the replacement of missing teeth in especially atrophic alveolar ridges. The advanced technology and improvement of the implant surfaces have encouraged the success of short implants to a comparable level to that of standard implants. However, further randomized controlled clinical trials and prospective studies with longer follow-up periods are needed.

Elevated serum levels of ghrelin and TNF-α in patients with cyanotic and acyanotic congenital heart disease.

PubMed

Zhang, Sai; Guo, Gong-Liang; Yang, Li-Li; Sun, Li-Qun

2017-04-01

The levels of ghrelin and tumor necrosis factor alpha (TNF-α) are considered biological markers of congenital heart diseases (CHD). The present meta-analysis was conducted to investigate the clinical significance of serum levels of ghrelin and TNF-α in children with (CHD). Chinese and English scientific literature databases were searched to retrieve published studies relevant to ghrelin, TNF-α and CHD. Manual search was additionally employed to identify other relevant studies from cross-references. The retrieved studies were screened on the basis of our stringent inclusion and exclusion criteria to select high quality case-control studies for meta-analysis. We initially retrieved 108 published studies (20 in Chinese and 88 in English) from database searches. Finally, 6 case-control studies (5 in English and 1 in Chinese) were enrolled in our meta-analysis, and contained a total of 160 cyanotic congenital heart disease (CCHD) patients and 215 acyanotic congenital heart disease (ACHD) patients, along with 162 healthy controls. The results of meta-analysis showed that serum levels of ghrelin and TNF-α in CCHD or ACHD children were significantly higher than those in healthy controls. Our meta-analysis results showed that serum levels of ghrelin and TNF-α are elevated in children with CHD, and could be used as effective biologic markers in early diagnosis of CHD.

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

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

Braams, Bastiaan J.; Chung, Hyun-Kyung

2012-05-25

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

Cancer Internet search activity on a major search engine, United States 2001-2003.

PubMed

Cooper, Crystale Purvis; Mallon, Kenneth P; Leadbetter, Steven; Pollack, Lori A; Peipins, Lucy A

2005-07-01

To locate online health information, Internet users typically use a search engine, such as Yahoo! or Google. We studied Yahoo! search activity related to the 23 most common cancers in the United States. The objective was to test three potential correlates of Yahoo! cancer search activity--estimated cancer incidence, estimated cancer mortality, and the volume of cancer news coverage--and to study the periodicity of and peaks in Yahoo! cancer search activity. Yahoo! cancer search activity was obtained from a proprietary database called the Yahoo! Buzz Index. The American Cancer Society's estimates of cancer incidence and mortality were used. News reports associated with specific cancer types were identified using the LexisNexis "US News" database, which includes more than 400 national and regional newspapers and a variety of newswire services. The Yahoo! search activity associated with specific cancers correlated with their estimated incidence (Spearman rank correlation, rho = 0.50, P = .015), estimated mortality (rho = 0.66, P = .001), and volume of related news coverage (rho = 0.88, P < .001). Yahoo! cancer search activity tended to be higher on weekdays and during national cancer awareness months but lower during summer months; cancer news coverage also tended to follow these trends. Sharp increases in Yahoo! search activity scores from one day to the next appeared to be associated with increases in relevant news coverage. Media coverage appears to play a powerful role in prompting online searches for cancer information. Internet search activity offers an innovative tool for passive surveillance of health information-seeking behavior.

Cancer Internet Search Activity on a Major Search Engine, United States 2001-2003

PubMed Central

Cooper, Crystale Purvis; Mallon, Kenneth P; Leadbetter, Steven; Peipins, Lucy A

2005-01-01

Background To locate online health information, Internet users typically use a search engine, such as Yahoo! or Google. We studied Yahoo! search activity related to the 23 most common cancers in the United States. Objective The objective was to test three potential correlates of Yahoo! cancer search activity—estimated cancer incidence, estimated cancer mortality, and the volume of cancer news coverage—and to study the periodicity of and peaks in Yahoo! cancer search activity. Methods Yahoo! cancer search activity was obtained from a proprietary database called the Yahoo! Buzz Index. The American Cancer Society's estimates of cancer incidence and mortality were used. News reports associated with specific cancer types were identified using the LexisNexis “US News” database, which includes more than 400 national and regional newspapers and a variety of newswire services. Results The Yahoo! search activity associated with specific cancers correlated with their estimated incidence (Spearman rank correlation, ρ = 0.50, P = .015), estimated mortality (ρ = 0.66, P = .001), and volume of related news coverage (ρ = 0.88, P < .001). Yahoo! cancer search activity tended to be higher on weekdays and during national cancer awareness months but lower during summer months; cancer news coverage also tended to follow these trends. Sharp increases in Yahoo! search activity scores from one day to the next appeared to be associated with increases in relevant news coverage. Conclusions Media coverage appears to play a powerful role in prompting online searches for cancer information. Internet search activity offers an innovative tool for passive surveillance of health information–seeking behavior. PMID:15998627

Intelligent Text Retrieval and Knowledge Acquisition from Texts for NASA Applications: Preprocessing Issues

NASA Technical Reports Server (NTRS)

2002-01-01

A system that retrieves problem reports from a NASA database is described. The database is queried with natural language questions. Part-of-speech tags are first assigned to each word in the question using a rule based tagger. A partial parse of the question is then produced with independent sets of deterministic finite state a utomata. Using partial parse information, a look up strategy searches the database for problem reports relevant to the question. A bigram stemmer and irregular verb conjugates have been incorporated into the system to improve accuracy. The system is evaluated by a set of fifty five questions posed by NASA engineers. A discussion of future research is also presented.

A comparison of Boolean-based retrieval to the WAIS system for retrieval of aeronautical information

NASA Technical Reports Server (NTRS)

Marchionini, Gary; Barlow, Diane

1994-01-01

An evaluation of an information retrieval system using a Boolean-based retrieval engine and inverted file architecture and WAIS, which uses a vector-based engine, was conducted. Four research questions in aeronautical engineering were used to retrieve sets of citations from the NASA Aerospace Database which was mounted on a WAIS server and available through Dialog File 108 which served as the Boolean-based system (BBS). High recall and high precision searches were done in the BBS and terse and verbose queries were used in the WAIS condition. Precision values for the WAIS searches were consistently above the precision values for high recall BBS searches and consistently below the precision values for high precision BBS searches. Terse WAIS queries gave somewhat better precision performance than verbose WAIS queries. In every case, a small number of relevant documents retrieved by one system were not retrieved by the other, indicating the incomplete nature of the results from either retrieval system. Relevant documents in the WAIS searches were found to be randomly distributed in the retrieved sets rather than distributed by ranks. Advantages and limitations of both types of systems are discussed.

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.

Decision fatigue: A conceptual analysis.

PubMed

Pignatiello, Grant A; Martin, Richard J; Hickman, Ronald L

2018-03-01

Decision fatigue is an applicable concept to healthcare psychology. Due to a lack of conceptual clarity, we present a concept analysis of decision fatigue. A search of the term "decision fatigue" was conducted across seven research databases, which yielded 17 relevant articles. The authors identified three antecedent themes (decisional, self-regulatory, and situational) and three attributional themes (behavioral, cognitive, and physiological) of decision fatigue. However, the extant literature failed to adequately describe consequences of decision fatigue. This concept analysis provides needed conceptual clarity for decision fatigue, a concept possessing relevance to nursing and allied health sciences.

Selecting CD-ROM databases for nursing students: a comparison of MEDLINE and the Cumulative Index to Nursing and Allied Health Literature (CINAHL).

PubMed

Okuma, E

1994-01-01

With the introduction of the Cumulative Index to Nursing and Allied Health Literature (CINAHL) on CD-ROM, research was initiated to compare coverage of nursing journals by CINAHL and MEDLINE in this format, expanding on previous comparison of these databases in print and online. The study assessed search results for eight topics in 1989 and 1990 citations in both databases, each produced by SilverPlatter. Results were tallied and analyzed for number of records retrieved, unique and overlapping records, relevance, and appropriateness. An overall precision score was developed. The goal of the research was to develop quantifiable tools to help determine which database to purchase for an academic library serving an undergraduate nursing program.

Selecting CD-ROM databases for nursing students: a comparison of MEDLINE and the Cumulative Index to Nursing and Allied Health Literature (CINAHL).

PubMed Central

Okuma, E

1994-01-01

With the introduction of the Cumulative Index to Nursing and Allied Health Literature (CINAHL) on CD-ROM, research was initiated to compare coverage of nursing journals by CINAHL and MEDLINE in this format, expanding on previous comparison of these databases in print and online. The study assessed search results for eight topics in 1989 and 1990 citations in both databases, each produced by SilverPlatter. Results were tallied and analyzed for number of records retrieved, unique and overlapping records, relevance, and appropriateness. An overall precision score was developed. The goal of the research was to develop quantifiable tools to help determine which database to purchase for an academic library serving an undergraduate nursing program. PMID:8136757

The effectiveness of knowledge translation strategies used in public health: a systematic review

PubMed Central

2012-01-01

Background Literature related to the effectiveness of knowledge translation (KT) strategies used in public health is lacking. The capacity to seek, analyze, and synthesize evidence-based information in public health is linked to greater success in making policy choices that have the best potential to yield positive outcomes for populations. The purpose of this systematic review is to identify the effectiveness of KT strategies used to promote evidence-informed decision making (EIDM) among public health decision makers. Methods A search strategy was developed to identify primary studies published between 2000–2010. Studies were obtained from multiple electronic databases (CINAHL, Medline, EMBASE, and the Cochrane Database of Systematic Reviews). Searches were supplemented by hand searching and checking the reference lists of included articles. Two independent review authors screened studies for relevance, assessed methodological quality of relevant studies, and extracted data from studies using standardized tools. Results After removal of duplicates, the search identified 64, 391 titles related to KT strategies. Following title and abstract review, 346 publications were deemed potentially relevant, of which 5 met all relevance criteria on full text screen. The included publications were of moderate quality and consisted of five primary studies (four randomized controlled trials and one interrupted time series analysis). Results were synthesized narratively. Simple or single KT strategies were shown in some circumstances to be as effective as complex, multifaceted ones when changing practice including tailored and targeted messaging. Multifaceted KT strategies led to changes in knowledge but not practice. Knowledge translation strategies shown to be less effective were passive and included access to registries of pre-processed research evidence or print materials. While knowledge brokering did not have a significant effect generally, results suggested that it did have a positive effect on those organizations that at baseline perceived their organization to place little value on evidence-informed decision making. Conclusions No singular KT strategy was shown to be effective in all contexts. Conclusions about interventions cannot be taken on their own without considering the characteristics of the knowledge that was being transferred, providers, participants and organizations. PMID:22958371

School-Based Sex Education Policies and Indicators of Sexual Health among Young People: A Comparison of the Netherlands, France, Australia and the United States

ERIC Educational Resources Information Center

Weaver, Heather; Smith, Gary; Kippax, Susan

2005-01-01

This paper investigates the relationship between school-based sex education policies and sexual health-related statistics of young people in four developed countries: the Netherlands, France, Australia, and the United States of America. Drawing upon literature searches in relevant CD-ROM databases, Internet websites, government reports and…

What Works in Developing Nations to Get Children into School or Keep Them There?: A Systematic Review of Rigorous Impact Studies

ERIC Educational Resources Information Center

Petrosino, Anthony; Morgan, Claire; Fronius, Trevor; Tanner-Smith, Emily E.; Boruch, Robert F.

2015-01-01

Due to evidence linking education and development, funding has been invested in interventions relevant to getting youth into school and keeping them there. This article reports on a systematic review of impact studies of these school enrollment interventions. Reports were identified through electronic searches of bibliographic databases and other…

Psychological Interventions in the Rehabilitation of Patients with Chronic Low Back Pain: Evidence and Recommendations from Systematic Reviews and Guidelines

ERIC Educational Resources Information Center

Reese, Christina; Mittag, Oskar

2013-01-01

The purpose of the article is to summarize evidence and recommendations for psychological interventions in the rehabilitation of patients with chronic low back pain. We carried out a systematic literature search in several databases and on the websites of professional associations to identify relevant reviews and guidelines. In addition to the…

Protocol: a systematic review of studies developing and/or evaluating search strategies to identify prognosis studies.

PubMed

Corp, Nadia; Jordan, Joanne L; Hayden, Jill A; Irvin, Emma; Parker, Robin; Smith, Andrea; van der Windt, Danielle A

2017-04-20

Prognosis research is on the rise, its importance recognised because chronic health conditions and diseases are increasingly common and costly. Prognosis systematic reviews are needed to collate and synthesise these research findings, especially to help inform effective clinical decision-making and healthcare policy. A detailed, comprehensive search strategy is central to any systematic review. However, within prognosis research, this is challenging due to poor reporting and inconsistent use of available indexing terms in electronic databases. Whilst many published search filters exist for finding clinical trials, this is not the case for prognosis studies. This systematic review aims to identify and compare existing methodological filters developed and evaluated to identify prognosis studies of any of the three main types: overall prognosis, prognostic factors, and prognostic [risk prediction] models. Primary studies reporting the development and/or evaluation of methodological search filters to retrieve any type of prognosis study will be included in this systematic review. Multiple electronic bibliographic databases will be searched, grey literature will be sought from relevant organisations and websites, experts will be contacted, and citation tracking of key papers and reference list checking of all included papers will be undertaken. Titles will be screened by one person, and abstracts and full articles will be reviewed for inclusion independently by two reviewers. Data extraction and quality assessment will also be undertaken independently by two reviewers with disagreements resolved by discussion or by a third reviewer if necessary. Filters' characteristics and performance metrics reported in the included studies will be extracted and tabulated. To enable comparisons, filters will be grouped according to database, platform, type of prognosis study, and type of filter for which it was intended. This systematic review will identify all existing validated prognosis search filters and synthesise evidence about their applicability and performance. These findings will identify if current filters provide a proficient means of searching electronic bibliographic databases or if further prognosis filters are needed and can feasibly be developed for systematic searches of prognosis studies.

Choosing Important Health Outcomes for Comparative Effectiveness Research: An Updated Review and Identification of Gaps.

PubMed

Gorst, Sarah L; Gargon, Elizabeth; Clarke, Mike; Smith, Valerie; Williamson, Paula R

2016-01-01

The COMET (Core Outcome Measures in Effectiveness Trials) Initiative promotes the development and application of core outcome sets (COS), including relevant studies in an online database. In order to keep the database current, an annual search of the literature is undertaken. This study aimed to update a previous systematic review, in order to identify any further studies where a COS has been developed. Furthermore, no prioritization for COS development has previously been undertaken, therefore this study also aimed to identify COS relevant to the world's most prevalent health conditions. The methods used in this updated review followed the same approach used in the original review and the previous update. A survey was also sent to the corresponding authors of COS identified for inclusion in this review, to ascertain what lessons they had learnt from developing their COS. Additionally, the COMET database was searched to identify COS that might be relevant to the conditions with the highest global prevalence. Twenty-five reports relating to 22 new studies were eligible for inclusion in the review. Further improvements were identified in relation to the description of the scope of the COS, use of the Delphi technique, and the inclusion of patient participants within the development process. Additionally, 33 published and ongoing COS were identified for 13 of the world's most prevalent conditions. The development of a reporting guideline and minimum standards should contribute towards future improvements in development and reporting of COS. This study has also described a first approach to identifying gaps in existing COS, and to priority setting in this area. Important gaps have been identified, on the basis of global burden of disease, and the development and application of COS in these areas should be considered a priority.

Investigational drugs in dry eye disease.

PubMed

Nebbioso, Marcella; Fameli, Valeria; Gharbiya, Magda; Sacchetti, Marta; Zicari, Anna Maria; Lambiase, Alessandro

2016-12-01

The dry eye disease (DED) is a chronic multifactorial disorder of the tears that also involves the ocular surface, the lacrimal glands, and meibomian dysfunction. Furthermore, DED is often associated with Sjögren's syndrome (SS) and other autoimmune disorders. Sometimes, this chronic or subclinical condition is difficult to diagnose and treat, due to its heterogeneity. Areas covered: A literature search of relevant publications about treatment of DED was performed. All relevant articles published between 2011 and 2016 were identified through a computerized search for reviews and clinical trials using the Pub Med database. In particular, investigational treatments have been reported in this peer-reviewed publication. Relevant articles identified were manually searched and reviewed, then data concerning with novel treatment for DED were included into the manuscript. Expert opinion: The treatment of dry eye patients evolves continuously because DED seriously impacts the quality of life of older adults. Indeed, as a chronic disease, DED prevalence is expected to worsen with the aging population. For this reason, current efforts focus on combined pharmacological strategies targeted towards multiple systems. Probably this is the correct way to reach a long lasting symptoms relief treatment that may allow an actual improvement of patients' quality of life.

An active visual search interface for Medline.

PubMed

Xuan, Weijian; Dai, Manhong; Mirel, Barbara; Wilson, Justin; Athey, Brian; Watson, Stanley J; Meng, Fan

2007-01-01

Searching the Medline database is almost a daily necessity for many biomedical researchers. However, available Medline search solutions are mainly designed for the quick retrieval of a small set of most relevant documents. Because of this search model, they are not suitable for the large-scale exploration of literature and the underlying biomedical conceptual relationships, which are common tasks in the age of high throughput experimental data analysis and cross-discipline research. We try to develop a new Medline exploration approach by incorporating interactive visualization together with powerful grouping, summary, sorting and active external content retrieval functions. Our solution, PubViz, is based on the FLEX platform designed for interactive web applications and its prototype is publicly available at: http://brainarray.mbni.med.umich.edu/Brainarray/DataMining/PubViz.

Exploring issues in the conduct of website searching and other online sources for systematic reviews: how can we be systematic?

PubMed

Stansfield, Claire; Dickson, Kelly; Bangpan, Mukdarut

2016-11-15

Websites and online resources outside academic bibliographic databases can be significant sources for identifying literature, though there are challenges in searching and managing the results. These are pertinent to systematic reviews that are underpinned by principles of transparency, accountability and reproducibility. We consider how the conduct of searching these resources can be compatible with the principles of a systematic search. We present an approach to address some of the challenges. This is particularly relevant when websites are relied upon to identify important literature for a review. We recommend considering the process as three stages and having a considered rationale and sufficient recordkeeping at each stage that balances transparency with practicality of purpose. Advances in technology and recommendations for website providers are briefly discussed.

Refining search terms for nanotechnology

NASA Astrophysics Data System (ADS)

Porter, Alan L.; Youtie, Jan; Shapira, Philip; Schoeneck, David J.

2008-05-01

The ability to delineate the boundaries of an emerging technology is central to obtaining an understanding of the technology's research paths and commercialization prospects. Nowhere is this more relevant than in the case of nanotechnology (hereafter identified as "nano") given its current rapid growth and multidisciplinary nature. (Under the rubric of nanotechnology, we also include nanoscience and nanoengineering.) Past efforts have utilized several strategies, including simple term search for the prefix nano, complex lexical and citation-based approaches, and bootstrapping techniques. This research introduces a modularized Boolean approach to defining nanotechnology which has been applied to several research and patenting databases. We explain our approach to downloading and cleaning data, and report initial results. Comparisons of this approach with other nanotechnology search formulations are presented. Implications for search strategy development and profiling of the nanotechnology field are discussed.

Quality tools and resources to support organisational improvement integral to high-quality primary care: a systematic review of published and grey literature.

PubMed

Janamian, Tina; Upham, Susan J; Crossland, Lisa; Jackson, Claire L

2016-04-18

To conduct a systematic review of the literature to identify existing online primary care quality improvement tools and resources to support organisational improvement related to the seven elements in the Primary Care Practice Improvement Tool (PC-PIT), with the identified tools and resources to progress to a Delphi study for further assessment of relevance and utility. Systematic review of the international published and grey literature. CINAHL, Embase and PubMed databases were searched in March 2014 for articles published between January 2004 and December 2013. GreyNet International and other relevant websites and repositories were also searched in March-April 2014 for documents dated between 1992 and 2012. All citations were imported into a bibliographic database. Published and unpublished tools and resources were included in the review if they were in English, related to primary care quality improvement and addressed any of the seven PC-PIT elements of a high-performing practice. Tools and resources that met the eligibility criteria were then evaluated for their accessibility, relevance, utility and comprehensiveness using a four-criteria appraisal framework. We used a data extraction template to systematically extract information from eligible tools and resources. A content analysis approach was used to explore the tools and resources and collate relevant information: name of the tool or resource, year and country of development, author, name of the organisation that provided access and its URL, accessibility information or problems, overview of each tool or resource and the quality improvement element(s) it addresses. If available, a copy of the tool or resource was downloaded into the bibliographic database, along with supporting evidence (published or unpublished) on its use in primary care. This systematic review identified 53 tools and resources that can potentially be provided as part of a suite of tools and resources to support primary care practices in improving the quality of their practice, to achieve improved health outcomes.

Mining large heterogeneous data sets in drug discovery.

PubMed

Wild, David J

2009-10-01

Increasingly, effective drug discovery involves the searching and data mining of large volumes of information from many sources covering the domains of chemistry, biology and pharmacology amongst others. This has led to a proliferation of databases and data sources relevant to drug discovery. This paper provides a review of the publicly-available large-scale databases relevant to drug discovery, describes the kinds of data mining approaches that can be applied to them and discusses recent work in integrative data mining that looks for associations that pan multiple sources, including the use of Semantic Web techniques. The future of mining large data sets for drug discovery requires intelligent, semantic aggregation of information from all of the data sources described in this review, along with the application of advanced methods such as intelligent agents and inference engines in client applications.

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

PubMed Central

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

2016-01-01

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

A Review on Recent Patents and Applications of Inorganic Material Binding Peptides.

PubMed

Thota, Veeranjaneyulu; Perry, Carole C

2017-01-01

Although the popularity of using combinatorial display techniques for recognising unique peptides having high affinity for inorganic (nano) particles has grown rapidly, there are no systematic reviews showcasing current developments or patents on binding peptides specific to these materials. In this review, we summarize and discuss recent progress in patents on material binding peptides specifically exploring inorganic nano surfaces such as metals, metal oxides, minerals, carbonbased materials, polymer based materials, magnetic materials and semiconductors. We consider both the peptide display strategies used and the exploitation of the identified peptides in the generation of advanced nanomaterials. In order to get a clear picture on the number of patents and literature present to date relevant to inorganic material binding biomolecules and their applications, a thorough online search was conducted using national and worldwide databases. The literature search include standard bibliographic databases while patents included EPO Espacenet, WIPO patent scope, USPTO, Google patent search, Patent lens, etc. along with commercial databases such as Derwent and Patbase. Both English and American spellings were included in the searches. The initial number of patents found related to material binders were 981. After reading and excluding irrelevant patents such as organic binding peptides, works published before 2001, repeated patents, documents not in English etc., 51 highly relevant patents published from 2001 onwards were selected and analysed. These patents were further separated into six categories based on their target inorganic material and combinatorial library used. They include relevant patents on metal, metal oxide or combination binding peptides (19), magnetic and semiconductor binding peptides (8), carbon based (3), mineral (5), polymer (8) and other binders (9). Further, how these material specific binders have been used to synthesize simple to complex bio- or nano-materials, mediate the controlled biomineralization process, direct self-assembly and nanofabrication of ordered structures, facilitate the immobilization of functional biomolecules and construct inorganic-inorganic or organic-inorganic nano hybrids are concisely described. From analysis of recent literature and patents, we clearly show that biomimetic material binders are in the vanguard of new design approaches for novel nanomaterials with improved/ controlled physical and chemical properties that have no adverse effect on the structural or functional activities of the nanomaterials themselves. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

What is the effect of chest physiotherapy in hospitalized children with pneumonia?

PubMed

Damiani, Felipe; Adasme, Rodrigo

2015-10-19

Chest physiotherapy is applied in clinical practice for the treatment of pneumonia. However, its use is still controversial. Searching in Epistemonikos database, which is maintained by screening 30 databases, we identified one systematic review including two relevant randomized controlled trials. We combined the evidence using meta-analysis and generated a summary of findings table following the GRADE approach. We concluded it is unclear whether chest physiotherapy increases or decreases the length of hospitalization, severity, or the time to clinical improvement in children with pneumonia because the certainty of the evidence is very low.

SAM: String-based sequence search algorithm for mitochondrial DNA database queries

PubMed Central

Röck, Alexander; Irwin, Jodi; Dür, Arne; Parsons, Thomas; Parson, Walther

2011-01-01

The analysis of the haploid mitochondrial (mt) genome has numerous applications in forensic and population genetics, as well as in disease studies. Although mtDNA haplotypes are usually determined by sequencing, they are rarely reported as a nucleotide string. Traditionally they are presented in a difference-coded position-based format relative to the corrected version of the first sequenced mtDNA. This convention requires recommendations for standardized sequence alignment that is known to vary between scientific disciplines, even between laboratories. As a consequence, database searches that are vital for the interpretation of mtDNA data can suffer from biased results when query and database haplotypes are annotated differently. In the forensic context that would usually lead to underestimation of the absolute and relative frequencies. To address this issue we introduce SAM, a string-based search algorithm that converts query and database sequences to position-free nucleotide strings and thus eliminates the possibility that identical sequences will be missed in a database query. The mere application of a BLAST algorithm would not be a sufficient remedy as it uses a heuristic approach and does not address properties specific to mtDNA, such as phylogenetically stable but also rapidly evolving insertion and deletion events. The software presented here provides additional flexibility to incorporate phylogenetic data, site-specific mutation rates, and other biologically relevant information that would refine the interpretation of mitochondrial DNA data. The manuscript is accompanied by freeware and example data sets that can be used to evaluate the new software (http://stringvalidation.org). PMID:21056022

Multidimensional indexing structure for use with linear optimization queries

NASA Technical Reports Server (NTRS)

Bergman, Lawrence David (Inventor); Castelli, Vittorio (Inventor); Chang, Yuan-Chi (Inventor); Li, Chung-Sheng (Inventor); Smith, John Richard (Inventor)

2002-01-01

Linear optimization queries, which usually arise in various decision support and resource planning applications, are queries that retrieve top N data records (where N is an integer greater than zero) which satisfy a specific optimization criterion. The optimization criterion is to either maximize or minimize a linear equation. The coefficients of the linear equation are given at query time. Methods and apparatus are disclosed for constructing, maintaining and utilizing a multidimensional indexing structure of database records to improve the execution speed of linear optimization queries. Database records with numerical attributes are organized into a number of layers and each layer represents a geometric structure called convex hull. Such linear optimization queries are processed by searching from the outer-most layer of this multi-layer indexing structure inwards. At least one record per layer will satisfy the query criterion and the number of layers needed to be searched depends on the spatial distribution of records, the query-issued linear coefficients, and N, the number of records to be returned. When N is small compared to the total size of the database, answering the query typically requires searching only a small fraction of all relevant records, resulting in a tremendous speedup as compared to linearly scanning the entire dataset.

Supported Decision-Making: Implications from Positive Psychology for Assessment and Intervention in Rehabilitation and Employment.

PubMed

Uyanik, Hatice; Shogren, Karrie A; Blanck, Peter

2017-12-01

Purpose This article reviews existing literature on positive psychology, supported decision-making (SDM), employment, and disability. It examines interventions and assessments that have been empirically evaluated for the enhancement of decision-making and overall well-being of people with disabilities. Additionally, conceptual themes present in the literature were explored. Methods A systematic review was conducted across two databases (ERIC and PsychINFO) using various combination of keywords of 'disabilit*', work rehabilitation and employment terms, positive psychology terms, and SDM components. Seven database searches were conducted with diverse combinations of keywords, which identified 1425 results in total to be screened for relevance using their titles and abstracts. Database search was supplemented with hand searches of oft-cited journals, ancestral search, and supplemental search from grey literature. Results Only four studies were identified in the literature targeting SDM and positive psychology related constructs in the employment and job development context. Results across the studies indicated small to moderate impacts of the assessment and interventions on decision-making and engagement outcomes. Conceptually there are thematic areas of potential overlap, although they are limited in the explicit integration of theory in supported decision-making, positive psychology, disability, and employment. Conclusion Results suggest a need for additional scholarship in this area that focuses on theory development and integration as well as empirical work. Such work should examine the potential utility of considering positive psychological interventions when planning for SDM in the context of career development activities to enhance positive outcomes related to decision-making, self-determination, and other positive psychological constructs.

Advanced Satellite Research Project: SCAR Research Database. Bibliographic analysis

NASA Technical Reports Server (NTRS)

Pelton, Joseph N.

1991-01-01

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

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

Adjacency and Proximity Searching in the Science Citation Index and Google

DTIC Science & Technology

2005-01-01

major database search engines , including commercial S&T database search engines (e.g., Science Citation Index (SCI), Engineering Compendex (EC...PubMed, OVID), Federal agency award database search engines (e.g., NSF, NIH, DOE, EPA, as accessed in Federal R&D Project Summaries), Web search Engines (e.g...searching. Some database search engines allow strict constrained co- occurrence searching as a user option (e.g., OVID, EC), while others do not (e.g., SCI

Flare-ups after endodontic treatment: a meta-analysis of literature.

PubMed

Tsesis, Igor; Faivishevsky, Vadim; Fuss, Zvi; Zukerman, Ofer

2008-10-01

The purpose of this study was to determine the frequency of flare-ups and to evaluate factors that affect it by using meta-analysis of results of previous studies. MEDLINE database was searched by using Entrez PubMed search engine and Medical Subject Headings (MeSH) search with EviDents Search Engine to identify the studies dealing with endodontic flare-up phenomenon. The search covered all articles published in dental journals in English from 1966-May 2007, and the relevancy of 119 selected articles was evaluated by reading their titles and abstracts, from which 54 were rejected as irrelevant and 65 were subjected to a suitability test. Six studies that met all the above mentioned criteria were included in the study. Average percentage of incidence of flare-ups for 982 patients was 8.4 (standard deviation +/-57). There were insufficient data to investigate the effect of the influencing factors.

Raising the IQ in full-text searching via intelligent querying

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

Kero, R.; Russell, L.; Swietlik, C.

1994-11-01

Current Information Retrieval (IR) technologies allow for efficient access to relevant information, provided that user selected query terms coincide with the specific linguistical choices made by the authors whose works constitute the text-base. Therefore, the challenge is to enhance the limited searching capability of state-of-the-practice IR. This can be done either with augmented clients that overcome current server searching deficiencies, or with added capabilities that can augment searching algorithms on the servers. The technology being investigated is that of deductive databases, with a set of new techniques called cooperative answering. This technology utilizes semantic networks to allow for navigation betweenmore » possible query search term alternatives. The augmented search terms are passed to an IR engine and the results can be compared. The project utilizes the OSTI Environment, Safety and Health Thesaurus to populate the domain specific semantic network and the text base of ES&H related documents from the Facility Profile Information Management System as the domain specific search space.« less

Database Resources of the BIG Data Center in 2018

PubMed Central

Xu, Xingjian; Hao, Lili; Zhu, Junwei; Tang, Bixia; Zhou, Qing; Song, Fuhai; Chen, Tingting; Zhang, Sisi; Dong, Lili; Lan, Li; Wang, Yanqing; Sang, Jian; Hao, Lili; Liang, Fang; Cao, Jiabao; Liu, Fang; Liu, Lin; Wang, Fan; Ma, Yingke; Xu, Xingjian; Zhang, Lijuan; Chen, Meili; Tian, Dongmei; Li, Cuiping; Dong, Lili; Du, Zhenglin; Yuan, Na; Zeng, Jingyao; Zhang, Zhewen; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Pan, Mengyu; Tang, Bixia; Zou, Dong; Song, Shuhui; Sang, Jian; Xia, Lin; Wang, Zhennan; Li, Man; Cao, Jiabao; Niu, Guangyi; Zhang, Yang; Sheng, Xin; Lu, Mingming; Wang, Qi; Xiao, Jingfa; Zou, Dong; Wang, Fan; Hao, Lili; Liang, Fang; Li, Mengwei; Sun, Shixiang; Zou, Dong; Li, Rujiao; Yu, Chunlei; Wang, Guangyu; Sang, Jian; Liu, Lin; Li, Mengwei; Li, Man; Niu, Guangyi; Cao, Jiabao; Sun, Shixiang; Xia, Lin; Yin, Hongyan; Zou, Dong; Xu, Xingjian; Ma, Lina; Chen, Huanxin; Sun, Yubin; Yu, Lei; Zhai, Shuang; Sun, Mingyuan; Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa; Bao, Yiming; Song, Shuhui; Hao, Lili; Li, Rujiao; Ma, Lina; Sang, Jian; Wang, Yanqing; Tang, Bixia; Zou, Dong; Wang, Fan

2018-01-01

Abstract The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. PMID:29036542

Comet: an open-source MS/MS sequence database search tool.

PubMed

Eng, Jimmy K; Jahan, Tahmina A; Hoopmann, Michael R

2013-01-01

Proteomics research routinely involves identifying peptides and proteins via MS/MS sequence database search. Thus the database search engine is an integral tool in many proteomics research groups. Here, we introduce the Comet search engine to the existing landscape of commercial and open-source database search tools. Comet is open source, freely available, and based on one of the original sequence database search tools that has been widely used for many years. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Database Search Engines: Paradigms, Challenges and Solutions.

PubMed

Verheggen, Kenneth; Martens, Lennart; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

2016-01-01

The first step in identifying proteins from mass spectrometry based shotgun proteomics data is to infer peptides from tandem mass spectra, a task generally achieved using database search engines. In this chapter, the basic principles of database search engines are introduced with a focus on open source software, and the use of database search engines is demonstrated using the freely available SearchGUI interface. This chapter also discusses how to tackle general issues related to sequence database searching and shows how to minimize their impact.

Determining conserved metabolic biomarkers from a million database queries.

PubMed

Kurczy, Michael E; Ivanisevic, Julijana; Johnson, Caroline H; Uritboonthai, Winnie; Hoang, Linh; Fang, Mingliang; Hicks, Matthew; Aldebot, Anthony; Rinehart, Duane; Mellander, Lisa J; Tautenhahn, Ralf; Patti, Gary J; Spilker, Mary E; Benton, H Paul; Siuzdak, Gary

2015-12-01

Metabolite databases provide a unique window into metabolome research allowing the most commonly searched biomarkers to be catalogued. Omic scale metabolite profiling, or metabolomics, is finding increased utility in biomarker discovery largely driven by improvements in analytical technologies and the concurrent developments in bioinformatics. However, the successful translation of biomarkers into clinical or biologically relevant indicators is limited. With the aim of improving the discovery of translatable metabolite biomarkers, we present search analytics for over one million METLIN metabolite database queries. The most common metabolites found in METLIN were cross-correlated against XCMS Online, the widely used cloud-based data processing and pathway analysis platform. Analysis of the METLIN and XCMS common metabolite data has two primary implications: these metabolites, might indicate a conserved metabolic response to stressors and, this data may be used to gauge the relative uniqueness of potential biomarkers. METLIN can be accessed by logging on to: https://metlin.scripps.edu siuzdak@scripps.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Challenges of the information age: the impact of false discovery on pathway identification.

PubMed

Rog, Colin J; Chekuri, Srinivasa C; Edgerton, Mary E

2012-11-21

Pathways with members that have known relevance to a disease are used to support hypotheses generated from analyses of gene expression and proteomic studies. Using cancer as an example, the pitfalls of searching pathways databases as support for genes and proteins that could represent false discoveries are explored. The frequency with which networks could be generated from 100 instances each of randomly selected five and ten genes sets as input to MetaCore, a commercial pathways database, was measured. A PubMed search enumerated cancer-related literature published for any gene in the networks. Using three, two, and one maximum intervening step between input genes to populate the network, networks were generated with frequencies of 97%, 77%, and 7% using ten gene sets and 73%, 27%, and 1% using five gene sets. PubMed reported an average of 4225 cancer-related articles per network gene. This can be attributed to the richly populated pathways databases and the interest in the molecular basis of cancer. As information sources become enriched, they are more likely to generate plausible mechanisms for false discoveries.

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.

Diagnostic Evaluation of Nontraumatic Chest Pain in Athletes.

PubMed

Moran, Byron; Bryan, Sean; Farrar, Ted; Salud, Chris; Visser, Gary; Decuba, Raymond; Renelus, Deborah; Buckley, Tyler; Dressing, Michael; Peterkin, Nicholas; Coris, Eric

This article is a clinically relevant review of the existing medical literature relating to the assessment and diagnostic evaluation for athletes complaining of nontraumatic chest pain. The literature was searched using the following databases for the years 1975 forward: Cochrane Database of Systematic Reviews; CINAHL; PubMed (MEDLINE); and SportDiscus. The general search used the keywords chest pain and athletes. The search was revised to include subject headings and subheadings, including chest pain and prevalence and athletes. Cross-referencing published articles from the databases searched discovered additional articles. No dissertations, theses, or meeting proceedings were reviewed. The authors discuss the scope of this complex problem and the diagnostic dilemma chest pain in athletes can provide. Next, the authors delve into the vast differential and attempt to simplify this process for the sports medicine physician by dividing potential etiologies into cardiac and noncardiac conditions. Life-threatening causes of chest pain in athletes may be cardiac or noncardiac in origin, which highlights the need for the sports medicine physician to consider pathology in multiple organ systems simultaneously. This article emphasizes the importance of ruling out immediately life threatening diagnoses, while acknowledging the most common causes of noncardiac chest pain in young athletes are benign. The authors propose a practical algorithm the sports medicine physician can use as a guide for the assessment and diagnostic work-up of the athlete with chest pain designed to help the physician arrive at the correct diagnosis in a clinically efficient and cost-effective manner.

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.

A knowledge based search tool for performance measures in health care systems.

PubMed

Beyan, Oya D; Baykal, Nazife

2012-02-01

Performance measurement is vital for improving the health care systems. However, we are still far from having accepted performance measurement models. Researchers and developers are seeking comparable performance indicators. We developed an intelligent search tool to identify appropriate measures for specific requirements by matching diverse care settings. We reviewed the literature and analyzed 229 performance measurement studies published after 2000. These studies are evaluated with an original theoretical framework and stored in the database. A semantic network is designed for representing domain knowledge and supporting reasoning. We have applied knowledge based decision support techniques to cope with uncertainty problems. As a result we designed a tool which simplifies the performance indicator search process and provides most relevant indicators by employing knowledge based systems.

An approach in building a chemical compound search engine in oracle database.

PubMed

Wang, H; Volarath, P; Harrison, R

2005-01-01

A searching or identifying of chemical compounds is an important process in drug design and in chemistry research. An efficient search engine involves a close coupling of the search algorithm and database implementation. The database must process chemical structures, which demands the approaches to represent, store, and retrieve structures in a database system. In this paper, a general database framework for working as a chemical compound search engine in Oracle database is described. The framework is devoted to eliminate data type constrains for potential search algorithms, which is a crucial step toward building a domain specific query language on top of SQL. A search engine implementation based on the database framework is also demonstrated. The convenience of the implementation emphasizes the efficiency and simplicity of the framework.

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.…

Reporting guidelines in health research: A review.

