Abstract‐to‐publication ratio for papers presented at scientific meetings: a quality marker for UK emergency medicine research

PubMed Central

Macmillan, Craig D; Moore, Anthony K; Cook, Ronald J; Pedley, David K

2007-01-01

Objectives To determine the publication rate of abstracts presented by UK emergency physicians at major emergency medicine meetings, and to identify the site of publication of papers. Method All abstracts presented to the annual scientific meetings of both the British Association of Emergency Medicine and the Faculty of Accident and Emergency Medicine between 2001 and 2002 were identified retrospectively from conference programmes. To identify whether the work relating to the abstract had been published in a peer‐reviewed journal, the Medline database (Ovid interface) was searched using the first and last authors as well as key words from the abstract. Results Of the 404 abstracts identified, 124 (30%) had been published as full articles. For abstracts presented in the oral sessions, 83 (57%) resulted in publication. A range of journals accepted papers for publication. Conclusion The abstract‐to‐publication ratio for UK emergency medicine is lower than for other specialties, but broadly similar to emergency medicine in the US and Australia. PMID:17513542

An analysis of abstracts presented to the College on Problems of Drug Dependence meeting and subsequent publication in peer review journals

PubMed Central

Valderrama-Zurián, Juan Carlos; Bolaños-Pizarro, Máxima; Bueno-Cañigral, Francisco Jesús; Álvarez, F Javier; Ontalba-Ruipérez, José Antonio; Aleixandre-Benavent, Rafael

2009-01-01

Background Subsequent publication rate of abstracts presented at meetings is seen as an indicator of the interest and quality of the meeting. We have analyzed characteristics and rate publication in peer-reviewed journals derived from oral communications and posters presented at the 1999 College on Problems of Drug Dependence (CPDD) meeting. Methods All 689 abstracts presented at the 1999 CPDD meeting were reviewed. In order to find the existence of publications derived from abstracts presented at that meeting, a set of bibliographical searches in the database Medline was developed in July 2006. Information was gathered concerning the abstracts, articles and journals in which they were published. Results 254 out of 689 abstracts (36.9%) gave rise to at least one publication. The oral communications had a greater likelihood of being published than did the posters (OR = 2.53, 95% CI 1.80-3.55). The average time lapse to publication of an article was 672.97 days. The number of authors per work in the subsequent publications was 4.55. The articles were published in a total of 84 journals, of which eight were indexed with the subject term Substance-Related Disorders. Psychopharmacology (37 articles, 14.5%) was the journal that published the greatest number of articles subsequent to the abstracts presented at the 1999 CPDD meeting. Conclusion One out of every three abstracts presented to the 1999 CPDD meeting were later published in peer-reviewed journals indexed in Medline. The subsequent publication of the abstracts presented in the CPDD meetings should be actively encouraged, as this maximizes the dissemination of the scientific research and therefore the investment. PMID:19889211

Interactive bibliographical database on color

NASA Astrophysics Data System (ADS)

Caivano, Jose L.

2002-06-01

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

Effectiveness of open versus endovascular abdominal aortic aneurysm repair in population settings: A systematic review of statewide databases.

PubMed

Williams, Christopher R; Brooke, Benjamin S

2017-10-01

Patient outcomes after open abdominal aortic aneurysm and endovascular aortic aneurysm repair have been widely reported from several large, randomized, controlled trials. It is not clear whether these trial outcomes are representative of abdominal aortic aneurysm repair procedures performed in real-world hospital settings across the United States. This study was designed to evaluate population-based outcomes after endovascular aortic aneurysm repair versus open abdominal aortic aneurysm repair using statewide inpatient databases and examine how they have helped improve our understanding of abdominal aortic aneurysm repair. A systematic search of MEDLINE, EMBASE, and CINAHL databases was performed to identify articles comparing endovascular aortic aneurysm repair and open abdominal aortic aneurysm repair using data from statewide inpatient databases. This search was limited to studies published in the English language after 1990, and abstracts were screened and abstracted by 2 authors. Our search yielded 17 studies published between 2004 and 2016 that used data from 29 different statewide inpatient databases to compare endovascular aortic aneurysm repair versus open abdominal aortic aneurysm repair. These studies support the randomized, controlled trial results, including a lower mortality associated with endovascular aortic aneurysm repair extended from the perioperative period up to 3 years after operation, as well as a higher complication rate after endovascular aortic aneurysm repair. The evidence from statewide inpatient database analyses has also elucidated trends in procedure volume, patient case mix, volume-outcome relationships, and health care disparities associated with endovascular aortic aneurysm repair versus open abdominal aortic aneurysm repair. Population analyses of endovascular aortic aneurysm repair and open abdominal aortic aneurysm repair using statewide inpatient databases have confirmed short- and long-term mortality outcomes obtained from large, randomized, controlled trials. Moreover, these analyses have allowed us to assess the effect of endovascular aortic aneurysm repair adoption on population outcomes and patient case mix over time. Published by Elsevier Inc.

Library information services.

NASA Astrophysics Data System (ADS)

Michold, U.; Cummins, M.; Watson, J. M.; Holmquist, J.; Shobbrook, R.

Contents: library catalogs and holdings; indexing and abstract services; preprint services; electronic journals and newsletters; alerting services; commercial databases; informal networking; use of a thesaurus for on-line searching. An extensive list of access pointers for library catalogs and services, electronic newsletters, and publishers and bookshops is enclosed.

Abstract to publication ratio for papers presented at scientific meetings: how does emergency medicine compare?

PubMed

Walby, A; Kelly, A M; Georgakas, C

2001-12-01

The aims of the present study were to determine the publication rate of abstracts presented by Australasian emergency physicians at major emergency medicine meetings and to identify the site of publication of papers. All free paper abstracts presented (oral and poster) by Australasian emergency physicians and trainees at five Australasian College for Emergency Medicine/Australasian Society for Emergency Medicine and International Conference on Emergency Medicine meetings between 1995 and 1998 were identified retrospectively from conference programmes. In order to determine whether or not the abstract had been published, the PubMed database (http://www4.ncbi.nlm.nih.gov/PubMed/) was searched using the presenter's name and key words from the abstract. In addition, a hand search of the non-abstracted journal Emergency Medicine was conducted. Of the 207 free paper abstracts identified, 73 (35%) had been published as full articles. Papers were published in a variety of journals; however, Emergency Medicine accounted for almost half the published papers. The mean time between presentation and publication was 12.6 months (median 11 months). The abstract to publication rate for papers presented by Australasian emergency physicians and trainees at Australasian College for Emergency Medicine/Australasian Society for Emergency Medicine and International Conference on Emergency Medicine meetings is 35%, which is lower than that reported by some other established specialities, but comparable to rates reported for US-based national and international emergency medicine meetings. Future research should look at barriers to the publication of findings and ways to assist the publication process.

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.

Techniques of Photometry and Astrometry with APASS, Gaia, and Pan-STARRs Results (Abstract)

NASA Astrophysics Data System (ADS)

Green, W.

2017-12-01

(Abstract only) The databases with the APASS DR9, Gaia DR1, and the Pan-STARRs 3pi DR1 data releases are publicly available for use. There is a bit of data-mining involved to download and manage these reference stars. This paper discusses the use of these databases to acquire accurate photometric references as well as techniques for improving results. Images are prepared in the usual way: zero, dark, flat-fields, and WCS solutions with Astrometry.net. Images are then processed with Sextractor to produce an ASCII table of identifying photometric features. The database manages photometics catalogs and images converted to ASCII tables. Scripts convert the files into SQL and assimilate them into database tables. Using SQL techniques, each image star is merged with reference data to produce publishable results. The VYSOS has over 13,000 images of the ONC5 field to process with roughly 100 total fields in the campaign. This paper provides the overview for this daunting task.

Fate of abstracts presented at the annual scientific meeting of the Undersea and Hyperbaric Medical Society.

PubMed

Uzun, Günalp; Mutluoğlu, Mesut; Bakir, Alev; Senocak, Mustafa S

2013-01-01

The full-text publication of abstracts presented at any given scientific meeting in peer-reviewed journals is accepted as a measure of scientific quality of that particular meeting. The aim of this study is to determine the full-text publication rate of abstracts presented at the 2005 Scientific Meeting of the Undersea and Hyperbaric Medical Society (UHMS). We identified the scientific abstracts presented at the 2005 UHMS meeting and searched the PubMed database (June 2005 to July 2010) for their corresponding full-text publication. We recorded the following parameters for each of the abstracts: number of authors, number of centers involved in the study, statistical methods used, country of origin of the study, study type, and subject of the abstract. We recorded the time to publication and the title of the journal if the abstract had been published in a peer-reviewed journal. Overall, we identified 187 abstracts presented at the 2005 UHMS meeting. Two of the abstracts were excluded from the study because they had been retracted from the meeting and six more because they had been already published as full-text articles at the time the meeting was held. Of the 179 abstracts, 62 (34.6%) were published as full-text articles within the succeeding five years. The mean (+/- SD) time to publication was 18.5 (+/- 13.6) months. Multivariate analysis with logistic regression identified "country of origin" and "the subject of the abstract" as independent predictors of full-text publication. We found that only one-third of the abstracts presented at the 2005 UHMS meeting were published as full-text articles within the succeeding five years. Although this rate is consistent with similar studies from various disciplines, further research is needed to identify the specific barriers to full-text publication of abstracts in the field of underwater and hyperbaric medicine.

Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD).

PubMed

Jiang, Xiangying; Ringwald, Martin; Blake, Judith; Shatkay, Hagit

2017-01-01

The Gene Expression Database (GXD) is a comprehensive online database within the Mouse Genome Informatics resource, aiming to provide available information about endogenous gene expression during mouse development. The information stems primarily from many thousands of biomedical publications that database curators must go through and read. Given the very large number of biomedical papers published each year, automatic document classification plays an important role in biomedical research. Specifically, an effective and efficient document classifier is needed for supporting the GXD annotation workflow. We present here an effective yet relatively simple classification scheme, which uses readily available tools while employing feature selection, aiming to assist curators in identifying publications relevant to GXD. We examine the performance of our method over a large manually curated dataset, consisting of more than 25 000 PubMed abstracts, of which about half are curated as relevant to GXD while the other half as irrelevant to GXD. In addition to text from title-and-abstract, we also consider image captions, an important information source that we integrate into our method. We apply a captions-based classifier to a subset of about 3300 documents, for which the full text of the curated articles is available. The results demonstrate that our proposed approach is robust and effectively addresses the GXD document classification. Moreover, using information obtained from image captions clearly improves performance, compared to title and abstract alone, affirming the utility of image captions as a substantial evidence source for automatically determining the relevance of biomedical publications to a specific subject area. www.informatics.jax.org. © The Author(s) 2017. Published by Oxford University Press.

Incomplete evidence: the inadequacy of databases in tracing published adverse drug reactions in clinical trials

PubMed Central

Derry, Sheena; Kong Loke, Yoon; Aronson, Jeffrey K

2001-01-01

Background We would expect information on adverse drug reactions in randomised clinical trials to be easily retrievable from specific searches of electronic databases. However, complete retrieval of such information may not be straightforward, for two reasons. First, not all clinical drug trials provide data on the frequency of adverse effects. Secondly, not all electronic records of trials include terms in the abstract or indexing fields that enable us to select those with adverse effects data. We have determined how often automated search methods, using indexing terms and/or textwords in the title or abstract, would fail to retrieve trials with adverse effects data. Methods We used a sample set of 107 trials known to report frequencies of adverse drug effects, and measured the proportion that (i) were not assigned the appropriate adverse effects indexing terms in the electronic databases, and (ii) did not contain identifiable adverse effects textwords in the title or abstract. Results Of the 81 trials with records on both MEDLINE and EMBASE, 25 were not indexed for adverse effects in either database. Twenty-six trials were indexed in one database but not the other. Only 66 of the 107 trials reporting adverse effects data mentioned this in the abstract or title of the paper. Simultaneous use of textword and indexing terms retrieved only 82/107 (77%) papers. Conclusions Specific search strategies based on adverse effects textwords and indexing terms will fail to identify nearly a quarter of trials that report on the rate of drug adverse effects. PMID:11591220

Discrepancies and rates of publication in orthopaedic sports medicine abstracts.

PubMed

Kleweno, Conor P; Bryant, Whitney K; Jacir, Albert M; Levine, William N; Ahmad, Christopher S

2008-10-01

Presentations of clinically relevant data at AOSSM national meetings are presented yearly and may influence clinical decision making. The incidence of presentations that do not subsequently get published is high, and the numbers of major and minor inconsistencies, once published, are also high. Systematic review. A database was created of all abstracts presented at AOSSM meetings from 1999 to 2001 from official program books. To assess whether each abstract had been followed by publication in a peer-reviewed journal, a PubMed search was conducted to include a 5-year follow-up for each conference. Minor inconsistencies included differences in title, authors, presentation of all outcomes, and authors' interpretation of data. Major inconsistencies included discrepancies in study objective and/or hypothesis, study design, primary and secondary outcome measures, sample size, statistical analysis, results, and standard deviations/confidence intervals. Overall, 98 of the 165 abstracts presented at AOSSM national meetings from 1999 to 2001 were published in a peer-reviewed journal within 5 years, a publication rate of 59.4%. The median time to publication for all articles was 21 (range, 1-60) months. The majority of articles (61) were published in the American Journal of Sports Medicine (62.2%). The median number of major and minor inconsistencies from abstract to publication was 1 (range, 0-5) and 1 (range, 0-4), respectively. Sixty-two of the 98 published abstracts (63%) had at least 1 major inconsistency, while 79 (81%) had at least 1 minor inconsistency. In 5 manuscripts (5%), the authors' interpretation of the data had changed, and in 2 (2%), the change essentially invalidated the abstract. A large number of scientific presentations do not get published in a peer-reviewed journal. In addition, those published have a significant number of changes that, in a small percentage of cases, alter the validity of the original presentation. Orthopaedic surgeons and other attendees as well as nonattendees who reference conference abstracts need to exercise good judgment when considering the implications of oral presentations of unpublished materials. When reviewing meeting presentation abstracts, readers should remember that the material being presented is often not in its definitive or ultimate form.

Nato-Pco Database

NASA Astrophysics Data System (ADS)

Wtv Gmbh

This new CD-ROM is a reference database. It covers almost twenty years of non-military scientific/technical meetings and publications sponsored by the NATO Science Committee. It contains full references (with keywords and/or abstracts) to more than 30,000 contributions from scientists all over the world and is published in more than 1,000 volumes. With the easy-to-follow menu options of the retrieval software, access to the data is simple and fast. Updates are planned on a yearly basis.

Seventy Years of RN Effectiveness: A Database Development Project to Inform Best Practice.

PubMed

Lulat, Zainab; Blain-McLeod, Julie; Grinspun, Doris; Penney, Tasha; Harripaul-Yhap, Anastasia; Rey, Michelle

2018-03-23

The appropriate nursing staff mix is imperative to the provision of quality care. Nurse staffing levels and staff mix vary from country to country, as well as between care settings. Understanding how staffing skill mix impacts patient, organizational, and financial outcomes is critical in order to allow policymakers and clinicians to make evidence-informed staffing decisions. This paper reports on the methodology for creation of an electronic database of studies exploring the effectiveness of Registered Nurses (RNs) on clinical and patient outcomes, organizational and nurse outcomes, and financial outcomes. Comprehensive literature searches were conducted in four electronic databases. Inclusion criteria for the database included studies published from 1946 to 2016, peer-reviewed international literature, and studies focused on RNs in all health-care disciplines, settings, and sectors. Masters-prepared nurse researchers conducted title and abstract screening and relevance review to determine eligibility of studies for the database. High-level analysis was conducted to determine key outcomes and the frequency at which they appeared within the database. Of the initial 90,352 records, a total of 626 abstracts were included within the database. Studies were organized into three groups corresponding to clinical and patient outcomes, organizational and nurse-related outcomes, and financial outcomes. Organizational and nurse-related outcomes represented the largest category in the database with 282 studies, followed by clinical and patient outcomes with 244 studies, and lastly financial outcomes, which included 124 studies. The comprehensive database of evidence for RN effectiveness is freely available at https://rnao.ca/bpg/initiatives/RNEffectiveness. The database will serve as a resource for the Registered Nurses' Association of Ontario, as well as a tool for researchers, clinicians, and policymakers for making evidence-informed staffing decisions. © 2018 The Authors. Worldviews on Evidence-Based Nursing published by Wiley Periodicals, Inc. on behalf of Sigma Theta Tau International The Honor Society of Nursing.

Finding Qualitative Research Evidence for Health Technology Assessment.

PubMed

DeJean, Deirdre; Giacomini, Mita; Simeonov, Dorina; Smith, Andrea

2016-08-01

Health technology assessment (HTA) agencies increasingly use reviews of qualitative research as evidence for evaluating social, experiential, and ethical aspects of health technologies. We systematically searched three bibliographic databases (MEDLINE, CINAHL, and Social Science Citation Index [SSCI]) using published search filters or "hedges" and our hybrid filter to identify qualitative research studies pertaining to chronic obstructive pulmonary disease and early breast cancer. The search filters were compared in terms of sensitivity, specificity, and precision. Our screening by title and abstract revealed that qualitative research constituted only slightly more than 1% of all published research on each health topic. The performance of the published search filters varied greatly across topics and databases. Compared with existing search filters, our hybrid filter demonstrated a consistently high sensitivity across databases and topics, and minimized the resource-intensive process of sifting through false positives. We identify opportunities for qualitative health researchers to improve the uptake of qualitative research into evidence-informed policy making. © The Author(s) 2016.

[Gone with the wind or... Fate of scientific articles presented at large anesthesia congresses--an update].