PubMed

Simon, Arun K; Rao, Ashwini; Rajesh, Gururaghavendran; Shenoy, Ramya; Pai, Mithun B

2015-01-01

Contemporary health research has come under close scrutiny, exposing alarming flaws in the reporting of research. The reporting guidelines can aid in identification of poorly reported studies and can bring transparency to health research. The guidelines also help journal editors, peer reviewers, funding agencies, and readers to better discern health research. Reporting guidelines encourage accurate and thorough reporting of fundamental aspects of health research so that the results of studies can be replicated by others. Reporting guidelines are potent tools to improve the practice of research and in reducing reporting bias. For the present review, both electronic and manual literature search was carried out. Electronic databases like PubMed, MEDLINE, EBSCO host, and Science Direct were searched for extracting relevant articles. Various key words and their combinations were used for literature search like reporting guidelines, checklist, research, publishing standards, study design, medicine, and dentistry. The search results were scrutinized for relevance to the topic and only full text articles in English were incorporated. Various reporting guidelines were identified and grouped under headings based on study design. This review article attempts to highlight the various reporting guidelines in literature relating to health research, its potential applications, and its limitations.

Mobile phone interference with medical equipment and its clinical relevance: a systematic review.

PubMed

Lawrentschuk, Nathan; Bolton, Damien M

2004-08-02

To conduct a systematic review of studies on clinically relevant digital mobile phone electromagnetic interference with medical equipment. MEDLINE and SUMSEARCH were searched for the period 1966-2004. The Cochrane Library and Database of Abstracts of Reviews of Effects were also searched for systematic reviews. Studies were eligible if published in a peer-reviewed journal in English, and if they included testing of digital mobile phones for clinically relevant interference with medical equipment used to monitor or treat patients, but not implantable medical devices. As there was considerable heterogeneity in medical equipment studied and the conduct of testing, results were summarised rather than subjected to meta-analysis. Clinically relevant electromagnetic interference (EMI) secondary to mobile phones potentially endangering patients occurred in 45 of 479 devices tested at 900 MHz and 14 of 457 devices tested at 1800 MHz. However, in the largest studies, the prevalence of clinically relevant EMI was low. Most clinically relevant EMI occurred when mobile phones were used within 1 m of medical equipment. Although testing was not standardised between studies and equipment tested was not identical, it is of concern that at least 4% of devices tested in any study were susceptible to clinically relevant EMI. All studies recommend some type of restriction of mobile phone use in hospitals, with use greater than 1 m from equipment and restrictions in clinical areas being the most common.

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

PubMed

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

2015-04-01

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

Towards a model of surgeons' leadership in the operating room.

PubMed

Henrickson Parker, Sarah; Yule, Steven; Flin, Rhona; McKinley, Aileen

2011-07-01

There is widespread recognition that leadership skills are essential for effective performance in the workplace, but the evidence detailing effective leadership behaviours for surgeons during operations is unclear. Boolean searches of four on-line databases and detailed hand search of relevant references were conducted. A four stage screening process was adopted stipulating that articles presented empirical data on surgeons' intraoperative leadership behaviours. Ten relevant articles were identified and organised by method of investigation into (i) observation, (ii) questionnaire and (iii) interview studies. This review summarises the limited literature on surgeons' intraoperative leadership, and proposes a preliminary theoretically based structure for intraoperative leadership behaviours. This structure comprises seven categories with corresponding leadership components and covers two overarching themes related to task- and team-focus. Selected leadership theories which may be applicable to the operating room environment are also discussed. Further research is required to determine effective intraoperative leadership behaviours for safe surgical practice.

[Is combining metronidazole and alcohol really hazardous?].

PubMed

Fjeld, Hilde; Raknes, Guttorm

2014-09-16

It is common practice to warn against intake of alcohol (ethanol) when taking metronidazole because of the risk of an effect similar to disulfiram (Antabuse). In this article we investigate whether such a warning has any real basis. KNOWLEDGE BASE: The article is based on a review of relevant literature retrieved through a search in PubMed. A search was also made in the WHO's database on adverse effects. No in-vitro studies, animal models, reports of adverse effects or clinical studies provide any convincing evidence of a disulfiram-like interaction between ethanol and metronidazole. The warning against simultaneous use of alcohol and metronidazole appear to be based on laboratory experiments and individual case histories in which the reported reactions are equally likely to have been caused by ethanol alone or by adverse effects of metronidazole. Recent research does not confirm a clinically relevant interaction between ethanol and metronidazole.

Evidence-based dental practice: part I. Formulating clinical questions and searching for answers.

PubMed

Adeyemo, W L; Akinwande, J A; Bamgbose, B O

2007-01-01

Evidence-based dentistry (EBD) is an approach to oral health care that requires the judicious integration of systematic assessments of clinically relevant scientific evidence, relating to the patient's oral and medical condition and history, with the dentist's clinical expertise and the patient's treatment needs and preferences. Evidence-based care is now regarded as the "gold standard" in health care delivery worldwide. EBD involves tracking down the available evidence, assessing its validity and relevance, and then using the "best" evidence to inform decisions regarding care. Although, the concept of evidence-based dentistry is not new, however, anecdotal evidence suggests that the awareness of this concept among Nigerian dental practitioners is low. This first of three articles on evidence-based dental practice discusses the historical background of evidence-based medicine/evidence-based dentistry, how to formulate clear clinical questions and how to track down (search) the available evidence in the literature databases.

[Scientometrics and bibliometrics of biomedical engineering periodicals and papers].

PubMed

Zhao, Ping; Xu, Ping; Li, Bingyan; Wang, Zhengrong

2003-09-01

This investigation was made to reveal the current status, research trend and research level of biomedical engineering in Chinese mainland by means of scientometrics and to assess the quality of the four domestic publications by bibliometrics. We identified all articles of four related publications by searching Chinese and foreign databases from 1997 to 2001. All articles collected or cited by these databases were searched and statistically analyzed for finding out the relevant distributions, including databases, years, authors, institutions, subject headings and subheadings. The source of sustentation funds and the related articles were analyzed too. The results showed that two journals were cited by two foreign databases and five Chinese databases simultaneously. The output of Journal of Biomedical Engineering was the highest. Its quantity of original papers cited by EI, CA and the totality of papers sponsored by funds were higher than those of the others, but the quantity and percentage per year of biomedical articles cited by EI were decreased in all. Inland core authors and institutions had come into being in the field of biomedical engineering. Their research topics were mainly concentrated on ten subject headings which included biocompatible materials, computer-assisted signal processing, electrocardiography, computer-assisted image processing, biomechanics, algorithms, electroencephalography, automatic data processing, mechanical stress, hemodynamics, mathematical computing, microcomputers, theoretical models, etc. The main subheadings were concentrated on instrumentation, physiopathology, diagnosis, therapy, ultrasonography, physiology, analysis, surgery, pathology, method, etc.

Nursing record systems: effects on nursing practice and health care outcomes.

PubMed

Currell, R; Urquhart, C

2003-01-01

A nursing record system is the record of care planned and/or given to individual patients/clients by qualified nurses or other caregivers under the direction of a qualified nurse. Nursing record systems may be an effective way of influencing nurse practice. To assess the effects of nursing record systems on nursing practice and patient outcomes. We searched The Cochrane Library, the EPOC trial register (October 2002), MEDLINE, Cinahl, Sigle, and databases of the Royal College of Nursing, King's Fund, the NHS Centre for Reviews and Dissemination, and the Institute of Electrical Engineers up to August 1999; and OCLC First Search, Department of Health database, NHS Register of Computer Applications and the Health Visitors' Association database up to the end of 1995. We hand searched the Journal of Nursing Administration (1971-1999), Computers in Nursing (1984-1999), Information Technology in Nursing (1989-1999) and reference lists of articles. We also hand searched the major health informatics conference proceedings. We contacted experts in the field of nursing informatics, suppliers of nursing computer systems, and relevant Internet groups. To update the review the Medline, Cinahl, British Nursing Index, Aslib Index to Theses databases were all searched from 1998 to 2002. The Journal of Nursing Administration, Computers in Nursing, Information Technology in Nursing were all hand searched up to 2002. The searches of the other databases and grey literature included in the original review, were not updated (except for Health Care Computing Conference and Med Info) as the original searches produced little relevant material. Randomised trials, controlled before and after studies and interrupted time series comparing one kind of nursing record system with another, in hospital, community or primary care settings. The participants were qualified nurses, students or health care assistants working under the direction of a qualified nurse and patients receiving care recorded and/or planned using nursing record systems. Two reviewers independently assessed trial quality and extracted data. Eight trials involving 1497 people were included. In three studies of client held records, there were no overall positive or negative effects, although some administrative benefits through fewer missing notes were suggested. A paediatric pain management sheet study showed a positive effect on the children's pain intensity. A computerised nursing care planning study showed a negative effect on documented nursing care planning, although two other computerised nursing information studies showed an increase in recording but no change in patient outcomes. Care planning took longer with these computerised systems, but the numbers of patients and nurses included in these studies was small. A controlled before-and-after study of two paper nursing record systems showed improvement in meeting documentation standards. No evidence was found of effects on practice attributable to changes in record systems. Although there is a paucity of studies of sufficient methodological rigour to yield reliable results in this area, it is clear from the literature that it is possible to set up randomised trials or other quasi-experimental designs needed to produce evidence for practice. The research undertaken so far may have suffered both from methodological problems and faulty hypotheses. Qualitative nursing research to explore the relationship between practice and information use, could be used as a precursor to the design and testing of nursing information systems.

SU-D-BRD-06: Automated Population-Based Planning for Whole Brain Radiation Therapy

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

Schreibmann, E; Fox, T; Crocker, I

2014-06-01

Purpose: Treatment planning for whole brain radiation treatment is technically a simple process but in practice it takes valuable clinical time of repetitive and tedious tasks. This report presents a method that automatically segments the relevant target and normal tissues and creates a treatment plan in only a few minutes after patient simulation. Methods: Segmentation is performed automatically through morphological operations on the soft tissue. The treatment plan is generated by searching a database of previous cases for patients with similar anatomy. In this search, each database case is ranked in terms of similarity using a customized metric designed formore » sensitivity by including only geometrical changes that affect the dose distribution. The database case with the best match is automatically modified to replace relevant patient info and isocenter position while maintaining original beam and MLC settings. Results: Fifteen patients were used to validate the method. In each of these cases the anatomy was accurately segmented to mean Dice coefficients of 0.970 ± 0.008 for the brain, 0.846 ± 0.009 for the eyes and 0.672 ± 0.111 for the lens as compared to clinical segmentations. Each case was then subsequently matched against a database of 70 validated treatment plans and the best matching plan (termed auto-planned), was compared retrospectively with the clinical plans in terms of brain coverage and maximum doses to critical structures. Maximum doses were reduced by a maximum of 20.809 Gy for the left eye (mean 3.533), by 13.352 (1.311) for the right eye, and by 27.471 (4.856), 25.218 (6.315) for the left and right lens. Time from simulation to auto-plan was 3-4 minutes. Conclusion: Automated database- based matching is an alternative to classical treatment planning that improves quality while providing a cost—effective solution to planning through modifying previous validated plans to match a current patient's anatomy.« less

HER-2 expression in biopsy and surgical specimen on prognosis of osteosarcoma: A systematic review and meta-analysis of 16 studies.

PubMed

Zhang, Qingyu; Liu, Fanxiao; Wang, Bomin; Li, Zhenfeng; Zhou, Dongsheng; Yang, Qiang; Dong, Jinlei; Li, Jianmin

2016-06-01

Numerous original clinical studies have attempted to investigate the prognostic value of HER-2 overexpression in osteosarcoma, but the results of these studies are not consistent. This meta-analysis and systematic review was performed to further assess the correlation between HER-2 expression and prognosis in patients with osteosarcoma. A detailed search of relevant publications was conducted using 7 electronic databases: PubMed, Embase, the Cochrane library, the Wanfang database, the China National Knowledge Internet (CNKI) database, the Chinese VIP database, and the Chinese Biological Medical (CBM) Database for publications through August 1, 2015, using the following keywords (HER-2 OR ErbB-2 OR C-erbB-2 OR neu) AND (osteosarcoma OR osteogenic tumor). The bibliographies of potentially relevant articles and identified articles were then searched by hand. Eligible studies were those that enrolled participants with osteosarcoma and provided survival outcome in HER-2 positive and negative groups. The hazard ratio (HR) and 95% confidence interval (CI) for each individual study was calculated and pooled to obtain integrated estimates, using random effects modeling. Sixteen studies involving 934 participants with osteosarcoma met our inclusion criteria. HER-2 overexpression was documented in 42.2% of patients with osteosarcoma. Compared with patients without HER-2 overexpression, those overexpressing HER-2 had decreased overall survival (HR = 2.03, 95% CI: 1.36-3.03, P < 0.001). Statistical associations between HER-2 overexpression and unfavorable overall survival (OS) were observed for both biopsy and surgical removal specimens (HR = 2.07, 95%CI: 1.16-3.72, P = 0.014; and HR = 2.02, 95%CI: 1.10-3.71, P = 0.024). Results for disease-free survival (DFS) were similar. Overexpression of HER-2 is significantly associated with poor outcome for patients with osteosarcoma and should be assessed at diagnosis and after surgery as a prognostic factor. However, larger-scale multicenter clinical studies are needed to further support these findings.

Are Bibliographic Management Software Search Interfaces Reliable?: A Comparison between Search Results Obtained Using Database Interfaces and the EndNote Online Search Function

ERIC Educational Resources Information Center

Fitzgibbons, Megan; Meert, Deborah

2010-01-01

The use of bibliographic management software and its internal search interfaces is now pervasive among researchers. This study compares the results between searches conducted in academic databases' search interfaces versus the EndNote search interface. The results show mixed search reliability, depending on the database and type of search…

PRIM versus CART in subgroup discovery: when patience is harmful.

PubMed

Abu-Hanna, Ameen; Nannings, Barry; Dongelmans, Dave; Hasman, Arie

2010-10-01

We systematically compare the established algorithms CART (Classification and Regression Trees) and PRIM (Patient Rule Induction Method) in a subgroup discovery task on a large real-world high-dimensional clinical database. Contrary to current conjectures, PRIM's performance was generally inferior to CART's. PRIM often considered "peeling of" a large chunk of data at a value of a relevant discrete ordinal variable unattractive, ultimately missing an important subgroup. This finding has considerable significance in clinical medicine where ordinal scores are ubiquitous. PRIM's utility in clinical databases would increase when global information about (ordinal) variables is better put to use and when the search algorithm keeps track of alternative solutions.

Divorce and Single-Parent Family Counseling. Searchlight Plus: Relevant Resources in High Interest Areas. No 26+.

ERIC Educational Resources Information Center

Hale, Lynelle C.

This document, based on a computer search of the ERIC database, presents a review of the literature on divorce and single parent families. Statistics from the 1980 census are presented which show that 19.7 percent of children under 18 live with a single parent, who in the overwhelming number of cases is the mother. The document presents data on…

Guidelines for preventing common medical complications of catatonia: case report and literature review.

PubMed

Clinebell, Kimberly; Azzam, Pierre N; Gopalan, Priya; Haskett, Roger

2014-06-01

Comprehensive hospital-based care for individuals with catatonia relies on preventive approaches to reduce medical morbidity and mortality. Without syndrome-specific guidelines, psychiatrists must draw from measures used for general medical and surgical inpatients. We employ a prototypical case to highlight medical complications of catatonia and review preventive guidelines for implementation in the inpatient setting. Searches of the PubMed and Ovid databases were conducted from September-November 2013 using keywords relevant to 4 medical complications of catatonia: deep vein thrombosis/pulmonary embolism, pressure ulcers, muscle contractures, and nutritional deficiencies. A complementary general web-browser search was performed to help ensure that unpublished guidelines were considered. A search for deep vein thrombosis/pulmonary embolism guidelines yielded 478 articles that were appraised for relevance, and 6 were chosen for review; the pressure ulcer guideline search yielded 5,665 articles, and 5 were chosen; the muscle contractures guideline search yielded 1,481 articles, and 3 were chosen; and the nutritional deficiencies guideline search yielded 16,937 articles, and 4 were chosen. Guidelines were reviewed for content and summarized in a manner relevant to the audience. No quantitative analyses were conducted. Guidelines for deep vein thrombosis/pulmonary embolism prophylaxis support use of anticoagulant therapies for patients with catatonia who are at lower risk for acute bleeding. Pressure ulcer prevention hinges on frequent skin evaluation, use of support surfaces, and repositioning. Muscle contracture data are less clear and must be extrapolated from studies of patients with neurologic injuries. Early initiation of enteral nutrition should be considered in patients with prolonged immobility. As medical complications are common with catatonia, implementation of preventive measures is imperative. © Copyright 2014 Physicians Postgraduate Press, Inc.

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

Omicseq: a web-based search engine for exploring omics datasets

PubMed Central

Sun, Xiaobo; Pittard, William S.; Xu, Tianlei; Chen, Li; Zwick, Michael E.; Jiang, Xiaoqian; Wang, Fusheng

2017-01-01

Abstract The development and application of high-throughput genomics technologies has resulted in massive quantities of diverse omics data that continue to accumulate rapidly. These rich datasets offer unprecedented and exciting opportunities to address long standing questions in biomedical research. However, our ability to explore and query the content of diverse omics data is very limited. Existing dataset search tools rely almost exclusively on the metadata. A text-based query for gene name(s) does not work well on datasets wherein the vast majority of their content is numeric. To overcome this barrier, we have developed Omicseq, a novel web-based platform that facilitates the easy interrogation of omics datasets holistically to improve ‘findability’ of relevant data. The core component of Omicseq is trackRank, a novel algorithm for ranking omics datasets that fully uses the numerical content of the dataset to determine relevance to the query entity. The Omicseq system is supported by a scalable and elastic, NoSQL database that hosts a large collection of processed omics datasets. In the front end, a simple, web-based interface allows users to enter queries and instantly receive search results as a list of ranked datasets deemed to be the most relevant. Omicseq is freely available at http://www.omicseq.org. PMID:28402462

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.

EuPathDB: the eukaryotic pathogen genomics database resource

PubMed Central

Aurrecoechea, Cristina; Barreto, Ana; Basenko, Evelina Y.; Brestelli, John; Brunk, Brian P.; Cade, Shon; Crouch, Kathryn; Doherty, Ryan; Falke, Dave; Fischer, Steve; Gajria, Bindu; Harb, Omar S.; Heiges, Mark; Hertz-Fowler, Christiane; Hu, Sufen; Iodice, John; Kissinger, Jessica C.; Lawrence, Cris; Li, Wei; Pinney, Deborah F.; Pulman, Jane A.; Roos, David S.; Shanmugasundram, Achchuthan; Silva-Franco, Fatima; Steinbiss, Sascha; Stoeckert, Christian J.; Spruill, Drew; Wang, Haiming; Warrenfeltz, Susanne; Zheng, Jie

2017-01-01

The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of host–pathogen interactions. PMID:27903906

Zirconia in dental implantology: A review

PubMed Central

Apratim, Abhishek; Eachempati, Prashanti; Krishnappa Salian, Kiran Kumar; Singh, Vijendra; Chhabra, Saurabh; Shah, Sanket

2015-01-01

Background: Titanium has been the most popular material of choice for dental implantology over the past few decades. Its properties have been found to be most suitable for the success of implant treatment. But recently, zirconia is slowly emerging as one of the materials which might replace the gold standard of dental implant, i.e., titanium. Materials and Methods: Literature was searched to retrieve information about zirconia dental implant and studies were critically analyzed. PubMed database was searched for information about zirconia dental implant regarding mechanical properties, osseointegration, surface roughness, biocompatibility, and soft tissue health around it. The literature search was limited to English language articles published from 1975 to 2015. Results: A total of 45 papers met the inclusion criteria for this review, among the relevant search in the database. Conclusion: Literature search showed that some of the properties of zirconia seem to be suitable for making it an ideal dental implant, such as biocompatibility, osseointegration, favourable soft tissue response and aesthetics due to light transmission and its color. At the same time, some studies also point out its drawbacks. It was also found that most of the studies on zirconia dental implants are short-term studies and there is a need for more long-term clinical trials to prove that zirconia is worth enough to replace titanium as a biomaterial in dental implantology. PMID:26236672

Antileishmanial and Immunomodulatory Activity of Allium sativum (Garlic): A Review.

PubMed

Foroutan-Rad, Masoud; Tappeh, Khosrow Hazrati; Khademvatan, Shahram

2017-01-01

Leishmaniasis is caused by an obligate intracellular protozoa belonging to Leishmania genus. The current drugs for treatment of leishmaniasis possess many disadvantages; therefore, researchers are continuously looking for the more effective and safer drugs. The aim of this study is to review the effectiveness, toxicities, and possible mechanisms of pharmaceutical actions of different garlic extracts and organosulfur compounds isolated from garlic against Leishmania spp. in a variety of in vitro, in vivo and clinical trials reports. All relevant databases were searched using the terms "Allium sativum," "Garlic," "Allicin," "Ajoene," "Leishmania," "in vitro," "in vivo," and "clinical trial," alone or in combination from 5 English databases (Web of Science, PubMed, Science Direct, Scopus, Google Scholar) and 3 Persian databases (Scientific Information Database, Iran Medex, and Magiran) from 1990 to 2014. In summary, garlic with immunomodulatory effects and apoptosis induction contributes to the treatment of leishmaniasis. © The Author(s) 2015.

Cutaneous lichen planus: A systematic review of treatments.

PubMed

Fazel, Nasim

2015-06-01

Various treatment modalities are available for cutaneous lichen planus. Pubmed, EMBASE, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, Database of Abstracts of Reviews of Effects, and Health Technology Assessment Database were searched for all the systematic reviews and randomized controlled trials related to cutaneous lichen planus. Two systematic reviews and nine relevant randomized controlled trials were identified. Acitretin, griseofulvin, hydroxychloroquine and narrow band ultraviolet B are demonstrated to be effective in the treatment of cutaneous lichen planus. Sulfasalazine is effective, but has an unfavorable safety profile. KH1060, a vitamin D analogue, is not beneficial in the management of cutaneous lichen planus. Evidence from large scale randomized trials demonstrating the safety and efficacy for many other treatment modalities used to treat cutaneous lichen planus is simply not available.

Innovations in health service organization and delivery in northern rural and remote regions: a review of the literature.

PubMed

Mitton, Craig; Dionne, Francois; Masucci, Lisa; Wong, Sabrina; Law, Susan

2011-01-01

To identify and review innovations relevant to improving access, quality, efficiency and/or effectiveness in the organization and delivery of health care services in rural and remote areas. Literature review. Key bibliographic databases that index health research were searched: MEDLINE, EMBASE and CINAHL. Other databases relevant to Arctic health were also accessed. Abstracts were assessed for relevancy and full articles were reviewed and categorized according to emergent themes. Many innovations in delivering services to rural and remote areas were identified, particularly in the public health realm. These innovations were grouped into 4 key themes: organizational structure of health services; utilization of telehealth and ehealth; medical transportation; and public health challenges. Despite the challenges facing rural and remote regions, there is a distinctly positive message from this broad literature review. Evidence-based initiatives exist across a range of areas - which include operational efficiency and integration, access to care, organizational structure, public health, continuing education and workforce composition - that have the potential to positively impact health care quality and health-related outcomes.

Understanding the processes of writing papers reflectively.

PubMed

Regmi, Krishna; Naidoo, Jennie

2013-07-01

This paper explores the writing of research papers using reflective frameworks. Reflective practice is integral to professional education and development. However, healthcare students, academics and practitioners have given limited attention to how to write reflectively. In addition, there are limited resources on the practical aspects of writing papers reflectively. The following major databases were searched: PubMed, Medline, King's Library, Excerpta Medica Database, Department of Health database, Cumulative Index to Nursing and Allied Health Literature. The searches were conducted using 'free text' and 'index' terms. Only relevant papers published in English were reviewed and scrutinised. Unpublished reports, internal publications, snowballing from the reference lists and personal contacts were also included in the search. This is a review paper that critiques the frameworks used for reflective practice. Writing papers reflectively is a complex task. Healthcare professionals and researchers need to understand the meaning of reflection and make appropriate use of reflective frameworks. Demystifying the process of reflectively writing papers will help professionals develop skills and competencies. IMPLICATION FOR RESEARCH/PRACTICE: This article provides a practical guide to reflection and how nursing and allied healthcare students, academics and practitioners can practise it. The paper identifies four generic stages in frameworks: description, assessment, evaluation and action, which are illustrated by annotated 'skeletal' examples. It is hoped that this will assist the process of reflective practice, writing and learning.

Analysis of human serum phosphopeptidome by a focused database searching strategy.

PubMed

Zhu, Jun; Wang, Fangjun; Cheng, Kai; Song, Chunxia; Qin, Hongqiang; Hu, Lianghai; Figeys, Daniel; Ye, Mingliang; Zou, Hanfa

2013-01-14

As human serum is an important source for early diagnosis of many serious diseases, analysis of serum proteome and peptidome has been extensively performed. However, the serum phosphopeptidome was less explored probably because the effective method for database searching is lacking. Conventional database searching strategy always uses the whole proteome database, which is very time-consuming for phosphopeptidome search due to the huge searching space resulted from the high redundancy of the database and the setting of dynamic modifications during searching. In this work, a focused database searching strategy using an in-house collected human serum pro-peptidome target/decoy database (HuSPep) was established. It was found that the searching time was significantly decreased without compromising the identification sensitivity. By combining size-selective Ti (IV)-MCM-41 enrichment, RP-RP off-line separation, and complementary CID and ETD fragmentation with the new searching strategy, 143 unique endogenous phosphopeptides and 133 phosphorylation sites (109 novel sites) were identified from human serum with high reliability. Copyright © 2012 Elsevier B.V. All rights reserved.

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.

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

Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification.

PubMed

Li, Honglan; Joh, Yoon Sung; Kim, Hyunwoo; Paek, Eunok; Lee, Sang-Won; Hwang, Kyu-Baek

2016-12-22

Proteogenomics is a promising approach for various tasks ranging from gene annotation to cancer research. Databases for proteogenomic searches are often constructed by adding peptide sequences inferred from genomic or transcriptomic evidence to reference protein sequences. Such inflation of databases has potential of identifying novel peptides. However, it also raises concerns on sensitive and reliable peptide identification. Spurious peptides included in target databases may result in underestimated false discovery rate (FDR). On the other hand, inflation of decoy databases could decrease the sensitivity of peptide identification due to the increased number of high-scoring random hits. Although several studies have addressed these issues, widely applicable guidelines for sensitive and reliable proteogenomic search have hardly been available. To systematically evaluate the effect of database inflation in proteogenomic searches, we constructed a variety of real and simulated proteogenomic databases for yeast and human tandem mass spectrometry (MS/MS) data, respectively. Against these databases, we tested two popular database search tools with various approaches to search result validation: the target-decoy search strategy (with and without a refined scoring-metric) and a mixture model-based method. The effect of separate filtering of known and novel peptides was also examined. The results from real and simulated proteogenomic searches confirmed that separate filtering increases the sensitivity and reliability in proteogenomic search. However, no one method consistently identified the largest (or the smallest) number of novel peptides from real proteogenomic searches. We propose to use a set of search result validation methods with separate filtering, for sensitive and reliable identification of peptides in proteogenomic search.

Disbiome database: linking the microbiome to disease.

PubMed

Janssens, Yorick; Nielandt, Joachim; Bronselaer, Antoon; Debunne, Nathan; Verbeke, Frederick; Wynendaele, Evelien; Van Immerseel, Filip; Vandewynckel, Yves-Paul; De Tré, Guy; De Spiegeleer, Bart

2018-06-04

Recent research has provided fascinating indications and evidence that the host health is linked to its microbial inhabitants. Due to the development of high-throughput sequencing technologies, more and more data covering microbial composition changes in different disease types are emerging. However, this information is dispersed over a wide variety of medical and biomedical disciplines. Disbiome is a database which collects and presents published microbiota-disease information in a standardized way. The diseases are classified using the MedDRA classification system and the micro-organisms are linked to their NCBI and SILVA taxonomy. Finally, each study included in the Disbiome database is assessed for its reporting quality using a standardized questionnaire. Disbiome is the first database giving a clear, concise and up-to-date overview of microbial composition differences in diseases, together with the relevant information of the studies published. The strength of this database lies within the combination of the presence of references to other databases, which enables both specific and diverse search strategies within the Disbiome database, and the human annotation which ensures a simple and structured presentation of the available data.

Searching for Clinically Relevant Biomarkers in Geriatric Oncology.

PubMed

Katsila, Theodora; Patrinos, George P; Kardamakis, Dimitrios

2018-01-01

Ageing, which is associated with a progressive decline and functional deterioration in multiple organ systems, is highly heterogeneous, both inter- and intraindividually. For this, tailored-made theranostics and optimum patient stratification become fundamental, when decision-making in elderly patients is considered. In particular, when cancer incidence and cancer-related mortality and morbidity are taken into account, elderly patient care is a public health concern. In this review, we focus on oncogeriatrics and highlight current opportunities and challenges with an emphasis on the unmet need of clinically relevant biomarkers in elderly cancer patients. We performed a literature search on PubMed and Scopus databases for articles published in English between 2000 and 2017 coupled to text mining and analysis. Considering the top insights, we derived from our literature analysis that information knowledge needs to turn into knowledge growth in oncogeriatrics towards clinically relevant biomarkers, cost-effective practices, updated educational schemes for health professionals (in particular, geriatricians and oncologists), and awareness of ethical issues. We conclude with an interdisciplinary call to omics, geriatricians, oncologists, informatics, and policy-makers communities that Big Data should be translated into decision-making in the clinic.

Database Resources of the BIG Data Center in 2018.

PubMed

2018-01-04

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

MememxGATE: Unearthing Latent Content Features for Improved Search and Relevancy Ranking Across Scientific Literature

NASA Astrophysics Data System (ADS)

Wilson, B. D.; McGibbney, L. J.; Mattmann, C. A.; Ramirez, P.; Joyce, M.; Whitehall, K. D.

2015-12-01

Quantifying scientific relevancy is of increasing importance to NASA and the research community. Scientific relevancy may be defined by mapping the impacts of a particular NASA mission, instrument, and/or retrieved variables to disciplines such as climate predictions, natural hazards detection and mitigation processes, education, and scientific discoveries. Related to relevancy, is the ability to expose data with similar attributes. This in turn depends upon the ability for us to extract latent, implicit document features from scientific data and resources and make them explicit, accessible and useable for search activities amongst others. This paper presents MemexGATE; a server side application, command line interface and computing environment for running large scale metadata extraction, general architecture text engineering, document classification and indexing tasks over document resources such as social media streams, scientific literature archives, legal documentation, etc. This work builds on existing experiences using MemexGATE (funded, developed and validated through the DARPA Memex Progrjam PI Mattmann) for extracting and leveraging latent content features from document resources within the Materials Research domain. We extend the software functionality capability to the domain of scientific literature with emphasis on the expansion of gazetteer lists, named entity rules, natural language construct labeling (e.g. synonym, antonym, hyponym, etc.) efforts to enable extraction of latent content features from data hosted by wide variety of scientific literature vendors (AGU Meeting Abstract Database, Springer, Wiley Online, Elsevier, etc.) hosting earth science literature. Such literature makes both implicit and explicit references to NASA datasets and relationships between such concepts stored across EOSDIS DAAC's hence we envisage that a significant part of this effort will also include development and understanding of relevancy signals which can ultimately be utilized for improved search and relevancy ranking across scientific literature.

The Relevancy of paracetamol and Breastfeeding Post Infant Vaccination: A Systematic Review.

PubMed

Suleiman, Nurain; Shamsuddin, Siti Hadijah; Mohd Rus, Razman; Drahman, Shamsul; Taib, Mai Nurul Ashikin Mohd

2018-03-28

Background: Paracetamol may be used as an antipyretic agent for the treatment of fever, as well as an analgesic in the treatment of mild to moderate pain post-vaccination in infants. The use of paracetamol during fever may be or may not be recommended since it may alter the natural human body immune response, although it may reduce pain. Objectives: The aims of this study are to describe the effectiveness of breastfeeding in reducing pain and paracetamol in reducing fever and pain post infant vaccination. Methods: Data sources and study selection was conducted by electronic searching of six databases. Manual reference checks of all articles on paracetamol and breastfeeding post infant vaccination published in the English language between 1978 and 2017. Two levels of screening were used on 9614 citations, which include screening of abstracts and titles followed by full text screening. The data synthesis were tabulated into study characteristics, quality, and effects. Results: Systematic review of breastfeeding included three studies from 9614 database searches found significant benefit from breastfeeding in pain scores and the duration of crying, as well as behavioural changes. None of the studies stated the detriment of breastfeeding before, during, and after immunization. Systematic review of paracetamol effectiveness included four studies from 1177 database searches found significant benefit from prophylaxis paracetamol in fever, one study found significant benefit from prophylaxis paracetamol in fussiness, and one study's results were found to be not significant. Two studies on evaluating the safety of prophylactic paracetamol in 2009 found that antibody responses to several antigens were significantly reduced, and the other study in 1988 found that antibody titres to DTP bacteria of placebo and PCM did not differ significantly. Conclusions: The relevancy of giving paracetamol post all types of vaccination may be questionable. Breastfeeding before, during, and after immunization are recommended for pain reduction and are proven effective. Further research is required in deciding if paracetamol is to be of rational use following infant immunization.

A method of searching for related literature on protein structure analysis by considering a user's intention

PubMed Central

2015-01-01

Background In recent years, with advances in techniques for protein structure analysis, the knowledge about protein structure and function has been published in a vast number of articles. A method to search for specific publications from such a large pool of articles is needed. In this paper, we propose a method to search for related articles on protein structure analysis by using an article itself as a query. Results Each article is represented as a set of concepts in the proposed method. Then, by using similarities among concepts formulated from databases such as Gene Ontology, similarities between articles are evaluated. In this framework, the desired search results vary depending on the user's search intention because a variety of information is included in a single article. Therefore, the proposed method provides not only one input article (primary article) but also additional articles related to it as an input query to determine the search intention of the user, based on the relationship between two query articles. In other words, based on the concepts contained in the input article and additional articles, we actualize a relevant literature search that considers user intention by varying the degree of attention given to each concept and modifying the concept hierarchy graph. Conclusions We performed an experiment to retrieve relevant papers from articles on protein structure analysis registered in the Protein Data Bank by using three query datasets. The experimental results yielded search results with better accuracy than when user intention was not considered, confirming the effectiveness of the proposed method. PMID:25952498

Available studies fail to provide strong evidence of increased risk of diarrhea mortality due to measles in the period 4-26 weeks after measles rash onset.

PubMed

Jackson, Bianca D; Black, Robert E

2017-11-07

Measles vaccination effectiveness studies showed dramatic decreases in all-cause mortality in excess of what would be expected from the prevention of measles disease alone. This invited speculation that measles infection may increase the risk of diarrhea morbidity and mortality subsequent to the acute phase of the disease. The aim of the present systematic review is to summarize the existing evidence in the publically available literature pertaining to the putative causal link between measles and diarrhea in the period 4-26 weeks following measles rash onset. We searched the PubMed, Embase, Open Grey and Grey Literature Report databases for relevant literature using broad search terms. Prospective, retrospective and case-control studies in low- and middle-income countries involving children under five wherein relevant evidence were presented were included. Data were extracted from the articles and summarized. Fifty abstracts retrieved through the database searches met the initial screening criteria. Twelve additional documents were identified by review of the references of the documents found in the initial searches. Six documents representing five unique studies that presented evidence relevant to the research question were found. Four of the included studies took place in Bangladesh. One of the included studies took place in Sudan. Some measles vaccine effectiveness studies show lower diarrhea morbidity and mortality among the vaccinated. However, children who received vaccine may have differed in important ways from children who did not, such as health service utilization. Additionally, cohort studies following unvaccinated children showed no difference in diarrhea morbidity and mortality between cases and controls more than 4 weeks after measles rash onset. One study showed some evidence that severe measles may predispose children to gastroenteritis, but was not able to show a corresponding increase in the risk of diarrhea mortality. The available evidence suggests that the risk of measles-associated diarrhea mortality is largely limited to the 5-week period 1 week prior to and 4 weeks after measles rash onset, and that there is no increased risk of diarrhea mortality in the longer-term caused by measles.

A systematic review of the cost of data collection for performance monitoring in hospitals.

PubMed

Jones, Cheryl; Gannon, Brenda; Wakai, Abel; O'Sullivan, Ronan

2015-04-01

Key performance indicators (KPIs) are used to identify where organisational performance is meeting desired standards and where performance requires improvement. Valid and reliable KPIs depend on the availability of high-quality data, specifically the relevant minimum data set ((MDS) the core data identified as the minimum required to measure performance for a KPI) elements. However, the feasibility of collecting the relevant MDS elements is always a limitation of performance monitoring using KPIs. Preferably, data should be integrated into service delivery, and, where additional data are required that are not currently collected as part of routine service delivery, there should be an economic evaluation to determine the cost of data collection. The aim of this systematic review was to synthesise the evidence base concerning the costs of data collection in hospitals for performance monitoring using KPI, and to identify hospital data collection systems that have proven to be cost minimising. We searched MEDLINE (1946 to May week 4 2014), Embase (1974 to May week 2 2014), and CINAHL (1937 to date). The database searches were supplemented by searching for grey literature through the OpenGrey database. Data was extracted, tabulated, and summarised as part of a narrative synthesis. The searches yielded a total of 1,135 publications. After assessing each identified study against specific inclusion exclusion criteria only eight studies were deemed as relevant for this review. The studies attempt to evaluate different types of data collection interventions including the installation of information communication technology (ICT), improvements to current ICT systems, and how different analysis techniques may be used to monitor performance. The evaluation methods used to measure the costs and benefits of data collection interventions are inconsistent across the identified literature. Overall, the results weakly indicate that collection of hospital data and improvements in data recording can be cost-saving. Given the limitations of this systematic review, it is difficult to conclude whether improvements in data collection systems can save money, increase quality of care, and assist performance monitoring of hospitals. With that said, the results are positive and suggest that data collection improvements may lead to cost savings and aid quality of care. PROSPERO CRD42014007450 .

EasyKSORD: A Platform of Keyword Search Over Relational Databases

NASA Astrophysics Data System (ADS)

Peng, Zhaohui; Li, Jing; Wang, Shan

Keyword Search Over Relational Databases (KSORD) enables casual users to use keyword queries (a set of keywords) to search relational databases just like searching the Web, without any knowledge of the database schema or any need of writing SQL queries. Based on our previous work, we design and implement a novel KSORD platform named EasyKSORD for users and system administrators to use and manage different KSORD systems in a novel and simple manner. EasyKSORD supports advanced queries, efficient data-graph-based search engines, multiform result presentations, and system logging and analysis. Through EasyKSORD, users can search relational databases easily and read search results conveniently, and system administrators can easily monitor and analyze the operations of KSORD and manage KSORD systems much better.

Suicide and Murder-Suicide Involving Aircraft.

PubMed

Kenedi, Christopher; Friedman, Susan Hatters; Watson, Dougal; Preitner, Claude

2016-04-01

This is a systematic review of suicide and homicide-suicide events involving aircraft. In aeromedical literature and in the media, these very different events are both described as pilot suicide, but in psychiatry they are considered separate events with distinct risk factors. Medical databases, internet search engines, and aviation safety databases were searched in a systematic way to obtain relevant cases. Relevant articles were searched for additional references. There were 65 cases of pilot suicide and 6 cases of passengers who jumped from aircraft found. There were also 18 cases of homicide-suicide found involving 732 deaths. Pilots perpetrated 13 homicide-suicide events. Compared to non-aviation samples, a large percentage of pilot suicides in this study were homicide-suicides (17%). Homicide-suicide events occur extremely rarely. However, their impact in terms of the proportion of deaths is significant when compared to deaths from accidents. There is evidence of clustering where pilot suicides occur after by media reports of suicide or homicide-suicide. Five of six homicide-suicide events by pilots of commercial airliners occurred after they were left alone in the cockpit. This, along with a sixth incident in which active intervention by a Japan Air crew saved 147 lives, suggests that having two flight members in the cockpit is potentially protective. No single factor was associated with the risk for suicide or homicide-suicide. Factors associated with both events included legal and financial crises, occupational conflict, mental illness, and relationship stressors. Drugs and/or alcohol played a role in almost half of suicides, but not in homicide-suicides.

Using SQL Databases for Sequence Similarity Searching and Analysis.

PubMed

Pearson, William R; Mackey, Aaron J

2017-09-13

Relational databases can integrate diverse types of information and manage large sets of similarity search results, greatly simplifying genome-scale analyses. By focusing on taxonomic subsets of sequences, relational databases can reduce the size and redundancy of sequence libraries and improve the statistical significance of homologs. In addition, by loading similarity search results into a relational database, it becomes possible to explore and summarize the relationships between all of the proteins in an organism and those in other biological kingdoms. This unit describes how to use relational databases to improve the efficiency of sequence similarity searching and demonstrates various large-scale genomic analyses of homology-related data. It also describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. The unit also introduces search_demo, a database that stores sequence similarity search results. The search_demo database is then used to explore the evolutionary relationships between E. coli proteins and proteins in other organisms in a large-scale comparative genomic analysis. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Environmental health impacts of unconventional natural gas development: a review of the current strength of evidence.

PubMed

Werner, Angela K; Vink, Sue; Watt, Kerrianne; Jagals, Paul

2015-02-01

Rapid global expansion of unconventional natural gas development (UNGD) raises environmental health concerns. Many studies present information on these concerns, yet the strength of epidemiological evidence remains tenuous. This paper is a review of the strength of evidence in scientific reporting of environmental hazards from UNGD activities associated with adverse human health outcomes. Studies were drawn from peer-reviewed and grey literature following a systematic search. Five databases were searched for studies published from January 1995 through March 2014 using key search terms relevant to environmental health. Studies were screened, ranked and then reviewed according to the strength of the evidence presented on adverse environmental health outcomes associated with UNGD. The initial searches yielded >1000 studies, but this was reduced to 109 relevant studies after the ranking process. Only seven studies were considered highly relevant based on strength of evidence. Articles spanned several relevant topics, but most focussed on impacts on typical environmental media, such as water and air, with much of the health impacts inferred rather than evidenced. Additionally, the majority of studies focussed on short-term, rather than long-term, health impacts, which is expected considering the timeframe of UNGD; therefore, very few studies examined health outcomes with longer latencies such as cancer or developmental outcomes. Current scientific evidence for UNGD that demonstrates associations between adverse health outcomes directly with environmental health hazards resulting from UNGD activities generally lacks methodological rigour. Importantly, however, there is also no evidence to rule out such health impacts. While the current evidence in the scientific research reporting leaves questions unanswered about the actual environmental health impacts, public health concerns remain intense. This is a clear gap in the scientific knowledge that requires urgent attention. Copyright © 2014. Published by Elsevier B.V.

Clinical Research Informatics: Supporting the Research Study Lifecycle.

PubMed

Johnson, S B

2017-08-01

Objectives: The primary goal of this review is to summarize significant developments in the field of Clinical Research Informatics (CRI) over the years 2015-2016. The secondary goal is to contribute to a deeper understanding of CRI as a field, through the development of a strategy for searching and classifying CRI publications. Methods: A search strategy was developed to query the PubMed database, using medical subject headings to both select and exclude articles, and filtering publications by date and other characteristics. A manual review classified publications using stages in the "research study lifecycle", with key stages that include study definition, participant enrollment, data management, data analysis, and results dissemination. Results: The search strategy generated 510 publications. The manual classification identified 125 publications as relevant to CRI, which were classified into seven different stages of the research lifecycle, and one additional class that pertained to multiple stages, referring to general infrastructure or standards. Important cross-cutting themes included new applications of electronic media (Internet, social media, mobile devices), standardization of data and procedures, and increased automation through the use of data mining and big data methods. Conclusions: The review revealed increased interest and support for CRI in large-scale projects across institutions, regionally, nationally, and internationally. A search strategy based on medical subject headings can find many relevant papers, but a large number of non-relevant papers need to be detected using text words which pertain to closely related fields such as computational statistics and clinical informatics. The research lifecycle was useful as a classification scheme by highlighting the relevance to the users of clinical research informatics solutions. Georg Thieme Verlag KG Stuttgart.

Agency, Social and Healthcare Supports for Adults with Intellectual Disability at the End of Life in Out-of-Home, Non-Institutional Community Residences in Western Nations: A Literature Review

ERIC Educational Resources Information Center

Moro, Teresa T.; Savage, Teresa A.; Gehlert, Sarah

2017-01-01

Background: The nature and quality of end-of-life care received by adults with intellectual disabilities in out-of-home, non-institutional community agency residences in Western nations is not well understood. Method: A range of databases and search engines were used to locate conceptual, clinical and research articles from relevant peer-reviewed…

DECADE Web Portal: Integrating MaGa, EarthChem and GVP Will Further Our Knowledge on Earth Degassing

NASA Astrophysics Data System (ADS)

Cardellini, C.; Frigeri, A.; Lehnert, K. A.; Ash, J.; McCormick, B.; Chiodini, G.; Fischer, T. P.; Cottrell, E.

2014-12-01

The release of gases from the Earth's interior to the exosphere takes place in both volcanic and non-volcanic areas of the planet. Fully understanding this complex process requires the integration of geochemical, petrological and volcanological data. At present, major online data repositories relevant to studies of degassing are not linked and interoperable. We are developing interoperability between three of those, which will support more powerful synoptic studies of degassing. The three data systems that will make their data accessible via the DECADE portal are: (1) the Smithsonian Institution's Global Volcanism Program database (GVP) of volcanic activity data, (2) EarthChem databases for geochemical and geochronological data of rocks and melt inclusions, and (3) the MaGa database (Mapping Gas emissions) which contains compositional and flux data of gases released at volcanic and non-volcanic degassing sites. These databases are developed and maintained by institutions or groups of experts in a specific field, and data are archived in formats specific to these databases. In the framework of the Deep Earth Carbon Degassing (DECADE) initiative of the Deep Carbon Observatory (DCO), we are developing a web portal that will create a powerful search engine of these databases from a single entry point. The portal will return comprehensive multi-component datasets, based on the search criteria selected by the user. For example, a single geographic or temporal search will return data relating to compositions of emitted gases and erupted products, the age of the erupted products, and coincident activity at the volcano. The development of this level of capability for the DECADE Portal requires complete synergy between these databases, including availability of standard-based web services (WMS, WFS) at all data systems. Data and metadata can thus be extracted from each system without interfering with each database's local schema or being replicated to achieve integration at the DECADE web portal. The DECADE portal will enable new synoptic perspectives on the Earth degassing process. Other data systems can be easily plugged in using the existing framework. Our vision is to explore Earth degassing related datasets over previously unexplored spatial or temporal ranges.

ProtaBank: A repository for protein design and engineering data.

PubMed

Wang, Connie Y; Chang, Paul M; Ary, Marie L; Allen, Benjamin D; Chica, Roberto A; Mayo, Stephen L; Olafson, Barry D

2018-03-25

We present ProtaBank, a repository for storing, querying, analyzing, and sharing protein design and engineering data in an actively maintained and updated database. ProtaBank provides a format to describe and compare all types of protein mutational data, spanning a wide range of properties and techniques. It features a user-friendly web interface and programming layer that streamlines data deposition and allows for batch input and queries. The database schema design incorporates a standard format for reporting protein sequences and experimental data that facilitates comparison of results across different data sets. A suite of analysis and visualization tools are provided to facilitate discovery, to guide future designs, and to benchmark and train new predictive tools and algorithms. ProtaBank will provide a valuable resource to the protein engineering community by storing and safeguarding newly generated data, allowing for fast searching and identification of relevant data from the existing literature, and exploring correlations between disparate data sets. ProtaBank invites researchers to contribute data to the database to make it accessible for search and analysis. ProtaBank is available at https://protabank.org. © 2018 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Native Health Research Database

MedlinePlus

... Indian Health Board) Welcome to the Native Health Database. Please enter your search terms. Basic Search Advanced ... To learn more about searching the Native Health Database, click here. Tutorial Video The NHD has made ...

What are the indications for using probiotics in children?

PubMed

Szajewska, Hania

2016-04-01

The health benefits of probiotics have been the subject of extensive research. Still, some questions are being repeatedly asked: should one use or not use probiotics? If yes, how and when should probiotics be used? The purpose of this review is to summarise current evidence on specific probiotics' efficacy and safety to help healthcare professionals make evidence-based decisions on the indications for using specific probiotic strains or combinations in children. To identify relevant data, searches of MEDLINE and the Cochrane Library databases were performed in July 2015 to locate randomised controlled trials or their meta-analyses published in the last five years. The MEDLINE database also was searched for evidence-based clinical practice guidelines, developed by scientific societies. Considering that probiotics have strain-specific effects, the main focus was on data on individual probiotic strains, not on probiotics in general. 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/

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.

Theories of behaviour and behaviour change across the social and behavioural sciences: a scoping review.

PubMed

Davis, Rachel; Campbell, Rona; Hildon, Zoe; Hobbs, Lorna; Michie, Susan

2015-01-01

Interventions to change health-related behaviours typically have modest effects and may be more effective if grounded in appropriate theory. Most theories applied to public health interventions tend to emphasise individual capabilities and motivation, with limited reference to context and social factors. Intervention effectiveness may be increased by drawing on a wider range of theories incorporating social, cultural and economic factors that influence behaviour. The primary aim of this paper is to identify theories of behaviour and behaviour change of potential relevance to public health interventions across four scientific disciplines: psychology, sociology, anthropology and economics. We report in detail the methodology of our scoping review used to identify these theories including which involved a systematic search of electronic databases, consultation with a multidisciplinary advisory group, web searching, searching of reference lists and hand searching of key behavioural science journals. Of secondary interest we developed a list of agreed criteria for judging the quality of the theories. We identified 82 theories and 9 criteria for assessing theory quality. The potential relevance of this wide-ranging number of theories to public health interventions and the ease and usefulness of evaluating the theories in terms of the quality criteria are however yet to be determined.

Theories of behaviour and behaviour change across the social and behavioural sciences: a scoping review

PubMed Central

Davis, Rachel; Campbell, Rona; Hildon, Zoe; Hobbs, Lorna; Michie, Susan

2015-01-01

Interventions to change health-related behaviours typically have modest effects and may be more effective if grounded in appropriate theory. Most theories applied to public health interventions tend to emphasise individual capabilities and motivation, with limited reference to context and social factors. Intervention effectiveness may be increased by drawing on a wider range of theories incorporating social, cultural and economic factors that influence behaviour. The primary aim of this paper is to identify theories of behaviour and behaviour change of potential relevance to public health interventions across four scientific disciplines: psychology, sociology, anthropology and economics. We report in detail the methodology of our scoping review used to identify these theories including which involved a systematic search of electronic databases, consultation with a multidisciplinary advisory group, web searching, searching of reference lists and hand searching of key behavioural science journals. Of secondary interest we developed a list of agreed criteria for judging the quality of the theories. We identified 82 theories and 9 criteria for assessing theory quality. The potential relevance of this wide-ranging number of theories to public health interventions and the ease and usefulness of evaluating the theories in terms of the quality criteria are however yet to be determined. PMID:25104107

Library Instruction and Online Database Searching.

ERIC Educational Resources Information Center

Mercado, Heidi

1999-01-01

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

HOWDY: an integrated database system for human genome research

PubMed Central

Hirakawa, Mika

2002-01-01

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

Choosing an Optimal Database for Protein Identification from Tandem Mass Spectrometry Data.

PubMed

Kumar, Dhirendra; Yadav, Amit Kumar; Dash, Debasis

2017-01-01

Database searching is the preferred method for protein identification from digital spectra of mass to charge ratios (m/z) detected for protein samples through mass spectrometers. The search database is one of the major influencing factors in discovering proteins present in the sample and thus in deriving biological conclusions. In most cases the choice of search database is arbitrary. Here we describe common search databases used in proteomic studies and their impact on final list of identified proteins. We also elaborate upon factors like composition and size of the search database that can influence the protein identification process. In conclusion, we suggest that choice of the database depends on the type of inferences to be derived from proteomics data. However, making additional efforts to build a compact and concise database for a targeted question should generally be rewarding in achieving confident protein identifications.

Driving towards obesity: a systematized literature review on the association between motor vehicle travel time and distance and weight status in adults.

PubMed

McCormack, Gavin R; Virk, Jagdeep S

2014-09-01

Higher levels of sedentary behavior are associated with adverse health outcomes. Over-reliance on private motor vehicles for transportation is a potential contributor to the obesity epidemic. The objective of this study was to review evidence on the relationship between motor vehicle travel distance and time and weight status among adults. Keywords associated with driving and weight status were entered into four databases (PubMed Medline Transportation Research Information Database and Web of Science) and retrieved article titles and abstracts screened for relevance. Relevant articles were assessed for their eligibility for inclusion in the review (English-language articles a sample ≥ 16 years of age included a measure of time or distance traveling in a motor vehicle and weight status and estimated the association between driving and weight status). The database search yielded 2781 articles, from which 88 were deemed relevant and 10 studies met the inclusion criteria. Of the 10 studies included in the review, 8 found a statistically significant positive association between time and distance traveled in a motor vehicle and weight status. Multilevel interventions that make alternatives to driving private motor vehicles more convenient, such as walking and cycling, are needed to promote healthy weight in the adult population. Copyright © 2014 Elsevier Inc. All rights reserved.

Access and use of the GUDMAP database of genitourinary development.

PubMed

Davies, Jamie A; Little, Melissa H; Aronow, Bruce; Armstrong, Jane; Brennan, Jane; Lloyd-MacGilp, Sue; Armit, Chris; Harding, Simon; Piu, Xinjun; Roochun, Yogmatee; Haggarty, Bernard; Houghton, Derek; Davidson, Duncan; Baldock, Richard

2012-01-01

The Genitourinary Development Molecular Atlas Project (GUDMAP) aims to document gene expression across time and space in the developing urogenital system of the mouse, and to provide access to a variety of relevant practical and educational resources. Data come from microarray gene expression profiling (from laser-dissected and FACS-sorted samples) and in situ hybridization at both low (whole-mount) and high (section) resolutions. Data are annotated to a published, high-resolution anatomical ontology and can be accessed using a variety of search interfaces. Here, we explain how to run typical queries on the database, by gene or anatomical location, how to view data, how to perform complex queries, and how to submit data.

Semantic Annotation of Complex Text Structures in Problem Reports

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Throop, David R.; Fleming, Land D.

2011-01-01

Text analysis is important for effective information retrieval from databases where the critical information is embedded in text fields. Aerospace safety depends on effective retrieval of relevant and related problem reports for the purpose of trend analysis. The complex text syntax in problem descriptions has limited statistical text mining of problem reports. The presentation describes an intelligent tagging approach that applies syntactic and then semantic analysis to overcome this problem. The tags identify types of problems and equipment that are embedded in the text descriptions. The power of these tags is illustrated in a faceted searching and browsing interface for problem report trending that combines automatically generated tags with database code fields and temporal information.

A portal for the ocean biogeographic information system

USGS Publications Warehouse

Zhang, Yunqing; Grassle, J. F.

2002-01-01

Since its inception in 1999 the Ocean Biogeographic Information System (OBIS) has developed into an international science program as well as a globally distributed network of biogeographic databases. An OBIS portal at Rutgers University provides the links and functional interoperability among member database systems. Protocols and standards have been established to support effective communication between the portal and these functional units. The portal provides distributed data searching, a taxonomy name service, a GIS with access to relevant environmental data, biological modeling, and education modules for mariners, students, environmental managers, and scientists. The portal will integrate Census of Marine Life field projects, national data archives, and other functional modules, and provides for network-wide analyses and modeling tools.

ALDB: a domestic-animal long noncoding RNA database.

PubMed

Li, Aimin; Zhang, Junying; Zhou, Zhongyin; Wang, Lei; Liu, Yujuan; Liu, Yajun

2015-01-01

Long noncoding RNAs (lncRNAs) have attracted significant attention in recent years due to their important roles in many biological processes. Domestic animals constitute a unique resource for understanding the genetic basis of phenotypic variation and are ideal models relevant to diverse areas of biomedical research. With improving sequencing technologies, numerous domestic-animal lncRNAs are now available. Thus, there is an immediate need for a database resource that can assist researchers to store, organize, analyze and visualize domestic-animal lncRNAs. The domestic-animal lncRNA database, named ALDB, is the first comprehensive database with a focus on the domestic-animal lncRNAs. It currently archives 12,103 pig intergenic lncRNAs (lincRNAs), 8,923 chicken lincRNAs and 8,250 cow lincRNAs. In addition to the annotations of lincRNAs, it offers related data that is not available yet in existing lncRNA databases (lncRNAdb and NONCODE), such as genome-wide expression profiles and animal quantitative trait loci (QTLs) of domestic animals. Moreover, a collection of interfaces and applications, such as the Basic Local Alignment Search Tool (BLAST), the Generic Genome Browser (GBrowse) and flexible search functionalities, are available to help users effectively explore, analyze and download data related to domestic-animal lncRNAs. ALDB enables the exploration and comparative analysis of lncRNAs in domestic animals. A user-friendly web interface, integrated information and tools make it valuable to researchers in their studies. ALDB is freely available from http://res.xaut.edu.cn/aldb/index.jsp.

Polyamines in foods: development of a food database

PubMed Central

Ali, Mohamed Atiya; Poortvliet, Eric; Strömberg, Roger; Yngve, Agneta

2011-01-01

Background Knowing the levels of polyamines (putrescine, spermidine, and spermine) in different foods is of interest due to the association of these bioactive nutrients to health and diseases. There is a lack of relevant information on their contents in foods. Objective To develop a food polyamine database from published data by which polyamine intake and food contribution to this intake can be estimated, and to determine the levels of polyamines in Swedish dairy products. Design Extensive literature search and laboratory analysis of selected Swedish dairy products. Polyamine contents in foods were collected using an extensive literature search of databases. Polyamines in different types of Swedish dairy products (milk with different fat percentages, yogurt, cheeses, and sour milk) were determined using high performance liquid chromatography (HPLC) equipped with a UV detector. Results Fruits and cheese were the highest sources of putrescine, while vegetables and meat products were found to be rich in spermidine and spermine, respectively. The content of polyamines in cheese varied considerably between studies. In analyzed Swedish dairy products, matured cheese had the highest total polyamine contents with values of 52.3, 1.2, and 2.6 mg/kg for putrescine, spermidine, and spermine, respectively. Low fat milk had higher putrescine and spermidine, 1.2 and 1.0 mg/kg, respectively, than the other types of milk. Conclusions The database aids other researchers in their quest for information regarding polyamine intake from foods. Connecting the polyamine contents in food with the Swedish Food Database allows for estimation of polyamine contents per portion. PMID:21249159

Nurse-led ranibizumab intravitreal injections in wet age-related macular degeneration: a literature review.

PubMed

Gregg, Emma

2017-04-12

Aim The aim of this literature review was to explore the development of the role of specialist ophthalmic nurses in delivering ranibizumab intravitreal injections to patients with wet age-related macular degeneration (AMD), and to evaluate their contribution to reducing capacity pressures in medical retina services, while maintaining safe and effective standards of care. Method A systematic literature search was undertaken to identify relevant articles published between January 2000 and June 2015. A search of electronic databases was undertaken, and selected relevant journals were searched manually. A free text and subject heading search strategy was conducted, in which the abstracts of publications identified for review were assessed for relevance. Inclusion criteria were: nurses delivering ranibizumab intravitreal treatment; studies performed in the UK and other countries; and patients with AMD, diabetic macular oedema or central retinal vein occlusion receiving nurse-led ranibizumab (Lucentis) intravitreal treatment. Findings Five studies were identified from the literature search, which audited a total of 31,303 injections delivered by nurse practitioners between January 2007 and November 2013. The visual outcomes and the rate of complications from intravitreal injections delivered by trained ophthalmic nurse practitioners were comparable to intravitreal injections delivered by ophthalmologists. Four of the five studies reported increased patient satisfaction, patients consenting to nurse-delivered intravitreal injections, favourable pain experience, and absence of complaints. Conclusion Practice innovation is an example of a quality, innovation, productivity and prevention process. Role expansion, in which specialist ophthalmic nurses deliver intravitreal injections, has been shown to be economical, safe and effective. It enables timely delivery of the service, thereby preventing irreversible blindness for individuals with wet AMD.

Rapid identification of anonymous subjects in large criminal databases: problems and solutions in IAFIS III/FBI subject searches

NASA Astrophysics Data System (ADS)

Kutzleb, C. D.

1997-02-01

The high incidence of recidivism (repeat offenders) in the criminal population makes the use of the IAFIS III/FBI criminal database an important tool in law enforcement. The problems and solutions employed by IAFIS III/FBI criminal subject searches are discussed for the following topics: (1) subject search selectivity and reliability; (2) the difficulty and limitations of identifying subjects whose anonymity may be a prime objective; (3) database size, search workload, and search response time; (4) techniques and advantages of normalizing the variability in an individual's name and identifying features into identifiable and discrete categories; and (5) the use of database demographics to estimate the likelihood of a match between a search subject and database subjects.

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

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

Cutler, Debbie

2010-06-28

A study was performed comparing user search results from the specialized scientific database on energy-related information, ETDEWEB, with search results from the internet search engines Google and Google Scholar. The primary objective of the study was to determine if ETDEWEB (the Energy Technology Data Exchange – World Energy Base) continues to bring the user search results that are not being found by Google and Google Scholar. As a multilateral information exchange initiative, ETDE’s member countries and partners contribute cost- and task-sharing resources to build the largest database of energy-related information in the world. As of early 2010, the ETDEWEB databasemore » has 4.3 million citations to world-wide energy literature. One of ETDEWEB’s strengths is its focused scientific content and direct access to full text for its grey literature (over 300,000 documents in PDF available for viewing from the ETDE site and over a million additional links to where the documents can be found at research organizations and major publishers globally). Google and Google Scholar are well-known for the wide breadth of the information they search, with Google bringing in news, factual and opinion-related information, and Google Scholar also emphasizing scientific content across many disciplines. The analysis compared the results of 15 energy-related queries performed on all three systems using identical words/phrases. A variety of subjects was chosen, although the topics were mostly in renewable energy areas due to broad international interest. Over 40,000 search result records from the three sources were evaluated. The study concluded that ETDEWEB is a significant resource to energy experts for discovering relevant energy information. For the 15 topics in this study, ETDEWEB was shown to bring the user unique results not shown by Google or Google Scholar 86.7% of the time. Much was learned from the study beyond just metric comparisons. Observations about the strengths of each system and factors impacting the search results are also shared along with background information and summary tables of the results. If a user knows a very specific title of a document, all three systems are helpful in finding the user a source for the document. But if the user is looking to discover relevant documents on a specific topic, each of the three systems will bring back a considerable volume of data, but quite different in focus. Google is certainly a highly-used and valuable tool to find significant ‘non-specialist’ information, and Google Scholar does help the user focus on scientific disciplines. But if a user’s interest is scientific and energy-specific, ETDEWEB continues to hold a strong position in the energy research, technology and development (RTD) information field and adds considerable value in knowledge discovery. (auth)« less

Preconception risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease.

PubMed

Hussein, Norita; Weng, Stephen F; Kai, Joe; Kleijnen, Jos; Qureshi, Nadeem

2015-08-12

Globally, about five per cent of children are born with congenital or genetic disorders. The most common autosomal recessive conditions are thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease, with higher carrier rates in specific patient populations. Identifying and counselling couples at genetic risk of the conditions before pregnancy enables them to make fully informed reproductive decisions, with some of these choices not being available if genetic counselling is only offered in an antenatal setting. To assess the effectiveness of systematic preconception genetic risk assessment to improve reproductive outcomes in women and their partners who are identified as carriers of thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease in healthcare settings when compared to usual care. We searched the Cochrane Cystic Fibrosis and Genetic Disorders Group's Trials Registers. In addition, we searched for all relevant trials from 1970 (or the date at which the database was first available if after 1970) to date using electronic databases (MEDLINE, Embase, CINAHL, PsycINFO), clinical trial databases (National Institutes of Health, Clinical Trials Search portal of the World Health Organization, metaRegister of controlled clinical trials), and hand searching of key journals and conference abstract books from 1998 to date (European Journal of Human Genetics, Genetics in Medicine, Journal of Community Genetics). We also searched the reference lists of relevant articles, reviews and guidelines and also contacted subject experts in the field to request any unpublished or other published trials.Date of latest search of the registers: 25 June 2015.Date of latest search of all other sources: 10 December 2014. Any randomised or quasi-randomised control trials (published or unpublished) comparing reproductive outcomes of systematic preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease when compared to usual care. We identified 19 papers, describing 13 unique trials which were potentially eligible for inclusion in the review. However, after assessment, no randomised controlled trials of preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease were found. No randomised controlled trials of preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease were found. As no randomised controlled trials of preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis, or Tay-Sachs disease were found for inclusion in this review, the research evidence for current policy recommendations is limited to non-randomised studies.Information from well-designed, adequately powered, randomised trials is desirable in order to make more robust recommendations for practice. However, such trials must also consider the legal, ethical, and cultural barriers to implementation of preconception genetic risk assessment.

Effect of educational components and strategies associated with insulin pump therapy: a systematic review.

PubMed

Jayasekara, Rasika Sirilal; Munn, Zachary; Lockwood, Craig

2011-12-01

The objectives of this review were to establish the effectiveness of approaches to the provision of education for adults with type 1 diabetes using or initiating insulin pump therapy (IPT), and identify the best available evidence on the association between intervals and duration of follow up and the stated outcome criteria. This review considered all studies and papers that involved adults (aged 16 years or over) with type 1 diabetes using IPT as their primary form of therapy who participated in education or training, with no restrictions placed on gender or comorbidities. All forms of education, including resources utilised during education were included in the review. The search strategy sought to find both published and unpublished studies and papers written in the English language. An initial limited search of MEDLINE and CINAHL databases was undertaken to identify optimal search terms. A second search using all identified key words and index terms was then undertaken based on key words specific to each database across all included databases from 1998 to February 2008. Thirdly, the reference lists of all identified reports and articles were searched for additional studies. Two independent reviewers assessed the methodological quality of retrieved papers using the corresponding checklist from the System for the Unified Management, Assessment and Review of Information (SUMARI) package. A total of 142 studies were identified as potentially relevant to the review question in the first and second steps of the literature search. Based on the title and abstract, 24 papers that were relevant to the review topic were retrieved for evaluation of methodological quality. Following this stage, 20 papers were excluded. Whilst searching the reference lists of the selected studies (n = 4), one paper met the inclusion criteria. Therefore, a total of five descriptive studies were included in the review. The included papers reported a variety of educational methods and different outcome measures. In general, it is difficult to draw a strong conclusion regarding the effectiveness of components and strategies associated with IPT because of a lack of high-quality comparative studies, small sample sizes and a variability of reported methods in the included studies. However, included descriptive studies explored a range of issues related to the effectiveness of IPT therapy, and the educative requirements of patients. It is clear that type 1 diabetes patients initiating and utilising IPT need a comprehensive range of advice, education and training. The mixture of group and individual teaching, multidisciplinary teams as educators, educational materials, long-term training with multiple sessions and a variety of educational contents may all be effective for delivering IPT education and training. 2011 The Authors. International Journal of Evidence-Based Healthcare. 2011 The Joanna Briggs Institute.

A Systematic Evaluation of Field-Based Screening Methods for the Assessment of Anterior Cruciate Ligament (ACL) Injury Risk.

PubMed

Fox, Aaron S; Bonacci, Jason; McLean, Scott G; Spittle, Michael; Saunders, Natalie

2016-05-01

Laboratory-based measures provide an accurate method to identify risk factors for anterior cruciate ligament (ACL) injury; however, these methods are generally prohibitive to the wider community. Screening methods that can be completed in a field or clinical setting may be more applicable for wider community use. Examination of field-based screening methods for ACL injury risk can aid in identifying the most applicable method(s) for use in these settings. The objective of this systematic review was to evaluate and compare field-based screening methods for ACL injury risk to determine their efficacy of use in wider community settings. An electronic database search was conducted on the SPORTDiscus™, MEDLINE, AMED and CINAHL databases (January 1990-July 2015) using a combination of relevant keywords. A secondary search of the same databases, using relevant keywords from identified screening methods, was also undertaken. Studies identified as potentially relevant were independently examined by two reviewers for inclusion. Where consensus could not be reached, a third reviewer was consulted. Original research articles that examined screening methods for ACL injury risk that could be undertaken outside of a laboratory setting were included for review. Two reviewers independently assessed the quality of included studies. Included studies were categorized according to the screening method they examined. A description of each screening method, and data pertaining to the ability to prospectively identify ACL injuries, validity and reliability, recommendations for identifying 'at-risk' athletes, equipment and training required to complete screening, time taken to screen athletes, and applicability of the screening method across sports and athletes were extracted from relevant studies. Of 1077 citations from the initial search, a total of 25 articles were identified as potentially relevant, with 12 meeting all inclusion/exclusion criteria. From the secondary search, eight further studies met all criteria, resulting in 20 studies being included for review. Five ACL-screening methods-the Landing Error Scoring System (LESS), Clinic-Based Algorithm, Observational Screening of Dynamic Knee Valgus (OSDKV), 2D-Cam Method, and Tuck Jump Assessment-were identified. There was limited evidence supporting the use of field-based screening methods in predicting ACL injuries across a range of populations. Differences relating to the equipment and time required to complete screening methods were identified. Only screening methods for ACL injury risk were included for review. Field-based screening methods developed for lower-limb injury risk in general may also incorporate, and be useful in, screening for ACL injury risk. Limited studies were available relating to the OSDKV and 2D-Cam Method. The LESS showed predictive validity in identifying ACL injuries, however only in a youth athlete population. The LESS also appears practical for community-wide use due to the minimal equipment and set-up/analysis time required. The Clinic-Based Algorithm may have predictive value for ACL injury risk as it identifies athletes who exhibit high frontal plane knee loads during a landing task, but requires extensive additional equipment and time, which may limit its application to wider community settings.

Systematic review of use of β-blockers in sepsis.

PubMed

Chacko, Cyril Jacob; Gopal, Shameer

2015-01-01

We proposed a review of present literature and systematic analysis of present literature to summarize the evidence on the use of β-blockers on the outcome of a patient with severe sepsis and septic shock. Medline, EMBASE, Cochrane Library were searched from 1946 to December 2013. The bibliography of all relevant articles was hand searched. Full-text search of the grey literature was done through the medical institution database. The database search identified a total of 1241 possible studies. The citation list was hand searched by both the authors. A total of 9 studies were identified. Most studies found a benefit from β-blocker administration in sepsis. This included improved heart rate (HR) control, decreased mortality and improvement in acid-base parameters. Chronic β-blocker usage in sepsis was also associated with improved mortality. The administration of β-blockers during sepsis was associated with better control of HR. The methodological quality of all the included studies, however, was poor. There is insufficient evidence to justify the routine use of β-blockers in sepsis. A large adequately powered multi-centered randomized controlled clinical trial is required to address the question on the efficacy of β-blocker usage in sepsis. This trial should also consider a number of important questions including the choice of β-blocker used, optimal dosing, timing of intervention, duration of intervention and discontinuation of the drug. Until such time based on the available evidence, there is no place for the use of β-blockers in sepsis in current clinical practice.

Omicseq: a web-based search engine for exploring omics datasets.

PubMed

Sun, Xiaobo; Pittard, William S; Xu, Tianlei; Chen, Li; Zwick, Michael E; Jiang, Xiaoqian; Wang, Fusheng; Qin, Zhaohui S

2017-07-03

The development and application of high-throughput genomics technologies has resulted in massive quantities of diverse omics data that continue to accumulate rapidly. These rich datasets offer unprecedented and exciting opportunities to address long standing questions in biomedical research. However, our ability to explore and query the content of diverse omics data is very limited. Existing dataset search tools rely almost exclusively on the metadata. A text-based query for gene name(s) does not work well on datasets wherein the vast majority of their content is numeric. To overcome this barrier, we have developed Omicseq, a novel web-based platform that facilitates the easy interrogation of omics datasets holistically to improve 'findability' of relevant data. The core component of Omicseq is trackRank, a novel algorithm for ranking omics datasets that fully uses the numerical content of the dataset to determine relevance to the query entity. The Omicseq system is supported by a scalable and elastic, NoSQL database that hosts a large collection of processed omics datasets. In the front end, a simple, web-based interface allows users to enter queries and instantly receive search results as a list of ranked datasets deemed to be the most relevant. Omicseq is freely available at http://www.omicseq.org. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Toward a definition of competency-based education in medicine: a systematic review of published definitions.

PubMed

Frank, Jason R; Mungroo, Rani; Ahmad, Yasmine; Wang, Mimi; De Rossi, Stefanie; Horsley, Tanya

2010-01-01

Competency-based education (CBE) has emerged in the health professions to address criticisms of contemporary approaches to training. However, the literature has no clear, widely accepted definition of CBE that furthers innovation, debate, and scholarship in this area. To systematically review CBE-related literature in order to identify key terms and constructs to inform the development of a useful working definition of CBE for medical education. We searched electronic databases and supplemented searches by using authors' files, checking reference lists, contacting relevant organizations and conducting Internet searches. Screening was carried out by duplicate assessment, and disagreements were resolved by consensus. We included any English- or French-language sources that defined competency-based education. Data were analyzed qualitatively and summarized descriptively. We identified 15,956 records for initial relevancy screening by title and abstract. The full text of 1,826 records was then retrieved and assessed further for relevance. A total of 173 records were analyzed. We identified 4 major themes (organizing framework, rationale, contrast with time, and implementing CBE) and 6 sub-themes (outcomes defined, curriculum of competencies, demonstrable, assessment, learner-centred and societal needs). From these themes, a new definition of CBE was synthesized. This is the first comprehensive systematic review of the medical education literature related to CBE definitions. The themes and definition identified should be considered by educators to advance the field.

Beyond Keyword Search: Discovering Relevant Scientific Literature

DTIC Science & Technology

2011-06-01

Information genealogy: uncovering the flow of ideas in non-hyperlinked document databases. In KDD, 2007. 18 [44] Thomson Reuters Web of Knowledge. http...stimulation 2001 98 14386-14391 10123 In vivo evidence for a cochlear amplifier in the hair-cell bundle of lizards 2001 98 2826-2831 22 Table 1 (cont...2000 97 4856-4861 12134 Arabidopsis RelA/SpoT homologs implicate (p)ppGpp in plant signal- ing 2000 97 3747-3752 12176 Cochlear mechanisms from a

A Systematic Review of Techniques and Sources of Big Data in the Healthcare Sector.

PubMed

Alonso, Susel Góngora; de la Torre Díez, Isabel; Rodrigues, Joel J P C; Hamrioui, Sofiane; López-Coronado, Miguel

2017-10-14

The main objective of this paper is to present a review of existing researches in the literature, referring to Big Data sources and techniques in health sector and to identify which of these techniques are the most used in the prediction of chronic diseases. Academic databases and systems such as IEEE Xplore, Scopus, PubMed and Science Direct were searched, considering the date of publication from 2006 until the present time. Several search criteria were established as 'techniques' OR 'sources' AND 'Big Data' AND 'medicine' OR 'health', 'techniques' AND 'Big Data' AND 'chronic diseases', etc. Selecting the paper considered of interest regarding the description of the techniques and sources of Big Data in healthcare. It found a total of 110 articles on techniques and sources of Big Data on health from which only 32 have been identified as relevant work. Many of the articles show the platforms of Big Data, sources, databases used and identify the techniques most used in the prediction of chronic diseases. From the review of the analyzed research articles, it can be noticed that the sources and techniques of Big Data used in the health sector represent a relevant factor in terms of effectiveness, since it allows the application of predictive analysis techniques in tasks such as: identification of patients at risk of reentry or prevention of hospital or chronic diseases infections, obtaining predictive models of quality.

Interactive decision support in hepatic surgery

PubMed Central

Dugas, Martin; Schauer, Rolf; Volk, Andreas; Rau, Horst

2002-01-01

Background Hepatic surgery is characterized by complicated operations with a significant peri- and postoperative risk for the patient. We developed a web-based, high-granular research database for comprehensive documentation of all relevant variables to evaluate new surgical techniques. Methods To integrate this research system into the clinical setting, we designed an interactive decision support component. The objective is to provide relevant information for the surgeon and the patient to assess preoperatively the risk of a specific surgical procedure. Based on five established predictors of patient outcomes, the risk assessment tool searches for similar cases in the database and aggregates the information to estimate the risk for an individual patient. Results The physician can verify the analysis and exclude manually non-matching cases according to his expertise. The analysis is visualized by means of a Kaplan-Meier plot. To evaluate the decision support component we analyzed data on 165 patients diagnosed with hepatocellular carcinoma (period 1996–2000). The similarity search provides a two-peak distribution indicating there are groups of similar patients and singular cases which are quite different to the average. The results of the risk estimation are consistent with the observed survival data, but must be interpreted with caution because of the limited number of matching reference cases. Conclusion Critical issues for the decision support system are clinical integration, a transparent and reliable knowledge base and user feedback. PMID:12003639

The STEP database through the end-users eyes--USABILITY STUDY.

PubMed

Salunke, Smita; Tuleu, Catherine

2015-08-15

The user-designed database of Safety and Toxicity of Excipients for Paediatrics ("STEP") is created to address the shared need of drug development community to access the relevant information of excipients effortlessly. Usability testing was performed to validate if the database satisfies the need of the end-users. Evaluation framework was developed to assess the usability. The participants performed scenario based tasks and provided feedback and post-session usability ratings. Failure Mode Effect Analysis (FMEA) was performed to prioritize the problems and improvements to the STEP database design and functionalities. The study revealed several design vulnerabilities. Tasks such as limiting the results, running complex queries, location of data and registering to access the database were challenging. The three critical attributes identified to have impact on the usability of the STEP database included (1) content and presentation (2) the navigation and search features (3) potential end-users. Evaluation framework proved to be an effective method for evaluating database effectiveness and user satisfaction. This study provides strong initial support for the usability of the STEP database. Recommendations would be incorporated into the refinement of the database to improve its usability and increase user participation towards the advancement of the database. Copyright © 2015 Elsevier B.V. All rights reserved.

Content based information retrieval in forensic image databases.