PubMed

Meininger, D; Bück, M; Bohlmann, S; Weber, C F; Strouhal, U; Ihlow, K; Zacharowski, K; Byhahn, C

2011-02-01

The goal of the present study was to evaluate the publication rate of abstracts presented during the German Anesthesia Congress (Deutscher Anästhesiecongress, DAC) and the meeting of the European Society of Anesthesiologists (ESA) in the years 2000 and 2005 in Medline listed journals (http://www.ncbi.nlm.nih.gov/pubmed). In addition, the respective impact factors of the journals in which the articles were published were evaluated (http://www.isiknowledge.com). All abstracts of free papers and posters presented at the DAC and ESA from the years 2000 and 2005 were included into the study. The presence of authors and the topics of abstracts in the literature were analyzed by a Medline based inquiry over a time period of 5 years. The search was based on the last name and initials of authors and when these could not be identified in Medline the search was extended by keywords of relevant topics of the abstract. Umlauts "ä/ö/ü" were replaced by "ae/oe/ue" and "ß" was replaced by "ss". Only original papers were included in this analysis. Once an original paper was found the impact factor of the journal in that year was identified. A total of 465 abstracts from the DAC 2000, 378 abstracts from the DAC 2005, 644 abstracts from the ESA 2000 and 720 abstracts from the ESA 2005 were included. Of the abstracts from the DAC 2000, 183 (39%) were published in Medline listed journals, 179 (47%) from DAC 2005, 218 (34%) from ESA 2000 and 233 (32%) from ESA 2005. The ESA abstracts were published in English more often than the DAC abstracts (ESA 2000: 95%; ESA 2005: 95%; DAC 2000: 78%; DAC 2005: 86%). While the publication rate after the ESA remained nearly unchanged between 2000 and 2005, the publication rate after the DAC increased by about 7%. The average impact factors of the publications were 1.777 (DAC 2000), 2.836 (DAC 2005), 1.825 (ESA 2000) and 2.36 (ESA 2005). Independent of the congress (DAC or ESA) where the abstract was presented, most articles were published in the journal Anesthesia & Analgesia. In the year 2005 more abstracts of the DAC were published in Medline listed papers than in 2000. When comparing the number of abstracts published in Medline listed journals, more abstracts of the DAC were published compared to abstracts of the ESA. The increase in papers written in English after abstract presentation on the DAC is mostly due to the wider readership which can be reached with manuscripts in the English language. Besides a larger readership, English journals often also have a higher ranked impact factor. This analysis does not claim to be a complete registration of all published abstracts due to the limitation on Medline listed journals and publications in other journals were not rated. Medline was selected because of the widespread and international use of this database.

Comparison of published and unpublished phase I clinical cancer trials: an analysis of the CliniclTrials.gov database.

PubMed

Shepshelovich, D; Goldvaser, H; Wang, L; Abdul Razak, A R

2017-12-13

Introduction The role of phase I cancer trials is constantly evolving and they are increasingly being used in 'go/no' decisions in drug development. As a result, there is a growing need to ensure trials are published when completed. There are limited data on the publication rate and the factors associated with publication in phase I trials. Methods The ClinicalTrials.gov database was searched for completed adult phase I cancer trials with reported results. PubMed was searched for matching publications published prior to April 1, 2017. Logistic regression was used to identify factors associated with unpublished trials. Linear regression was used to explore factors associated with time lag from study database lock to publication for published trials. Results The study cohort included 319 trials. 95 (30%) trials had no matching publication. Thirty (9%) trials were not published in abstract form as well. On multivariable analysis, the most significant factor associated with unpublished trials was industry funding (odds ratio 3.3, 95% confidence interval 1.7-6.6, p=0.019). For published trials, time lag between database lock and publication was longer by 10.9 months (standard error 3.6, p<0.001) for industry funded trials compared with medical center funded trials. Conclusions Timely publishing of early cancer clinical trials results remains unsatisfactory. Industry funded phase I cancer trials were more likely to remain unpublished, and were associated with a longer time lag from database lock to publication. Policies that promote transparency and data sharing in clinical trial research might improve accountability among industry and investigators and improve timely results publication.

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

PubMed Central

Livingston, Kara A.; Chung, Mei; Sawicki, Caleigh M.; Lyle, Barbara J.; Wang, Ding Ding; Roberts, Susan B.; McKeown, Nicola M.

2016-01-01

Background Dietary fiber is a broad category of compounds historically defined as partially or completely indigestible plant-based carbohydrates and lignin with, more recently, the additional criteria that fibers incorporated into foods as additives should demonstrate functional human health outcomes to receive a fiber classification. Thousands of research studies have been published examining fibers and health outcomes. Objectives (1) Develop a database listing studies testing fiber and physiological health outcomes identified by experts at the Ninth Vahouny Conference; (2) Use evidence mapping methodology to summarize this body of literature. This paper summarizes the rationale, methodology, and resulting database. The database will help both scientists and policy-makers to evaluate evidence linking specific fibers with physiological health outcomes, and identify missing information. Methods To build this database, we conducted a systematic literature search for human intervention studies published in English from 1946 to May 2015. Our search strategy included a broad definition of fiber search terms, as well as search terms for nine physiological health outcomes identified at the Ninth Vahouny Fiber Symposium. Abstracts were screened using a priori defined eligibility criteria and a low threshold for inclusion to minimize the likelihood of rejecting articles of interest. Publications then were reviewed in full text, applying additional a priori defined exclusion criteria. The database was built and published on the Systematic Review Data Repository (SRDR™), a web-based, publicly available application. Conclusions A fiber database was created. This resource will reduce the unnecessary replication of effort in conducting systematic reviews by serving as both a central database archiving PICO (population, intervention, comparator, outcome) data on published studies and as a searchable tool through which this data can be extracted and updated. PMID:27348733

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

PubMed Central

Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B

2018-01-01

Abstract The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. PMID:29040670

PASCAL Data Base: File Description and On Line Access on ESA/IRS.

ERIC Educational Resources Information Center

Pelissier, Denise

This report describes the PASCAL database, a machine readable version of the French abstract journal Bulletin Signaletique, which allows use of the file for (1) batch and online retrieval of information, (2) selective dissemination of information, and (3) publishing of the 50 sections of Bulletin Signaletique. The system, which covers nine…

Does the CONSORT checklist for abstracts improve the quality of reports of randomized controlled trials on clinical pathways?

PubMed

Cui, Qi; Tian, Jinhui; Song, Xuping; Yang, Kehu

2014-12-01

The extension of the Consolidated Standards of Reporting Trials (CONSORT) statement provides reporting guidelines to improve the reporting quality of randomized controlled trials (RCTs). This present study was aim to assess the reporting quality of abstracts of RCTs on clinical pathway. Eight databases were searched from inception to November 2012 to identify RCTs. We extracted basic information and CONSORT items from abstracts. Each abstract was assessed independently by two reviewers. Statistical analyses were performed with SPSS 13.0. Level of significance was set at P < 0.05. 328 abstracts were included. 300 (91.5%) were published in Chinese, of which 292 were published on high impact factor journals. 28 English abstracts were all published on Science Citation Index (SCI) journals. (1) Intervention, objective and outcome were almost fully reported in all abstracts, while recruitment and funding were never reported. (2) There are nine items (P < 0.05) in Chinese that were of low quality compared with in English. There was statistically difference on total score between Chinese and English abstracts (P < 0.00001). (3) There was no difference in any items between high and low impact factor journal in China. (4) In SCI journals, there were significant changes in reporting for three items trial design (P = 0.026), harms (P = 0.039) and trial registration (P = 0.019) in different periods (pre- and post-CONSORT), but only the numbers of randomized (P = 0.003) changed in Chinese abstracts. The reporting quality of abstracts of RCTs on clinical pathway still should be improved. After the publication of CONSORT for abstracts guideline, the RCT abstracts reporting quality were improvement to some extent. The abstracts in Chinese journals showed non-adherence to the CONSORT for abstracts guidelines. © 2014 John Wiley & Sons, Ltd.

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

PubMed Central

Morgan, Steve; Hanley, Gillian; Greyson, Devon

2009-01-01

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

Korean association of medical journal editors at the forefront of improving the quality and indexing chances of its member journals.

PubMed

Suh, Chang-Ok; Oh, Se Jeong; Hong, Sung-Tae

2013-05-01

The article overviews some achievements and problems of Korean medical journals published in the highly competitive journal environment. Activities of Korean Association of Medical Journal Editors (KAMJE) are viewed as instrumental for improving the quality of Korean articles, indexing large number of local journals in prestigious bibliographic databases and launching new abstract and citation tracking databases or platforms (eg KoreaMed, KoreaMed Synapse, the Western Pacific Regional Index Medicus [WPRIM]). KAMJE encourages its member journals to upgrade science editing standards and to legitimately increase citation rates, primarily by publishing more great articles with global influence. Experience gained by KAMJE and problems faced by Korean editors may have global implications.

Publication rate of abstracts presented at the emergency medicine congresses held by the European Society for Emergency Medicine (EUSEM) in 2011 and 2012.