PubMed

Geradts, Zeno; Bijhold, Jurrien

2002-03-01

This paper gives an overview of the various available image databases and ways of searching these databases on image contents. The developments in research groups of searching in image databases is evaluated and compared with the forensic databases that exist. Forensic image databases of fingerprints, faces, shoeprints, handwriting, cartridge cases, drugs tablets, and tool marks are described. The developments in these fields appear to be valuable for forensic databases, especially that of the framework in MPEG-7, where the searching in image databases is standardized. In the future, the combination of the databases (also DNA-databases) and possibilities to combine these can result in stronger forensic evidence.

Developing a national framework of quality indicators for public hospitals.

PubMed

Simou, Effie; Pliatsika, Paraskevi; Koutsogeorgou, Eleni; Roumeliotou, Anastasia

2014-01-01

The current study describes the development of a preliminary set of quality indicators for public Greek National Health System (GNHS) hospitals, which were used in the "Health Monitoring Indicators System: Health Map" (Ygeionomikos Chartis) project, with the purpose that these quality indicators would assess the quality of all the aspects relevant to public hospital healthcare workforce and services provided. A literature review was conducted in the MEDLINE database to identify articles referring to international and national hospital quality assessment projects, together with an online search for relevant projects. Studies were included if they were published in English, from 1980 to 2010. A consensus panel took place afterwards with 40 experts in the field and tele-voting procedure. Twenty relevant projects and their 1698 indicators were selected through the literature search, and after the consensus panel process, a list of 67 indicators were selected to be implemented for the assessment of the public hospitals categorized under six distinct dimensions: Quality, Responsiveness, Efficiency, Utilization, Timeliness, and Resources and Capacity. Data gathered and analyzed in this manner provided a novel evaluation and monitoring system for Greece, which can assist decision-makers, healthcare professionals, and patients in Greece to retrieve relevant information, with the long-term goal to improve quality in care in the GNHS hospital sector. Copyright © 2014 John Wiley & Sons, Ltd.

Systematic review of "filling" procedures for lip augmentation regarding types of material, outcomes and complications.

PubMed

San Miguel Moragas, Joan; Reddy, Rajgopal R; Hernández Alfaro, Federico; Mommaerts, Maurice Y

2015-07-01

The ideal lip augmentation technique provides the longest period of efficacy, lowest complication rate, and best aesthetic results. A myriad of techniques have been described for lip augmentation, but the optimal approach has not yet been established. This systematic review with meta-regression will focus on the various filling procedures for lip augmentation (FPLA), with the goal of determining the optimal approach. A systematic search for all English, French, Spanish, German, Italian, Portuguese and Dutch language studies involving FPLA was performed using these databases: Elsevier Science Direct, PubMed, Highwire Press, Springer Standard Collection, SAGE, DOAJ, Sweetswise, Free E-Journals, Ovid Lippincott Williams & Wilkins, Willey Online Library Journals, and Cochrane Plus. The reference section of every study selected through this database search was subsequently examined to identify additional relevant studies. The database search yielded 29 studies. Nine more studies were retrieved from the reference sections of these 29 studies. The level of evidence ratings of these 38 studies were as follows: level Ib, four studies; level IIb, four studies; level IIIb, one study; and level IV, 29 studies. Ten studies were prospective. This systematic review sought to highlight all the quality data currently available regarding FPLA. Because of the considerable diversity of procedures, no definitive comparisons or conclusions were possible. Additional prospective studies and clinical trials are required to more conclusively determine the most appropriate approach for this procedure. IV. Copyright © 2015 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Federated Access to Heterogeneous Information Resources in the Neuroscience Information Framework (NIF)

PubMed Central

Gupta, Amarnath; Bug, William; Marenco, Luis; Qian, Xufei; Condit, Christopher; Rangarajan, Arun; Müller, Hans Michael; Miller, Perry L.; Sanders, Brian; Grethe, Jeffrey S.; Astakhov, Vadim; Shepherd, Gordon; Sternberg, Paul W.; Martone, Maryann E.

2009-01-01

The overarching goal of the NIF (Neuroscience Information Framework) project is to be a one-stop-shop for Neuroscience. This paper provides a technical overview of how the system is designed. The technical goal of the first version of the NIF system was to develop an information system that a neuroscientist can use to locate relevant information from a wide variety of information sources by simple keyword queries. Although the user would provide only keywords to retrieve information, the NIF system is designed to treat them as concepts whose meanings are interpreted by the system. Thus, a search for term should find a record containing synonyms of the term. The system is targeted to find information from web pages, publications, databases, web sites built upon databases, XML documents and any other modality in which such information may be published. We have designed a system to achieve this functionality. A central element in the system is an ontology called NIFSTD (for NIF Standard) constructed by amalgamating a number of known and newly developed ontologies. NIFSTD is used by our ontology management module, called OntoQuest to perform ontology-based search over data sources. The NIF architecture currently provides three different mechanisms for searching heterogeneous data sources including relational databases, web sites, XML documents and full text of publications. Version 1.0 of the NIF system is currently in beta test and may be accessed through http://nif.nih.gov. PMID:18958629

Federated access to heterogeneous information resources in the Neuroscience Information Framework (NIF).

PubMed

Gupta, Amarnath; Bug, William; Marenco, Luis; Qian, Xufei; Condit, Christopher; Rangarajan, Arun; Müller, Hans Michael; Miller, Perry L; Sanders, Brian; Grethe, Jeffrey S; Astakhov, Vadim; Shepherd, Gordon; Sternberg, Paul W; Martone, Maryann E

2008-09-01

The overarching goal of the NIF (Neuroscience Information Framework) project is to be a one-stop-shop for Neuroscience. This paper provides a technical overview of how the system is designed. The technical goal of the first version of the NIF system was to develop an information system that a neuroscientist can use to locate relevant information from a wide variety of information sources by simple keyword queries. Although the user would provide only keywords to retrieve information, the NIF system is designed to treat them as concepts whose meanings are interpreted by the system. Thus, a search for term should find a record containing synonyms of the term. The system is targeted to find information from web pages, publications, databases, web sites built upon databases, XML documents and any other modality in which such information may be published. We have designed a system to achieve this functionality. A central element in the system is an ontology called NIFSTD (for NIF Standard) constructed by amalgamating a number of known and newly developed ontologies. NIFSTD is used by our ontology management module, called OntoQuest to perform ontology-based search over data sources. The NIF architecture currently provides three different mechanisms for searching heterogeneous data sources including relational databases, web sites, XML documents and full text of publications. Version 1.0 of the NIF system is currently in beta test and may be accessed through http://nif.nih.gov.

neXtA5: accelerating annotation of articles via automated approaches in neXtProt.

PubMed

Mottin, Luc; Gobeill, Julien; Pasche, Emilie; Michel, Pierre-André; Cusin, Isabelle; Gaudet, Pascale; Ruch, Patrick

2016-01-01

The rapid increase in the number of published articles poses a challenge for curated databases to remain up-to-date. To help the scientific community and database curators deal with this issue, we have developed an application, neXtA5, which prioritizes the literature for specific curation requirements. Our system, neXtA5, is a curation service composed of three main elements. The first component is a named-entity recognition module, which annotates MEDLINE over some predefined axes. This report focuses on three axes: Diseases, the Molecular Function and Biological Process sub-ontologies of the Gene Ontology (GO). The automatic annotations are then stored in a local database, BioMed, for each annotation axis. Additional entities such as species and chemical compounds are also identified. The second component is an existing search engine, which retrieves the most relevant MEDLINE records for any given query. The third component uses the content of BioMed to generate an axis-specific ranking, which takes into account the density of named-entities as stored in the Biomed database. The two ranked lists are ultimately merged using a linear combination, which has been specifically tuned to support the annotation of each axis. The fine-tuning of the coefficients is formally reported for each axis-driven search. Compared with PubMed, which is the system used by most curators, the improvement is the following: +231% for Diseases, +236% for Molecular Functions and +3153% for Biological Process when measuring the precision of the top-returned PMID (P0 or mean reciprocal rank). The current search methods significantly improve the search effectiveness of curators for three important curation axes. Further experiments are being performed to extend the curation types, in particular protein-protein interactions, which require specific relationship extraction capabilities. In parallel, user-friendly interfaces powered with a set of JSON web services are currently being implemented into the neXtProt annotation pipeline.Available on: http://babar.unige.ch:8082/neXtA5Database URL: http://babar.unige.ch:8082/neXtA5/fetcher.jsp. © The Author(s) 2016. Published by Oxford University Press.

neXtA5: accelerating annotation of articles via automated approaches in neXtProt

PubMed Central

Mottin, Luc; Gobeill, Julien; Pasche, Emilie; Michel, Pierre-André; Cusin, Isabelle; Gaudet, Pascale; Ruch, Patrick

2016-01-01

The rapid increase in the number of published articles poses a challenge for curated databases to remain up-to-date. To help the scientific community and database curators deal with this issue, we have developed an application, neXtA5, which prioritizes the literature for specific curation requirements. Our system, neXtA5, is a curation service composed of three main elements. The first component is a named-entity recognition module, which annotates MEDLINE over some predefined axes. This report focuses on three axes: Diseases, the Molecular Function and Biological Process sub-ontologies of the Gene Ontology (GO). The automatic annotations are then stored in a local database, BioMed, for each annotation axis. Additional entities such as species and chemical compounds are also identified. The second component is an existing search engine, which retrieves the most relevant MEDLINE records for any given query. The third component uses the content of BioMed to generate an axis-specific ranking, which takes into account the density of named-entities as stored in the Biomed database. The two ranked lists are ultimately merged using a linear combination, which has been specifically tuned to support the annotation of each axis. The fine-tuning of the coefficients is formally reported for each axis-driven search. Compared with PubMed, which is the system used by most curators, the improvement is the following: +231% for Diseases, +236% for Molecular Functions and +3153% for Biological Process when measuring the precision of the top-returned PMID (P0 or mean reciprocal rank). The current search methods significantly improve the search effectiveness of curators for three important curation axes. Further experiments are being performed to extend the curation types, in particular protein–protein interactions, which require specific relationship extraction capabilities. In parallel, user-friendly interfaces powered with a set of JSON web services are currently being implemented into the neXtProt annotation pipeline. Available on: http://babar.unige.ch:8082/neXtA5 Database URL: http://babar.unige.ch:8082/neXtA5/fetcher.jsp PMID:27374119

Identification of Fur, Aconitase, and Other Proteins Expressed by Mycobacterium tuberculosis under Conditions of Low and High Concentrations of Iron by Combined Two-Dimensional Gel Electrophoresis and Mass Spectrometry

PubMed Central

Wong, Diane K.; Lee, Bai-Yu; Horwitz, Marcus A.; Gibson, Bradford W.

1999-01-01

Iron plays a critical role in the pathophysiology of Mycobacterium tuberculosis. To gain a better understanding of iron regulation by this organism, we have used two-dimensional (2-D) gel electrophoresis, mass spectrometry, and database searching to study protein expression in M. tuberculosis under conditions of high and low iron concentration. Proteins in cellular extracts from M. tuberculosis Erdman strain grown under low-iron (1 μM) and high-iron (70 μM) conditions were separated by 2-D polyacrylamide gel electrophoresis, which allowed high-resolution separation of several hundred proteins, as visualized by Coomassie staining. The expression of at least 15 proteins was induced, and the expression of at least 12 proteins was decreased under low-iron conditions. In-gel trypsin digestion was performed on these differentially expressed proteins, and the digestion mixtures were analyzed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry to determine the molecular masses of the resulting tryptic peptides. Partial sequence data on some of the peptides were obtained by using after source decay and/or collision-induced dissociation. The fragmentation data were used to search computerized peptide mass and protein sequence databases for known proteins. Ten iron-regulated proteins were identified, including Fur and aconitase proteins, both of which are known to be regulated by iron in other bacterial systems. Our study shows that, where large protein sequence databases are available from genomic studies, the combined use of 2-D gel electrophoresis, mass spectrometry, and database searching to analyze proteins expressed under defined environmental conditions is a powerful tool for identifying expressed proteins and their physiologic relevance. PMID:9864233

Huperzine A for vascular dementia

PubMed Central

Hao, Zilong; Liu, Ming; Liu, Zhiqin; Lu, DongHao

2014-01-01

Background Huperzine A, a form of herbal medicine, has been considered as an alternative treatment for vascular dementia (VaD) in China. Objectives To assess the efficacy and safety of Huperzine A in patients with vascular dementia. Search methods We searched ALOIS: the Cochrane Dementia and Cognitive Improvement Group’s Specialized Register on 10 February 2011 using the terms: chinese, plants, huperzine, HUP, ayapin, scoparon. ALOIS contains records of clinical trials identified from monthly searches of a number of major healthcare databases (The Cochrane Library, MEDLINE, EMBASE, PsycINFO, CINAHL, LILACS), numerous trial registries and grey literature sources. We also searched the following databases in March 2011 using the terms ‘Huperzine A’, ‘Shishanjianjia’, ‘Haboyin’ and ‘Shuangyiping’: The Chinese Biomedical Database (CBM) (1977 to March 2011); Chinese Science and Technique Journals Database (VIP) (1989 to March 2011); China National Knowledge Infrastructure (CNKI) (1979 to March 2011); Google (March 2011). In addition, we searched relevant reference lists. We also contacted researchers to request additional information where necessary. Selection criteria We considered randomized controlled trials comparing Huperzine A with placebo in people with vascular dementia eligible for inclusion. Data collection and analysis Two review authors independently applied the inclusion criteria, assessed trial quality and extracted the data. We resolved any disagreement by discussion. Main results We included only one small trial, involving 14 participants with vascular dementia. No significant effect of Huperzine A on cognitive function measured by MMSE (WMD 2.40; 95% CI −4.78 to 9.58) was observed. There was a significant beneficial effect of Huperzine A on performance of activities of daily living (WMD −13.00; 95% CI −23.24 to −2.76) after six months of treatment. No deaths from any cause at the end of treatment were reported. Behaviour, quality of life and caregiver burden were not assessed in the included trial. Authors’ conclusions There is currently no high quality evidence to support the use of Huperzine A for the treatment of vascular dementia. Further randomized placebo controlled trials are needed to determine whether there is worthwhile benefit. PMID:19370686

International patent applications for non-injectable naloxone for opioid overdose reversal: Exploratory search and retrieve analysis of the PatentScope database.

PubMed

McDonald, Rebecca; Danielsson Glende, Øyvind; Dale, Ola; Strang, John

2018-02-01

Non-injectable naloxone formulations are being developed for opioid overdose reversal, but only limited data have been published in the peer-reviewed domain. Through examination of a hitherto-unsearched database, we expand public knowledge of non-injectable formulations, tracing their development and novelty, with the aim to describe and compare their pharmacokinetic properties. (i) The PatentScope database of the World Intellectual Property Organization was searched for relevant English-language patent applications; (ii) Pharmacokinetic data were extracted, collated and analysed; (iii) PubMed was searched using Boolean search query '(nasal OR intranasal OR nose OR buccal OR sublingual) AND naloxone AND pharmacokinetics'. Five hundred and twenty-two PatentScope and 56 PubMed records were identified: three published international patent applications and five peer-reviewed papers were eligible. Pharmacokinetic data were available for intranasal, sublingual, and reference routes. Highly concentrated formulations (10-40 mg mL -1 ) had been developed and tested. Sublingual bioavailability was very low (1%; relative to intravenous). Non-concentrated intranasal spray (1 mg mL -1 ; 1 mL per nostril) had low bioavailability (11%). Concentrated intranasal formulations (≥10 mg mL -1 ) had bioavailability of 21-42% (relative to intravenous) and 26-57% (relative to intramuscular), with peak concentrations (dose-adjusted C max  = 0.8-1.7 ng mL -1 ) reached in 19-30 min (t max ). Exploratory analysis identified intranasal bioavailability as associated positively with dose and negatively with volume. We find consistent direction of development of intranasal sprays to high-concentration, low-volume formulations with bioavailability in the 20-60% range. These have potential to deliver a therapeutic dose in 0.1 mL volume. [McDonald R, Danielsson Glende Ø, Dale O, Strang J. International patent applications for non-injectable naloxone for opioid overdose reversal: Exploratory search and retrieve analysis of the PatentScope database. Drug Alcohol Rev 2017;00:000-000]. © 2017 Australasian Professional Society on Alcohol and other Drugs.

The EMBL-EBI bioinformatics web and programmatic tools framework.

PubMed

Li, Weizhong; Cowley, Andrew; Uludag, Mahmut; Gur, Tamer; McWilliam, Hamish; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Lopez, Rodrigo

2015-07-01

Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi.ac.uk/Tools/sss/) such as BLAST, FASTA and PSI-Search, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa/) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically through Web Services interfaces (https://www.ebi.ac.uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https://www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, InterProScan 5 and PfamScan, new categories such as RNA analysis tools (https://www.ebi.ac.uk/Tools/rna/), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Human genetic factors in tuberculosis: an update.

PubMed

van Tong, Hoang; Velavan, Thirumalaisamy P; Thye, Thorsten; Meyer, Christian G

2017-09-01

Tuberculosis (TB) is a major threat to human health, especially in many developing countries. Human genetic variability has been recognised to be of great relevance in host responses to Mycobacterium tuberculosis infection and in regulating both the establishment and the progression of the disease. An increasing number of candidate gene and genome-wide association studies (GWAS) have focused on human genetic factors contributing to susceptibility or resistance to TB. To update previous reviews on human genetic factors in TB we searched the MEDLINE database and PubMed for articles from 1 January 2014 through 31 March 2017 and reviewed the role of human genetic variability in TB. Search terms applied in various combinations were 'tuberculosis', 'human genetics', 'candidate gene studies', 'genome-wide association studies' and 'Mycobacterium tuberculosis'. Articles in English retrieved and relevant references cited in these articles were reviewed. Abstracts and reports from meetings were also included. This review provides a recent summary of associations of polymorphisms of human genes with susceptibility/resistance to TB. © 2017 John Wiley & Sons Ltd.

Astrobiological complexity with probabilistic cellular automata.

PubMed

Vukotić, Branislav; Ćirković, Milan M

2012-08-01

The search for extraterrestrial life and intelligence constitutes one of the major endeavors in science, but has yet been quantitatively modeled only rarely and in a cursory and superficial fashion. We argue that probabilistic cellular automata (PCA) represent the best quantitative framework for modeling the astrobiological history of the Milky Way and its Galactic Habitable Zone. The relevant astrobiological parameters are to be modeled as the elements of the input probability matrix for the PCA kernel. With the underlying simplicity of the cellular automata constructs, this approach enables a quick analysis of large and ambiguous space of the input parameters. We perform a simple clustering analysis of typical astrobiological histories with "Copernican" choice of input parameters and discuss the relevant boundary conditions of practical importance for planning and guiding empirical astrobiological and SETI projects. In addition to showing how the present framework is adaptable to more complex situations and updated observational databases from current and near-future space missions, we demonstrate how numerical results could offer a cautious rationale for continuation of practical SETI searches.

Posterior lamellar reconstruction: a comprehensive review of the literature.

PubMed

Fin, Alessandra; De Biasio, Fabrizio; Lanzetta, Paolo; Mura, Sebastiano; Tarantini, Anna; Parodi, Pier Camillo

2018-05-21

The aim of the review is to describe the different techniques and materials available to reconstruct the tarsoconjunctival layer of the eyelid; to analyze their indications, advantages, and disadvantages. We searched the Cochrane, PubMed, and Ovid MEDLINE databases for English articles published between January 1990 and January 2017 using variations of the following key words: "posterior lamella," "eyelid reconstruction," "tarsoconjunctival," "flap," and "graft." Two reviewers checked the abstracts of the articles found to eliminate redundant or not relevant articles. The references of the identified articles were screened manually to include relevant works not found through the initial search. The search identified 174 articles. Only a few articles with a therapeutic level of evidence were found. Techniques for the posterior lamellar reconstruction can be categorized as local, regional, and distant flaps; tarsoconjunctival, heterotopic, homologous, and heterologous grafts. Several techniques and variations on the techniques exist to reconstruct the posterior lamella, and, for similar indications, there's no evidence of the primacy of one over the other. Defect size and location as well as patient features must guide the oculoplastic surgeon's choice. The use of biomaterials can avoid possible complications of the donor site.

Drug-drug interactions as a result of co-administering Δ9-THC and CBD with other psychotropic agents.

PubMed

Rong, Carola; Carmona, Nicole E; Lee, Yena L; Ragguett, Renee-Marie; Pan, Zihang; Rosenblat, Joshua D; Subramaniapillai, Mehala; Shekotikhina, Margarita; Almatham, Fahad; Alageel, Asem; Mansur, Rodrigo; Ho, Roger C; McIntyre, Roger S

2018-01-01

To determine, via narrative, non-systematic review of pre-clinical and clinical studies, whether the effect of cannabis on hepatic biotransformation pathways would be predicted to result in clinically significant drug-drug interactions (DDIs) with commonly prescribed psychotropic agents. Areas covered: A non-systematic literature search was conducted using the following databases: PubMed, PsycInfo, and Scopus from inception to January 2017. The search term cannabis was cross-referenced with the terms drug interactions, cytochrome, cannabinoids, cannabidiol, and medical marijuana. Pharmacological, molecular, and physiologic studies evaluating the pharmacokinetics of Δ 9 -tetrahydrocannabinol (Δ 9 -THC) and cannabidiol (CBD), both in vitro and in vivo, were included. Bibliographies were also manually searched for additional citations that were relevant to the overarching aim of this paper. Expert opinion: Δ 9 -Tetrahydrocannabinol and CBD are substrates and inhibitors of cytochrome P450 enzymatic pathways relevant to the biotransformation of commonly prescribed psychotropic agents. The high frequency and increasing use of cannabis invites the need for healthcare providers to familiarize themselves with potential DDIs in persons receiving select psychotropic agents, and additionally consuming medical marijuana and/or recreational marijuana.

Current knowledge and trends in age-related macular degeneration: today's and future treatments.

PubMed

Velez-Montoya, Raul; Oliver, Scott C N; Olson, Jeffrey L; Fine, Stuart L; Mandava, Naresh; Quiroz-Mercado, Hugo

2013-09-01

To address the most dynamic and current issues concerning today's treatment options and promising research efforts regarding treatment for age-related macular degeneration. This review is aimed to serve as a practical reference for more in-depth reviews on the subject. An online review of the database PubMed and Ovid were performed, searching for the key words age-related macular degeneration, AMD, VEGF, treatment, PDT, steroids, bevacizumab, ranibizumab, VEGF-trap, radiation, combined therapy, as well as their compound phrases. The search was limited to articles published since 1985. All returned articles were carefully screened, and their references were manually reviewed for additional relevant data. The web page www.clinicaltrials.gov was also accessed in search of relevant research trials. A total of 363 articles were reviewed, including 64 additional articles extracted from the references. At the end, only 160 references were included in this review. Treatment for age-related macular degeneration is a very dynamic research field. While current treatments are mainly aimed at blocking vascular endothelial growth factor, future treatments seek to prevent vision loss because of scarring. Promising efforts have been made to address the dry form of the disease, which has lacked effective treatment.

Reliability and Validity of Survey Instruments to Measure Work-Related Fatigue in the Emergency Medical Services Setting: A Systematic Review.

PubMed

Patterson, P Daniel; Weaver, Matthew D; Fabio, Anthony; Teasley, Ellen M; Renn, Megan L; Curtis, Brett R; Matthews, Margaret E; Kroemer, Andrew J; Xun, Xiaoshuang; Bizhanova, Zhadyra; Weiss, Patricia M; Sequeira, Denisse J; Coppler, Patrick J; Lang, Eddy S; Higgins, J Stephen

2018-02-15

This study sought to systematically search the literature to identify reliable and valid survey instruments for fatigue measurement in the Emergency Medical Services (EMS) occupational setting. A systematic review study design was used and searched six databases, including one website. The research question guiding the search was developed a priori and registered with the PROSPERO database of systematic reviews: "Are there reliable and valid instruments for measuring fatigue among EMS personnel?" (2016:CRD42016040097). The primary outcome of interest was criterion-related validity. Important outcomes of interest included reliability (e.g., internal consistency), and indicators of sensitivity and specificity. Members of the research team independently screened records from the databases. Full-text articles were evaluated by adapting the Bolster and Rourke system for categorizing findings of systematic reviews, and the rated data abstracted from the body of literature as favorable, unfavorable, mixed/inconclusive, or no impact. The Grading of Recommendations, Assessment, Development and Evaluation (GRADE) methodology was used to evaluate the quality of evidence. The search strategy yielded 1,257 unique records. Thirty-four unique experimental and non-experimental studies were determined relevant following full-text review. Nineteen studies reported on the reliability and/or validity of ten different fatigue survey instruments. Eighteen different studies evaluated the reliability and/or validity of four different sleepiness survey instruments. None of the retained studies reported sensitivity or specificity. Evidence quality was rated as very low across all outcomes. In this systematic review, limited evidence of the reliability and validity of 14 different survey instruments to assess the fatigue and/or sleepiness status of EMS personnel and related shift worker groups was identified.

Validity of 2D lateral cephalometry in orthodontics: a systematic review

PubMed Central

2013-01-01

Lateral cephalometric radiography is commonly used as a standard tool in orthodontic assessment and treatment planning. The aim of this study was to evaluate the available scientific literature and existing evidence for the validation of using lateral cephalometric imaging for orthodontic treatment planning. The secondary objective was to determine the accuracy and reliability of this technique. We did not attempt to evaluate the value of this radiographic technique for other purposes. A literature search was performed using specific keywords on electronic databases: Ovid MEDLINE, Scopus and Web of Science. Two reviewers selected relevant articles, corresponding to predetermined inclusion criteria. The electronic search was followed by a hand search of the reference lists of relevant papers. Two reviewers assessed the level of evidence of relevant publications as high, moderate or low. Based on this, the evidence grade for diagnostic efficacy was rated as strong, moderately strong, limited or insufficient. The initial search revealed 784 articles listed in MEDLINE (Ovid), 1,034 in Scopus and 264 articles in the Web of Science. Only 17 articles met the inclusion criteria and were selected for qualitative synthesis. Results showed seven studies on the role of cephalometry in orthodontic treatment planning, eight concerning cephalometric measurements and landmark identification and two on cephalometric analysis. It is surprising that, notwithstanding the 968 articles published in peer-reviewed journals, scientific evidence on the usefulness of this radiographic technique in orthodontics is still lacking, with contradictory results. More rigorous research on a larger study population should be performed to achieve full evidence on this topic. PMID:24325757

Indexing of randomised controlled trials of physiotherapy interventions: a comparison of AMED, CENTRAL, CINAHL, EMBASE, hooked on evidence, PEDro, PsycINFO and PubMed.

PubMed

Moseley, Anne M; Sherrington, Catherine; Elkins, Mark R; Herbert, Robert D; Maher, Christopher G

2009-09-01

To compare the comprehensiveness of indexing the reports of randomised controlled trials of physiotherapy interventions by eight bibliographic databases (AMED, CENTRAL, CINAHL, EMBASE, Hooked on Evidence, PEDro, PsycINFO and PubMed). Audit of bibliographic databases. Two hundred and eighty-one reports of randomised controlled trials of physiotherapy interventions were identified by screening the reference lists of 30 relevant systematic reviews published in four consecutive issues of the Cochrane Database of Systematic Reviews (Issue 3, 2007 to Issue 2, 2008). AMED, CENTRAL, CINAHL, EMBASE, Hooked on Evidence, PEDro, PsycINFO and PubMed were used to search for the trial reports. The number of trial reports indexed in each database was calculated. PEDro indexed 99% of the trial reports, CENTRAL indexed 98%, PubMed indexed 91%, EMBASE indexed 82%, CINAHL indexed 61%, Hooked on Evidence indexed 40%, AMED indexed 36% and PsycINFO indexed 17%. Most trial reports (92%) were indexed on four or more of the databases. One trial report was indexed on a single database (PEDro). Of the eight bibliographic databases examined, PEDro and CENTRAL provide the most comprehensive indexing of reports of randomised trials of physiotherapy interventions.

Molecule database framework: a framework for creating database applications with chemical structure search capability

PubMed Central

2013-01-01

Background Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Results Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes: • Support for multi-component compounds (mixtures) • Import and export of SD-files • Optional security (authorization) For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures). Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. Conclusions By using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework. PMID:24325762

Molecule database framework: a framework for creating database applications with chemical structure search capability.

PubMed

Kiener, Joos

2013-12-11

Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:•Support for multi-component compounds (mixtures)•Import and export of SD-files•Optional security (authorization)For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures).Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. By using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework.

Monitoring ethical, legal, and social issues in developing population genetic databases.

PubMed

Austin, Melissa A; Harding, Sarah E; McElroy, Courtney E

2003-01-01

To characterize ethical, legal, and social issues unique to population genetic database research and to determine the relevance of international recommendations and guidelines for addressing these issues in the development of "genebank" projects globally. Building on our previous description of eight international genebanks, we conducted a comprehensive electronic search and literature review of relevant publications and consulted national and international documents applicable to genebank research. We identified and characterized five categories of ethical, legal, and social issues unique to genebank development: sponsorship and benefit-sharing, neutrality and regulatory power of ethics committees, public engagement, consent, and data protection. We illustrate these issues with examples from specific genebanks. Not all of the issues are addressed in current international guidelines, many of which are nonspecific and unenforceable. The trend of genebank development promises to provide new discoveries to the field of medical science and to greatly improve public health. However, there is a growing need for more explicit, enforceable, and coordinated international guidelines relevant to the development and implementation of genebanks. By comparing ethical, legal and social issues as they arise in genebanks, researchers can better evaluate how to best use these projects to improve public health while protecting participating populations.

Citation of prior research has increased in introduction and discussion sections with time: A survey of clinical trials in physiotherapy.

PubMed

Hoderlein, Xenia; Moseley, Anne M; Elkins, Mark R

2017-08-01

Many clinical trials are reported without reference to the existing relevant high-quality research. This study aimed to investigate the extent to which authors of reports of clinical trials of physiotherapy interventions try to use high-quality clinical research to (1) help justify the need for the trial in the introduction and (2) help interpret the trial's results in the discussion. Data were extracted from 221 clinical trials that were randomly selected from the Physiotherapy Evidence Database: 70 published in 2001 (10% sample) and 151 published in 2015 (10% sample). The Physiotherapy Evidence Database score (which rates methodological quality and completeness of reporting) for each trial was also downloaded. Overall 41% of trial reports cited a systematic review or the results of a search for other evidence in the introduction section: 20% for 2001 and 50% for 2015 (relative risk = 2.3, 95% confidence interval = 1.5-3.8). For the discussion section, only 1 of 221 trials integrated the results of the trial into an existing meta-analysis, but citation of a relevant systematic review did increase from 17% in 2001 to 34% in 2015. There was no relationship between citation of existing research and the total Physiotherapy Evidence Database score. Published reports of clinical trials of physiotherapy interventions increasingly cite a systematic review or the results of a search for other evidence in the introduction, but integration with existing research in the discussion section is very rare. To encourage the use of existing research, stronger recommendations to refer to existing systematic reviews (where available) could be incorporated into reporting checklists and journal editorial guidelines.

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.

Economics methods in Cochrane systematic reviews of health promotion and public health related interventions.

PubMed

Shemilt, Ian; Mugford, Miranda; Drummond, Michael; Eisenstein, Eric; Mallender, Jacqueline; McDaid, David; Vale, Luke; Walker, Damian

2006-11-15

Provision of evidence on costs alongside evidence on the effects of interventions can enhance the relevance of systematic reviews to decision-making. However, patterns of use of economics methods alongside systematic review remain unclear. Reviews of evidence on the effects of interventions are published by both the Cochrane and Campbell Collaborations. Although it is not a requirement that Cochrane or Campbell Reviews should consider economic aspects of interventions, many do. This study aims to explore and describe approaches to incorporating economics methods in a selection of Cochrane systematic reviews in the area of health promotion and public health, to help inform development of methodological guidance on economics for reviewers. The Cochrane Database of Systematic Reviews was searched using a search strategy for potential economic evaluation studies. We included current Cochrane reviews and review protocols retrieved using the search that are also identified as relevant to health promotion or public health topics. A reviewer extracted data which describe the economics components of included reviews. Extracted data were summarised in tables and analysed qualitatively. Twenty-one completed Cochrane reviews and seven review protocols met inclusion criteria. None incorporate formal economic evaluation methods. Ten completed reviews explicitly aim to incorporate economics studies and data. There is a lack of transparent reporting of methods underpinning the incorporation of economics studies and data. Some reviews are likely to exclude useful economics studies and data due to a failure to incorporate search strategies tailored to the retrieval of such data or use of key specialist databases, and application of inclusion criteria designed for effectiveness studies. There is a need for consistency and transparency in the reporting and conduct of the economics components of Cochrane reviews, as well as regular dialogue between Cochrane reviewers and economists to develop increased capacity for economic analyses alongside such reviews. Use of applicable economics methods in Cochrane reviews can help provide the international context within which economics data can be interpreted and assessed as a preliminary to full economic evaluation.

Motor abilities of children and adolescents with a psychiatric condition: A systematic literature review

PubMed Central

Damme, Tine Van; Simons, Johan; Sabbe, Bernard; van West, Dirk

2015-01-01

AIM: To summarize research regarding the motor abilities of children and adolescents who suffer from a common psychiatric condition. METHODS: In order to outline the current knowledge regarding the motor abilities of children and adolescents with autism spectrum disorders (ASD), attention deficit hyperactivity disorder (ADHD), disruptive behavior disorders (DBD) and depression, a comprehensive systematic literature search was carried out using PubMed, Medline and ERIC databases. The databases were searched for relevant English language articles published between January 1990 and April 2014. Only studies that conducted a quantitative evaluation of motor ability and concerned individuals aged 0-18 years were included. A separate search was conducted for each disorder (ASD, ADHD, DBD, depression) in conjunction with each of the following keywords: (psycho/perceptuo) motor/movement skill(s), (psycho/perceptuo) motor/movement abilities, (psycho/perceptuo) motor/movement impairment, (psycho/perceptuo) motor/movement problem(s), motor function, motor coordination, motor performance, motor deficit(s). To detect supplementary relevant literature, the reference lists of the retrieved articles were examined. RESULTS: The search strategy yielded 51 studies meeting the inclusion criteria. In total, 28 studies were included that examined the motor abilities of children and adolescents with ASD. All studies indicated that they performed below average on various standardized motor assessment instruments. The overall prevalence rate for impairment in motor abilities ranged from 33% to 100%. Twenty-seven studies examined the motor abilities of children and adolescents with ADHD. Depending on the type of motor assessment tool and the cut-off points used by different researchers, prevalence rates of impairment in motor abilities are highly variable and ranged from 8% to 73%. Remarkably, there is a paucity of research addressing the motor abilities of individuals with DBD or depression. Furthermore, methodological problems, such as measurement and comorbidity issues, complicate the generalization of the findings. CONCLUSION: Research suggests that motor impairment is highly prevalent in some psychiatric conditions, particularly ASD and ADHD. However, future work is necessary to draw sound conclusions. PMID:26425445

Inclusion of individuals with special needs in regular education: a literature review.

PubMed

Silva, Fabiana Trevisani; Gonçalves, Eduardo Augusto Vella; Alvarenga, Kátia de Freitas

2012-01-01

To critically analyze the inclusion of individuals with special needs in regular education in Brazil, considering social and legal aspects, through literature review. The literature search was conducted in open access databases: LILACS, SciELO, Portal Cochrane and IUSDATA, the latter belonging to the Library of the Law School of the University of São Paulo, considering all articles published until December 2010. The search strategy used the following keywords: inclusive education; special education; inclusive proposal; individuals with special needs. In the search, only studies in which the summary or the body of the article were related to the purpose of the study were evaluated and selected. The potentially relevant articles for review were presented in a protocol form containing the eligibility criteria of the study, methods used, characteristics of the analyzed group or manuscripts, type of intervention used in the study, and results obtained. Articles classified as expert opinions, despite their low level of scientific evidence, were considered in this work, since they are often found in the literature on the issue. A total of 1,399 articles was found and 120 potentially relevant articles were selected after reading their abstracts. From these, 67 articles were cited in more than one database, which resulted in 53 articles to be fully read. Fifteen of these articles were excluded after reading because they did not meet the inclusion criteria. Thus, 38 studies were included and analyzed. Following a critical analysis of the literature in the field, it was concluded that, so far, in general, the school receives individuals with special needs; however, there is a long way to go to actually include these individuals, although Brazil has the scope of inclusion. Therefore, it is necessary to establish public policies and guidelines aimed at effective inclusion.

Methods for systematic reviews of health economic evaluations: a systematic review, comparison, and synthesis of method literature.

PubMed

Mathes, Tim; Walgenbach, Maren; Antoine, Sunya-Lee; Pieper, Dawid; Eikermann, Michaela

2014-10-01

The quality of systematic reviews of health economic evaluations (SR-HE) is often limited because of methodological shortcomings. One reason for this poor quality is that there are no established standards for the preparation of SR-HE. The objective of this study is to compare existing methods and suggest best practices for the preparation of SR-HE. To identify the relevant methodological literature on SR-HE, a systematic literature search was performed in Embase, Medline, the National Health System Economic Evaluation Database, the Health Technology Assessment Database, and the Cochrane methodology register, and webpages of international health technology assessment agencies were searched. The study selection was performed independently by 2 reviewers. Data were extracted by one reviewer and verified by a second reviewer. On the basis of the overlaps in the recommendations for the methods of SR-HE in the included papers, suggestions for best practices for the preparation of SR-HE were developed. Nineteen relevant publications were identified. The recommendations within them often differed. However, for most process steps there was some overlap between recommendations for the methods of preparation. The overlaps were taken as basis on which to develop suggestions for the following process steps of preparation: defining the research question, developing eligibility criteria, conducting a literature search, selecting studies, assessing the methodological study quality, assessing transferability, and synthesizing data. The differences in the proposed recommendations are not always explainable by the focus on certain evaluation types, target audiences, or integration in the decision process. Currently, there seem to be no standard methods for the preparation of SR-HE. The suggestions presented here can contribute to the harmonization of methods for the preparation of SR-HE. © The Author(s) 2014.

Profiling modifications for glioblastoma proteome using ultra-tolerant database search: Are the peptide mass shifts biologically relevant or chemically induced?

PubMed

Tarasova, Irina A; Chumakov, Peter M; Moshkovskii, Sergei A; Gorshkov, Mikhail V

2018-05-17

Peptide mass shifts were profiled using ultra-tolerant database search strategy for shotgun proteomics data sets of human glioblastoma cell lines demonstrating strong response to the type I interferon (IFNα-2b) treatment. The main objective of this profiling was revealing the cell response to IFN treatment at the level of protein modifications. To achieve this objective, statistically significant changes in peptide mass shift profiles between IFN treated and untreated glioblastoma samples were analyzed. Detailed analysis of MS/MS spectra allowed further interpretation of the observed mass shifts and differentiation between post-translational and artifact modifications. Malignant cells typically acquire increased sensitivity to viruses due to the deregulated antiviral mechanisms. Therefore, a viral therapy is considered as one of the promising approaches to treat cancer. However, recent studies have demonstrated that malignant cells can preserve intact antiviral mechanisms, e.g. interferon signaling, and develop resistance to virus infection in response to interferon treatment. Post translational modifications, e.g. tyrosine phosphorylation, are the interferon signaling drivers. Thus, comprehensive characterization of modifications is crucially important, yet, most challenging problem in cancer proteomics. Here, we report on the application of the recently introduced ultra-tolerant search strategy for profiling peptide modifications in the human glioblastoma cell lines demonstrating strong response to the type I interferon (IFNα-2b) treatment. The specific aim of the study was identification of statistically significant changes in peptide mass shift profiles between IFN treated and untreated glioblastoma samples, as well as determination of whether these shifts represent the biologically relevant modification. Copyright © 2018 Elsevier B.V. All rights reserved.