PubMed

Kalkan, Asim; Kose, Ozkan; Bilir, Ozlem; Ersunan, Gokhan; Ozel, Deniz; Guler, Ferhat

2015-09-01

The purpose of this study was to assess the publication rate of the abstracts presented at the 6th Mediterranean Emergency Medicine Congress, 2011 and the 7th European Congress on Emergency Medicine, 2012. All abstracts, both posters and oral presentations, from the international emergency medicine congresses held by the European Society for Emergency Medicine (EUSEM) in 2011 and 2012 were identified. To establish whether these abstracts were subsequently published in peer-reviewed medical journals, the names of all the authors and the title of the abstracts were searched for in the databases of Clinical Key/Elsevier, EBSCO Discovery Service, MD Consult, Science Direct, Scopus, EMBASE, Medscape, Google Scholar and local ULAKBIM. The year of publication, consistency of author names and titles, the type of study, the journals in which papers were published and countries from which reports were submitted were all recorded. A total of 1721 abstracts were examined; 626 from 2011 (307 oral presentations and 319 posters) and 1095 from 2012 (154 oral presentations and 941 posters). Of all abstracts in 2011, 172 (27.5%) and of all abstracts in 2012, 265 (24.2%) were subsequently published as full-text reports in peer-reviewed journals. Of the 172 papers published in 2011, 152 (88.4%) were accepted by Science Citation Index (SCI) and/or SCI Expanded (SCI-E) journals and 155 (58.5%) of 265 papers were accepted by SCI and/or SCI-E journals in 2012 (p=0.0001). The publication rate of abstracts submitted to international emergency medicine congresses held by EUSEM over those 2 years was low compared with that of abstracts presented in other emergency medicine congresses. Presenters should be encouraged to send their studies to peer-reviewed journals. During the selection process by the scientific panel, constructive critics should be notified to the presenters instead of simply accepting or rejecting the studies that submitted to the congress, which may increase the subsequent publication rate. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Assessment of the quality of reporting in abstracts of systematic reviews with meta-analyses in periodontology and implant dentistry.

PubMed

Faggion, C M; Liu, J; Huda, F; Atieh, M

2014-04-01

Proper scientific reporting is necessary to ensure the correct interpretation of study results by readers. The main objective of this study was to assess the quality of reporting in abstracts of systematic reviews (SRs) with meta-analyses in periodontology and implant dentistry. Differences in reporting of abstracts in Cochrane and paper-based reviews were also assessed. The PubMed electronic database and the Cochrane database for SRs were searched on November 11, 2012, independently and in duplicate, for SRs with meta-analyses related to interventions in periodontology and implant dentistry. Assessment of the quality of reporting was performed independently and in duplicate, taking into account items related to the effect direction, numerical estimates of effect size, measures of precision, probability and consistency. We initially screened 433 papers and included 146 (127 paper-based and 19 Cochrane reviews, respectively). The direction of evidence was reported in two-thirds of the abstracts while strength of evidence and measure of precision (i.e., confidence interval) were reported in less than half the selected abstracts. Measures of consistency such as I(2) statistics were reported in only 5% of the selected sample of abstracts. Cochrane abstracts reported the limitations of evidence and precision better than paper-based ones. Two items ("meta-analysis" in title and abstract, respectively), were nevertheless better reported in paper-based abstracts. Abstracts of SRs with meta-analyses in periodontology and implant dentistry currently have no uniform standard of reporting, which may hinder readers' understanding of study outcomes. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

A possible extension to the RInChI as a means of providing machine readable process data.

PubMed

Jacob, Philipp-Maximilian; Lan, Tian; Goodman, Jonathan M; Lapkin, Alexei A

2017-04-11

The algorithmic, large-scale use and analysis of reaction databases such as Reaxys is currently hindered by the absence of widely adopted standards for publishing reaction data in machine readable formats. Crucial data such as yields of all products or stoichiometry are frequently not explicitly stated in the published papers and, hence, not reported in the database entry for those reactions, limiting their usefulness for algorithmic analysis. This paper presents a possible extension to the IUPAC RInChI standard via an auxiliary layer, termed ProcAuxInfo, which is a standardised, extensible form in which to report certain key reaction parameters such as declaration of all products and reactants as well as auxiliaries known in the reaction, reaction stoichiometry, amounts of substances used, conversion, yield and operating conditions. The standard is demonstrated via creation of the RInChI including the ProcAuxInfo layer based on three published reactions and demonstrates accurate data recoverability via reverse translation of the created strings. Implementation of this or another method of reporting process data by the publishing community would ensure that databases, such as Reaxys, would be able to abstract crucial data for big data analysis of their contents.

Development and Uses of Offline and Web-Searchable Metabolism Databases - The Case of Benzo[a]pyrene.

PubMed

Rendic, Slobodan P; Guengerich, Frederick P

2018-01-01

The present work describes development of offline and web-searchable metabolism databases for drugs, other chemicals, and physiological compounds using human and model species, prompted by the large amount of data published after year 1990. The intent was to provide a rapid and accurate approach to published data to be applied both in science and to assist therapy. Searches for the data were done using the Pub Med database, accessing the Medline database of references and abstracts. In addition, data presented at scientific conferences (e.g., ISSX conferences) are included covering the publishing period beginning with the year 1976. Application of the data is illustrated by the properties of benzo[a]pyrene (B[a]P) and its metabolites. Analysis show higher activity of P450 1A1 for activation of the (-)- isomer of trans-B[a]P-7,8-diol, while P4501B1 exerts higher activity for the (+)- isomer. P450 1A2 showed equally low activity in the metabolic activation of both isomers. The information collected in the databases is applicable in prediction of metabolic drug-drug and/or drug-chemical interactions in clinical and environmental studies. The data on the metabolism of searched compound (exemplified by benzo[a]pyrene and its metabolites) also indicate toxicological properties of the products of specific reactions. The offline and web-searchable databases had wide range of applications (e.g. computer assisted drug design and development, optimization of clinical therapy, toxicological applications) and adjustment in everyday life styles. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

[Over- or underestimated? Bibliographic survey of the biomedical periodicals published in Hungary].

PubMed

Berhidi, Anna; Horváth, Katalin; Horváth, Gabriella; Vasas, Lívia

2013-06-30

This publication - based on an article published in 2006 - emphasises the qualities of the current biomedical periodicals of Hungarian editions. The aim of this study was to analyse how Hungarian journals meet the requirements of the scientific aspect and international visibility. Authors evaluated 93 Hungarian biomedical periodicals by 4 viewpoints of the two criteria mentioned above. 35% of the analysed journals complete the attributes of scientific aspect, 5% the international visibility, 6% fulfill all examined criteria, and 25% are indexed in international databases. 6 biomedical Hungarian periodicals covered by each of the three main bibliographic databases (Medline, Scopus, Web of Science) have the best qualities. Authors recommend to improve viewpoints of the scientific aspect and international visibility. The basis of qualitative adequacy are the accurate authors' guidelines, title, abstract, keywords of the articles in English, and the ability to publish on time.

A survey of the current status of web-based databases indexing Iranian journals.

PubMed

Merat, Shahin; Khatibzadeh, Shahab; Mesgarpour, Bita; Malekzadeh, Reza

2009-05-01

The scientific output of Iran is increasing rapidly during the recent years. Unfortunately, most papers are published in journals which are not indexed by popular indexing systems and many of them are in Persian without English translation. This makes the results of Iranian scientific research unavailable to other researchers, including Iranians. The aim of this study was to evaluate the quality of current web-based databases indexing scientific articles published in Iran. We identified web-based databases which indexed scientific journals published in Iran using popular search engines. The sites were then subjected to a series of tests to evaluate their coverage, search capabilities, stability, accuracy of information, consistency, accessibility, ease of use, and other features. Results were compared with each other to identify strengths and shortcomings of each site. Five web sites were indentified. None had a complete coverage on scientific Iranian journals. The search capabilities were less than optimal in most sites. English translations of research titles, author names, keywords, and abstracts of Persian-language articles did not follow standards. Some sites did not cover abstracts. Numerous typing errors make searches ineffective and citation indexing unreliable. None of the currently available indexing sites are capable of presenting Iranian research to the international scientific community. The government should intervene by enforcing policies designed to facilitate indexing through a systematic approach. The policies should address Iranian journals, authors, and indexing sites. Iranian journals should be required to provide their indexing data, including references, electronically; authors should provide correct indexing information to journals; and indexing sites should improve their software to meet standards set by the government.

Quality of reporting in abstracts of randomized controlled trials published in leading journals of periodontology and implant dentistry: a survey.

PubMed

Faggion, Clovis Mariano; Giannakopoulos, Nikolaos Nikitas

2012-10-01

Most readers, reviewers, and editors rely on abstracts to decide whether to assess the full text of an article. A research abstract should, therefore, be as informative as possible. The standard of reporting in abstracts of randomized controlled trials (RCTs) in periodontology and implant dentistry has not yet been assessed. The objectives of this review are: 1) to assess the quality of reporting in abstracts of RCTs in periodontology and implant dentistry, and 2) to investigate changes in the quality of reporting by comparing samples from different periods. The authors searched the PubMed electronic database, independently and in duplicate, for abstracts of RCTs published in seven leading journals of periodontology and implant dentistry from 2005 to 2007 and from 2009 to 2011. The quality of reporting in selected abstracts with reference to the CONSORT (Consolidated Standards of Reporting Trials) for Abstracts checklist published in January 2008 was assessed independently and in duplicate. Cohen κ statistic was used to determine the extent of agreement of the reviewers. Pearson χ(2) test and/or Fisher exact test were used to assess differences in reporting in the two samples. Level of significance was set at P <0.05. Three hundred ninety-two abstracts are included in this review. Three items (intervention, objective, and conclusions) were almost fully reported in both samples. In contrast, other items (randomization, trial registration, and funding) were never reported. There were significant changes in reporting for only two items, trial design and title (items better reported in the pre- and post-CONSORT samples, respectively). Most topics, however, were similarly poorly reported in both samples of abstracts. The quality of reporting in abstracts of RCTs in periodontology and implant dentistry can be improved. Authors should follow the CONSORT for Abstracts guidelines, and journal editors should promote clear rules to improve authors' adherence to these guidelines.

Learning from research on the information behaviour of healthcare professionals: a review of the literature 2004-2008 with a focus on emotion.

PubMed

Fourie, Ina

2009-09-01

A review, focusing on emotion, was conducted of reported studies on the information behaviour of healthcare professionals (2004-2008). Findings were intended to offer guidelines on information services and information literacy training, to note gaps in research and to raise research interest. Databases were searched for literature published from January 2004 to December 2008 and indexed on eric, Library and Information Science Abstracts, medline, PsycINFO, Social Services Abstracts, Sociological Abstracts, Health Source: Nursing/Academic Edition; Library, Information Science & Technology Abstracts; Psychology and Behavioral Sciences Collection; Social Work Abstracts; SocINDEX with Full Text; SPORTDiscus; cinhal; and the ISI Web of Knowledge databases. Key journals were manually scanned and citations followed. Literature was included if reporting on issues concerning emotion. Emotion in information behaviour in healthcare contexts is scantily addressed. This review, however, offers some insight into the difficulty in identifying and expressing information needs; sense making and the need to fill knowledge gaps; uncertainty; personality and coping skills; motivation to seeking information; emotional experiences during information seeking; self-confidence and attitude; emotional factors in the selection of information channels; and seeking information for psychological or emotional reasons. Suggestions following findings, address information literacy programs, information services and research gaps.

Occupational dose reduction at Department of Energy contractor facilities: Bibliography of selected readings in radiation protection and ALARA

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

Dionne, B.J.; Sullivan, S.G.; Baum, J.W.

1993-12-01

This bibliography contains abstracts relating to various aspects of ALARA program implementation and dose reduction activities, with a focus on DOE facilities. Abstracts included in this bibliography were selected from proceedings of technical meetings, journals, research reports, searches of the DOE Energy, Science and Technology Database (in general, the citation and abstract information is presented as obtained from this database), and reprints of published articles provided by the authors. Facility types and activities covered in the scope of this report include: radioactive waste, uranium enrichment, fuel fabrication, spent fuel storage and reprocessing, facility decommissioning, hot laboratories, tritium production, research, testmore » and production reactors, weapons fabrication and testing, fusion, uranium and plutonium processing, radiography, and aocelerators. Information on improved shielding design, decontamination, containments, robotics, source prevention and control, job planning, improved operational and design techniques, as well as on other topics, has been included. In addition, DOE/EH reports not included in previous volumes of the bibliography are in this volume (abstracts 611 to 684). This volume (Volume 5 of the series) contains 217 abstracts. An author index and a subject index are provided to facilitate use. Both indices contain the abstract numbers from previous volumes, as well as the current volume. Information that the reader feels might be included in the next volume of this bibliography should be submitted to the BNL ALARA Center.« less

Publication Rates of Abstracts Presented at Five National Pharmacy Association Meetings

PubMed Central

Prohaska, Emily; Generali, Joyce; Zak, Kevin; Grauer, Dennis

2013-01-01

Background: Abstract presentations at professional meetings provide a medium for disseminating the findings of scholarly activity. Rates of abstract publication from various biomedical disciplines have been evaluated, with pharmacy noted to be lower than other specialties. Previous research on pharmacy abstract publication rates was conducted for a limited number of professional meetings but has not been assessed using Google Scholar. Objective: To determine the full publication rate of abstracts presented at the 2005 American College of Clinical Pharmacy (ACCP) Spring and Annual Meetings, American Pharmacists Association (APhA) Annual Meeting, and American Society of Health-System Pharmacists (ASHP) Summer and Midyear Clinical Meetings. Methods: Publication status was assessed for abstracts presented during the 2005 ACCP Spring and Annual Meetings, APhA Annual Meeting, and ASHP Summer and Midyear Clinical Meetings using PubMed and Google Scholar. Data collected included abstract category, study category, practice site, database(s) in which publication appeared, time in months to publication, publication type, and journal of publication. Results: Evaluation of 2,000 abstracts presented in 2005 revealed an overall full publication rate of 19.8% (n = 384). Nearly all pharmacy abstracts were published as manuscripts (98.4%; n=378) and indexed in PubMed and Google Scholar (91.9%; n = 353), although a significant percentage were indexed in Google Scholar only (7.8%; n = 30). The mean time to full publication was 16.8 months (SD ±11.9 months). Conclusions: Results were consistent with previously reported full publication rates of abstracts from pharmacy association meetings, indicating that abstracts presented at pharmacy meetings continue to have a lower full publication rate than other health disciplines. PMID:24421465

Publication trend, resource utilization, and impact of the US National Cancer Database

PubMed Central

Su, Chang; Peng, Cuiying; Agbodza, Ena; Bai, Harrison X.; Huang, Yuqian; Karakousis, Giorgos; Zhang, Paul J.; Zhang, Zishu

2018-01-01

Abstract Background: The utilization and impact of the studies published using the National Cancer Database (NCDB) is currently unclear. In this study, we aim to characterize the published studies, and identify relatively unexplored areas for future investigations. Methods: A literature search was performed using PubMed in January 2017 to identify all papers published using NCDB data. Characteristics of the publications were extracted. Citation frequencies were obtained through the Web of Science. Results: Three hundred 2 articles written by 230 first authors met the inclusion criteria. The number of publications grew exponentially since 2013, with 108 articles published in 2016. Articles were published in 86 journals. The majority of the published papers focused on digestive system cancer, while bone and joints, eye and orbit, myeloma, mesothelioma, and Kaposi Sarcoma were never studied. Thirteen institutions in the United States were associated with more than 5 publications. The papers have been cited for a total of 9858 times since the publication of the first paper in 1992. Frequently appearing keywords congregated into 3 clusters: “demographics,” “treatments and survival,” and “statistical analysis method.” Even though the main focuses of the articles captured a extremely wide range, they can be classified into 2 main categories: survival analysis and characterization. Other focuses include database(s) analysis and/or comparison, and hospital reporting. Conclusion: The surging interest in the use of NCDB is accompanied by unequal utilization of resources by individuals and institutions. Certain areas were relatively understudied and should be further explored. PMID:29489679

Database resources of the National Center for Biotechnology Information.

PubMed

2016-01-04

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (PubMed Central (PMC), Bookshelf and PubReader), health (ClinVar, dbGaP, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen), genomes (BioProject, Assembly, Genome, BioSample, dbSNP, dbVar, Epigenomics, the Map Viewer, Nucleotide, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser and the Trace Archive), genes (Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and chemicals (Biosystems and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for most of these databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Database resources of the National Center for Biotechnology Information.

PubMed

2015-01-01

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (Bookshelf, PubMed Central (PMC) and PubReader); medical genetics (ClinVar, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen); genes and genomics (BioProject, BioSample, dbSNP, dbVar, Epigenomics, Gene, Gene Expression Omnibus (GEO), Genome, HomoloGene, the Map Viewer, Nucleotide, PopSet, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser, Trace Archive and UniGene); and proteins and chemicals (Biosystems, COBALT, the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB), Protein Clusters, Protein and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for many of these databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Full journal publication of abstracts presented at the Nordic Congress of General Practice in 2009 and 2011.

PubMed

Waldorff, Frans Boch; Petersen, Kristine; Vinther, Siri; Sandholdt, Håkon; Siersma, Volkert; Andersen, John Sahl

2017-03-01

To determine the overall publication rates for abstracts presented at two consecutive Nordic Congresses of General Practice and to evaluate determinants for these publication rates. Prospective study. MEDLINE (PubMed) and Google Scholar were searched for relevant publications from 1 January 2009 up until 31 August 2014. Abstracts accepted for oral or poster presentation were identified from the original congress booklets from the Nordic Congresses of General Practice in 2009 and 2011. Based on PubMed and Google Scholar searches, we subsequently identified full journal publications within a 36-month follow-up from both congresses. In cases of doubt, the first author was contacted directly. Full journal publication within 36 months after the congress. A total of 200 abstracts were analyzed. Of these, 85 (42.5%) were identified with a full publication within 36 months after the congress. More abstracts from the 2011 congress were published compared to the 2009 congress odds ratio (OR) 1.97, 95% confidence interval (CI) (1.10; 3.50). Abstracts accepted for oral presentation were more often published OR 1.94, 95% CI (1.08; 3.50) than accepted poster abstracts. In the multivariate analysis, a university affiliation for both first and last author increased the probability for publication OR 4.23, 95% CI (1.71; 10.42), as well as more than two authors. An optimal number, based on the highest OR, seems to be 3-4 authors with OR 2.43, 95% CI (1.07; 5.54). Qualitative studies were published at the same frequency as quantitative studies OR 1.36, 95% CI (0.57; 3.24). Less than half of the abstracts accepted for oral or poster presentation at two consecutive Nordic Congresses of General Practice were published as full text articles within 36 months. Key points Congress abstracts accepted for Nordic Congress of General Practice are not indexed in international search databases. Less than half of the abstracts accepted for oral or poster presentation at two consecutive Nordic Congresses of General Practice were published as full text articles within 36 months. Future congress committees could address this aspect in order to increase the visibility of and accessibility to research within the field of general practice.