Pain perception during levonorgestrel-releasing intrauterine device insertion in nulliparous women: a systematic review.

PubMed

Anthoulakis, Christos; Iordanidou, Eirini; Vatopolou, Anastasia

2018-06-08

Intrauterine devices (IUDs) still remain underused in adolescents. Pain during insertion may prevent adolescents to opt for a levonorgestrel (LNG) - releasing IUD. This study aimed to conduct a systematic review, following the PRISMA guidelines, and critically appraise published data with respect to the efficacy of various substances (analgesics or not) in preventing pain during LNG-IUD insertion in nulliparous women as a proxy for adolescents. DESIGN, SETTING, PARTICIPANTS, INTERVENTIONS, AND MAIN OUTCOME MEASURES: A comprehensive computerized systematic literature search of all English language studies between 2006 and 2016 was performed in PubMed, EMBASE, Scopus, Evidence Based Medicine Reviews (Cochrane Database and Cochrane Central Register of Controlled Trials), and Google Scholar. Relevant article reference lists were hand searched. Computerised database search revealed 31 citations of relevance, 9 of which with a total of 355 treated women and 345 controls fulfilled the inclusion/exclusion criteria. In women treated with misoprostol (n=150) versus placebo (n=145), the median visual analog scale (VAS) score ± standard deviation (SD) were 5.7 ± 2.1 versus 5.1 ± 2.2, respectively. In the abovementioned population, there was a non-significant change in VAS score (OR=1.44, 95%CI 0.86-2.40). In women treated with lidocaine (n=140) versus placebo (n=136), the median VAS score ± SD were 4.6 ± 2.1 versus 5.8 ± 2, respectively. In the aforementioned population, there was a significant decrease in VAS score (OR=0.12, 95%CI 0.02-0.91). In nulliparous women, lidocaine treatment seems to be a reasonable choice. However, further studies are required to examine the different routes and modes of administration as well as optimal quantities. Copyright © 2018. Published by Elsevier Inc.

Scientists Admitting to Plagiarism: A Meta-analysis of Surveys.

PubMed

Pupovac, Vanja; Fanelli, Daniele

2015-10-01

We conducted a systematic review and meta-analysis of anonymous surveys asking scientists whether they ever committed various forms of plagiarism. From May to December 2011 we searched 35 bibliographic databases, five grey literature databases and hand searched nine journals for potentially relevant studies. We included surveys that asked scientists if, in a given recall period, they had committed or knew of a colleague who committed plagiarism, and from each survey extracted the proportion of those who reported at least one case. Studies that focused on academic (i.e. student) plagiarism were excluded. Literature searches returned 12,460 titles from which 17 relevant survey studies were identified. Meta-analysis of studies reporting committed (N = 7) and witnessed (N = 11) plagiarism yielded a pooled estimate of, respectively, 1.7% (95% CI 1.2-2.4) and 30% (95% CI 17-46). Basic methodological factors, including sample size, year of survey, delivery method and whether survey questions were explicit rather than indirect made a significant difference on survey results. Even after controlling for these methodological factors, between-study differences in admission rates were significantly above those expected by sampling error alone and remained largely unexplained. Despite several limitations of the data and of this meta-analysis, we draw three robust conclusions: (1) The rate at which scientists report knowing a colleague who committed plagiarism is higher than for data fabrication and falsification; (2) The rate at which scientists report knowing a colleague who committed plagiarism is correlated to that of fabrication and falsification; (3) The rate at which scientists admit having committed either form of misconduct (i.e. fabrication, falsification and plagiarism) in surveys has declined over time.

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters.

PubMed

Wang, Chunlin; Lefkowitz, Elliot J

2004-10-28

Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist.

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

PubMed Central

Wang, Chunlin; Lefkowitz, Elliot J

2004-01-01

Background Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. Results We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Conclusions Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist. PMID:15511296

Large-scale feature searches of collections of medical imagery

NASA Astrophysics Data System (ADS)

Hedgcock, Marcus W.; Karshat, Walter B.; Levitt, Tod S.; Vosky, D. N.

1993-09-01

Large scale feature searches of accumulated collections of medical imagery are required for multiple purposes, including clinical studies, administrative planning, epidemiology, teaching, quality improvement, and research. To perform a feature search of large collections of medical imagery, one can either search text descriptors of the imagery in the collection (usually the interpretation), or (if the imagery is in digital format) the imagery itself. At our institution, text interpretations of medical imagery are all available in our VA Hospital Information System. These are downloaded daily into an off-line computer. The text descriptors of most medical imagery are usually formatted as free text, and so require a user friendly database search tool to make searches quick and easy for any user to design and execute. We are tailoring such a database search tool (Liveview), developed by one of the authors (Karshat). To further facilitate search construction, we are constructing (from our accumulated interpretation data) a dictionary of medical and radiological terms and synonyms. If the imagery database is digital, the imagery which the search discovers is easily retrieved from the computer archive. We describe our database search user interface, with examples, and compare the efficacy of computer assisted imagery searches from a clinical text database with manual searches. Our initial work on direct feature searches of digital medical imagery is outlined.

Antileishmanial and Immunomodulatory Activity of Allium sativum (Garlic)

PubMed Central

Foroutan-Rad, Masoud; Tappeh, Khosrow Hazrati; Khademvatan, Shahram

2015-01-01

Leishmaniasis is caused by an obligate intracellular protozoa belonging to Leishmania genus. The current drugs for treatment of leishmaniasis possess many disadvantages; therefore, researchers are continuously looking for the more effective and safer drugs. The aim of this study is to review the effectiveness, toxicities, and possible mechanisms of pharmaceutical actions of different garlic extracts and organosulfur compounds isolated from garlic against Leishmania spp. in a variety of in vitro, in vivo and clinical trials reports. All relevant databases were searched using the terms “Allium sativum,” “Garlic,” “Allicin,” “Ajoene,” “Leishmania,” “in vitro,” “in vivo,” and “clinical trial,” alone or in combination from 5 English databases (Web of Science, PubMed, Science Direct, Scopus, Google Scholar) and 3 Persian databases (Scientific Information Database, Iran Medex, and Magiran) from 1990 to 2014. In summary, garlic with immunomodulatory effects and apoptosis induction contributes to the treatment of leishmaniasis. PMID:26721553

SCRIPDB: a portal for easy access to syntheses, chemicals and reactions in patents

PubMed Central

Heifets, Abraham; Jurisica, Igor

2012-01-01

The patent literature is a rich catalog of biologically relevant chemicals; many public and commercial molecular databases contain the structures disclosed in patent claims. However, patents are an equally rich source of metadata about bioactive molecules, including mechanism of action, disease class, homologous experimental series, structural alternatives, or the synthetic pathways used to produce molecules of interest. Unfortunately, this metadata is discarded when chemical structures are deposited separately in databases. SCRIPDB is a chemical structure database designed to make this metadata accessible. SCRIPDB provides the full original patent text, reactions and relationships described within any individual patent, in addition to the molecular files common to structural databases. We discuss how such information is valuable in medical text mining, chemical image analysis, reaction extraction and in silico pharmaceutical lead optimization. SCRIPDB may be searched by exact chemical structure, substructure or molecular similarity and the results may be restricted to patents describing synthetic routes. SCRIPDB is available at http://dcv.uhnres.utoronto.ca/SCRIPDB. PMID:22067445

VIEWCACHE: An incremental pointer-based access method for autonomous interoperable databases

NASA Technical Reports Server (NTRS)

Roussopoulos, N.; Sellis, Timos

1992-01-01

One of biggest problems facing NASA today is to provide scientists efficient access to a large number of distributed databases. Our pointer-based incremental database access method, VIEWCACHE, provides such an interface for accessing distributed data sets and directories. VIEWCACHE allows database browsing and search performing inter-database cross-referencing with no actual data movement between database sites. This organization and processing is especially suitable for managing Astrophysics databases which are physically distributed all over the world. Once the search is complete, the set of collected pointers pointing to the desired data are cached. VIEWCACHE includes spatial access methods for accessing image data sets, which provide much easier query formulation by referring directly to the image and very efficient search for objects contained within a two-dimensional window. We will develop and optimize a VIEWCACHE External Gateway Access to database management systems to facilitate distributed database search.

Evaluation of Federated Searching Options for the School Library

ERIC Educational Resources Information Center

Abercrombie, Sarah E.

2008-01-01

Three hosted federated search tools, Follett One Search, Gale PowerSearch Plus, and WebFeat Express, were configured and implemented in a school library. Databases from five vendors and the OPAC were systematically searched. Federated search results were compared with each other and to the results of the same searches in the database's native…

Online Patent Searching: The Realities.

ERIC Educational Resources Information Center

Kaback, Stuart M.

1983-01-01

Considers patent subject searching capabilities of major online databases, noting patent claims, "deep-indexed" files, test searches, retrieval of related references, multi-database searching, improvements needed in indexing of chemical structures, full text searching, improvements needed in handling numerical data, and augmenting a…

Huperzine A for vascular dementia.

PubMed

Hao, Zilong; Liu, Ming; Liu, Zhiqin; Lv, Donghao

2009-04-15

Huperzine A, a form of herbal medicine, has been considered as an alternative treatment for vascular dementia (VaD) in China. To assess the efficacy and safety of Huperzine A in patients with vascular dementia. The Specialized Register of the Cochrane Dementia and Cognitive Improvement Group (CDCIG) was searched on 7 July 2008 using the terms: huperzi* OR ayapin OR scoparon*. The CDCIG Specialized Register contains records from all major health care databases (The Cochrane Library, MEDLINE, EMBASE, PsycINFO, CINAHL, LILACS) as well as from many trials databases and grey literature sources. The review authors searched the following databases in August 2008 using the terms 'Huperzine A', 'Shishanjianjia', 'Haboyin' and 'Shuangyiping': The Chinese Biomedical Database (CBM) (1977 to August 2008); Chinese Science and Technique Journals Database (VIP) (1989 to August 2008); China National Knowledge Infrastructure (CNKI) (1979 to August 2008); The Chinese Clinical Trials Register (ChiCTR, August 2008); Google (August 2008). In addition, the review authors searched reference lists, relevant clinical trials and contacted researchers in an effort to identify further published and unpublished studies. Randomized controlled trials comparing Huperzine A with placebo in patients with vascular dementia were considered eligible for inclusion. Two review authors independently selected trials for inclusion, assessed trial quality, and extracted data. Only one small trial, involving 14 participants, was included. No significant beneficial effect of Huperzine A on the improvement of cognitive function measured by MMSE for VaD (WMD 2.40; 95% CI -4.78 to 9.58) was observed. No death from all causes at the end of treatment were reported. At present, other outcome measures were not available in any of the trials. Although no statistically significant differences were found between the Huperzine A-treated and control groups, the confidence intervals for the treatment effect estimates were wide and included both clinically significant benefits and clinically significant harms. There is no [convincing] evidence that Huperzine A is of value in vascular dementia based on one small trial. It deserves further research.

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…

Application of kernel functions for accurate similarity search in large chemical databases.

PubMed

Wang, Xiaohong; Huan, Jun; Smalter, Aaron; Lushington, Gerald H

2010-04-29

Similarity search in chemical structure databases is an important problem with many applications in chemical genomics, drug design, and efficient chemical probe screening among others. It is widely believed that structure based methods provide an efficient way to do the query. Recently various graph kernel functions have been designed to capture the intrinsic similarity of graphs. Though successful in constructing accurate predictive and classification models, graph kernel functions can not be applied to large chemical compound database due to the high computational complexity and the difficulties in indexing similarity search for large databases. To bridge graph kernel function and similarity search in chemical databases, we applied a novel kernel-based similarity measurement, developed in our team, to measure similarity of graph represented chemicals. In our method, we utilize a hash table to support new graph kernel function definition, efficient storage and fast search. We have applied our method, named G-hash, to large chemical databases. Our results show that the G-hash method achieves state-of-the-art performance for k-nearest neighbor (k-NN) classification. Moreover, the similarity measurement and the index structure is scalable to large chemical databases with smaller indexing size, and faster query processing time as compared to state-of-the-art indexing methods such as Daylight fingerprints, C-tree and GraphGrep. Efficient similarity query processing method for large chemical databases is challenging since we need to balance running time efficiency and similarity search accuracy. Our previous similarity search method, G-hash, provides a new way to perform similarity search in chemical databases. Experimental study validates the utility of G-hash in chemical databases.

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.

An evidence based review of the assessment and management of penetrating neck trauma.

PubMed

Burgess, C A; Dale, O T; Almeyda, R; Corbridge, R J

2012-02-01

Although relatively uncommon, penetrating neck trauma has the potential for serious morbidity and an estimated mortality of up to 6%. The assessment and management of patients who have sustained a penetrating neck injury has historically been an issue surrounded by significant controversy. OBJECTIVES OF REVIEW: To assess recent evidence relating to the assessment and management of penetrating neck trauma, highlighting areas of controversy with an overall aim of formulating clinical guidelines according to a care pathway format. Structured, non-systematic review of recent medical literature. An electronic literature search was performed in May 2011. The Medline database was searched using the Medical Subject Headings terms 'neck injuries' and 'wounds, penetrating' in conjunction with the terms 'assessment' or 'management'. Embase was searched with the terms 'penetrating trauma' and 'neck injury', also in conjunction with the terms 'assessment' and 'management'. Results were limited to articles published in English from 1990 to the present day. Abstracts were reviewed by the first three authors to select full-text articles for further critical appraisal. The references and citation links of these articles were hand-searched to identify further articles of relevance. 147 relevant articles were identified by the electronic literature search, comprising case series, case reports and reviews. 33 were initially selected for further evaluation. Although controversy continues to surround the management of penetrating neck trauma, the role of selective non-operative management and the utility of CT angiography to investigate potential vascular injuries appears to be increasingly accepted. © 2011 Blackwell Publishing Ltd.

The use of the exit interview to reduce turnover amongst healthcare professionals.

PubMed

Flint, Anndrea; Webster, Joan

2011-01-19

Exit interviews are widely used in healthcare organisations to identify reasons for staff attrition, yet their usefulness in limiting turnover is unclear. To determine the effectiveness of various exit interview strategies in decreasing turnover rates amongst healthcare professionals. We used a comprehensive search strategy including an electronic search of the following databases: DARE, CENTRAL, MEDLINE, EMBASE, CINAHL, PsycINFO, ERIC (search date: 7 September 2010) and EPOC Specialised Register (search date: 30 September 2009). We also screened the reference lists of included studies and relevant reviews. Randomised controlled trials, controlled clinical trials, controlled before and after studies and interrupted time series studies comparing turnover rates between healthcare professionals who had undergone one form of exit interview with another form of exit interview or with no interview. Two review authors independently assessed trial quality and extracted data. The search identified 1560 citations of which we considered 19 potentially relevant. The two authors independently reviewed the abstracts of these studies and retrieved the full texts of eight studies. We excluded all eight following independent assessment. They were either interviews, commentaries on how to do an exit interview or descriptive studies about reasons for leaving. We found no trials that matched our inclusion criteria. Evidence about the effectiveness of exit interviews to reduce turnover is currently not available. However, exit interviews may provide useful information about the work environment which, in turn, may be useful in the development of interventions to reduce turnover.

Utilisation of oral health services provided by non-dental health practitioners in developed countries: a review of the literature.

PubMed

Barnett, T; Hoang, Ha; Stuart, J; Crocombe, L; Bell, E

2014-12-01

People who have limited access to dental care may present to non-dental health practitioners for dental treatment and advice. This review synthesised the available evidence regarding the use of non-dental health practitioners for oral health problems and the services provided by non-dental health practitioners to manage such presentations. PubMed and CINAHL databases were searched using key search terms to identify all relevant quantitative and qualitative English-language studies published between 1990 and March 2014. Snowballing techniques were then applied whereby the reference lists of retrieved articles were searched for other relevant citations. Grey literature was searched via Google using the same search terms to identify unpublished work and government reports. Of the 43 papers which met the review criteria, 25 papers reported on the use of non-dental health practitioners for oral health problems and 18 on dental care education and training for non-dental health practitioners. Four reports were located from the grey literature on the involvement of non-dental health practitioners in the management of oral health care. The review of literature showed that both children and adults utilise non-dental health practitioners for oral health problems. Despite this, Emergency Department medical staff, medical practitioners and pharmacists generally lacked training and knowledge in the maragement of oral health. Services from non-dental health practitioners mainly focussed on children. The literature on education and training for non-dental health practitioners was limited.

Informatics in radiology: RADTF: a semantic search-enabled, natural language processor-generated radiology teaching file.

PubMed

Do, Bao H; Wu, Andrew; Biswal, Sandip; Kamaya, Aya; Rubin, Daniel L

2010-11-01

Storing and retrieving radiology cases is an important activity for education and clinical research, but this process can be time-consuming. In the process of structuring reports and images into organized teaching files, incidental pathologic conditions not pertinent to the primary teaching point can be omitted, as when a user saves images of an aortic dissection case but disregards the incidental osteoid osteoma. An alternate strategy for identifying teaching cases is text search of reports in radiology information systems (RIS), but retrieved reports are unstructured, teaching-related content is not highlighted, and patient identifying information is not removed. Furthermore, searching unstructured reports requires sophisticated retrieval methods to achieve useful results. An open-source, RadLex(®)-compatible teaching file solution called RADTF, which uses natural language processing (NLP) methods to process radiology reports, was developed to create a searchable teaching resource from the RIS and the picture archiving and communication system (PACS). The NLP system extracts and de-identifies teaching-relevant statements from full reports to generate a stand-alone database, thus converting existing RIS archives into an on-demand source of teaching material. Using RADTF, the authors generated a semantic search-enabled, Web-based radiology archive containing over 700,000 cases with millions of images. RADTF combines a compact representation of the teaching-relevant content in radiology reports and a versatile search engine with the scale of the entire RIS-PACS collection of case material. ©RSNA, 2010

Using relational databases for improved sequence similarity searching and large-scale genomic analyses.

PubMed

Mackey, Aaron J; Pearson, William R

2004-10-01

Relational databases are designed to integrate diverse types of information and manage large sets of search results, greatly simplifying genome-scale analyses. Relational databases are essential for management and analysis of large-scale sequence analyses, and can also be used to improve the statistical significance of similarity searches by focusing on subsets of sequence libraries most likely to contain homologs. This unit describes using relational databases to improve the efficiency of sequence similarity searching and to demonstrate various large-scale genomic analyses of homology-related data. This unit describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. These include basic use of the database to generate a novel sequence library subset, how to extend and use seqdb_demo for the storage of sequence similarity search results and making use of various kinds of stored search results to address aspects of comparative genomic analysis.

DNA profiles, computer searches, and the Fourth Amendment.

PubMed

Kimel, Catherine W

2013-01-01

Pursuant to federal statutes and to laws in all fifty states, the United States government has assembled a database containing the DNA profiles of over eleven million citizens. Without judicial authorization, the government searches each of these profiles one-hundred thousand times every day, seeking to link database subjects to crimes they are not suspected of committing. Yet, courts and scholars that have addressed DNA databasing have focused their attention almost exclusively on the constitutionality of the government's seizure of the biological samples from which the profiles are generated. This Note fills a gap in the scholarship by examining the Fourth Amendment problems that arise when the government searches its vast DNA database. This Note argues that each attempt to match two DNA profiles constitutes a Fourth Amendment search because each attempted match infringes upon database subjects' expectations of privacy in their biological relationships and physical movements. The Note further argues that database searches are unreasonable as they are currently conducted, and it suggests an adaptation of computer-search procedures to remedy the constitutional deficiency.

[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.

Chapter 51: How to Build a Simple Cone Search Service Using a Local Database

NASA Astrophysics Data System (ADS)

Kent, B. R.; Greene, G. R.

The cone search service protocol will be examined from the server side in this chapter. A simple cone search service will be setup and configured locally using MySQL. Data will be read into a table, and the Java JDBC will be used to connect to the database. Readers will understand the VO cone search specification and how to use it to query a database on their local systems and return an XML/VOTable file based on an input of RA/DEC coordinates and a search radius. The cone search in this example will be deployed as a Java servlet. The resulting cone search can be tested with a verification service. This basic setup can be used with other languages and relational databases.

muBLASTP: database-indexed protein sequence search on multicore CPUs.

PubMed

Zhang, Jing; Misra, Sanchit; Wang, Hao; Feng, Wu-Chun

2016-11-04

The Basic Local Alignment Search Tool (BLAST) is a fundamental program in the life sciences that searches databases for sequences that are most similar to a query sequence. Currently, the BLAST algorithm utilizes a query-indexed approach. Although many approaches suggest that sequence search with a database index can achieve much higher throughput (e.g., BLAT, SSAHA, and CAFE), they cannot deliver the same level of sensitivity as the query-indexed BLAST, i.e., NCBI BLAST, or they can only support nucleotide sequence search, e.g., MegaBLAST. Due to different challenges and characteristics between query indexing and database indexing, the existing techniques for query-indexed search cannot be used into database indexed search. muBLASTP, a novel database-indexed BLAST for protein sequence search, delivers identical hits returned to NCBI BLAST. On Intel Haswell multicore CPUs, for a single query, the single-threaded muBLASTP achieves up to a 4.41-fold speedup for alignment stages, and up to a 1.75-fold end-to-end speedup over single-threaded NCBI BLAST. For a batch of queries, the multithreaded muBLASTP achieves up to a 5.7-fold speedups for alignment stages, and up to a 4.56-fold end-to-end speedup over multithreaded NCBI BLAST. With a newly designed index structure for protein database and associated optimizations in BLASTP algorithm, we re-factored BLASTP algorithm for modern multicore processors that achieves much higher throughput with acceptable memory footprint for the database index.

[Quality Indicators of Primary Health Care Facilities in Austria].

PubMed

Semlitsch, Thomas; Abuzahra, Muna; Stigler, Florian; Jeitler, Klaus; Posch, Nicole; Siebenhofer, Andrea

2017-07-11

Background The strengthening of primary health care is one major goal of the current national health reform in Austria. In this context, a new interdisciplinary concept was developed in 2014 that defines structures and requirements for future primary health care facilities. Objective The aim of this project was the development of quality indicators for the evaluation of the scheduled primary health care facilities in Austria, which are in accordance with the new Austrian concept. Methods We used the RAND/NPCRDC method for the development and selection of the quality indicators. We conducted systematic literature searches for existing measures in international databases for quality indicators as well as in bibliographic databases. All retrieved measures were evaluated and rated by an expert panel in a 2-step process regarding relevance and feasibility. Results Overall, the literature searches yielded 281 potentially relevant quality indicators, which were summarized to 65 different quality measures for primary health care. Out of these, the panel rated and accepted 30 measures as relevant and feasible for use in Austria. Five of these indicators were structure measures, 14 were process measures and the remaining 11 were outcome measures. Based on the Austrian primary health care concept, the final set of quality indicators was grouped in the 5 following domains: Access to primary health care (5), quality of care (15), continuity of care (5), coordination of care (4), and safety (1). Conclusion This set of quality measures largely covers the four defined functions of primary health care. It enables standardized evaluation of primary health care facilities in Austria regarding the implementation of the Austrian primary health care concept as well as improvement in healthcare of the population. © Georg Thieme Verlag KG Stuttgart · New York.

Political and institutional influences on the use of evidence in public health policy. A systematic review.

PubMed

Liverani, Marco; Hawkins, Benjamin; Parkhurst, Justin O

2013-01-01

There is increasing recognition that the development of evidence-informed health policy is not only a technical problem of knowledge exchange or translation, but also a political challenge. Yet, while political scientists have long considered the nature of political systems, the role of institutional structures, and the political contestation of policy issues as central to understanding policy decisions, these issues remain largely unexplored by scholars of evidence-informed policy making. We conducted a systematic review of empirical studies that examined the influence of key features of political systems and institutional mechanisms on evidence use, and contextual factors that may contribute to the politicisation of health evidence. Eligible studies were identified through searches of seven health and social sciences databases, websites of relevant organisations, the British Library database, and manual searches of academic journals. Relevant findings were extracted using a uniform data extraction tool and synthesised by narrative review. 56 studies were selected for inclusion. Relevant political and institutional aspects affecting the use of health evidence included the level of state centralisation and democratisation, the influence of external donors and organisations, the organisation and function of bureaucracies, and the framing of evidence in relation to social norms and values. However, our understanding of such influences remains piecemeal given the limited number of empirical analyses on this subject, the paucity of comparative works, and the limited consideration of political and institutional theory in these studies. This review highlights the need for a more explicit engagement with the political and institutional factors affecting the use of health evidence in decision-making. A more nuanced understanding of evidence use in health policy making requires both additional empirical studies of evidence use, and an engagement with theories and approaches beyond the current remit of public health or knowledge utilisation studies.

Health-Related Resource-Use Measurement Instruments for Intersectoral Costs and Benefits in the Education and Criminal Justice Sectors.

PubMed

Mayer, Susanne; Paulus, Aggie T G; Łaszewska, Agata; Simon, Judit; Drost, Ruben M W A; Ruwaard, Dirk; Evers, Silvia M A A

2017-09-01

Intersectoral costs and benefits (ICBs), i.e. costs and benefits of healthcare interventions outside the healthcare sector, can be a crucial component in economic evaluations from the societal perspective. Pivotal to their estimation is the existence of sound resource-use measurement (RUM) instruments; however, RUM instruments for ICBs in the education or criminal justice sectors have not yet been systematically collated or their psychometric quality assessed. This review aims to fill this gap. To identify relevant instruments, the Database of Instruments for Resource Use Measurement (DIRUM) was searched. Additionally, a systematic literature review was conducted in seven electronic databases to detect instruments containing ICB items used in economic evaluations. Finally, studies evaluating the psychometric quality of these instruments were searched. Twenty-six unique instruments were included. Most frequently, ICB items measured school absenteeism, tutoring, classroom assistance or contacts with legal representatives, police custody/prison detainment and court appearances, with the highest number of items listed in the Client Service Receipt Inventory/Client Sociodemographic and Service Receipt Inventory/Client Service Receipt Inventory-Children's Version (CSRI/CSSRI/CSRI-C), Studying the Scope of Parental Expenditures (SCOPE) and Self-Harm Intervention, Family Therapy (SHIFT) instruments. ICBs in the education sector were especially relevant for age-related developmental disorders and chronic diseases, while criminal justice resource use seems more important in mental health, including alcohol-related disorders or substance abuse. Evidence on the validity or reliability of ICB items was published for two instruments only. With a heterogeneous variety of ICBs found to be relevant for several disease areas but many ICB instruments applied in one study only (21/26 instruments), setting-up an international task force to, for example, develop an internationally adaptable instrument is recommended.

Strategies to explore functional genomics data sets in NCBI's GEO database.

PubMed

Wilhite, Stephen E; Barrett, Tanya

2012-01-01

The Gene Expression Omnibus (GEO) database is a major repository that stores high-throughput functional genomics data sets that are generated using both microarray-based and sequence-based technologies. Data sets are submitted to GEO primarily by researchers who are publishing their results in journals that require original data to be made freely available for review and analysis. In addition to serving as a public archive for these data, GEO has a suite of tools that allow users to identify, analyze, and visualize data relevant to their specific interests. These tools include sample comparison applications, gene expression profile charts, data set clusters, genome browser tracks, and a powerful search engine that enables users to construct complex queries.

Strategies to Explore Functional Genomics Data Sets in NCBI’s GEO Database

PubMed Central

Wilhite, Stephen E.; Barrett, Tanya

2012-01-01

The Gene Expression Omnibus (GEO) database is a major repository that stores high-throughput functional genomics data sets that are generated using both microarray-based and sequence-based technologies. Data sets are submitted to GEO primarily by researchers who are publishing their results in journals that require original data to be made freely available for review and analysis. In addition to serving as a public archive for these data, GEO has a suite of tools that allow users to identify, analyze and visualize data relevant to their specific interests. These tools include sample comparison applications, gene expression profile charts, data set clusters, genome browser tracks, and a powerful search engine that enables users to construct complex queries. PMID:22130872

Long-Term Neurodevelopmental Outcomes After Preterm Birth

PubMed Central

Soleimani, Farin; Zaheri, Farzaneh; Abdi, Fatemeh

2014-01-01

Context: All over the the world, preterm birth is a major cause of death and important neurodevelopmental disorders. Approximately 9.6% (12.9 million) births worldwide are preterm. Evidence Acquisition: In this review, databases such as PubMed, EMBASE, ISI, Scopus, Google Scholar and Iranian databases including Iranmedex, and SID were researched to review relevant literature. A comprehensive search was performed using combinations of various keywords. Results: Cerebral palsy especially spastic diplegia, intellectual disability, visual (retinopathy of prematurity) and hearing impairments are the main neurodevelopmental disorders associated with prematurity. Conclusions: The increased survival of preterm infants was not associated with lower complications. There is now increasing evidence of sustained adverse outcomes into school age and adolescence, for preterm infants. PMID:25068052

Review of the Gene-Environment Interaction Literature in Cancer: What Do We Know?

PubMed

Simonds, Naoko I; Ghazarian, Armen A; Pimentel, Camilla B; Schully, Sheri D; Ellison, Gary L; Gillanders, Elizabeth M; Mechanic, Leah E

2016-07-01

Risk of cancer is determined by a complex interplay of genetic and environmental factors. Although the study of gene-environment interactions (G×E) has been an active area of research, little is reported about the known findings in the literature. To examine the state of the science in G×E research in cancer, we performed a systematic review of published literature using gene-environment or pharmacogenomic flags from two curated databases of genetic association studies, the Human Genome Epidemiology (HuGE) literature finder and Cancer Genome-Wide Association and Meta Analyses Database (CancerGAMAdb), from January 1, 2001, to January 31, 2011. A supplemental search using HuGE was conducted for articles published from February 1, 2011, to April 11, 2013. A 25% sample of the supplemental publications was reviewed. A total of 3,019 articles were identified in the original search. From these articles, 243 articles were determined to be relevant based on inclusion criteria (more than 3,500 interactions). From the supplemental search (1,400 articles identified), 29 additional relevant articles (1,370 interactions) were included. The majority of publications in both searches examined G×E in colon, rectal, or colorectal; breast; or lung cancer. Specific interactions examined most frequently included environmental factors categorized as energy balance (e.g., body mass index, diet), exogenous (e.g., oral contraceptives) and endogenous hormones (e.g., menopausal status), chemical environment (e.g., grilled meats), and lifestyle (e.g., smoking, alcohol intake). In both searches, the majority of interactions examined were using loci from candidate genes studies and none of the studies were genome-wide interaction studies (GEWIS). The most commonly reported measure was the interaction P-value, of which a sizable number of P-values were considered statistically significant (i.e., <0.05). In addition, the magnitude of interactions reported was modest. Observations of published literature suggest that opportunity exists for increased sample size in G×E research, including GWAS-identified loci in G×E studies, exploring more GWAS approaches in G×E such as GEWIS, and improving the reporting of G×E findings. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Review of the Gene-Environment Interaction Literature in Cancer: What do we know?

PubMed Central

Simonds, Naoko I.; Ghazarian, Armen A.; Pimentel, Camilla B.; Schully, Sheri D.; Ellison, Gary L.; Gillanders, Elizabeth M.; Mechanic, Leah E.

2016-01-01

Background Risk of cancer is determined by a complex interplay of genetic and environmental factors. Although the study of gene-environment (GxE) interactions has been an active area of research, little is reported about the known findings in the literature. Methods To examine the state of the science in GxE research in cancer, we performed a systematic review of published literature using gene-environment or pharmacogenomic flags from two curated databases of genetic association studies, the Human Genome Epidemiology (HuGE) literature finder and Cancer Genome-Wide Association and Meta Analyses Database (CancerGAMAdb), from January 1, 2001, to January 31, 2011. A supplemental search using HuGE was conducted for articles published February 1, 2011, to April 11, 2013. A 25% sample of the supplemental publications was reviewed. Results A total of 3,019 articles were identified in the original search. From these articles, 243 articles were determined to be relevant based on inclusion criteria (more than 3,500 interactions). From the supplemental search (1,400 articles identified), 29 additional relevant articles (1,370 interactions) were included. The majority of publications in both searches examined GxE in colon, rectal, or colorectal cancer types; breast; or lung cancer. Specific interactions examined most frequently included environmental factors categorized as energy balance (e.g., body mass index (BMI), diet), exogenous (e.g., oral contraceptives) and endogenous hormones (e.g., menopausal status), chemical environment (e.g., grilled meats), and lifestyle (e.g., smoking, alcohol intake). In both searches, the majority of interactions examined were using loci from candidate genes studies and none of the studies were genome-wide interaction studies (GEWIS). The most commonly reported measure was the interaction p-value, of which a sizable number of p-values were considered statistically significant (i.e., < 0.05). In addition, the magnitudes of interactions reported were modest. Conclusion Observations of published literature suggest that opportunity exists for increased sample size in GxE research, including GWAS identified loci in GxE studies, exploring more GWAS approaches in GxE such as GEWIS, and improving the reporting of GxE findings. PMID:27061572

What Is eHealth (3): A Systematic Review of Published Definitions

PubMed Central

Oh, Hans; Rizo, Carlos; Enkin, Murray

2005-01-01

Context The term eHealth is widely used by many individuals, academic institutions, professional bodies, and funding organizations. It has become an accepted neologism despite the lack of an agreed-upon clear or precise definition. We believe that communication among the many individuals and organizations that use the term could be improved by comprehensive data about the range of meanings encompassed by the term. Objective To report the results of a systematic review of published, suggested, or proposed definitions of eHealth. Data Sources Using the search query string “eHealth” OR “e-Health” OR “electronic health”, we searched the following databases: Medline and Premedline (1966-June 2004), EMBASE (1980-May 2004), International Pharmaceutical Abstracts (1970-May 2004), Web of Science (all years), Information Sciences Abstracts (1966-May 2004), Library Information Sciences Abstracts (1969-May 2004), and Wilson Business Abstracts (1982-March 2004). In addition, we searched dictionaries and an Internet search engine. Study Selection We included any source published in either print format or on the Internet, available in English, and containing text that defines or attempts to define eHealth in explicit terms. Two of us independently reviewed titles and abstracts of citations identified in the bibliographic databases and Internet search, reaching consensus on relevance by discussion. Data Extraction We retrieved relevant reports, articles, references, letters, and websites containing definitions of eHealth. Two of us qualitatively analyzed the definitions and coded them for content, emerging themes, patterns, and novel ideas. Data Synthesis The 51 unique definitions that we retrieved showed a wide range of themes, but no clear consensus about the meaning of the term eHealth. We identified 2 universal themes (health and technology) and 6 less general (commerce, activities, stakeholders, outcomes, place, and perspectives). Conclusions The widespread use of the term eHealth suggests that it is an important concept, and that there is a tacit understanding of its meaning. This compendium of proposed definitions may improve communication among the many individuals and organizations that use the term. PMID:15829471

Montreal Cognitive Assessment for the diagnosis of Alzheimer's disease and other dementias.

PubMed

Davis, Daniel H J; Creavin, Sam T; Yip, Jennifer L Y; Noel-Storr, Anna H; Brayne, Carol; Cullum, Sarah

2015-10-29

Dementia is a progressive syndrome of global cognitive impairment with significant health and social care costs. Global prevalence is projected to increase, particularly in resource-limited settings. Recent policy changes in Western countries to increase detection mandates a careful examination of the diagnostic accuracy of neuropsychological tests for dementia. To determine the diagnostic accuracy of the Montreal Cognitive Assessment (MoCA) at various thresholds for dementia and its subtypes. We searched MEDLINE, EMBASE, BIOSIS Previews, Science Citation Index, PsycINFO and LILACS databases to August 2012. In addition, we searched specialised sources containing diagnostic studies and reviews, including MEDION (Meta-analyses van Diagnostisch Onderzoek), DARE (Database of Abstracts of Reviews of Effects), HTA (Health Technology Assessment Database), ARIF (Aggressive Research Intelligence Facility) and C-EBLM (International Federation of Clinical Chemistry and Laboratory Medicine Committee for Evidence-based Laboratory Medicine) databases. We also searched ALOIS (Cochrane Dementia and Cognitive Improvement Group specialized register of diagnostic and intervention studies). We identified further relevant studies from the PubMed 'related articles' feature and by tracking key studies in Science Citation Index and Scopus. We also searched for relevant grey literature from the Web of Science Core Collection, including Science Citation Index and Conference Proceedings Citation Index (Thomson Reuters Web of Science), PhD theses and contacted researchers with potential relevant data. Cross-sectional designs where all participants were recruited from the same sample were sought; case-control studies were excluded due to high chance of bias. We searched for studies from memory clinics, hospital clinics, primary care and community populations. We excluded studies of early onset dementia, dementia from a secondary cause, or studies where participants were selected on the basis of a specific disease type such as Parkinson's disease or specific settings such as nursing homes. We extracted dementia study prevalence and dichotomised test positive/test negative results with thresholds used to diagnose dementia. This allowed calculation of sensitivity and specificity if not already reported in the study. Study authors were contacted where there was insufficient information to complete the 2x2 tables. We performed quality assessment according to the QUADAS-2 criteria.Methodological variation in selected studies precluded quantitative meta-analysis, therefore results from individual studies were presented with a narrative synthesis. Seven studies were selected: three in memory clinics, two in hospital clinics, none in primary care and two in population-derived samples. There were 9422 participants in total, but most of studies recruited only small samples, with only one having more than 350 participants. The prevalence of dementia was 22% to 54% in the clinic-based studies, and 5% to 10% in population samples. In the four studies that used the recommended threshold score of 26 or over indicating normal cognition, the MoCA had high sensitivity of 0.94 or more but low specificity of 0.60 or less. The overall quality and quantity of information is insufficient to make recommendations on the clinical utility of MoCA for detecting dementia in different settings. Further studies that do not recruit participants based on diagnoses already present (case-control design) but apply diagnostic tests and reference standards prospectively are required. Methodological clarity could be improved in subsequent DTA studies of MoCA by reporting findings using recommended guidelines (e.g. STARDdem). Thresholds lower than 26 are likely to be more useful for optimal diagnostic accuracy of MoCA in dementia, but this requires confirmation in further studies.

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.

MortalityPredictors.org: a manually-curated database of published biomarkers of human all-cause mortality

PubMed Central

Winslow, Ksenia; Ho, Andrew; Fortney, Kristen; Morgen, Eric

2017-01-01

Biomarkers of all-cause mortality are of tremendous clinical and research interest. Because of the long potential duration of prospective human lifespan studies, such biomarkers can play a key role in quantifying human aging and quickly evaluating any potential therapies. Decades of research into mortality biomarkers have resulted in numerous associations documented across hundreds of publications. Here, we present MortalityPredictors.org, a manually-curated, publicly accessible database, housing published, statistically-significant relationships between biomarkers and all-cause mortality in population-based or generally healthy samples. To gather the information for this database, we searched PubMed for appropriate research papers and then manually curated relevant data from each paper. We manually curated 1,576 biomarker associations, involving 471 distinct biomarkers. Biomarkers ranged in type from hematologic (red blood cell distribution width) to molecular (DNA methylation changes) to physical (grip strength). Via the web interface, the resulting data can be easily browsed, searched, and downloaded for further analysis. MortalityPredictors.org provides comprehensive results on published biomarkers of human all-cause mortality that can be used to compare biomarkers, facilitate meta-analysis, assist with the experimental design of aging studies, and serve as a central resource for analysis. We hope that it will facilitate future research into human mortality and aging. PMID:28858850

Mapping the Iranian Research Literature in the Field of Traditional Medicine in Scopus Database 2010-2014.