Full journal publication of abstracts presented at the Nordic Congress of General Practice in 2009 and 2011

PubMed Central

Waldorff, Frans Boch; Petersen, Kristine; Vinther, Siri; Sandholdt, Håkon; Siersma, Volkert; Andersen, John Sahl

2017-01-01

Objective To determine the overall publication rates for abstracts presented at two consecutive Nordic Congresses of General Practice and to evaluate determinants for these publication rates. Design Prospective study. Setting MEDLINE (PubMed) and Google Scholar were searched for relevant publications from 1 January 2009 up until 31 August 2014. Methods Abstracts accepted for oral or poster presentation were identified from the original congress booklets from the Nordic Congresses of General Practice in 2009 and 2011. Based on PubMed and Google Scholar searches, we subsequently identified full journal publications within a 36-month follow-up from both congresses. In cases of doubt, the first author was contacted directly. Main outcome measures Full journal publication within 36 months after the congress. Results A total of 200 abstracts were analyzed. Of these, 85 (42.5%) were identified with a full publication within 36 months after the congress. More abstracts from the 2011 congress were published compared to the 2009 congress odds ratio (OR) 1.97, 95% confidence interval (CI) (1.10; 3.50). Abstracts accepted for oral presentation were more often published OR 1.94, 95% CI (1.08; 3.50) than accepted poster abstracts. In the multivariate analysis, a university affiliation for both first and last author increased the probability for publication OR 4.23, 95% CI (1.71; 10.42), as well as more than two authors. An optimal number, based on the highest OR, seems to be 3–4 authors with OR 2.43, 95% CI (1.07; 5.54). Qualitative studies were published at the same frequency as quantitative studies OR 1.36, 95% CI (0.57; 3.24). Conclusion Less than half of the abstracts accepted for oral or poster presentation at two consecutive Nordic Congresses of General Practice were published as full text articles within 36 months. Key points Congress abstracts accepted for Nordic Congress of General Practice are not indexed in international search databases. Less than half of the abstracts accepted for oral or poster presentation at two consecutive Nordic Congresses of General Practice were published as full text articles within 36 months. Future congress committees could address this aspect in order to increase the visibility of and accessibility to research within the field of general practice. PMID:28277049

Interventions for family members caring for an elder with dementia.

PubMed

Acton, Gayle J; Winter, Mary A

2002-01-01

This chapter reviews 73 published and unpublished research reports of interventions for family members caring for an elder with dementia by nurse researchers and researchers from other disciplines. Reports were identified through searches of MEDLINE, CINAHL, Social Science Index, PsycINFO, ERIC, Social Work Abstracts, American Association of Retired Persons database, CRISP index of the National Institutes of Health, Cochrane Center database, and Dissertation Abstracts using the following search terms: caregiver, caregiving, dementia, Alzheimer's, intervention study, evaluation study, experimental, and quasi-experimental design. Additional keywords were used to narrow or expand the search as necessary. All nursing research was included in the review and nonnursing research was included if published between 1991 and 2001. Studies were included if they used a design that included a treatment and control group or a one-group, pretest-posttest design (ex post facto designs were included if they used a comparison group). Key findings show that approximately 32% of the study outcomes (e.g., burden, depression, knowledge) were changed after intervention in the desired direction. In addition, several problematic issues were identified including small, diverse samples; lack of intervention specificity; diversity in the length, duration, and intensity of the intervention strategies; and problematic outcome measures.

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

Publication outcomes for research presented at a Canadian surgical conference.

PubMed

Crawford, Sean A; Roche-Nagle, Graham

2017-04-01

The failure of investigators to publish research in peer-reviewed journals following acceptance at a national or international meeting can lead to significant publication biases in the literature. Our objective was to evaluate the abstract to manuscript conversion rate for abstracts presented at the Canadian Society for Vascular Surgery (CSVS) annual meeting and to evaluate the conversion rate for CSVS-awarded research grants. We searched for authors of abstracts accepted at the CSVS Annual Meeting (2007-2013) and recipients of CSVS research awards (2005-2013) on Scopus and PubMed databases to identify related publications. We identified 84 publications from 188 research abstracts (45%) and 17 publications from 39 research grants (44%). The mean time to publication was 1.8 years and the mean impact factor was 2.7. Studies related to endovascular therapies demonstrated a trend toward a higher rate of publication relative to open surgical therapies (64 [56%] v. 37 [27%]). Additionally, we observed a similar trend in research grant topics related to endovascular therapies relative to open surgical therapies (9 [67%] v. 8 [38%]). Finally, CSVS research grant recipients who subsequently published had a significantly higher h-index at the time of receipt than those who had not published. The CSVS annual meeting's abstract to publication conversion rate is comparable to that of its Canadian peers as well as to other medical specialties; however, a substantial publication gap remains. We identified several potential areas that may help to improve the effectiveness of CSVS research grants.

The prescribable drugs with efficacy in experimental epilepsies (PDE3) database for drug repurposing research in epilepsy.

PubMed

Sivapalarajah, Shayeeshan; Krishnakumar, Mathangi; Bickerstaffe, Harry; Chan, YikYing; Clarkson, Joseph; Hampden-Martin, Alistair; Mirza, Ahmad; Tanti, Matthew; Marson, Anthony; Pirmohamed, Munir; Mirza, Nasir

2018-02-01

Current antiepileptic drugs (AEDs) have several shortcomings. For example, they fail to control seizures in 30% of patients. Hence, there is a need to identify new AEDs. Drug repurposing is the discovery of new indications for approved drugs. This drug "recycling" offers the potential of significant savings in the time and cost of drug development. Many drugs licensed for other indications exhibit antiepileptic efficacy in animal models. Our aim was to create a database of "prescribable" drugs, approved for other conditions, with published evidence of efficacy in animal models of epilepsy, and to collate data that would assist in choosing the most promising candidates for drug repurposing. The database was created by the following: (1) computational literature-mining using novel software that identifies Medline abstracts containing the name of a prescribable drug, a rodent model of epilepsy, and a phrase indicating seizure reduction; then (2) crowdsourced manual curation of the identified abstracts. The final database includes 173 drugs and 500 abstracts. It is made freely available at www.liverpool.ac.uk/D3RE/PDE3. The database is reliable: 94% of the included drugs have corroborative evidence of efficacy in animal models (for example, evidence from multiple independent studies). The database includes many drugs that are appealing candidates for repurposing, as they are widely accepted by prescribers and patients-the database includes half of the 20 most commonly prescribed drugs in England-and they target many proteins involved in epilepsy but not targeted by current AEDs. It is important to note that the drugs are of potential relevance to human epilepsy-the database is highly enriched with drugs that target proteins of known causal human epilepsy genes (Fisher's exact test P-value < 3 × 10 -5 ). We present data to help prioritize the most promising candidates for repurposing from the database. The PDE3 database is an important new resource for drug repurposing research in epilepsy. Wiley Periodicals, Inc. © 2018 International League Against Epilepsy.

Choosing a Database for Social Work: A Comparison of Social Work Abstracts and Social Service Abstracts

ERIC Educational Resources Information Center

Flatley, Robert K.; Lilla, Rick; Widner, Jack

2007-01-01

This study compared Social Work Abstracts and Social Services Abstracts databases in terms of indexing, journal coverage, and searches. The authors interviewed editors, analyzed journal coverage, and compared searches. It was determined that the databases complement one another more than compete. The authors conclude with some considerations.

The Biological Macromolecule Crystallization Database and NASA Protein Crystal Growth Archive

PubMed Central

Gilliland, Gary L.; Tung, Michael; Ladner, Jane

1996-01-01

The NIST/NASA/CARB Biological Macromolecule Crystallization Database (BMCD), NIST Standard Reference Database 21, contains crystal data and crystallization conditions for biological macromolecules. The database entries include data abstracted from published crystallographic reports. Each entry consists of information describing the biological macromolecule crystallized and crystal data and the crystallization conditions for each crystal form. The BMCD serves as the NASA Protein Crystal Growth Archive in that it contains protocols and results of crystallization experiments undertaken in microgravity (space). These database entries report the results, whether successful or not, from NASA-sponsored protein crystal growth experiments in microgravity and from microgravity crystallization studies sponsored by other international organizations. The BMCD was designed as a tool to assist x-ray crystallographers in the development of protocols to crystallize biological macromolecules, those that have previously been crystallized, and those that have not been crystallized. PMID:11542472

The development of digital library system for drug research information.

PubMed

Kim, H J; Kim, S R; Yoo, D S; Lee, S H; Suh, O K; Cho, J H; Shin, H T; Yoon, J P

1998-01-01

The sophistication of computer technology and information transmission on internet has made various cyber information repository available to information consumers. In the era of information super-highway, the digital library which can be accessed from remote sites at any time is considered the prototype of information repository. Using object-oriented DBMS, the very first model of digital library for pharmaceutical researchers and related professionals in Korea has been developed. The published research papers and researchers' personal information was included in the database. For database with research papers, 13 domestic journals were abstracted and scanned for full-text image files which can be viewed by Internet web browsers. The database with researchers' personal information was also developed and interlinked to the database with research papers. These database will be continuously updated and will be combined with world-wide information as the unique digital library in the field of pharmacy.

New Features in the ADS Abstract Service

NASA Astrophysics Data System (ADS)

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

2001-11-01

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

Fresh Ideas, Perspectives, and Protocols Associated with Forest Inventory and Analysis Surveys: Graduate Reports, 1974 to July 2001

Treesearch

Victor A. Rudis

2003-01-01

Graduate M.S. theses and Ph.D. dissertations were searched to provide a body of information associated with the U.S. Department of Agriculture, Forest Service, Forest Inventory and Analysis (FIA) database. Authors' abstracts were included if available in electronic form and published since 1974. Novel technical and nontraditional FIA data uses, as well as the...

The Publication Rate of Abstracts Presented at the 2003 Urological Brazilian Meeting

PubMed Central

Oliveira, Leonardo Resende Sousa; Figueiredo, André Avarese; Choi, Mauro; Ferrarez, Carlos Eduardo Prata Fernandes; Bastos, Andre Netto; Netto, Jose Murillo Bastos

2009-01-01

OBJECTIVE: To determine the publication rate of orally-presented abstracts from the 2003 Urological Brazilian Meeting, as well as the factors determining this publication rate. MATERIALS AND METHODS: The publication rate of the 313 orally-presented abstracts at the 2003 Urological Brazilian Meeting was evaluated by scanning the Lilacs, Scielo and Medline databases. The time between presentation and publication, the state and country of the abstract, the research methodology (cross-sectional, case-control, retrospective case series, prospective case series or clinical trial), whether drugs were utilized and the topic of the study were all characterized. RESULTS: Thirty-nine percent of the abstracts were published after a median time of 14 months (range: 1 to 51 months). There were high publication rates for cross-sectional abstracts (75%), drug utilization studies (51.3%), clinical trials (50%) and prospective case series’ (48.1%). However, there was only a moderate statistical trend towards a higher publication rate in the prospective case series (p=0.07), while the retrospective case series’ showed statistically lower publication rates than the other groups (33.7%, p=0.04). Abstracts on laparoscopic surgery had the highest publication rate (61.9%, p=0.03) compared to others topics. In 57% of the unpublished abstracts, there was no interest in or attempt to publish, and rejection was responsible for the lack of publication of only 4% of the abstracts. CONCLUSION: The publication rate of the orally-presented abstracts from the 2003 Urological Brazilian Meeting was comparable to that of international congresses. The subsequent publication of presented abstracts and the selection of prospective studies with stronger evidence should be encouraged and may improve the scientific quality of the meeting. PMID:19488593

Supporting parents and parenting: An overview of data-based papers recently published in Contemporary Nurse.

PubMed

Jackson, Debra; Power, Tamara; Dean, Sue; Potgieter, Ingrid; Cleary, Michelle

2013-10-02

Abstract Nurses have a crucial role in play in supporting parents and in delivering and referring parents to family-support services. In this editorial, we reflect on papers recently published in Contemporary Nurse. We sought to consider data-based papers on parenting published between 2008 and 2012 and elucidate the role/s and potential roles of nurses in enhancing and supporting parenting. Parenting is recognised as a crucial variable for achieving positive outcomes for children (Dawson et al 2012). Poor, inconsistent or abusive parenting is linked to poor outcomes (Griffin et al. 2000, Holt et al.2008, Patterson et al.1989), while consistent and effective parenting is associated with enhanced child outcomes (Lamb 2012, Landry et al.2001). In addition to being important to outcomes for children, perceived parenting quality is also important to parents themselves. Disrupted relationships between parents and their children have been identified as distressing and potentially damaging to both parties (Jackson 2000; East 2006, 2007; Power 2012).

Publication of papers presented in a Brazilian Trauma Congress.

PubMed

de Andrade, Vitor Augusto; Carpini, Stela; Schwingel, Ricardo; Calderan, Thiago Rodrigues Araújo; Fraga, Gustavo Pereira

2011-01-01

To assess the proportion of papers presented at the XXI Panamerican Congress of Trauma, VIII Congress of the Brazilian Society of Integrated Assistance to the Traumatized (SBAIT) and X Brazilian Congress of Trauma Leagues (CoLT) that were published in full. In the events cited, based in Campinas in 2008, 347 papers abstracts of were presented and published. To evaluate the proportion of complete published works a retrospective observational study was conducted, reviewing the biomedical databases PubMed and SciELO, with support from Google, from the title of the abstracts and list of authors. Of 347 papers considered, 25 (7.3%) were from foreign services and 322 (92.7%) national. Ten (2.9%) papers were published, of which six (1.7%) of nursing and four (1.2%) medical. Among these, four thesis publications were identified and only one international work has been published. Despite a large number of papers presented at trauma conferences in Brazil, the publications in this area are rare. The academy and the societies of surgery need to encourage the submission of scientific papers even before the presentation in Congresses in order for them to be evaluated for publication in indexed journals.

Scientific meeting abstracts: significance, access, and trends.

PubMed Central

Kelly, J A

1998-01-01

Abstracts of scientific papers and posters that are presented at annual scientific meetings of professional societies are part of the broader category of conference literature. They are an important avenue for the dissemination of current data. While timely and succinct, these abstracts present problems such as an abbreviated peer review and incomplete bibliographic access. METHODS: Seventy societies of health sciences professionals were surveyed about the publication of abstracts from their annual meetings. Nineteen frequently cited journals also were contacted about their policies on the citation of meeting abstracts. Ten databases were searched for the presence of meetings abstracts. RESULTS: Ninety percent of the seventy societies publish their abstracts, with nearly half appearing in the society's journal. Seventy-seven percent of the societies supply meeting attendees with a copy of each abstract, and 43% make their abstracts available in an electronic format. Most of the journals surveyed allow meeting abstracts to be cited. Bibliographic access to these abstracts does not appear to be widespread. CONCLUSIONS: Meeting abstracts play an important role in the dissemination of scientific knowledge. Bibliographic access to meeting abstracts is very limited. The trend toward making meeting abstracts available via the Internet has the potential to give a broader audience access to the information they contain. PMID:9549015

Analysis of full-text publication and publishing predictors of abstracts presented at an Italian public health meeting (2005-2007).

PubMed

Castaldi, S; Giacometti, M; Toigo, W; Bert, F; Siliquini, R

2015-09-29

In Public Health, a thorough review of abstract quality evaluations and the publication history of studies presented at scientific meetings has never been conducted. To analyse the long-term outcome of quality abstracts submitted to conferences of Italian Society of Hygiene and Public Health (SItI) from 2005 to 2007, we conducted a second analysis of previously published material aiming to estimate full-text publication rate of high quality abstract presented at Italian public health meetings, and to identify predictors of full-text publication. The search was undertaken through scientific databases and search engines and through the web sites of the major Italian journals of Public Health. For each publication confirmed as a full text paper, the journal name, impact factor, year of publication, gender of the first author, type of study design, characteristics of the results and sample size were collected. The overall publication rate of the abstracts presented is 23.5%; most of the papers were published in Public Health journals (average impact factor: 3.007). Non universitary affiliation had resulted in a lower probability of publication, while some of the Conference topics had predisposed the studies to an increased likelihood of publication as well as poster form presentation. The method presented in this study provides a good framework for the evaluation of the scientific evidence. The findings achieved should be taken into consideration by the Scientific Societies during the contributions selection phase, with the aim of achieving a continuous improvement of work quality. In the future, it would be interesting to survey the abstract authors to identify reasons for unpublished data.

Full-text publication of abstracts presented at European Orthodontic Society congresses.

PubMed

Livas, Christos; Pandis, Nikolaos; Ren, Yijin

2014-10-01

Empirical evidence has indicated that only a subsample of studies conducted reach full-text publication and this phenomenon has become known as publication bias. A form of publication bias is the selectively delayed full publication of conference abstracts. The objective of this article was to examine the publication status of oral abstracts and poster-presentation abstracts, included in the scientific program of the 82nd and 83rd European Orthodontic Society (EOS) congresses, held in 2006 and 2007, and to identify factors associated with full-length publication. A systematic search of PubMed and Google Scholar databases was performed in April 2013 using author names and keywords from the abstract title to locate abstract and full-article publications. Information regarding mode of presentation, type of affiliation, geographical origin, statistical results, and publication details were collected and analyzed using univariable and multivariable logistic regression. Approximately 51 per cent of the EOS 2006 and 55 per cent of the EOS 2007 abstracts appeared in print more than 5 years post congress. A mean period of 1.32 years elapsed between conference and publication date. Mode of presentation (oral or poster), use of statistical analysis, and research subject area were significant predictors for publication success. Inherent discrepancies of abstract reporting, mainly related to presentation of preliminary results and incomplete description of methods, may be considered in analogous studies. On average 52.2 per cent of the abstracts presented at the two EOS conferences reached full publication. Abstracts presented orally, including statistical analysis, were more likely to get published. © The Author 2013. Published by Oxford University Press on behalf of the European Orthodontic Society. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Assessing the Eventual Publication of Clinical Trial Abstracts Submitted to a Large Annual Oncology Meeting.