PubMed

GhaedAmini, Hossein; Okhovati, Maryam; Zare, Morteza; Saghafi, Zahra; Bazrafshan, Azam; GhaedAmini, Alireza; GhaedAmini, Mohammadreza

2016-05-01

The aim of this study was to provide research and collaboration overview of Iranian research efforts in the field of traditional medicine during 2010-2014. This is a bibliometric study using the Scopus database as data source, using search affiliation address relevant to traditional medicine and Iran as the search strategy. Subject and geographical overlay maps were also applied to visualize the network activities of the Iranian authors. Highly cited articles (citations >10) were further explored to highlight the impact of research domains more specifically. About 3,683 articles were published by Iranian authors in Scopus database. The compound annual growth rate of Iranian publications was 0.14% during 2010-2014. Tehran University of Medical Sciences (932 articles), Shiraz University of Medical Sciences (404 articles) and Tabriz Islamic Medical University (391 articles), were the leading institutions in the field of traditional medicine. Medicinal plants (72%), digestive system's disease (21%), basics of traditional medicine (13%), mental disorders (8%) were the major research topics. United States (7%), Netherlands (3%), and Canada (2.6%) were the most important collaborators of Iranian authors. Iranian research efforts in the field of traditional medicine have been increased slightly over the last years. Yet, joint multi-disciplinary collaborations are needed to cover inadequately described areas of traditional medicine in the country.

MortalityPredictors.org: a manually-curated database of published biomarkers of human all-cause mortality.

PubMed

Peto, Maximus V; De la Guardia, Carlos; Winslow, Ksenia; Ho, Andrew; Fortney, Kristen; Morgen, Eric

2017-08-31

Biomarkers of all-cause mortality are of tremendous clinical and research interest. Because of the long potential duration of prospective human lifespan studies, such biomarkers can play a key role in quantifying human aging and quickly evaluating any potential therapies. Decades of research into mortality biomarkers have resulted in numerous associations documented across hundreds of publications. Here, we present MortalityPredictors.org , a manually-curated, publicly accessible database, housing published, statistically-significant relationships between biomarkers and all-cause mortality in population-based or generally healthy samples. To gather the information for this database, we searched PubMed for appropriate research papers and then manually curated relevant data from each paper. We manually curated 1,576 biomarker associations, involving 471 distinct biomarkers. Biomarkers ranged in type from hematologic (red blood cell distribution width) to molecular (DNA methylation changes) to physical (grip strength). Via the web interface, the resulting data can be easily browsed, searched, and downloaded for further analysis. MortalityPredictors.org provides comprehensive results on published biomarkers of human all-cause mortality that can be used to compare biomarkers, facilitate meta-analysis, assist with the experimental design of aging studies, and serve as a central resource for analysis. We hope that it will facilitate future research into human mortality and aging.

Complementary and Alternative Medicines Use during Pregnancy: A Systematic Review of Pregnant Women and Healthcare Professional Views and Experiences

PubMed Central

Pallivalappila, Abdul Rouf; Stewart, Derek; Shetty, Ashalatha; Pande, Binita; McLay, James S.

2013-01-01

Aims. To undertake a systematic review of the recent (2008–2013) primary literature, describing views and experiences of CAM use during pregnancy by women and healthcare professionals. Method. Medline, Cumulative Index to Nursing and Allied Health Literature, Cochrane Database of Systematic Review Library and Allied, and Complementary Medicine Database were searched. Studies reporting systemic CAM products (homeopathic preparations, herbal medicines, Vitamins and minerals, homeopathy, and special diets) alone or in combination with other nonsystemic CAM modalities (e.g., acupuncture) were included. Results. Database searches retrieved 2,549 citations. Removal of duplicates followed by review of titles and abstracts yielded 32 relevant studies. Twenty-two reported the perspectives of women and their CAM use during pregnancy, while 10 focused on healthcare professionals. The majority of studies had significant flaws in study design and reporting, including a lack of appropriate definitions of CAM and associated modalities, absence of detailed checklists provided to participants, the use of convenience sampling, and a general lack of scientific robustness in terms of data validity and reliability. Conclusion. To permit generalisability of study findings, there is an urgent need to expand the evidence base assessing CAMs use during pregnancy using appropriately designed studies. PMID:24194778

When is a search not a search? A comparison of searching the AMED complementary health database via EBSCOhost, OVID and DIALOG.

PubMed

Younger, Paula; Boddy, Kate

2009-06-01

The researchers involved in this study work at Exeter Health library and at the Complementary Medicine Unit, Peninsula School of Medicine and Dentistry (PCMD). Within this collaborative environment it is possible to access the electronic resources of three institutions. This includes access to AMED and other databases using different interfaces. The aim of this study was to investigate whether searching different interfaces to the AMED allied health and complementary medicine database produced the same results when using identical search terms. The following Internet-based AMED interfaces were searched: DIALOG DataStar; EBSCOhost and OVID SP_UI01.00.02. Search results from all three databases were saved in an endnote database to facilitate analysis. A checklist was also compiled comparing interface features. In our initial search, DIALOG returned 29 hits, OVID 14 and Ebsco 8. If we assume that DIALOG returned 100% of potential hits, OVID initially returned only 48% of hits and EBSCOhost only 28%. In our search, a researcher using the Ebsco interface to carry out a simple search on AMED would miss over 70% of possible search hits. Subsequent EBSCOhost searches on different subjects failed to find between 21 and 86% of the hits retrieved using the same keywords via DIALOG DataStar. In two cases, the simple EBSCOhost search failed to find any of the results found via DIALOG DataStar. Depending on the interface, the number of hits retrieved from the same database with the same simple search can vary dramatically. Some simple searches fail to retrieve a substantial percentage of citations. This may result in an uninformed literature review, research funding application or treatment intervention. In addition to ensuring that keywords, spelling and medical subject headings (MeSH) accurately reflect the nature of the search, database users should include wildcards and truncation and adapt their search strategy substantially to retrieve the maximum number of appropriate citations possible. Librarians should be aware of these differences when making purchasing decisions, carrying out literature searches and planning user education.

Factors influencing community nursing roles and health service provision in rural areas: a review of literature.

PubMed

Barrett, Annette; Terry, Daniel R; Lê, Quynh; Hoang, Ha

2016-02-01

This review sought to better understand the issues and challenges experienced by community nurses working in rural areas and how these factors shape their role. Databases were searched to identify relevant studies, published between 1990 and 2015, that focussed on issues and challenges experienced by rural community nurses. Generic and grey literature relating to the subject was also searched. The search was systematically conducted multiple times to assure accuracy. A total of 14 articles met the inclusion criteria. This critical review identified common issues impacting community nursing and included role definition, organisational change, human resource, workplace and geographic challenges. Community nurses are flexible, autonomous, able to adapt care to the service delivery setting, and have a diversity of knowledge and skills. Considerably more research is essential to identify factors that impact rural community nursing practice. In addition, greater advocacy is required to develop the role.

Intelligent search in Big Data

NASA Astrophysics Data System (ADS)

Birialtsev, E.; Bukharaev, N.; Gusenkov, A.

2017-10-01

An approach to data integration, aimed on the ontology-based intelligent search in Big Data, is considered in the case when information objects are represented in the form of relational databases (RDB), structurally marked by their schemes. The source of information for constructing an ontology and, later on, the organization of the search are texts in natural language, treated as semi-structured data. For the RDBs, these are comments on the names of tables and their attributes. Formal definition of RDBs integration model in terms of ontologies is given. Within framework of the model universal RDB representation ontology, oil production subject domain ontology and linguistic thesaurus of subject domain language are built. Technique of automatic SQL queries generation for subject domain specialists is proposed. On the base of it, information system for TATNEFT oil-producing company RDBs was implemented. Exploitation of the system showed good relevance with majority of queries.

VIEWCACHE: An incremental pointer-based access method for autonomous interoperable databases

NASA Technical Reports Server (NTRS)

Roussopoulos, N.; Sellis, Timos

1993-01-01

One of the biggest problems facing NASA today is to provide scientists efficient access to a large number of distributed databases. Our pointer-based incremental data base access method, VIEWCACHE, provides such an interface for accessing distributed datasets and directories. VIEWCACHE allows database browsing and search performing inter-database cross-referencing with no actual data movement between database sites. This organization and processing is especially suitable for managing Astrophysics databases which are physically distributed all over the world. Once the search is complete, the set of collected pointers pointing to the desired data are cached. VIEWCACHE includes spatial access methods for accessing image datasets, which provide much easier query formulation by referring directly to the image and very efficient search for objects contained within a two-dimensional window. We will develop and optimize a VIEWCACHE External Gateway Access to database management systems to facilitate database search.

Automatically finding relevant citations for clinical guideline development.

PubMed

Bui, Duy Duc An; Jonnalagadda, Siddhartha; Del Fiol, Guilherme

2015-10-01

Literature database search is a crucial step in the development of clinical practice guidelines and systematic reviews. In the age of information technology, the process of literature search is still conducted manually, therefore it is costly, slow and subject to human errors. In this research, we sought to improve the traditional search approach using innovative query expansion and citation ranking approaches. We developed a citation retrieval system composed of query expansion and citation ranking methods. The methods are unsupervised and easily integrated over the PubMed search engine. To validate the system, we developed a gold standard consisting of citations that were systematically searched and screened to support the development of cardiovascular clinical practice guidelines. The expansion and ranking methods were evaluated separately and compared with baseline approaches. Compared with the baseline PubMed expansion, the query expansion algorithm improved recall (80.2% vs. 51.5%) with small loss on precision (0.4% vs. 0.6%). The algorithm could find all citations used to support a larger number of guideline recommendations than the baseline approach (64.5% vs. 37.2%, p<0.001). In addition, the citation ranking approach performed better than PubMed's "most recent" ranking (average precision +6.5%, recall@k +21.1%, p<0.001), PubMed's rank by "relevance" (average precision +6.1%, recall@k +14.8%, p<0.001), and the machine learning classifier that identifies scientifically sound studies from MEDLINE citations (average precision +4.9%, recall@k +4.2%, p<0.001). Our unsupervised query expansion and ranking techniques are more flexible and effective than PubMed's default search engine behavior and the machine learning classifier. Automated citation finding is promising to augment the traditional literature search. Copyright © 2015 Elsevier Inc. All rights reserved.

Dental insurance: A systematic review.

PubMed

Garla, Bharath Kumar; Satish, G; Divya, K T

2014-12-01

To review uses of finance in dentistry. A search of 25 electronic databases and World Wide Web was conducted. Relevant journals were hand searched and further information was requested from authors. Inclusion criteria were a predefined hierarchy of evidence and objectives. Study validity was assessed with checklists. Two reviewers independently screened sources, extracted data, and assessed validity. Insurance has come of ages and has become the mainstay of payment in many developed countries. So much so that all the alternative forms of payment which originated as an alternative to fee for service now depend on insurance at one point or the other. Fee for service is still the major form of payment in many developing countries including India. It is preferred in many instances since the payment is made immediately.

Bioinformatics Approaches to Classifying Allergens and Predicting Cross-Reactivity

PubMed Central

Schein, Catherine H.; Ivanciuc, Ovidiu; Braun, Werner

2007-01-01

The major advances in understanding why patients respond to several seemingly different stimuli have been through the isolation, sequencing and structural analysis of proteins that induce an IgE response. The most significant finding is that allergenic proteins from very different sources can have nearly identical sequences and structures, and that this similarity can account for clinically observed cross-reactivity. The increasing amount of information on the sequence, structure and IgE epitopes of allergens is now available in several databases and powerful bioinformatics search tools allow user access to relevant information. Here, we provide an overview of these databases and describe state-of-the art bioinformatics tools to identify the common proteins that may be at the root of multiple allergy syndromes. Progress has also been made in quantitatively defining characteristics that discriminate allergens from non-allergens. Search and software tools for this purpose have been developed and implemented in the Structural Database of Allergenic Proteins (SDAP, http://fermi.utmb.edu/SDAP/). SDAP contains information for over 800 allergens and extensive bibliographic references in a relational database with links to other publicly available databases. SDAP is freely available on the Web to clinicians and patients, and can be used to find structural and functional relations among known allergens and to identify potentially cross-reacting antigens. Here we illustrate how these bioinformatics tools can be used to group allergens, and to detect areas that may account for common patterns of IgE binding and cross-reactivity. Such results can be used to guide treatment regimens for allergy sufferers. PMID:17276876

Global and public health core competencies for nursing education: A systematic review of essential competencies.

PubMed

Clark, Megan; Raffray, Marie; Hendricks, Kristin; Gagnon, Anita J

2016-05-01

Nurses are learning and practicing in an increasingly global world. Both nursing schools and nursing students are seeking guidance as they integrate global health into their learning and teaching. This systematic review is intended to identify the most common global and public health core competencies found in the literature and better inform schools of nursing wishing to include global health content in their curricula. Systematic review. An online search of CINAHL and Medline databases, as well as, inclusion of pertinent gray literature was conducted for articles published before 2013. Relevant literature for global health (GH) and public and community health (PH/CH) competencies was reviewed to determine recommendations of both competencies using a combination of search terms. Studies must have addressed competencies as defined in the literature and must have been pertinent to GH or PH/CH. The databases were systematically searched and after reading the full content of the included studies, key concepts were extracted and synthesized. Twenty-five studies were identified and resulted in a list of 14 global health core competencies. These competencies are applicable to a variety of health disciplines, but particularly can inform the efforts of nursing schools to integrate global health concepts into their curricula. Copyright © 2016 Elsevier Ltd. All rights reserved.

Risk factors, incidence, consequences and prevention strategies for falls and fall-injury within older indigenous populations: a systematic review.

PubMed

Lukaszyk, Caroline; Harvey, Lara; Sherrington, Cathie; Keay, Lisa; Tiedemann, Anne; Coombes, Julieann; Clemson, Lindy; Ivers, Rebecca

2016-12-01

To examine the risk factors, incidence, consequences and existing prevention strategies for falls and fall-related injury in older indigenous people. Relevant literature was identified through searching 14 electronic databases, a range of institutional websites, online search engines and government databases, using search terms pertaining to indigenous status, injury and ageing. Thirteen studies from Australia, the United States, Central America and Canada were identified. Few studies reported on fall rates but two reported that around 30% of indigenous people aged 45 years and above experienced at least one fall during the past year. The most common hospitalised fall injuries among older indigenous people were hip fracture and head injury. Risk factors significantly associated with falls within indigenous populations included poor mobility, a history of stroke, epilepsy, head injury, poor hearing and urinary incontinence. No formally evaluated, indigenous-specific fall prevention interventions were identified. Falls are a significant and growing health issue for older indigenous people worldwide that can lead to severe health consequences and even death. No fully-evaluated, indigenous-specific fall prevention programs were identified. Implications for Public Health: Research into fall patterns and fall-related injury among indigenous people is necessary for the development of appropriate fall prevention interventions. © 2016 Public Health Association of Australia.

Role of Nigella sativa and Its Constituent Thymoquinone on Chemotherapy-Induced Nephrotoxicity: Evidences from Experimental Animal Studies

PubMed Central

Cascella, Marco; Palma, Giuseppe; Barbieri, Antonio; Bimonte, Sabrina; Amruthraj, Nagoth Joseph; Muzio, Maria Rosaria; del Vecchio, Vitale; Rea, Domenica; Falco, Michela; Luciano, Antonio; Arra, Claudio; Cuomo, Arturo

2017-01-01

Background: Most chemotherapeutic drugs are known to cause nephrotoxicity. Therefore, new strategies have been considered to prevent chemotherapy-induced nephrotoxicity. It is of note that Nigella sativa (NS), or its isolated compound Thymoquinone (TQ), has a potential role in combating chemotherapy-induced nephrotoxicity. AIM: To analyze and report the outcome of experimental animal studies on the protective effects of NS/TQ on chemotherapy-associated kidney complications. Design: Standard systematic review and narrative synthesis. Data Sources: MEDLINE, EMBASE databases were searched for relevant articles published up to March 2017. Additionally, a manual search was performed. Criteria for a study’s inclusion were: conducted in animals, systematic reviews and meta-analysis, containing data on nephroprotective effects of NS/TQ compared to a placebo or other substance. All strains and genders were included. Results: The database search yielded 71 studies, of which 12 (cisplatin-induced nephrotoxicity 8; methotrexate-induced nephrotoxicity 1; doxorubicin-induced nephrotoxicity 2; ifosfamide-induced nephrotoxicity 1) were included in this review. Conclusions: Experimental animal studies showed the protective effect of NS, or TQ, on chemotherapy-induced nephrotoxicity. These effects are caused by decreasing lipid peroxidation and increasing activity of antioxidant enzymes in renal tissue of chemotherapy-treated animals. PMID:28629150

The role of sensory perception in the development and targeting of tobacco products.

PubMed

Carpenter, Carrie M; Wayne, Geoffrey Ferris; Connolly, Gregory N

2007-01-01

To examine tobacco industry research on smoking-related sensory effects, including differences in sensory perception across smoker groups, and to determine whether this research informed targeted product development and impacted the development of commercial tobacco products. We searched previously secret internal tobacco industry documents available online through document databases housed at Tobacco Documents Online, the British American Tobacco Document Archive and the Legacy Tobacco Documents Library. We identified relevant documents using a snowball sampling method to first search the databases using an initial set of key words and to then establish further search terms. Sensory research is a priority within the tobacco industry directly impacting commercial markets both in the United States and internationally. Sensory factors contribute to smoker satisfaction and product acceptance, and play an important role in controlling puffing behavior. Cigarette manufacturers have capitalized on distinct sensory preferences across gender, age and ethnic groups by tailoring products for specific populations. Regulation of tobacco products is needed to address product changes that are used to reinforce or contribute to tobacco dependence; for instance, the incorporation of additives that target attributes such as smoothness, harshness and aftertaste. Greater understanding of the role of sensory effects on smoking behavior may also help to inform the development of tobacco treatment options that support long-term tobacco abstinence.

Investigation of Financial Conflict of Interest among Published Ventral Hernia Research.

PubMed

Cherla, Deepa V; Olavarria, Oscar A; Bernardi, Karla; Viso, Cristina P; Moses, Maya L; Holihan, Julie L; Ko, Tien C; Kao, Lillian S; Liang, Mike K

2018-03-01

Discordance exists between author self-disclosure and the Open Payments Database in various surgical fields, but the effects of this discordance on study design and presentation are unknown. We hypothesized that, among ventral hernia publications, discordance exists between industry and physician self-reported conflicts of interest (COIs); authors disclose relevant COIs; and disclosure and relevant COIs affect study favorability. We conducted a double-blinded, prospective, observational study of published articles. PubMed was searched in reverse chronological order for clinical articles pertaining to ventral hernias. Authors' self-disclosed conflicts were compared with those on the Open Payments Database. Two reviewers blinded to article disclosure status determined jointly whether the COIs were relevant to the article. Three blinded referees independently voted whether each article was favorable to discussed subject matter. The primary end point was study favorability. Secondary outcomes included disclosure status and relevance. One hundred articles were included. Compared with authors with no COIs, authors with a COI, self-disclosed or not, were twice as likely to write results favorable to industry. Of those with a COI, most of the articles had a relevant COI (37 of 45 [82.2%]), and 25% of relevant COIs were not disclosed by authors. Among authors with a relevant COI, study favorability remained unchanged at 68.5% (control: no COI 33.3%; p < 0.001). Within the ventral hernia literature, 70% of articles have a COI. Self-reporting of COI is discordant in 63% of articles. Twenty-five percent of relevant COI are not disclosed. Having a COI increases the chances that an article will cast a favorable impression on the company paying the authors by 200%. Copyright © 2017 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

Database Searching by Managers.

ERIC Educational Resources Information Center

Arnold, Stephen E.

Managers and executives need the easy and quick access to business and management information that online databases can provide, but many have difficulty articulating their search needs to an intermediary. One possible solution would be to encourage managers and their immediate support staff members to search textual databases directly as they now…

Constructing Effective Search Strategies for Electronic Searching.

ERIC Educational Resources Information Center

Flanagan, Lynn; Parente, Sharon Campbell

Electronic databases have grown tremendously in both number and popularity since their development during the 1960s. Access to electronic databases in academic libraries was originally offered primarily through mediated search services by trained librarians; however, the advent of CD-ROM and end-user interfaces for online databases has shifted the…

Subject searching of monographs online in the medical literature.

PubMed

Brahmi, F A

1988-01-01

Searching by subject for monographic information online in the medical literature is a challenging task. The NLM database of choice is CATLINE. Other NLM databases of interest are BIOTHICSLINE, CANCERLIT, HEALTH, POPLINE, and TOXLINE. Ten BRS databases are also discussed. Of these, Books in Print, Bookinfo, and OCLC are explored further. The databases are compared as to number of total records and number and percentage of monographs. Three topics were searched on CROSS to compare hits on BBIP, BOOK, and OCLC. The same searches were run on CATLINE. The parameters of time coverage and language were equalized and the resulting citations were compared and analyzed for duplication and uniqueness. With the input of CATLINE tapes into OCLC, OCLC has become the database of choice for searching by subject for medical monographs.

mTM-align: a server for fast protein structure database search and multiple protein structure alignment.

PubMed

Dong, Runze; Pan, Shuo; Peng, Zhenling; Zhang, Yang; Yang, Jianyi

2018-05-21

With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop algorithms for efficient protein structure comparisons. In this article, we present the mTM-align server, which consists of two closely related modules: one for structure database search and the other for multiple structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization of the structures in the database. The multiple structure alignment is performed using the recently developed algorithm mTM-align. Benchmark tests demonstrate that our algorithms outperform other peering methods for both modules, in terms of speed and accuracy. One of the unique features for the server is the interplay between database search and multiple structure alignment. The server provides service not only for performing fast database search, but also for making accurate multiple structure alignment with the structures found by the search. For the database search, it takes about 2-5 min for a structure of a medium size (∼300 residues). For the multiple structure alignment, it takes a few seconds for ∼10 structures of medium sizes. The server is freely available at: http://yanglab.nankai.edu.cn/mTM-align/.

MScanner: a classifier for retrieving Medline citations

PubMed Central

Poulter, Graham L; Rubin, Daniel L; Altman, Russ B; Seoighe, Cathal

2008-01-01

Background Keyword searching through PubMed and other systems is the standard means of retrieving information from Medline. However, ad-hoc retrieval systems do not meet all of the needs of databases that curate information from literature, or of text miners developing a corpus on a topic that has many terms indicative of relevance. Several databases have developed supervised learning methods that operate on a filtered subset of Medline, to classify Medline records so that fewer articles have to be manually reviewed for relevance. A few studies have considered generalisation of Medline classification to operate on the entire Medline database in a non-domain-specific manner, but existing applications lack speed, available implementations, or a means to measure performance in new domains. Results MScanner is an implementation of a Bayesian classifier that provides a simple web interface for submitting a corpus of relevant training examples in the form of PubMed IDs and returning results ranked by decreasing probability of relevance. For maximum speed it uses the Medical Subject Headings (MeSH) and journal of publication as a concise document representation, and takes roughly 90 seconds to return results against the 16 million records in Medline. The web interface provides interactive exploration of the results, and cross validated performance evaluation on the relevant input against a random subset of Medline. We describe the classifier implementation, cross validate it on three domain-specific topics, and compare its performance to that of an expert PubMed query for a complex topic. In cross validation on the three sample topics against 100,000 random articles, the classifier achieved excellent separation of relevant and irrelevant article score distributions, ROC areas between 0.97 and 0.99, and averaged precision between 0.69 and 0.92. Conclusion MScanner is an effective non-domain-specific classifier that operates on the entire Medline database, and is suited to retrieving topics for which many features may indicate relevance. Its web interface simplifies the task of classifying Medline citations, compared to building a pre-filter and classifier specific to the topic. The data sets and open source code used to obtain the results in this paper are available on-line and as supplementary material, and the web interface may be accessed at . PMID:18284683

Getting the fundamentals of movement: a meta-analysis of the effectiveness of motor skill interventions in children.

PubMed

Logan, S W; Robinson, L E; Wilson, A E; Lucas, W A

2012-05-01

The development of fundamental movement skills (FMS) is associated with positive health-related outcomes. Children do not develop FMS naturally through maturational processes. These skills need to be learned, practised and reinforced. The objective was to determine the effectiveness of motor skill interventions in children. The following databases were searched for relevant articles: Academic Search Premier, PsycArticles, PsycInfo, SportDiscus and ERIC. No date range was specified and each search was conducted to include all possible years of publication specific to each database. Key terms for the search included motor, skill, movement, intervention, programme or children. Searches were conducted using single and combined terms. Pertinent journals and article reference lists were also manually searched. (1) implementation of any type of motor skill intervention; (2) pre- and post-qualitative assessment of FMS; and (3) availability of means and standard deviations of motor performance. A significant positive effect of motor skill interventions on the improvement of FMS in children was found (d= 0.39, P < 0.001). Results indicate that object control (d= 0.41, P < 0.001) and locomotor skills (d= 0.45, P < 0.001) improved similarly from pre- to post-intervention. The overall effect size for control groups (i.e. free play) was not significant (d= 0.06, P= 0.33). A Pearson correlation indicated a non-significant (P= 0.296), negative correlation (r=-0.18) between effect size of pre- to post-improvement of FMS and the duration of the intervention (in minutes). Motor skill interventions are effective in improving FMS in children. Early childhood education centres should implement 'planned' movement programmes as a strategy to promote motor skill development in children. © 2011 Blackwell Publishing Ltd.

Shuttle-Data-Tape XML Translator

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2005-01-01

JSDTImport is a computer program for translating native Shuttle Data Tape (SDT) files from American Standard Code for Information Interchange (ASCII) format into databases in other formats. JSDTImport solves the problem of organizing the SDT content, affording flexibility to enable users to choose how to store the information in a database to better support client and server applications. JSDTImport can be dynamically configured by use of a simple Extensible Markup Language (XML) file. JSDTImport uses this XML file to define how each record and field will be parsed, its layout and definition, and how the resulting database will be structured. JSDTImport also includes a client application programming interface (API) layer that provides abstraction for the data-querying process. The API enables a user to specify the search criteria to apply in gathering all the data relevant to a query. The API can be used to organize the SDT content and translate into a native XML database. The XML format is structured into efficient sections, enabling excellent query performance by use of the XPath query language. Optionally, the content can be translated into a Structured Query Language (SQL) database for fast, reliable SQL queries on standard database server computers.

Diagnosis, Prevalence, Awareness, Treatment, Prevention, and Control of Hypertension in Cameroon: Protocol for a Systematic Review and Meta-Analysis of Clinic-Based and Community-Based Studies.

PubMed

Kuate Defo, Barthelemy; Mbanya, Jean Claude; Tardif, Jean-Claude; Ekundayo, Olugbemiga; Perreault, Sylvie; Potvin, Louise; Cote, Robert; Kengne, Andre Pascal; Choukem, Simeon Pierre; Assah, Felix; Kingue, Samuel; Richard, Lucie; Pongou, Roland; Frohlich, Katherine; Saji, Jude; Fournier, Pierre; Sobngwi, Eugene; Ridde, Valery; Dubé, Marie-Pierre; De Denus, Simon; Mbacham, Wilfred; Lafrance, Jean-Philippe; Nsagha, Dickson Shey; Mampuya, Warner; Dzudie, Anastase; Cloutier, Lyne; Zarowsky, Christina; Tanya, Agatha; Ndom, Paul; Hatem, Marie; Rey, Evelyne; Roy, Louise; Borgès Da Silva, Roxane; Dagenais, Christian; Todem, David; Weladji, Robert; Mbanya, Dora; Emami, Elham; Njoumemi, Zakariaou; Monnais, Laurence; Dubois, Carl-Ardy

2017-05-29

Hypertension holds a unique place in population health and health care because it is the leading cause of cardiovascular disease and the most common noncommunicable condition seen in primary care worldwide. Without effective prevention and control, raised blood pressure significantly increases the risk of stroke, myocardial infarction, chronic kidney disease, heart failure, dementia, renal failure, and blindness. There is an urgent need for stakeholders-including individuals and families-across the health system, researchers, and decision makers to work collaboratively for improving prevention, screening and detection, diagnosis and evaluation, awareness, treatment and medication adherence, management, and control for people with or at high risk for hypertension. Meeting this need will help reduce the burden of hypertension-related disease, prevent complications, and reduce the need for hospitalization, costly interventions, and premature deaths. This review aims to synthesize evidence on the epidemiological landscape and control of hypertension in Cameroon, and to identify elements that could potentially inform interventions to combat hypertension in this setting and elsewhere in sub-Saharan Africa. The full search process will involve several steps, including selecting relevant databases, keywords, and Medical Subject Headings (MeSH); searching for relevant studies from the selected databases; searching OpenGrey and the Grey Literature Report for gray literature; hand searching in Google Scholar; and soliciting missed publications (if any) from relevant authors. We will select qualitative, quantitative, or mixed-methods studies with data on the epidemiology and control of hypertension in Cameroon. We will include published literature in French or English from electronic databases up to December 31, 2016, and involving adults aged 18 years or older. Both facility and population-based studies on hypertension will be included. Two reviewers of the team will independently search, screen, extract data, and assess the quality of selected studies using suitable tools. Selected studies will be analyzed by narrative synthesis, meta-analysis, or both, depending on the nature of the data retrieved in line with the review objectives. This review is part of an ongoing research program on disease prevention and control in the context of the dual burden of communicable and noncommunicable diseases in Africa. The first results are expected in 2017. This review will provide a comprehensive assessment of the burden of hypertension and control measures that have been designed and implemented in Cameroon. Findings will form the knowledge base relevant to stakeholders across the health system and researchers who are involved in hypertension prevention and control in the community and clinic settings in Cameroon, as a yardstick for similar African countries. PROSPERO registration number: CRD42017054950; http://www.crd.york.ac.uk/PROSPERO/ display_record.asp?ID=CRD42017054950 (Archived by WebCite at http://www.webcitation.org/6qYSjt9Jc). ©Barthelemy Kuate Defo, Jean Claude Mbanya, Jean-Claude Tardif, Olugbemiga Ekundayo, Sylvie Perreault, Louise Potvin, Robert Cote, Andre Pascal Kengne, Simeon Pierre Choukem, Felix Assah, Samuel Kingue, Lucie Richard, Roland Pongou, Katherine Frohlich, Jude Saji, Pierre Fournier, Eugene Sobngwi, Valery Ridde, Marie-Pierre Dubé, Simon De Denus, Wilfred Mbacham, Jean-Philippe Lafrance, Dickson Shey Nsagha, Warner Mampuya, Anastase Dzudie, Lyne Cloutier, Christina Zarowsky, Agatha Tanya, Paul Ndom, Marie Hatem, Evelyne Rey, Louise Roy, Roxane Borgès Da Silva, Christian Dagenais, David Todem, Robert Weladji, Dora Mbanya, Elham Emami, Zakariaou Njoumemi, Laurence Monnais, Carl-Ardy Dubois. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 29.05.2017.

The importance and complexity of regret in the measurement of ‘good’ decisions: a systematic review and a content analysis of existing assessment instruments

PubMed Central

Joseph‐Williams, Natalie; Edwards, Adrian; Elwyn, Glyn

2011-01-01

Abstract Background or context  Regret is a common consequence of decisions, including those decisions related to individuals’ health. Several assessment instruments have been developed that attempt to measure decision regret. However, recent research has highlighted the complexity of regret. Given its relevance to shared decision making, it is important to understand its conceptualization and the instruments used to measure it. Objectives  To review current conceptions of regret. To systematically identify instruments used to measure decision regret and assess whether they capture recent conceptualizations of regret. Search strategy  Five electronic databases were searched in 2008. Search strategies used a combination of MeSH terms (or database equivalent) and free text searching under the following key headings: ‘Decision’ and ‘regret’ and ‘measurement’. Follow‐up manual searches were also performed. Inclusion criteria  Articles were included if they reported the development and psychometric testing of an instrument designed to measure decision regret, or the use of a previously developed and tested instrument. Main results  Thirty‐two articles were included: 10 report the development and validation of an instrument that measures decision regret and 22 report the use of a previously developed and tested instrument. Content analysis found that existing instruments for the measurement of regret do not capture current conceptualizations of regret and they do not enable the construct of regret to be measured comprehensively. Conclusions  Existing instrumentation requires further development. There is also a need to clarify the purpose for using regret assessment instruments as this will, and should, focus their future application. PMID:20860776

Supplemental calcium in the chemoprevention of colorectal cancer: a systematic review and meta-analysis.

PubMed

Carroll, Christopher; Cooper, Katy; Papaioannou, Diana; Hind, Daniel; Pilgrim, Hazel; Tappenden, Paul

2010-05-01

The aim of the review was to assess the evidence for the effectiveness of calcium in reducing the recurrence of adenomas and the occurrence of colorectal cancer among populations at high, intermediate, and low risk of the disease. A systematic review of randomized controlled trials (RCTs) was performed to compare calcium alone, and with other agents, versus placebo. Nine databases (Cochrane Library, MEDLINE, PreMEDLINE, CINAHL, EMBASE, Web of Science, Biological Abstracts, the National Research Register, and Current Controlled Trials) were searched for published and unpublished trials. Searches were not restricted by either language or date of publication. All searches were completed in January 2010. Database thesaurus and free text terms for calcium and adenomas or colorectal cancer were used to search for trial reports; additional terms were used to search for other agents of interest, such as NSAIDs and folic acid. Search terms consisted of a combination of terms for colorectal cancer (eg, colon or colorectal and neoplasm or cancer or adenoma) and terms for calcium and RCTs. The initial searches were conducted in June 2008, with update searches in January 2010 to identify more recent studies. The reference lists of relevant studies were also searched for additional papers not identified by the search of electronic databases. Studies had to satisfy the following criteria to be included: RCTs about calcium, with or without other chemopreventive agents, in adults with familial adenomatous polyposis (FAP), hereditary nonpolyposis colorectal cancer, or a history of colorectal adenomas, or with no increased baseline risk of colorectal cancer. Meta-analysis was performed. For discrete and numerical outcomes, relative risks (RRs) and risk differences were reported with 95% CIs. The random-effects model was used to account for clinical and methodologic variations between trials. The original and update searches of electronic databases produced 3835 citations, of which 6 studies (8 papers) met the inclusion criteria. Supplemental calcium had no effect on the number of adenomas in 1 small trial of patients with FAP. Meta-analysis of 3 trials in individuals with a history of adenomas showed a statistically significant reduction in the RR for adenoma recurrence (RR = 0.80 [95% CI, 0.69-0.94], P = 0.006) for those receiving calcium 1200 to 2000 mg/d, but no effect was seen in advanced adenoma (RR = 0.77 [95% CI, 0.501.17], P = NS). Meta-analysis of 2 trials in populations with no increased baseline risk for colorectal cancer suggested that calcium, with or without vitamin D, had no effect on the RR for colorectal cancer (RR = 0.62 [95% CI, 0.11-3.40], P = NS). Published reports indicated that supplemental calcium was effective for the prevention of adenoma recurrence in populations with a history of adenomas, but no similar effect was apparent in populations at higher or lower risk. Copyright 2010 Excerpta Medica Inc. All rights reserved.

Identifying nurse staffing research in Medline: development and testing of empirically derived search strategies with the PubMed interface

PubMed Central

2010-01-01

Background The identification of health services research in databases such as PubMed/Medline is a cumbersome task. This task becomes even more difficult if the field of interest involves the use of diverse methods and data sources, as is the case with nurse staffing research. This type of research investigates the association between nurse staffing parameters and nursing and patient outcomes. A comprehensively developed search strategy may help identify nurse staffing research in PubMed/Medline. Methods A set of relevant references in PubMed/Medline was identified by means of three systematic reviews. This development set was used to detect candidate free-text and MeSH terms. The frequency of these terms was compared to a random sample from PubMed/Medline in order to identify terms specific to nurse staffing research, which were then used to develop a sensitive, precise and balanced search strategy. To determine their precision, the newly developed search strategies were tested against a) the pool of relevant references extracted from the systematic reviews, b) a reference set identified from an electronic journal screening, and c) a sample from PubMed/Medline. Finally, all newly developed strategies were compared to PubMed's Health Services Research Queries (PubMed's HSR Queries). Results The sensitivities of the newly developed search strategies were almost 100% in all of the three test sets applied; precision ranged from 6.1% to 32.0%. PubMed's HSR queries were less sensitive (83.3% to 88.2%) than the new search strategies. Only minor differences in precision were found (5.0% to 32.0%). Conclusions As with other literature on health services research, nurse staffing studies are difficult to identify in PubMed/Medline. Depending on the purpose of the search, researchers can choose between high sensitivity and retrieval of a large number of references or high precision, i.e. and an increased risk of missing relevant references, respectively. More standardized terminology (e.g. by consistent use of the term "nurse staffing") could improve the precision of future searches in this field. Empirically selected search terms can help to develop effective search strategies. The high consistency between all test sets confirmed the validity of our approach. PMID:20731858

Identifying nurse staffing research in Medline: development and testing of empirically derived search strategies with the PubMed interface.

PubMed

Simon, Michael; Hausner, Elke; Klaus, Susan F; Dunton, Nancy E

2010-08-23

The identification of health services research in databases such as PubMed/Medline is a cumbersome task. This task becomes even more difficult if the field of interest involves the use of diverse methods and data sources, as is the case with nurse staffing research. This type of research investigates the association between nurse staffing parameters and nursing and patient outcomes. A comprehensively developed search strategy may help identify nurse staffing research in PubMed/Medline. A set of relevant references in PubMed/Medline was identified by means of three systematic reviews. This development set was used to detect candidate free-text and MeSH terms. The frequency of these terms was compared to a random sample from PubMed/Medline in order to identify terms specific to nurse staffing research, which were then used to develop a sensitive, precise and balanced search strategy. To determine their precision, the newly developed search strategies were tested against a) the pool of relevant references extracted from the systematic reviews, b) a reference set identified from an electronic journal screening, and c) a sample from PubMed/Medline. Finally, all newly developed strategies were compared to PubMed's Health Services Research Queries (PubMed's HSR Queries). The sensitivities of the newly developed search strategies were almost 100% in all of the three test sets applied; precision ranged from 6.1% to 32.0%. PubMed's HSR queries were less sensitive (83.3% to 88.2%) than the new search strategies. Only minor differences in precision were found (5.0% to 32.0%). As with other literature on health services research, nurse staffing studies are difficult to identify in PubMed/Medline. Depending on the purpose of the search, researchers can choose between high sensitivity and retrieval of a large number of references or high precision, i.e. and an increased risk of missing relevant references, respectively. More standardized terminology (e.g. by consistent use of the term "nurse staffing") could improve the precision of future searches in this field. Empirically selected search terms can help to develop effective search strategies. The high consistency between all test sets confirmed the validity of our approach.

Search Fermilab Plant Database

Science.gov Websites

Select the characteristics of the plant you want to find below and click the Search button. To see Plants to see all the prairie plants in the database. Click Search All Plants at Fermilab to search for reflects observations at Fermilab. If you need a more sophisticated search, try the Advanced Search. Search

Reducing process delays for real-time earthquake parameter estimation - An application of KD tree to large databases for Earthquake Early Warning

NASA Astrophysics Data System (ADS)

Yin, Lucy; Andrews, Jennifer; Heaton, Thomas

2018-05-01

Earthquake parameter estimations using nearest neighbor searching among a large database of observations can lead to reliable prediction results. However, in the real-time application of Earthquake Early Warning (EEW) systems, the accurate prediction using a large database is penalized by a significant delay in the processing time. We propose to use a multidimensional binary search tree (KD tree) data structure to organize large seismic databases to reduce the processing time in nearest neighbor search for predictions. We evaluated the performance of KD tree on the Gutenberg Algorithm, a database-searching algorithm for EEW. We constructed an offline test to predict peak ground motions using a database with feature sets of waveform filter-bank characteristics, and compare the results with the observed seismic parameters. We concluded that large database provides more accurate predictions of the ground motion information, such as peak ground acceleration, velocity, and displacement (PGA, PGV, PGD), than source parameters, such as hypocenter distance. Application of the KD tree search to organize the database reduced the average searching process by 85% time cost of the exhaustive method, allowing the method to be feasible for real-time implementation. The algorithm is straightforward and the results will reduce the overall time of warning delivery for EEW.

Telescope Bibliography Cookbook: Creating a Database of Scientific Papers that Use Observational Data

NASA Astrophysics Data System (ADS)

Kitt, S.; Grothkopf, U.

2010-10-01

This paper explains the procedures involved in creating a database of scientific papers that use observational data and linking the records to the observations residing in a data archive. Based on our experiences with the ESO Telescope Bibliography, we describe the workflow we apply in order to retrieve relevant articles, assign tags to describe the observing facilities that generated the data, and identify the correct program identification numbers (IDs). These program identifiers are particularly important as they link the published papers and the underlying data and enable scientists to access the data for new studies. With the understanding that the difficulty of compiling correct and complete data varies, depending on the information readily provided in the published literature, this paper proposes an evolution of search options for finding appropriate ID numbers. To explore the process and its various stages, we use the analogy of the "cookbook." These search methodologies might be labeled fast, medium, and slow heat recipes within our culinary theme. We provide a step-by-step guide in order to assist other bibliography compilers, in particular those who are new to the field.

PPDB - A tool for investigation of plants physiology based on gene ontology.

PubMed

Sharma, Ajay Shiv; Gupta, Hari Om; Prasad, Rajendra

2014-09-02

Representing the way forward, from functional genomics and its ontology to functional understanding and physiological model, in a computationally tractable fashion is one of the ongoing challenges faced by computational biology. To tackle the standpoint, we herein feature the applications of contemporary database management to the development of PPDB, a searching and browsing tool for the Plants Physiology Database that is based upon the mining of a large amount of gene ontology data currently available. The working principles and search options associated with the PPDB are publicly available and freely accessible on-line ( http://www.iitr.ernet.in/ajayshiv/ ) through a user friendly environment generated by means of Drupal-6.24. By knowing that genes are expressed in temporally and spatially characteristic patterns and that their functionally distinct products often reside in specific cellular compartments and may be part of one or more multi-component complexes, this sort of work is intended to be relevant for investigating the functional relationships of gene products at a system level and, thus, helps us approach to the full physiology.

PPDB: A Tool for Investigation of Plants Physiology Based on Gene Ontology.

PubMed

Sharma, Ajay Shiv; Gupta, Hari Om; Prasad, Rajendra

2015-09-01

Representing the way forward, from functional genomics and its ontology to functional understanding and physiological model, in a computationally tractable fashion is one of the ongoing challenges faced by computational biology. To tackle the standpoint, we herein feature the applications of contemporary database management to the development of PPDB, a searching and browsing tool for the Plants Physiology Database that is based upon the mining of a large amount of gene ontology data currently available. The working principles and search options associated with the PPDB are publicly available and freely accessible online ( http://www.iitr.ac.in/ajayshiv/ ) through a user-friendly environment generated by means of Drupal-6.24. By knowing that genes are expressed in temporally and spatially characteristic patterns and that their functionally distinct products often reside in specific cellular compartments and may be part of one or more multicomponent complexes, this sort of work is intended to be relevant for investigating the functional relationships of gene products at a system level and, thus, helps us approach to the full physiology.

Interactive searching of facial image databases

NASA Astrophysics Data System (ADS)

Nicholls, Robert A.; Shepherd, John W.; Shepherd, Jean

1995-09-01

A set of psychological facial descriptors has been devised to enable computerized searching of criminal photograph albums. The descriptors have been used to encode image databased of up to twelve thousand images. Using a system called FACES, the databases are searched by translating a witness' verbal description into corresponding facial descriptors. Trials of FACES have shown that this coding scheme is more productive and efficient than searching traditional photograph albums. An alternative method of searching the encoded database using a genetic algorithm is currenly being tested. The genetic search method does not require the witness to verbalize a description of the target but merely to indicate a degree of similarity between the target and a limited selection of images from the database. The major drawback of FACES is that is requires a manual encoding of images. Research is being undertaken to automate the process, however, it will require an algorithm which can predict human descriptive values. Alternatives to human derived coding schemes exist using statistical classifications of images. Since databases encoded using statistical classifiers do not have an obvious direct mapping to human derived descriptors, a search method which does not require the entry of human descriptors is required. A genetic search algorithm is being tested for such a purpose.

Searching Harvard Business Review Online. . . Lessons in Searching a Full Text Database.

ERIC Educational Resources Information Center

Tenopir, Carol

1985-01-01

This article examines the Harvard Business Review Online (HBRO) database (bibliographic description fields, abstracts, extracted information, full text, subject descriptors) and reports on 31 sample HBRO searches conducted in Bibliographic Retrieval Services to test differences between searching full text and searching bibliographic record. Sample…

LAILAPS: the plant science search engine.

PubMed

Esch, Maria; Chen, Jinbo; Colmsee, Christian; Klapperstück, Matthias; Grafahrend-Belau, Eva; Scholz, Uwe; Lange, Matthias

2015-01-01

With the number of sequenced plant genomes growing, the number of predicted genes and functional annotations is also increasing. The association between genes and phenotypic traits is currently of great interest. Unfortunately, the information available today is widely scattered over a number of different databases. Information retrieval (IR) has become an all-encompassing bioinformatics methodology for extracting knowledge from complex, heterogeneous and distributed databases, and therefore can be a useful tool for obtaining a comprehensive view of plant genomics, from genes to traits. Here we describe LAILAPS (http://lailaps.ipk-gatersleben.de), an IR system designed to link plant genomic data in the context of phenotypic attributes for a detailed forward genetic research. LAILAPS comprises around 65 million indexed documents, encompassing >13 major life science databases with around 80 million links to plant genomic resources. The LAILAPS search engine allows fuzzy querying for candidate genes linked to specific traits over a loosely integrated system of indexed and interlinked genome databases. Query assistance and an evidence-based annotation system enable time-efficient and comprehensive information retrieval. An artificial neural network incorporating user feedback and behavior tracking allows relevance sorting of results. We fully describe LAILAPS's functionality and capabilities by comparing this system's performance with other widely used systems and by reporting both a validation in maize and a knowledge discovery use-case focusing on candidate genes in barley. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

Evaluating a NoSQL Alternative for Chilean Virtual Observatory Services

NASA Astrophysics Data System (ADS)

Antognini, J.; Araya, M.; Solar, M.; Valenzuela, C.; Lira, F.

2015-09-01

Currently, the standards and protocols for data access in the Virtual Observatory architecture (DAL) are generally implemented with relational databases based on SQL. In particular, the Astronomical Data Query Language (ADQL), language used by IVOA to represent queries to VO services, was created to satisfy the different data access protocols, such as Simple Cone Search. ADQL is based in SQL92, and has extra functionality implemented using PgSphere. An emergent alternative to SQL are the so called NoSQL databases, which can be classified in several categories such as Column, Document, Key-Value, Graph, Object, etc.; each one recommended for different scenarios. Within their notable characteristics we can find: schema-free, easy replication support, simple API, Big Data, etc. The Chilean Virtual Observatory (ChiVO) is developing a functional prototype based on the IVOA architecture, with the following relevant factors: Performance, Scalability, Flexibility, Complexity, and Functionality. Currently, it's very difficult to compare these factors, due to a lack of alternatives. The objective of this paper is to compare NoSQL alternatives with SQL through the implementation of a Web API REST that satisfies ChiVO's needs: a SESAME-style name resolver for the data from ALMA. Therefore, we propose a test scenario by configuring a NoSQL database with data from different sources and evaluating the feasibility of creating a Simple Cone Search service and its performance. This comparison will allow to pave the way for the application of Big Data databases in the Virtual Observatory.

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.

In search of the emotional face: anger versus happiness superiority in visual search.

PubMed

Savage, Ruth A; Lipp, Ottmar V; Craig, Belinda M; Becker, Stefanie I; Horstmann, Gernot

2013-08-01

Previous research has provided inconsistent results regarding visual search for emotional faces, yielding evidence for either anger superiority (i.e., more efficient search for angry faces) or happiness superiority effects (i.e., more efficient search for happy faces), suggesting that these results do not reflect on emotional expression, but on emotion (un-)related low-level perceptual features. The present study investigated possible factors mediating anger/happiness superiority effects; specifically search strategy (fixed vs. variable target search; Experiment 1), stimulus choice (Nimstim database vs. Ekman & Friesen database; Experiments 1 and 2), and emotional intensity (Experiment 3 and 3a). Angry faces were found faster than happy faces regardless of search strategy using faces from the Nimstim database (Experiment 1). By contrast, a happiness superiority effect was evident in Experiment 2 when using faces from the Ekman and Friesen database. Experiment 3 employed angry, happy, and exuberant expressions (Nimstim database) and yielded anger and happiness superiority effects, respectively, highlighting the importance of the choice of stimulus materials. Ratings of the stimulus materials collected in Experiment 3a indicate that differences in perceived emotional intensity, pleasantness, or arousal do not account for differences in search efficiency. Across three studies, the current investigation indicates that prior reports of anger or happiness superiority effects in visual search are likely to reflect on low-level visual features associated with the stimulus materials used, rather than on emotion. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Preconception risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease.

PubMed

Hussein, Norita; Weng, Stephen F; Kai, Joe; Kleijnen, Jos; Qureshi, Nadeem

2018-03-14

Globally, about five per cent of children are born with congenital or genetic disorders. The most common autosomal recessive conditions are thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease, with higher carrier rates in specific patient populations. Identifying and counselling couples at genetic risk of the conditions before pregnancy enables them to make fully informed reproductive decisions, with some of these choices not being available if genetic counselling is only offered in an antenatal setting. This is an update of a previously published review. To assess the effectiveness of systematic preconception genetic risk assessment to improve reproductive outcomes in women and their partners who are identified as carriers of thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease in healthcare settings when compared to usual care. We searched the Cochrane Cystic Fibrosis and Genetic Disorders Group's Trials Registers. In addition, we searched for all relevant trials from 1970 (or the date at which the database was first available if after 1970) to date using electronic databases (MEDLINE, Embase, CINAHL, PsycINFO), clinical trial databases (National Institutes of Health, Clinical Trials Search portal of the World Health Organization, metaRegister of controlled clinical trials), and hand searching of key journals and conference abstract books from 1998 to date (European Journal of Human Genetics, Genetics in Medicine, Journal of Community Genetics). We also searched the reference lists of relevant articles, reviews and guidelines and also contacted subject experts in the field to request any unpublished or other published trials.Date of latest search of the registers: 20 June 2017.Date of latest search of all other sources: 16 November 2017. Any randomised or quasi-randomised controlled trials (published or unpublished) comparing reproductive outcomes of systematic preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease when compared to usual care. We identified 25 papers, describing 16 unique trials which were potentially eligible for inclusion in the review. However, after assessment, no randomised controlled trials of preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease were found. No randomised controlled trials of preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease were included. One ongoing trial has been identified which may potentially eligible for inclusion once completed. As no randomised controlled trials of preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis, or Tay-Sachs disease were found for inclusion in this review, the research evidence for current policy recommendations is limited to non-randomised studies.Information from well-designed, adequately powered, randomised trials is desirable in order to make more robust recommendations for practice. However, such trials must also consider the legal, ethical, and cultural barriers to implementation of preconception genetic risk assessment.

Genetic Testing Registry

MedlinePlus

... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

Droperidol for acute psychosis.

PubMed

Cure, S; Rathbone, J; Carpenter, S

2004-10-18

People suffering from acute psychotic illnesses, especially those associated with agitated or violent behaviour, may require urgent pharmacological tranquillisation or sedation. Droperidol, a butyrophenone neuroleptic, has been used for this purpose in several countries. To estimate the effects of droperidol compared to other treatments for controlling disturbed behaviour and reducing psychotic symptoms for people with suspected acute psychotic illnesses. We updated previous searches by searching the Cochrane Schizophrenia Group Register (September 2003). References of all identified studies were searched for further trial citations and authors of trials were contacted. Twenty-one other databases were also searched as part of a broader project and this composite database was searched for this review. This was supplemented by hand searching reference lists and contacting both the pharmacological industry and relevant authors. The review included randomised controlled trials comparing droperidol to any other treatment for people with suspected acute psychotic illnesses, including schizophrenia, schizoaffective disorder, mixed affective disorders, the manic phase of bipolar disorder or a brief psychotic episode. Relevant studies were selected for inclusion, their quality was assessed and data extracted. Data were excluded when more than 50% of participants were lost to follow up. For binary outcomes, standard estimates of risk ratio (RR) and the corresponding 95% confidence intervals (CI) were calculated. Where possible, weighted number needed to treat or harm statistics (NNT, NNH), and the corresponding 95% confidence intervals (CI), were calculated. We identified only two relevant trials. One additional study focused on outcomes at 30 days rather than at a few hours. One small (n = 41) randomised trial compared intravenous (iv) droperidol (10 mg) with iv placebo and found that people allocated to droperidol were significantly less likely to need additional injections of another drug, haloperidol, in the first few minutes (n = 41, RR 0.37 CI 0.2 to 0.7, NNT 2 CI 1 to 10) compared to those given placebo. By 90 minutes this difference was still evident but not statistically significant (RR 0.46 CI 0.2 to 1.2). When 5 mg intramuscular (im) droperidol was compared with 5 mg im haloperidol, those given droperidol were also less likely to need additional injections by 30 minutes, than those given haloperidol, but this result was not statistically significant (n = 27, RR 0.45 CI 0.2 to 1.01). One person out of the 16 given haloperidol experienced a mild dystonic reaction (muscle spasms or abnormal contractions), while none of the 11 people allocated to droperidol were reported to have experienced adverse effects. This is an important, and surprisingly under-researched, area. To date, use of droperidol for emergency situations has been justified by experience rather than evidence from well conducted and reported randomised trials, but, as world reserves diminish, droperidol will no longer be a treatment option.

Curricular initiatives that enhance student knowledge and perceptions of sexual and gender minority groups: a critical interpretive synthesis.

PubMed

Desrosiers, Jennifer; Wilkinson, Tim; Abel, Gillian; Pitama, Suzanne

2016-10-01

There is no accepted best practice for optimizing tertiary student knowledge, perceptions, and skills to care for sexual and gender diverse groups. The objective of this research was to synthesize the relevant literature regarding effective curricular initiatives designed to enhance tertiary level student knowledge, perceptions, and skills to care for sexual and gender diverse populations. A modified Critical Interpretive Synthesis using a systematic search strategy was conducted in 2015. This method was chosen to synthesize the relevant qualitative and quantitative literature as it allows for the depth and breadth of information to be captured and new constructs to be illuminated. Databases searched include AMED, CINAHL EBM Reviews, ERIC, Ovid MEDLINE, Ovid Nursing Database, PsychInfo, and Google Scholar. Thirty-one articles were included in this review. Curricular initiatives ranging from discrete to multimodal approaches have been implemented. Successful initiatives included discrete sessions with time for processing, and multi-modal strategies. Multi-modal approaches that encouraged awareness of one's lens and privilege in conjunction with facilitated communication seemed the most effective. The literature is limited to the evaluation of explicit curricula. The wider cultural competence literature offers further insight by highlighting the importance of broad and embedded forces including social influences, the institutional climate, and the implicit, or hidden, curriculum. A combined interpretation of the complementary cultural competence and sexual and gender diversity literature provides a novel understanding of the optimal content and context for the delivery of a successful curricular initiative.

FLASHFLOOD: A 3D Field-based similarity search and alignment method for flexible molecules

NASA Astrophysics Data System (ADS)

Pitman, Michael C.; Huber, Wolfgang K.; Horn, Hans; Krämer, Andreas; Rice, Julia E.; Swope, William C.

2001-07-01

A three-dimensional field-based similarity search and alignment method for flexible molecules is introduced. The conformational space of a flexible molecule is represented in terms of fragments and torsional angles of allowed conformations. A user-definable property field is used to compute features of fragment pairs. Features are generalizations of CoMMA descriptors (Silverman, B.D. and Platt, D.E., J. Med. Chem., 39 (1996) 2129.) that characterize local regions of the property field by its local moments. The features are invariant under coordinate system transformations. Features taken from a query molecule are used to form alignments with fragment pairs in the database. An assembly algorithm is then used to merge the fragment pairs into full structures, aligned to the query. Key to the method is the use of a context adaptive descriptor scaling procedure as the basis for similarity. This allows the user to tune the weights of the various feature components based on examples relevant to the particular context under investigation. The property fields may range from simple, phenomenological fields, to fields derived from quantum mechanical calculations. We apply the method to the dihydrofolate/methotrexate benchmark system, and show that when one injects relevant contextual information into the descriptor scaling procedure, better results are obtained more efficiently. We also show how the method works and include computer times for a query from a database that represents approximately 23 million conformers of seventeen flexible molecules.

Database Search Strategies & Tips. Reprints from the Best of "ONLINE" [and]"DATABASE."

ERIC Educational Resources Information Center

Online, Inc., Weston, CT.

Reprints of 17 articles presenting strategies and tips for searching databases online appear in this collection, which is one in a series of volumes of reprints from "ONLINE" and "DATABASE" magazines. Edited for information professionals who use electronically distributed databases, these articles address such topics as: (1)…

SUGAR-FREE CHEWING GUM AND DENTAL CARIES – A SYSTEMATIC REVIEW

PubMed Central

Mickenautsch, Steffen; Leal, Soraya Coelho; Yengopal, Veerasamy; Bezerra, Ana Cristina; Cruvinel, Vanessa

2007-01-01

Objective: To appraise existing evidence for a therapeutic / anti-cariogenic effect of sugar-free chewing gum for patients. Method: 9 English and 2 Portuguese databases were searched using English and Portuguese keywords. Relevant articles in English, German, Portuguese and Spanish were included for review. Trials were excluded on lack of randomisation, control group, blinding and baseline data, drop out rate >33%, no statistical adjustment of baseline differences and no assessment of clinically important outcomes. Reviews were excluded on lack of information, article selection criteria, search strategy followed, search keywords, searched databases or lack of study-by-study critique tables. In cases of multiple reports from the same study, the report covering the longest period was included. Two reviewers independently reviewed and assessed the quality of accepted articles. Results: Thirty-nine articles were included for review. Thirty were excluded and 9 accepted. Of the 9 accepted, 2 trials of reasonable and good evidence value did not demonstrate any anti-cariogenic effect of sugar-free chewing gum. However, 7 articles, with 1 of strong, and 6 of good evidence value, demonstrated anti-cariogenic effects of chewing Sorbitol, Xylitol or Sorbitol/Xylitol gum. This effect can be ascribed to saliva stimulation through the chewing process, particularly when gum is used immediately after meals; the lack of sucrose and the inability of bacteria to metabolize polyols into acids. Conclusion: The evidence suggests that sugar-free chewing gum has a caries-reducing effect. Further well-designed randomised trials are needed to confirm these findings. PMID:19089107

Gastrosplenic fistula occurring in lymphoma patients: Systematic review with a new case of extranodal NK/T-cell lymphoma.

PubMed

Kang, Dong Hyeok; Huh, Jimi; Lee, Jong Hwa; Jeong, Yoong Ki; Cha, Hee Jeong

2017-09-21

To provide the overall spectrum of gastrosplenic fistula (GSF) occurring in lymphomas through a systematic review including a patient at our hospital. A comprehensive literature search was performed in the MEDLINE database to identify studies of GSF occurring in lymphomas. A computerized search of our institutional database was also performed. In all cases, we analyzed the clinicopathologic/radiologic features, treatment and outcome of GSF occurring in lymphomas. A literature search identified 25 relevant studies with 26 patients. Our institutional data search added 1 patient. Systematic review of the total 27 cases revealed that GSF occurred mainly in diffuse, large B-cell lymphoma ( n = 23), but also in diffuse, histiocytic lymphoma ( n = 1), Hodgkin's lymphoma ( n = 2), and NK/T-cell lymphoma ( n = 1, our patient). The common clinical presentations are constitutional symptoms ( n = 20) and abdominal pain ( n = 17), although acute gastrointestinal bleeding ( n = 6) and infection symptoms due to splenic abscess ( n = 3) are also noted. In all patients, computed tomography scanning was very helpful for diagnosing GSF and for evaluating the lymphoma extent. GSF could occur either post-chemotherapy ( n = 10) or spontaneously ( n = 17). Surgical resection has been the most common treatment. Once patients have recovered from the acute illness status after undergoing surgery, their long-term outcome has been favorable. This systematic review provides an overview of GSF occurring in lymphomas, and will be helpful in making physicians aware of this rare disease entity.

Effect of caffeine on vestibular evoked myogenic potential: a systematic review with meta-analysis.

PubMed

Souza, Maria Eduarda Di Cavalcanti Alves de; Costa, Klinger Vagner Teixeira da; Menezes, Pedro de Lemos

2017-12-24

Caffeine can be considered the most consumed drug by adults worldwide, and can be found in several foods, such as chocolate, coffee, tea, soda and others. Overall, caffeine in moderate doses, results in increased physical and intellectual productivity, increases the capacity of concentration and reduces the time of reaction to sensory stimuli. On the other hand, high doses can cause noticeable signs of mental confusion and error induction in intellectual tasks, anxiety, restlessness, muscle tremors, tachycardia, labyrinthine changes, and tinnitus. Considering that the vestibular evoked myogenic potential is a clinical test that evaluates the muscular response of high intensity auditory stimulation, the present systematic review aimed to analyze the effects of caffeine on vestibular evoked myogenic potential. This study consisted of the search of the following databases: MEDLINE, CENTRAL, ScienceDirect, Scopus, Web of Science, LILACS, SciELO and ClinicalTrials.gov. Additionally, the gray literature was also searched. The search strategy included terms related to intervention (caffeine or coffee consumption) and the primary outcome (vestibular evoked myogenic potential). Based on the 253 potentially relevant articles identified through the database search, only two full-text publications were retrieved for further evaluation, which were maintained for qualitative analysis. Analyzing the articles found, caffeine has no effect on vestibular evoked myogenic potential in normal individuals. Copyright © 2017 Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial. Published by Elsevier Editora Ltda. All rights reserved.

Searching for grey literature for systematic reviews: challenges and benefits.

PubMed

Mahood, Quenby; Van Eerd, Dwayne; Irvin, Emma

2014-09-01

There is ongoing interest in including grey literature in systematic reviews. Including grey literature can broaden the scope to more relevant studies, thereby providing a more complete view of available evidence. Searching for grey literature can be challenging despite greater access through the Internet, search engines and online bibliographic databases. There are a number of publications that list sources for finding grey literature in systematic reviews. However, there is scant information about how searches for grey literature are executed and how it is included in the review process. This level of detail is important to ensure that reviews follow explicit methodology to be systematic, transparent and reproducible. The purpose of this paper is to provide a detailed account of one systematic review team's experience in searching for grey literature and including it throughout the review. We provide a brief overview of grey literature before describing our search and review approach. We also discuss the benefits and challenges of including grey literature in our systematic review, as well as the strengths and limitations to our approach. Detailed information about incorporating grey literature in reviews is important in advancing methodology as review teams adapt and build upon the approaches described. Copyright © 2013 John Wiley & Sons, Ltd.

RadSearch: a RIS/PACS integrated query tool

NASA Astrophysics Data System (ADS)

Tsao, Sinchai; Documet, Jorge; Moin, Paymann; Wang, Kevin; Liu, Brent J.

2008-03-01

Radiology Information Systems (RIS) contain a wealth of information that can be used for research, education, and practice management. However, the sheer amount of information available makes querying specific data difficult and time consuming. Previous work has shown that a clinical RIS database and its RIS text reports can be extracted, duplicated and indexed for searches while complying with HIPAA and IRB requirements. This project's intent is to provide a software tool, the RadSearch Toolkit, to allow intelligent indexing and parsing of RIS reports for easy yet powerful searches. In addition, the project aims to seamlessly query and retrieve associated images from the Picture Archiving and Communication System (PACS) in situations where an integrated RIS/PACS is in place - even subselecting individual series, such as in an MRI study. RadSearch's application of simple text parsing techniques to index text-based radiology reports will allow the search engine to quickly return relevant results. This powerful combination will be useful in both private practice and academic settings; administrators can easily obtain complex practice management information such as referral patterns; researchers can conduct retrospective studies with specific, multiple criteria; teaching institutions can quickly and effectively create thorough teaching files.

A new approach to data evaluation in the non-target screening of organic trace substances in water analysis.

PubMed

Müller, Alexander; Schulz, Wolfgang; Ruck, Wolfgang K L; Weber, Walter H

2011-11-01

Non-target screening via high performance liquid chromatography-mass spectrometry (HPLC-MS) has gained increasingly in importance for monitoring organic trace substances in water resources targeted for the production of drinking water. In this article a new approach for evaluating the data from non-target HPLC-MS screening in water is introduced and its advantages are demonstrated using the supply of drinking water as an example. The crucial difference between this and other approaches is the comparison of samples based on compounds (features) determined by their full scan data. In so doing, we take advantage of the temporal, spatial, or process-based relationships among the samples by applying the set operators, UNION, INTERSECT, and COMPLEMENT to the features of each sample. This approach regards all compounds, detectable by the used analytical method. That is the fundamental meaning of non-target screening, which includes all analytical information from the applied technique for further data evaluation. In the given example, in just one step, all detected features (1729) of a landfill leachate sample could be examined for their relevant influences on water purification respectively drinking water. This study shows that 1721 out of 1729 features were not relevant for the water purification. Only eight features could be determined in the untreated water and three of them were found in the final drinking water after ozonation. In so doing, it was possible to identify 1-adamantylamine as contamination of the landfill in the drinking water at a concentration in the range of 20 ng L(-1). To support the identification of relevant compounds and their transformation products, the DAIOS database (Database-Assisted Identification of Organic Substances) was used. This database concept includes some functions such as product ion search to increase the efficiency of the database query after the screening. To identify related transformation products the database function "transformation tree" was used. Copyright © 2011 Elsevier Ltd. All rights reserved.

Assigning statistical significance to proteotypic peptides via database searches

PubMed Central

Alves, Gelio; Ogurtsov, Aleksey Y.; Yu, Yi-Kuo

2011-01-01

Querying MS/MS spectra against a database containing only proteotypic peptides reduces data analysis time due to reduction of database size. Despite the speed advantage, this search strategy is challenged by issues of statistical significance and coverage. The former requires separating systematically significant identifications from less confident identifications, while the latter arises when the underlying peptide is not present, due to single amino acid polymorphisms (SAPs) or post-translational modifications (PTMs), in the proteotypic peptide libraries searched. To address both issues simultaneously, we have extended RAId’s knowledge database to include proteotypic information, utilized RAId’s statistical strategy to assign statistical significance to proteotypic peptides, and modified RAId’s programs to allow for consideration of proteotypic information during database searches. The extended database alleviates the coverage problem since all annotated modifications, even those occurred within proteotypic peptides, may be considered. Taking into account the likelihoods of observation, the statistical strategy of RAId provides accurate E-value assignments regardless whether a candidate peptide is proteotypic or not. The advantage of including proteotypic information is evidenced by its superior retrieval performance when compared to regular database searches. PMID:21055489

National Center for Biotechnology Information

MedlinePlus

... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

The Global Evidence Mapping Initiative: scoping research in broad topic areas.

PubMed

Bragge, Peter; Clavisi, Ornella; Turner, Tari; Tavender, Emma; Collie, Alex; Gruen, Russell L

2011-06-17

Evidence mapping describes the quantity, design and characteristics of research in broad topic areas, in contrast to systematic reviews, which usually address narrowly-focused research questions. The breadth of evidence mapping helps to identify evidence gaps, and may guide future research efforts. The Global Evidence Mapping (GEM) Initiative was established in 2007 to create evidence maps providing an overview of existing research in Traumatic Brain Injury (TBI) and Spinal Cord Injury (SCI). The GEM evidence mapping method involved three core tasks:1. Setting the boundaries and context of the map: Definitions for the fields of TBI and SCI were clarified, the prehospital, acute inhospital and rehabilitation phases of care were delineated and relevant stakeholders (patients, carers, clinicians, researchers and policymakers) who could contribute to the mapping were identified. Researchable clinical questions were developed through consultation with key stakeholders and a broad literature search. 2. Searching for and selection of relevant studies: Evidence search and selection involved development of specific search strategies, development of inclusion and exclusion criteria, searching of relevant databases and independent screening and selection by two researchers. 3. Reporting on yield and study characteristics: Data extraction was performed at two levels - 'interventions and study design' and 'detailed study characteristics'. The evidence map and commentary reflected the depth of data extraction. One hundred and twenty-nine researchable clinical questions in TBI and SCI were identified. These questions were then prioritised into high (n = 60) and low (n = 69) importance by the stakeholders involved in question development. Since 2007, 58 263 abstracts have been screened, 3 731 full text articles have been reviewed and 1 644 relevant neurotrauma publications have been mapped, covering fifty-three high priority questions. GEM Initiative evidence maps have a broad range of potential end-users including funding agencies, researchers and clinicians. Evidence mapping is at least as resource-intensive as systematic reviewing. The GEM Initiative has made advancements in evidence mapping, most notably in the area of question development and prioritisation. Evidence mapping complements other review methods for describing existing research, informing future research efforts, and addressing evidence gaps.

The Global Evidence Mapping Initiative: Scoping research in broad topic areas

PubMed Central

2011-01-01

Background Evidence mapping describes the quantity, design and characteristics of research in broad topic areas, in contrast to systematic reviews, which usually address narrowly-focused research questions. The breadth of evidence mapping helps to identify evidence gaps, and may guide future research efforts. The Global Evidence Mapping (GEM) Initiative was established in 2007 to create evidence maps providing an overview of existing research in Traumatic Brain Injury (TBI) and Spinal Cord Injury (SCI). Methods The GEM evidence mapping method involved three core tasks: 1. Setting the boundaries and context of the map: Definitions for the fields of TBI and SCI were clarified, the prehospital, acute inhospital and rehabilitation phases of care were delineated and relevant stakeholders (patients, carers, clinicians, researchers and policymakers) who could contribute to the mapping were identified. Researchable clinical questions were developed through consultation with key stakeholders and a broad literature search. 2. Searching for and selection of relevant studies: Evidence search and selection involved development of specific search strategies, development of inclusion and exclusion criteria, searching of relevant databases and independent screening and selection by two researchers. 3. Reporting on yield and study characteristics: Data extraction was performed at two levels - 'interventions and study design' and 'detailed study characteristics'. The evidence map and commentary reflected the depth of data extraction. Results One hundred and twenty-nine researchable clinical questions in TBI and SCI were identified. These questions were then prioritised into high (n = 60) and low (n = 69) importance by the stakeholders involved in question development. Since 2007, 58 263 abstracts have been screened, 3 731 full text articles have been reviewed and 1 644 relevant neurotrauma publications have been mapped, covering fifty-three high priority questions. Conclusions GEM Initiative evidence maps have a broad range of potential end-users including funding agencies, researchers and clinicians. Evidence mapping is at least as resource-intensive as systematic reviewing. The GEM Initiative has made advancements in evidence mapping, most notably in the area of question development and prioritisation. Evidence mapping complements other review methods for describing existing research, informing future research efforts, and addressing evidence gaps. PMID:21682870

Transterm—extended search facilities and improved integration with other databases

PubMed Central

Jacobs, Grant H.; Stockwell, Peter A.; Tate, Warren P.; Brown, Chris M.

2006-01-01

Transterm has now been publicly available for >10 years. Major changes have been made since its last description in this database issue in 2002. The current database provides data for key regions of mRNA sequences, a curated database of mRNA motifs and tools to allow users to investigate their own motifs or mRNA sequences. The key mRNA regions database is derived computationally from Genbank. It contains 3′ and 5′ flanking regions, the initiation and termination signal context and coding sequence for annotated CDS features from Genbank and RefSeq. The database is non-redundant, enabling summary files and statistics to be prepared for each species. Advances include providing extended search facilities, the database may now be searched by BLAST in addition to regular expressions (patterns) allowing users to search for motifs such as known miRNA sequences, and the inclusion of RefSeq data. The database contains >40 motifs or structural patterns important for translational control. In this release, patterns from UTRsite and Rfam are also incorporated with cross-referencing. Users may search their sequence data with Transterm or user-defined patterns. The system is accessible at . PMID:16381889

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

PubMed

Famulari, Stevie; Witz, Kyla

2015-01-01

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

Applying systematic review search methods to the grey literature: a case study examining guidelines for school-based breakfast programs in Canada.

PubMed

Godin, Katelyn; Stapleton, Jackie; Kirkpatrick, Sharon I; Hanning, Rhona M; Leatherdale, Scott T

2015-10-22

Grey literature is an important source of information for large-scale review syntheses. However, there are many characteristics of grey literature that make it difficult to search systematically. Further, there is no 'gold standard' for rigorous systematic grey literature search methods and few resources on how to conduct this type of search. This paper describes systematic review search methods that were developed and applied to complete a case study systematic review of grey literature that examined guidelines for school-based breakfast programs in Canada. A grey literature search plan was developed to incorporate four different searching strategies: (1) grey literature databases, (2) customized Google search engines, (3) targeted websites, and (4) consultation with contact experts. These complementary strategies were used to minimize the risk of omitting relevant sources. Since abstracts are often unavailable in grey literature documents, items' abstracts, executive summaries, or table of contents (whichever was available) were screened. Screening of publications' full-text followed. Data were extracted on the organization, year published, who they were developed by, intended audience, goal/objectives of document, sources of evidence/resources cited, meals mentioned in the guidelines, and recommendations for program delivery. The search strategies for identifying and screening publications for inclusion in the case study review was found to be manageable, comprehensive, and intuitive when applied in practice. The four search strategies of the grey literature search plan yielded 302 potentially relevant items for screening. Following the screening process, 15 publications that met all eligibility criteria remained and were included in the case study systematic review. The high-level findings of the case study systematic review are briefly described. This article demonstrated a feasible and seemingly robust method for applying systematic search strategies to identify web-based resources in the grey literature. The search strategy we developed and tested is amenable to adaptation to identify other types of grey literature from other disciplines and answering a wide range of research questions. This method should be further adapted and tested in future research syntheses.

Influence of faith-based organisations on HIV prevention strategies in Africa: a systematic review.

PubMed

Ochillo, Marylyn A; van Teijlingen, Edwin; Hind, Martin

2017-09-01

The HIV/AIDS epidemic remains of global significance and there is a need to target sub-Saharan Africa since it is the hardest hit region worldwide. Religion and more specifically faith-based organisations can have an effect on socio-cultural factors that increase or decrease the risk of infection; and offer preventative interventions to the wider community. To understand the influence of faith-based organisations on HIV prevention in Africa. The main search engine of a British university 'mysearch' was used as this incorporates all relevant databases. Studies were also retrieved by searches within Google scholar, PubMed and reference lists of included papers were hand searched. The authors assessed the relevance of each article separately against the inclusion criteria. The data extraction form was piloted by the first author and cross-checked by the other authors. Seven studies met all inclusion criteria and were reviewed. Seven individual themes were identified. However, for the purposes of focus within this paper only two themes were focused on. Given the accessibility of faith-based organisations (FBOs) and the coverage of religion among the population, FBOs are potentially important players in HIV prevention. Therefore, more resources and support should be given to support their health promotion strategies.

Emergency treatment of hypoglycaemia: a guideline and evidence review.

PubMed

Villani, M; de Courten, B; Zoungas, S

2017-09-01

To examine the current treatment guidelines for the emergency management of hypoglycaemia and the evidence underpinning recommendations. International diabetes agencies were searched for hypoglycaemia treatment guidelines. Guidelines were assessed using the Appraisal of Guidelines Research and Evaluation II (AGREE II) instrument. An electronic database search was conducted for evidence regarding emergency treatment of hypoglycaemia in adults, and relevant articles were critically appraised. Of the international diabetes agencies, six sets of guidelines were deemed relevant and of sufficient detail for appraisal by AGREE II. The evidence search returned 2649 articles, of which 17 pertaining to the emergency management of hypoglycaemia were included. High-quality evidence for the management of hypoglycaemia was lacking, limiting treatment recommendations. In general, guidelines and studies were somewhat concordant and recommended 15-20 g of oral glucose or sucrose, repeated after 10-15 min for treatment of the responsive adult, and 10% intravenous dextrose or 1 mg intramuscular glucagon for treatment of the unresponsive adult. No evidence was found for other treatment approaches. Evidence for the emergency treatment of hypoglycaemia in adults is limited, is often low grade and mostly pre-dates contemporary management of diabetes. Guideline recommendations are limited by the lack of randomized trials. Further high-quality studies are required to inform the optimum management of this frequently occurring emergency condition. © 2017 Diabetes UK.

Utility of proteomics in obstetric disorders: a review

PubMed Central

Hernández-Núñez, Jónathan; Valdés-Yong, Magel

2015-01-01

The study of proteomics could explain many aspects of obstetric disorders. We undertook this review with the aim of assessing the utility of proteomics in the specialty of obstetrics. We searched the electronic databases of MEDLINE, EBSCOhost, BVS Bireme, and SciELO, using various search terms with the assistance of a librarian. We considered cohort studies, case-control studies, case series, and systematic review articles published until October 2014 in the English or Spanish language, and evaluated their quality and the internal validity of the evidence provided. Two reviewers extracted the data independently, then both researchers simultaneously revised the data later, to arrive at a consensus. The search retrieved 1,158 papers, of which 965 were excluded for being duplicates, not relevant, or unrelated studies. A further 86 papers were excluded for being guidelines, protocols, or case reports, along with another 64 that did not contain relevant information, leaving 43 studies for inclusion. Many of these studies showed the utility of proteomic techniques for prediction, pathophysiology, diagnosis, management, monitoring, and prognosis of pre-eclampsia, perinatal infection, premature rupture of membranes, preterm birth, intrauterine growth restriction, and ectopic pregnancy. Proteomic techniques have enormous clinical significance and constitute an invaluable weapon in the management of obstetric disorders that increase maternal and perinatal morbidity and mortality. PMID:25926758

[Tissue engineering of urinary bladder using acellular matrix].

PubMed

Glybochko, P V; Olefir, Yu V; Alyaev, Yu G; Butnaru, D V; Bezrukov, E A; Chaplenko, A A; Zharikova, T M

2017-04-01

Tissue engineering has become a new promising strategy for repairing damaged organs of the urinary system, including the bladder. The basic idea of tissue engineering is to integrate cellular technology and advanced bio-compatible materials to replace or repair tissues and organs. of the study is the objective reflection of the current trends and advances in tissue engineering of the bladder using acellular matrix through a systematic search of preclinical and clinical studies of interest. Relevant studies, including those on methods of tissue engineering of urinary bladder, was retrieved from multiple databases, including Scopus, Web of Science, PubMed, Embase. The reference lists of the retrieved review articles were analyzed for the presence of the missing relevant publications. In addition, a manual search for registered clinical trials was conducted in clinicaltrials.gov. Following the above search strategy, a total of 77 eligible studies were selected for further analysis. Studies differed in the types of animal models, supporting structures, cells and growth factors. Among those, studies using cell-free matrix were selected for a more detailed analysis. Partial restoration of urothelium layer was observed in most studies where acellular grafts were used for cystoplasty, but no the growth of the muscle layer was observed. This is the main reason why cellular structures are more commonly used in clinical practice.

National Rehabilitation Information Center

MedlinePlus

... search the NARIC website or one of our databases Select a database or search for a webpage A NARIC webpage ... Projects conducting research and/or development (NIDILRR Program Database). Organizations, agencies, and online resources that support people ...

Quantum search of a real unstructured database

NASA Astrophysics Data System (ADS)

Broda, Bogusław

2016-02-01

A simple circuit implementation of the oracle for Grover's quantum search of a real unstructured classical database is proposed. The oracle contains a kind of quantumly accessible classical memory, which stores the database.

Overcoming Species Boundaries in Peptide Identification with Bayesian Information Criterion-driven Error-tolerant Peptide Search (BICEPS)*

PubMed Central

Renard, Bernhard Y.; Xu, Buote; Kirchner, Marc; Zickmann, Franziska; Winter, Dominic; Korten, Simone; Brattig, Norbert W.; Tzur, Amit; Hamprecht, Fred A.; Steen, Hanno

2012-01-01

Currently, the reliable identification of peptides and proteins is only feasible when thoroughly annotated sequence databases are available. Although sequencing capacities continue to grow, many organisms remain without reliable, fully annotated reference genomes required for proteomic analyses. Standard database search algorithms fail to identify peptides that are not exactly contained in a protein database. De novo searches are generally hindered by their restricted reliability, and current error-tolerant search strategies are limited by global, heuristic tradeoffs between database and spectral information. We propose a Bayesian information criterion-driven error-tolerant peptide search (BICEPS) and offer an open source implementation based on this statistical criterion to automatically balance the information of each single spectrum and the database, while limiting the run time. We show that BICEPS performs as well as current database search algorithms when such algorithms are applied to sequenced organisms, whereas BICEPS only uses a remotely related organism database. For instance, we use a chicken instead of a human database corresponding to an evolutionary distance of more than 300 million years (International Chicken Genome Sequencing Consortium (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716). We demonstrate the successful application to cross-species proteomics with a 33% increase in the number of identified proteins for a filarial nematode sample of Litomosoides sigmodontis. PMID:22493179

LigandBox: A database for 3D structures of chemical compounds

PubMed Central

Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

2013-01-01

A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening. PMID:27493549

LigandBox: A database for 3D structures of chemical compounds.

PubMed

Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

2013-01-01

A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening.

The MAO NASU Plate Archive Database. Current Status and Perspectives

NASA Astrophysics Data System (ADS)

Pakuliak, L. K.; Sergeeva, T. P.

2006-04-01

The preliminary online version of the database of the MAO NASU plate archive is constructed on the basis of the relational database management system MySQL and permits an easy supplement of database with new collections of astronegatives, provides a high flexibility in constructing SQL-queries for data search optimization, PHP Basic Authorization protected access to administrative interface and wide range of search parameters. The current status of the database will be reported and the brief description of the search engine and means of the database integrity support will be given. Methods and means of the data verification and tasks for the further development will be discussed.

Adaptation of Decoy Fusion Strategy for Existing Multi-Stage Search Workflows

NASA Astrophysics Data System (ADS)

Ivanov, Mark V.; Levitsky, Lev I.; Gorshkov, Mikhail V.

2016-09-01

A number of proteomic database search engines implement multi-stage strategies aiming at increasing the sensitivity of proteome analysis. These approaches often employ a subset of the original database for the secondary stage of analysis. However, if target-decoy approach (TDA) is used for false discovery rate (FDR) estimation, the multi-stage strategies may violate the underlying assumption of TDA that false matches are distributed uniformly across the target and decoy databases. This violation occurs if the numbers of target and decoy proteins selected for the second search are not equal. Here, we propose a method of decoy database generation based on the previously reported decoy fusion strategy. This method allows unbiased TDA-based FDR estimation in multi-stage searches and can be easily integrated into existing workflows utilizing popular search engines and post-search algorithms.

Searching for evidence or approval? A commentary on database search in systematic reviews and alternative information retrieval methodologies.

PubMed

Delaney, Aogán; Tamás, Peter A

2018-03-01

Despite recognition that database search alone is inadequate even within the health sciences, it appears that reviewers in fields that have adopted systematic review are choosing to rely primarily, or only, on database search for information retrieval. This commentary reminds readers of factors that call into question the appropriateness of default reliance on database searches particularly as systematic review is adapted for use in new and lower consensus fields. It then discusses alternative methods for information retrieval that require development, formalisation, and evaluation. Our goals are to encourage reviewers to reflect critically and transparently on their choice of information retrieval methods and to encourage investment in research on alternatives. Copyright © 2017 John Wiley & Sons, Ltd.

Federated or cached searches: Providing expected performance from multiple invasive species databases

NASA Astrophysics Data System (ADS)

Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

2011-06-01

Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search "deep" web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

Federated or cached searches: providing expected performance from multiple invasive species databases

USGS Publications Warehouse

Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

2011-01-01

Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search “deep” web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

Psychopharmacological and Other Treatments in Preschool Children with Attention-Deficit/Hyperactivity Disorder: Current Evidence and Practice

PubMed Central

Arnold, L. Eugene; Anthony, Bruno J.

2008-01-01

Abstract Objective This article reviews rational approaches to treating attention-deficit/hyperactivity disorder (ADHD) in preschool children, including pharmacological and nonpharmacological treatments. Implications for clinical practice are discussed. Data Sources We searched MEDLINE, PsychINFO, Cumulative Index to Nursing & Allied Health, Educational Resources Information Center, Cochrane Database of Systematic Reviews and Database of Abstracts of Reviews of Effects for relevant literature published in English from 1967 to 2007 on preschool ADHD. We also reviewed the references cited in identified reports. Study Selection Studies were reviewed if the sample included at least some children younger than 6 years of age or attending kindergarten, the study participants had a diagnosis of ADHD or equivalent symptoms, received intervention aimed at ADHD symptoms, and included a relevant outcome measure. Data Extraction Studies were reviewed for type of intervention and outcome relevant to ADHD and were rated for the level of evidence for adequacy of the data to inform clinical practice. Conclusions The current level of evidence for adequacy of empirical data to inform clinical practice for short-term treatment of ADHD in preschool children is Level A for methylphenidate and Level B for parent behavior training, child training, and additive-free elimination diet. PMID:18844482

MICA: desktop software for comprehensive searching of DNA databases

PubMed Central

Stokes, William A; Glick, Benjamin S

2006-01-01

Background Molecular biologists work with DNA databases that often include entire genomes. A common requirement is to search a DNA database to find exact matches for a nondegenerate or partially degenerate query. The software programs available for such purposes are normally designed to run on remote servers, but an appealing alternative is to work with DNA databases stored on local computers. We describe a desktop software program termed MICA (K-Mer Indexing with Compact Arrays) that allows large DNA databases to be searched efficiently using very little memory. Results MICA rapidly indexes a DNA database. On a Macintosh G5 computer, the complete human genome could be indexed in about 5 minutes. The indexing algorithm recognizes all 15 characters of the DNA alphabet and fully captures the information in any DNA sequence, yet for a typical sequence of length L, the index occupies only about 2L bytes. The index can be searched to return a complete list of exact matches for a nondegenerate or partially degenerate query of any length. A typical search of a long DNA sequence involves reading only a small fraction of the index into memory. As a result, searches are fast even when the available RAM is limited. Conclusion MICA is suitable as a search engine for desktop DNA analysis software. PMID:17018144

Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules—Search Options and Applications in Food Science

PubMed Central

Minkiewicz, Piotr; Darewicz, Małgorzata; Iwaniak, Anna; Bucholska, Justyna; Starowicz, Piotr; Czyrko, Emilia

2016-01-01

Internet databases of small molecules, their enzymatic reactions, and metabolism have emerged as useful tools in food science. Database searching is also introduced as part of chemistry or enzymology courses for food technology students. Such resources support the search for information about single compounds and facilitate the introduction of secondary analyses of large datasets. Information can be retrieved from databases by searching for the compound name or structure, annotating with the help of chemical codes or drawn using molecule editing software. Data mining options may be enhanced by navigating through a network of links and cross-links between databases. Exemplary databases reviewed in this article belong to two classes: tools concerning small molecules (including general and specialized databases annotating food components) and tools annotating enzymes and metabolism. Some problems associated with database application are also discussed. Data summarized in computer databases may be used for calculation of daily intake of bioactive compounds, prediction of metabolism of food components, and their biological activity as well as for prediction of interactions between food component and drugs. PMID:27929431

Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules-Search Options and Applications in Food Science.

PubMed

Minkiewicz, Piotr; Darewicz, Małgorzata; Iwaniak, Anna; Bucholska, Justyna; Starowicz, Piotr; Czyrko, Emilia

2016-12-06

Internet databases of small molecules, their enzymatic reactions, and metabolism have emerged as useful tools in food science. Database searching is also introduced as part of chemistry or enzymology courses for food technology students. Such resources support the search for information about single compounds and facilitate the introduction of secondary analyses of large datasets. Information can be retrieved from databases by searching for the compound name or structure, annotating with the help of chemical codes or drawn using molecule editing software. Data mining options may be enhanced by navigating through a network of links and cross-links between databases. Exemplary databases reviewed in this article belong to two classes: tools concerning small molecules (including general and specialized databases annotating food components) and tools annotating enzymes and metabolism. Some problems associated with database application are also discussed. Data summarized in computer databases may be used for calculation of daily intake of bioactive compounds, prediction of metabolism of food components, and their biological activity as well as for prediction of interactions between food component and drugs.

Searching for Controlled Trials of Complementary and Alternative Medicine: A Comparison of 15 Databases

PubMed Central

Cogo, Elise; Sampson, Margaret; Ajiferuke, Isola; Manheimer, Eric; Campbell, Kaitryn; Daniel, Raymond; Moher, David

2011-01-01

This project aims to assess the utility of bibliographic databases beyond the three major ones (MEDLINE, EMBASE and Cochrane CENTRAL) for finding controlled trials of complementary and alternative medicine (CAM). Fifteen databases were searched to identify controlled clinical trials (CCTs) of CAM not also indexed in MEDLINE. Searches were conducted in May 2006 using the revised Cochrane highly sensitive search strategy (HSSS) and the PubMed CAM Subset. Yield of CAM trials per 100 records was determined, and databases were compared over a standardized period (2005). The Acudoc2 RCT, Acubriefs, Index to Chiropractic Literature (ICL) and Hom-Inform databases had the highest concentrations of non-MEDLINE records, with more than 100 non-MEDLINE records per 500. Other productive databases had ratios between 500 and 1500 records to 100 non-MEDLINE records—these were AMED, MANTIS, PsycINFO, CINAHL, Global Health and Alt HealthWatch. Five databases were found to be unproductive: AGRICOLA, CAIRSS, Datadiwan, Herb Research Foundation and IBIDS. Acudoc2 RCT yielded 100 CAM trials in the most recent 100 records screened. Acubriefs, AMED, Hom-Inform, MANTIS, PsycINFO and CINAHL had more than 25 CAM trials per 100 records screened. Global Health, ICL and Alt HealthWatch were below 25 in yield. There were 255 non-MEDLINE trials from eight databases in 2005, with only 10% indexed in more than one database. Yield varied greatly between databases; the most productive databases from both sampling methods were Acubriefs, Acudoc2 RCT, AMED and CINAHL. Low overlap between databases indicates comprehensive CAM literature searches will require multiple databases. PMID:19468052

Searching for controlled trials of complementary and alternative medicine: a comparison of 15 databases.

PubMed

Cogo, Elise; Sampson, Margaret; Ajiferuke, Isola; Manheimer, Eric; Campbell, Kaitryn; Daniel, Raymond; Moher, David

2011-01-01

This project aims to assess the utility of bibliographic databases beyond the three major ones (MEDLINE, EMBASE and Cochrane CENTRAL) for finding controlled trials of complementary and alternative medicine (CAM). Fifteen databases were searched to identify controlled clinical trials (CCTs) of CAM not also indexed in MEDLINE. Searches were conducted in May 2006 using the revised Cochrane highly sensitive search strategy (HSSS) and the PubMed CAM Subset. Yield of CAM trials per 100 records was determined, and databases were compared over a standardized period (2005). The Acudoc2 RCT, Acubriefs, Index to Chiropractic Literature (ICL) and Hom-Inform databases had the highest concentrations of non-MEDLINE records, with more than 100 non-MEDLINE records per 500. Other productive databases had ratios between 500 and 1500 records to 100 non-MEDLINE records-these were AMED, MANTIS, PsycINFO, CINAHL, Global Health and Alt HealthWatch. Five databases were found to be unproductive: AGRICOLA, CAIRSS, Datadiwan, Herb Research Foundation and IBIDS. Acudoc2 RCT yielded 100 CAM trials in the most recent 100 records screened. Acubriefs, AMED, Hom-Inform, MANTIS, PsycINFO and CINAHL had more than 25 CAM trials per 100 records screened. Global Health, ICL and Alt HealthWatch were below 25 in yield. There were 255 non-MEDLINE trials from eight databases in 2005, with only 10% indexed in more than one database. Yield varied greatly between databases; the most productive databases from both sampling methods were Acubriefs, Acudoc2 RCT, AMED and CINAHL. Low overlap between databases indicates comprehensive CAM literature searches will require multiple databases.

End User Information Searching on the Internet: How Do Users Search and What Do They Search For? (SIG USE)

ERIC Educational Resources Information Center

Saracevic, Tefko

2000-01-01

Summarizes a presentation that discussed findings and implications of research projects using an Internet search service and Internet-accessible vendor databases, representing the two sides of public database searching: query formulation and resource utilization. Presenters included: Tefko Saracevic, Amanda Spink, Dietmar Wolfram and Hong Xie.…

Assessment of Metabolome Annotation Quality: A Method for Evaluating the False Discovery Rate of Elemental Composition Searches

PubMed Central

Matsuda, Fumio; Shinbo, Yoko; Oikawa, Akira; Hirai, Masami Yokota; Fiehn, Oliver; Kanaya, Shigehiko; Saito, Kazuki

2009-01-01

Background In metabolomics researches using mass spectrometry (MS), systematic searching of high-resolution mass data against compound databases is often the first step of metabolite annotation to determine elemental compositions possessing similar theoretical mass numbers. However, incorrect hits derived from errors in mass analyses will be included in the results of elemental composition searches. To assess the quality of peak annotation information, a novel methodology for false discovery rates (FDR) evaluation is presented in this study. Based on the FDR analyses, several aspects of an elemental composition search, including setting a threshold, estimating FDR, and the types of elemental composition databases most reliable for searching are discussed. Methodology/Principal Findings The FDR can be determined from one measured value (i.e., the hit rate for search queries) and four parameters determined by Monte Carlo simulation. The results indicate that relatively high FDR values (30–50%) were obtained when searching time-of-flight (TOF)/MS data using the KNApSAcK and KEGG databases. In addition, searches against large all-in-one databases (e.g., PubChem) always produced unacceptable results (FDR >70%). The estimated FDRs suggest that the quality of search results can be improved not only by performing more accurate mass analysis but also by modifying the properties of the compound database. A theoretical analysis indicates that FDR could be improved by using compound database with smaller but higher completeness entries. Conclusions/Significance High accuracy mass analysis, such as Fourier transform (FT)-MS, is needed for reliable annotation (FDR <10%). In addition, a small, customized compound database is preferable for high-quality annotation of metabolome data. PMID:19847304

[Creativity and psychiatric disorders: recent neuroscientific insights].

PubMed

Thys, E; Sabbe, B; de Hert, M

2011-01-01

Creativity is an important human characteristic on which many of mankind's achievements are based. For centuries practitioners of various disciplines have deliberated over the possible connection between creativity and psychopathology. Even today the issue is still being investigated, mainly by groups working more or less independently; these range from art experts to psychiatrists and neuroscientists. In this article we bring together the foremost recent neuroscientific findings on the subject. We searched for relevant articles via electronic databases using a broad-band search strategy and concentrating mainly on neuroscientific publications. Our study of relevant articles showed that both the definition and the measurability of creativity are still problematic. Psychometric and psychodiagnostic research supports a link between creativity and the psychopathology of bipolar, schizophrenic and especially schizotypal disorders; the results of imaging techniques are less consistent and genetic research reveals a link between creativity and proneness to psychosis. There seems to be a connection between creativity and psychopathology in the bipolar-schizophrenic continuum. This connection is even more evident within the individual components of creativity and symptom groups of these pathologies. There is a need for accurate definitions, measuring instruments and multidisciplinary collaboration.

Ocular side effects of biological agents in oncology: what should the clinician be aware of?

PubMed Central

Hager, Tobias; Seitz, B

2014-01-01

During the last 20 years, biologicals have become increasingly relevant in oncologic therapy. Depending on the medication used, there are different profiles of ocular side effects. Although these can be present in up to 70% of patients, they are generally underreported in the literature. Therefore, the pathophysiological details of their development are often poorly understood. Herein we attempt to identify groups of biologicals to which a specific side effect profile can be assigned. We also tried to capture all relevant side effects and therefore conducted several database investigation including Medline, Cochrane library, and the drugs section of the US Food and Drug Administration (FDA), using the following search strings: “name of biological agent (both generic and commercial names)” AND “eye” OR “ocular”. If we found a side effect that has been associated with a drug, we researched Medline using the following search string: “name of biological agent” (both generic and commercial names) AND “term for the specific side effect”. Due to the wealth of material we report only the drugs that are approved by the FDA. PMID:24391443

NREL: Renewable Resource Data Center - Biomass Resource Publications

Science.gov Websites

Marginal Lands in APEC Economies NREL Publications Database For a comprehensive list of other NREL biomass resource publications, explore NREL's Publications Database. When searching the database, search on "

An assessment of the efficacy of searching in biomedical databases beyond MEDLINE in identifying studies for a systematic review on ward closures as an infection control intervention to control outbreaks.

PubMed

Kwon, Yoojin; Powelson, Susan E; Wong, Holly; Ghali, William A; Conly, John M

2014-11-11

The purpose of our study is to determine the value and efficacy of searching biomedical databases beyond MEDLINE for systematic reviews. We analyzed the results from a systematic review conducted by the authors and others on ward closure as an infection control practice. Ovid MEDLINE including In-Process & Other Non-Indexed Citations, Ovid Embase, CINAHL Plus, LILACS, and IndMED were systematically searched for articles of any study type discussing ward closure, as were bibliographies of selected articles and recent infection control conference abstracts. Search results were tracked, recorded, and analyzed using a relative recall method. The sensitivity of searching in each database was calculated. Two thousand ninety-five unique citations were identified and screened for inclusion in the systematic review: 2,060 from database searching and 35 from hand searching and other sources. Ninety-seven citations were included in the final review. MEDLINE and Embase searches each retrieved 80 of the 97 articles included, only 4 articles from each database were unique. The CINAHL search retrieved 35 included articles, and 4 were unique. The IndMED and LILACS searches did not retrieve any included articles, although 75 of the included articles were indexed in LILACS. The true value of using regional databases, particularly LILACS, may lie with the ability to search in the language spoken in the region. Eight articles were found only through hand searching. Identifying studies for a systematic review where the research is observational is complex. The value each individual study contributes to the review cannot be accurately measured. Consequently, we could not determine the value of results found from searching beyond MEDLINE, Embase, and CINAHL with accuracy. However, hand searching for serendipitous retrieval remains an important aspect due to indexing and keyword challenges inherent in this literature.

NBIC: Search Ballast Report Database

Science.gov Websites

Smithsonian Environmental Research Center Logo US Coast Guard Logo Submit BW Report | Search NBIC Database developed an online database that can be queried through our website. Data are accessible for all coastal Lakes, have been incorporated into the NBIC database as of August 2004. Information on data availability

Ocean Drilling Program: Science Operator Search Engine

Science.gov Websites

and products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main -USIO site, plus IODP, ODP, and DSDP Publications, together or separately. ODP | Search | Database

The Impact of Load Carriage on Measures of Power and Agility in Tactical Occupations: A Critical Review.

PubMed

Joseph, Aaron; Wiley, Amy; Orr, Robin; Schram, Benjamin; Dawes, J Jay

2018-01-07

The current literature suggests that load carriage can impact on a tactical officer's mobility, and that survival in the field may rely on the officer's mobility. The ability for humans to generate power and agility is critical for performance of the high-intensity movements required in the field of duty. The aims of this review were to critically examine the literature investigating the impacts of load carriage on measures of power and agility and to synthesize the findings. The authors completed a search of the literature using key search terms in four databases. After relevant studies were located using strict inclusion and exclusion criteria, the studies were critically appraised using the Downs and Black Checklist and relevant data were extracted and tabled. Fourteen studies were deemed relevant for this review, ranging in percentage quality scores from 42.85% to 71.43%. Outcome measures used in these studies to indicate levels of power and agility included short-distance sprints, vertical jumps, and agility runs, among others. Performance of both power and agility was shown to decrease when tactical load was added to the participants. This suggests that the increase in weight carried by tactical officers may put this population at risk of injury or fatality in the line of duty.

The Impact of Load Carriage on Measures of Power and Agility in Tactical Occupations: A Critical Review

PubMed Central

Joseph, Aaron; Wiley, Amy; Dawes, J. Jay

2018-01-01

The current literature suggests that load carriage can impact on a tactical officer’s mobility, and that survival in the field may rely on the officer’s mobility. The ability for humans to generate power and agility is critical for performance of the high-intensity movements required in the field of duty. The aims of this review were to critically examine the literature investigating the impacts of load carriage on measures of power and agility and to synthesize the findings. The authors completed a search of the literature using key search terms in four databases. After relevant studies were located using strict inclusion and exclusion criteria, the studies were critically appraised using the Downs and Black Checklist and relevant data were extracted and tabled. Fourteen studies were deemed relevant for this review, ranging in percentage quality scores from 42.85% to 71.43%. Outcome measures used in these studies to indicate levels of power and agility included short-distance sprints, vertical jumps, and agility runs, among others. Performance of both power and agility was shown to decrease when tactical load was added to the participants. This suggests that the increase in weight carried by tactical officers may put this population at risk of injury or fatality in the line of duty. PMID:29316674

A narrative review of recent developments in knowledge translation and implications for mental health care providers.

PubMed

Goldner, Elliot M; Jenkins, Emily K; Fischer, Benedikt

2014-03-01

Attention to knowledge translation (KT) has increased in the health care field in an effort to improve uptake and implementation of potentially beneficial knowledge. We provide an overview of the current state of KT literature and discuss the relevance of KT for health care professionals working in mental health. A systematic search was conducted using MEDLINE, PsycINFO, and CINAHL databases to identify review articles published in journals from 2007 to 2012. We selected articles on the basis of eligibility criteria and then added further articles deemed pertinent to the focus of ourpaper. After removing duplicates, we scanned 214 review articles for relevance and, subsequently, we added 46 articles identified through hand searches of reference lists or from other sources. A total of 61 papers were retained for full review. Qualitative synthesis identified 5 main themes: defining KT and development of KT science; effective KT strategies; factors influencing the effectiveness of KT; KT frameworks and guides; and relevance of KT to health care providers. Despite limitations in existing evidence, the concept and practice of KT holds potential value for mental health care providers. Understanding of, and familiarity with, effective approaches to KT holds the potential to enhance providers' treatment approaches and to promote the use of new knowledge in practice to enhance outcomes.

Using the TIGR gene index databases for biological discovery.

PubMed

Lee, Yuandan; Quackenbush, John

2003-11-01

The TIGR Gene Index web pages provide access to analyses of ESTs and gene sequences for nearly 60 species, as well as a number of resources derived from these. Each species-specific database is presented using a common format with a homepage. A variety of methods exist that allow users to search each species-specific database. Methods implemented currently include nucleotide or protein sequence queries using WU-BLAST, text-based searches using various sequence identifiers, searches by gene, tissue and library name, and searches using functional classes through Gene Ontology assignments. This protocol provides guidance for using the Gene Index Databases to extract information.

Health-care professionals' knowledge, attitudes and behaviours relating to patient capacity to consent to treatment: an integrative review.

PubMed

Lamont, Scott; Jeon, Yun-Hee; Chiarella, Mary

2013-09-01

This integrative review aims to provide a synthesis of research findings of health-care professionals' knowledge, attitudes and behaviours relating to patient capacity to consent to or refuse treatment within the general hospital setting. Search strategies included relevant health databases, hand searching of key journals, 'snowballing' and expert recommendations. The review identified various knowledge gaps and attitudinal dispositions of health-care professionals, which influence their behaviours and decision-making in relation to capacity to consent processes. The findings suggest that there is tension between legal, ethical and professional standards relating to the assessment of capacity and consent within health care. Legislation and policy guidance concerning capacity assessment processes are lacking, and this may contribute to inconsistencies in practice.

Ultra-wide-field imaging in diabetic retinopathy; an overview.

PubMed

Ghasemi Falavarjani, Khalil; Wang, Kang; Khadamy, Joobin; Sadda, Srinivas R

2016-06-01

To present an overview on ultra-wide-field imaging in diabetic retinopathy. A comprehensive search of the pubmed database was performed using the search terms of "ultra-wide-field imaging", "ultra-wide-field fluorescein angiography" and "diabetic retinopathy". The relevant original articles were reviewed. New advances in ultra-wide-field imaging allow for precise measurements of the peripheral retinal lesions. A consistent finding amongst these articles was that ultra-wide-field imaging improved detection of peripheral lesion. There was discordance among the studies, however, on the correlation between peripheral diabetic lesions and diabetic macular edema. Visualization of the peripheral retina using ultra-wide-field imaging improves diagnosis and classification of diabetic retinopathy. Additional studies are needed to better define the association of peripheral diabetic lesions with diabetic macular edema.

Finding research information on the web: how to make the most of Google and other free search tools.

PubMed

Blakeman, Karen

2013-01-01

The Internet and the World Wide Web has had a major impact on the accessibility of research information. The move towards open access and development of institutional repositories has resulted in increasing amounts of information being made available free of charge. Many of these resources are not included in conventional subscription databases and Google is not always the best way to ensure that one is picking up all relevant material on a topic. This article will look at how Google's search engine works, how to use Google more effectively for identifying research information, alternatives to Google and will review some of the specialist tools that have evolved to cope with the diverse forms of information that now exist in electronic form.

The Importance of Cholesterol in Psychopathology: A Review of Recent Contributions.

PubMed

Pereira, Henrique

2017-01-01

The aim of this study was to describe systematically recent studies that show the importance of cholesterol in psychopathology. This study was a review. The following databases were searched for relevant published articles on human studies: MEDLINE, Web of Science, EBSCOhost Academic Search Complete, and Psychology and Behavioral Sciences Collection (papers from January 2012 to March 2016). Eighteen recent papers were selected, and thematic dimensions showing correlations between cholesterol and behavioral and psychopathological variables were depression, suicide, personality, and aggression. This paper demonstrates that recent research corroborates the idea that cholesterol plays an important role in governing behavior and psychopathology in humans. Deepening the studies in this field could be a promising avenue for future research, with implications for treating people with behavior or mental health problems.

Accessing Biomedical Literature in the Current Information Landscape

PubMed Central

Khare, Ritu; Leaman, Robert; Lu, Zhiyong

2015-01-01

i. Summary Biomedical and life sciences literature is unique because of its exponentially increasing volume and interdisciplinary nature. Biomedical literature access is essential for several types of users including biomedical researchers, clinicians, database curators, and bibliometricians. In the past few decades, several online search tools and literature archives, generic as well as biomedicine-specific, have been developed. We present this chapter in the light of three consecutive steps of literature access: searching for citations, retrieving full-text, and viewing the article. The first section presents the current state of practice of biomedical literature access, including an analysis of the search tools most frequently used by the users, including PubMed, Google Scholar, Web of Science, Scopus, and Embase, and a study on biomedical literature archives such as PubMed Central. The next section describes current research and the state-of-the-art systems motivated by the challenges a user faces during query formulation and interpretation of search results. The research solutions are classified into five key areas related to text and data mining, text similarity search, semantic search, query support, relevance ranking, and clustering results. Finally, the last section describes some predicted future trends for improving biomedical literature access, such as searching and reading articles on portable devices, and adoption of the open access policy. PMID:24788259

Memory for found targets interferes with subsequent performance in multiple-target visual search.

PubMed

Cain, Matthew S; Mitroff, Stephen R

2013-10-01

Multiple-target visual searches--when more than 1 target can appear in a given search display--are commonplace in radiology, airport security screening, and the military. Whereas 1 target is often found accurately, additional targets are more likely to be missed in multiple-target searches. To better understand this decrement in 2nd-target detection, here we examined 2 potential forms of interference that can arise from finding a 1st target: interference from the perceptual salience of the 1st target (a now highly relevant distractor in a known location) and interference from a newly created memory representation for the 1st target. Here, we found that removing found targets from the display or making them salient and easily segregated color singletons improved subsequent search accuracy. However, replacing found targets with random distractor items did not improve subsequent search accuracy. Removing and highlighting found targets likely reduced both a target's visual salience and its memory load, whereas replacing a target removed its visual salience but not its representation in memory. Collectively, the current experiments suggest that the working memory load of a found target has a larger effect on subsequent search accuracy than does its perceptual salience. PsycINFO Database Record (c) 2013 APA, all rights reserved.

An Online Resource for Flight Test Safety Planning

NASA Technical Reports Server (NTRS)

Lewis, Greg

2007-01-01

A viewgraph presentation describing an online database for flight test safety techniques is shown. The topics include: 1) Goal; 2) Test Hazard Analyses; 3) Online Database Background; 4) Data Gathering; 5) NTPS Role; 6) Organizations; 7) Hazard Titles; 8) FAR Paragraphs; 9) Maneuver Name; 10) Identified Hazard; 11) Matured Hazard Titles; 12) Loss of Control Causes; 13) Mitigations; 14) Database Now Open to the Public; 15) FAR Reference Search; 16) Record Field Search; 17) Keyword Search; and 18) Results of FAR Reference Search.

Searching Databases without Query-Building Aids: Implications for Dyslexic Users

ERIC Educational Resources Information Center

Berget, Gerd; Sandnes, Frode Eika

2015-01-01

Introduction: Few studies document the information searching behaviour of users with cognitive impairments. This paper therefore addresses the effect of dyslexia on information searching in a database with no tolerance for spelling errors and no query-building aids. The purpose was to identify effective search interface design guidelines that…

Conducting a Web Search.

ERIC Educational Resources Information Center

Miller-Whitehead, Marie

Keyword and text string searches of online library catalogs often provide different results according to library and database used and depending upon how books and journals are indexed. For this reason, online databases such as ERIC often provide tutorials and recommendations for searching their site, such as how to use Boolean search strategies.…

Genetic polymorphisms associated with heart failure: A literature review.

PubMed

Guo, Mengqi; Guo, Guanlun; Ji, Xiaoping

2016-02-01

To review possible associations reported between genetic variants and the risk, therapeutic response and prognosis of heart failure. Electronic databases (PubMed, Web of Science and CNKI) were systematically searched for relevant papers, published between January 1995 and February 2015. Eighty-two articles covering 29 genes and 39 polymorphisms were identified. Genetic association studies of heart failure have been highly controversial. There may be interaction or synergism of several genetic variants that together result in the ultimate pathological phenotype for heart failure. © The Author(s) 2016.

Methodology for research I.

PubMed

Garg, Rakesh

2016-09-01

The conduct of research requires a systematic approach involving diligent planning and its execution as planned. It comprises various essential predefined components such as aims, population, conduct/technique, outcome and statistical considerations. These need to be objective, reliable and in a repeatable format. Hence, the understanding of the basic aspects of methodology is essential for any researcher. This is a narrative review and focuses on various aspects of the methodology for conduct of a clinical research. The relevant keywords were used for literature search from various databases and from bibliographies of the articles.

BEAUTY-X: enhanced BLAST searches for DNA queries.

PubMed

Worley, K C; Culpepper, P; Wiese, B A; Smith, R F

1998-01-01

BEAUTY (BLAST Enhanced Alignment Utility) is an enhanced version of the BLAST database search tool that facilitates identification of the functions of matched sequences. Three recent improvements to the BEAUTY program described here make the enhanced output (1) available for DNA queries, (2) available for searches of any protein database, and (3) more up-to-date, with periodic updates of the domain information. BEAUTY searches of the NCBI and EMBL non-redundant protein sequence databases are available from the BCM Search Launcher Web pages (http://gc.bcm.tmc. edu:8088/search-launcher/launcher.html). BEAUTY Post-Processing of submitted search results is available using the BCM Search Launcher Batch Client (version 2.6) (ftp://gc.bcm.tmc. edu/pub/software/search-launcher/). Example figures are available at http://dot.bcm.tmc. edu:9331/papers/beautypp.html (kworley,culpep)@bcm.tmc.edu

Database technology and the management of multimedia data in the Mirror project

NASA Astrophysics Data System (ADS)

de Vries, Arjen P.; Blanken, H. M.

1998-10-01

Multimedia digital libraries require an open distributed architecture instead of a monolithic database system. In the Mirror project, we use the Monet extensible database kernel to manage different representation of multimedia objects. To maintain independence between content, meta-data, and the creation of meta-data, we allow distribution of data and operations using CORBA. This open architecture introduces new problems for data access. From an end user's perspective, the problem is how to search the available representations to fulfill an actual information need; the conceptual gap between human perceptual processes and the meta-data is too large. From a system's perspective, several representations of the data may semantically overlap or be irrelevant. We address these problems with an iterative query process and active user participating through relevance feedback. A retrieval model based on inference networks assists the user with query formulation. The integration of this model into the database design has two advantages. First, the user can query both the logical and the content structure of multimedia objects. Second, the use of different data models in the logical and the physical database design provides data independence and allows algebraic query optimization. We illustrate query processing with a music retrieval application.

Systematic Review of Ossicular Chain Anatomy: Strategic Planning for Development of Novel Middle Ear Prostheses.

PubMed

Kamrava, Brandon; Roehm, Pamela C

2017-08-01

Objective To systematically review the anatomy of the ossicular chain. Data Sources Google Scholar, PubMed, and otologic textbooks. Review Methods A systematic literature search was performed on January 26, 2015. Search terms used to discover articles consisted of combinations of 2 keywords. One keyword from both groups was used: [ ossicular, ossicle, malleus, incus, stapes] and [ morphology, morphometric, anatomy, variation, physiology], yielding more than 50,000 hits. Articles were then screened by title and abstract if they did not contain information relevant to human ossicular chain anatomy. In addition to this search, references of selected articles were studied as well as suggested relevant articles from publication databases. Standard otologic textbooks were screened using the search criteria. Results Thirty-three sources were selected for use in this review. From these studies, data on the composition, physiology, morphology, and morphometrics were acquired. In addition, any correlations or lack of correlations between features of the ossicular chain and other features of the ossicular chain or patient were noted, with bilateral symmetry between ossicles being the only important correlation reported. Conclusion There was significant variation in all dimensions of each ossicle between individuals, given that degree of variation, custom fitting, or custom manufacturing of prostheses for each patient could optimize prosthesis fit. From published data, an accurate 3-dimensional model of the malleus, incus, and stapes can be created, which can then be further modified for each patient's individual anatomy.

Proton Pump Inhibitors: Risk for Myopathy?

PubMed

Colmenares, Evan W; Pappas, Ashley L

2017-01-01

The purpose of this article is to describe the relationship between proton pump inhibitors (PPIs) and symptoms of myopathy based on case reports. A literature search was conducted in PubMed (1946 to June 2016) using MeSH terms proton pump inhibitors, omeprazole, esomeprazole, lansoprazole, dexlansoprazole, rabeprazole, pantoprazole, and muscular diseases. Additionally, a search was conducted in ToxNet and EMBASE using similar search criteria. The resulting articles were scanned to assess relevance to the review. Bibliographies of all relevant articles were evaluated for additional sources; 26 articles resulted from the search of PubMed, ToxNet, and EMBASE; articles that involved medications typically considered to have myalgia-like side effects (eg, statins), or included patients who presented with a confounding disease state (eg, Guillain-Barré) were excluded. In total, 11 case reports as well as a review of an adverse event reporting database that included 292 cases were evaluated. Association of PPI use and myopathy symptoms does not have a clear etiology. Overall, the available published data do not show a high risk of myopathy with PPI use but should be considered if a patient presents with myopathy symptoms and concurrent PPI use. A limited body of published data suggests that PPI use has been associated with myopathy-like symptoms without long-term effects following discontinuation. Although myopathy is a rare adverse effect observed with PPIs, it can be a serious side effect to be considered when starting a patient on acid suppression therapy.

The efficacy of hydrogel dressings as a first aid measure for burn wound management in the pre-hospital setting: a systematic review of the literature.

PubMed

Goodwin, Nicholas S; Spinks, Anneliese; Wasiak, Jason

2016-08-01

The aim of this systematic review was to determine the supporting evidence for the clinical use of hydrogel dressings as a first aid measure for burn wound management in the pre-hospital setting. Two authors searched three databases (Ovid Medline, Ovid Embase and The Cochrane Library) for relevant English language articles published through September 2014. Reference lists, conference proceedings and non-indexed academic journals were manually searched. A separate search was conducted using the Internet search engine Google to source additional studies from burns advisory agencies, first aid bodies, military institutions, manufacturer and paramedic websites. Two authors independently assessed study eligibility and relevance of non-traditional data forms for inclusion. Studies were independently assessed and included if Hydrogel-based burn dressings (HBD) were examined in first aid practices in the pre-hospital setting. A total of 129 studies were considered for inclusion, of which no pre-hospital studies were identified. The review highlights that current use of HBD in the pre-hospital setting appears to be driven by sources of information that do not reflect the paramedic environment. We recommend researchers in the pre-hospital settings undertake clinical trials in this field. More so, the review supports the need for expert consensus to identify key demographic, clinical and injury outcomes for clinicians and researchers undertaking further research into the use of dressings as a first aid measure. © 2015 Medicalhelplines.com Inc and John Wiley & Sons Ltd.