PubMed

Massey, Paul R; Wang, Ruibin; Prasad, Vinay; Bates, Susan E; Fojo, Tito

2016-03-01

Despite the ethical imperative to publish clinical trials when human subjects are involved, such data frequently remain unpublished. The objectives were to tabulate the rate and ascertain factors associated with eventual publication of clinical trial results reported as abstracts in the Proceedings of the American Society of Clinical Oncology (American Society of Clinical Oncology). Abstracts describing clinical trials for patients with breast, lung, colorectal, ovarian, and prostate cancer from 2009 to 2011 were identified by using a comprehensive online database (http://meetinglibrary.asco.org/abstracts). Abstracts included reported results of a treatment or intervention assessed in a discrete, prospective clinical trial. Publication status at 4-6 years was determined by using a standardized search of PubMed. Primary outcomes were the rate of publication for abstracts of randomized and nonrandomized clinical trials. Secondary outcomes included factors influencing the publication of results. A total of 1,075 abstracts describing 378 randomized and 697 nonrandomized clinical trials were evaluated. Across all years, 75% of randomized and 54% of nonrandomized trials were published, with an overall publication rate of 61%. Sample size was a statistically significant predictor of publication for both randomized and nonrandomized trials (odds ratio [OR] per increase of 100 participants = 1.23 [1.11-1.36], p < .001; and 1.64 [1.15-2.34], p = .006, respectively). Among randomized studies, an industry coauthor or involvement of a cooperative group increased the likelihood of publication (OR 2.37, p = .013; and 2.21, p = .01, respectively). Among nonrandomized studies, phase II trials were more likely to be published than phase I (p < .001). Use of an experimental agent was not a predictor of publication in randomized (OR 0.76 [0.38-1.52]; p = .441) or nonrandomized trials (OR 0.89 [0.61-1.29]; p = .532). This is the largest reported study examining why oncology trials are not published. The data show that 4-6 years after appearing as abstracts, 39% of oncology clinical trials remain unpublished. Larger sample size and advanced trial phase were associated with eventual publication; among randomized trials, an industry-affiliated author or a cooperative group increased likelihood of publication. Unfortunately, we found that, despite widespread recognition of the problem and the creation of central data repositories, timely publishing of oncology clinical trials results remains unsatisfactory. ©AlphaMed Press.

Fate of abstracts presented at the 2008 European Congress of Physical and Rehabilitation Medicine.

PubMed

Allart, E; Beaucamp, F; Tiffreau, V; Thevenon, A

2015-08-01

The subsequent full-text publication of abstracts presented at a scientific congress reflects the latter's scientific quality. The aim of this paper was to evaluate the publication rate for abstracts presented at the 2008 European Congress of Physical and Rehabilitation Medicine (ECPRM), characterize the publications and identify factors that were predictive of publication. It is a bibliography search. We used the PubMed database to search for subsequent publication of abstracts. We screened the abstracts' characteristics for features that were predictive of publication among abstracts features, such the status of the authors, the topic and the type of work. We performed univariate analyses and a logistic regression analysis. Of 779 abstracts presented at ECPRM 2008, 169 (21.2%) were subsequently published. The mean time to publication was 12±15.7 months and the mean impact factor of the publishing journals was 2.05±2.1. In a univariate analysis, university status (P<10-6), geographic origin (P=10-3), oral presentation (P<10-6), and original research (P<10-6) (and particularly multicentre trials [P<0.01] and randomized controlled trials [P=10-3]) were predictive of publication. In a logistic regression analysis, oral presentation (odds ratio [OR]=0.37) and university status (OR=0.36) were significant, independent predictors of publication. ECPRM 2008 publication rate and impact factor were relatively low, when compared with most other national and international conferences in this field. University status, the type of abstract and oral presentation were predictive of subsequent publication.

STELAR: An experiment in the electronic distribution of astronomical literature

NASA Technical Reports Server (NTRS)

Warnock, A.; Vansteenburg, M. E.; Brotzman, L. E.; Gass, J.; Kovalsky, D.

1992-01-01

STELAR (Study of Electronic Literature for Astronomical Research) is a Goddard-based project designed to test methods of delivering technical literature in machine readable form. To that end, we have scanned a five year span of the ApJ, ApJ Supp, AJ and PASP, and have obtained abstracts for eight leading academic journals from NASA/STI CASI, which also makes these abstracts available through the NASA RECON system. We have also obtained machine readable versions of some journal volumes from the publishers, although in many instances, the final typeset versions are no longer available. The fundamental data object for the STELAR database is the article, a collection of items associated with a scientific paper - abstract, scanned pages (in a variety of formats), figures, OCR extractions, forward and backward references, errata and versions of the paper in various formats (e.g., TEX, SGML, PostScript, DVI). Articles are uniquely referenced in the database by journal name, volume number and page number. The selection and delivery of articles is accomplished through the WAIS (Wide Area Information Server) client/server models requiring only an Internet connection. Modest modifications to the server code have made it capable of delivering the multiple data types required by STELAR. WAIS is a platform independent and fully open multi-disciplinary delivery system, originally developed by Thinking Machines Corp. and made available free of charge. It is based on the ISO Z39.50 standard communications protocol. WAIS servers run under both UNIX and VMS. WAIS clients run on a wide variety of machines, from UNIX-based Xwindows systems to MS-DOS and macintosh microcomputers. The WAIS system includes full-test indexing and searching of documents, network interface and easy access to a variety of document viewers. ASCII versions of the CASI abstracts have been formatted for display and the full test of the abstracts has been indexed. The entire WAIS database of abstracts is now available for use by the astronomical community. Enhancements of the search and retrieval system are under investigation to include specialized searches (by reference, author or keyword, as opposed to full test searches), improved handling of word stems, improvements in relevancy criteria and other retrieval techniques, such as factor spaces. The STELAR project has been assisted by the full cooperation of the AAS, the ASP, the publishers of the academic journals, librarians from GSFC, NRAO and STScI, the Library of Congress, and the University of North Carolina at Chapel Hill.

Same family, different species: methodological conduct and quality varies according to purpose for five types of knowledge synthesis.

PubMed

Tricco, Andrea C; Zarin, Wasifa; Ghassemi, Marco; Nincic, Vera; Lillie, Erin; Page, Matthew J; Shamseer, Larissa; Antony, Jesmin; Rios, Patricia; Hwee, Jeremiah; Veroniki, Areti Angeliki; Moher, David; Hartling, Lisa; Pham, Ba'; Straus, Sharon E

2018-04-01

The aim of the study was to characterize methodological conduct, reporting, and quality of five knowledge synthesis (KS) approaches. Retrospective analysis of a convenience sample of five published databases of KS approaches: overview of reviews (n = 74), scoping reviews (n = 494), rapid reviews (n = 84), systematic reviews (n = 300), and network meta-analyses (NMAs; n = 456). Data in the five published databases were abstracted by two reviewers independently, any missing data for this retrospective analysis were abstracted by one experienced reviewer. Methods were appraised using the A MeaSurement Tool to Assess systematic Reviews (AMSTAR) tool. Descriptive analysis was performed. Reporting the use of a protocol ranged from 4% for rapid reviews to 32% for systematic reviews. The use of two reviewers for citation and full-text screening ranged from 20% for scoping reviews to 60% for NMAs. Data abstraction was performed in duplicate for 11% of rapid reviews and 54% of NMAs, and for risk of bias appraisal, this ranged from 6% for scoping reviews to 41% for NMAs. NMAs had the highest median percentage of maximum obtainable AMSTAR score (64%; Q1-Q3:45-73%), while scoping reviews had the lowest (25%; Q1-Q3:13-38%). NMAs consistently scored the highest on the AMSTAR tool likely because the purpose is to estimate treatment effects statistically. Scoping reviews scored the lowest (even after adjusting the score for not relevant items) likely because the purpose is to characterize the literature. Copyright © 2017 Elsevier Inc. All rights reserved.

Discrepancy between results and abstract conclusions in industry- vs nonindustry-funded studies comparing topical prostaglandins.

PubMed

Alasbali, Tariq; Smith, Michael; Geffen, Noa; Trope, Graham E; Flanagan, John G; Jin, Yaping; Buys, Yvonne M

2009-01-01

To investigate the relationship between industry- vs nonindustry-funded publications comparing the efficacy of topical prostaglandin analogs by evaluating the correspondence between the statistical significance of the publication's main outcome measure and its abstract conclusions. Retrospective, observational cohort study. English publications comparing the ocular hypotensive efficacy between any or all of latanoprost, travoprost, and bimatoprost were searched from the MEDLINE database. Each article was reviewed by three independent observers and was evaluated for source of funding, study quality, statistically significant main outcome measure, correspondence between results of main outcome measure and abstract conclusion, number of intraocular pressure outcomes compared, and journal impact factor. Funding was determined by published disclosure or, in cases of no documented disclosure, the corresponding author was contacted directly to confirm industry funding. Discrepancies were resolved by consensus. The main outcome measure was correspondence between abstract conclusion and reported statistical significance of the publications' main outcome measure. Thirty-nine publications were included, of which 29 were industry funded and 10 were nonindustry funded. The published abstract conclusion was not consistent with the results of the main outcome measure in 18 (62%) of 29 of the industry-funded studies compared with zero (0%) of 10 of the nonindustry-funded studies (P = .0006). Twenty-six (90%) of the industry-funded studies had proindustry abstract conclusions. Twenty-four percent of the industry-funded publications had a statistically significant main outcome measure; however, 90% of the industry-funded studies had proindustry abstract conclusions. Both readers and reviewers should scrutinize publications carefully to ensure that data support the authors' conclusions.

Database Management: Building, Changing and Using Databases. Collected Papers and Abstracts of the Mid-Year Meeting of the American Society for Information Science (15th, Portland, Oregon, May 1986).

ERIC Educational Resources Information Center

American Society for Information Science, Washington, DC.

This document contains abstracts of papers on database design and management which were presented at the 1986 mid-year meeting of the American Society for Information Science (ASIS). Topics considered include: knowledge representation in a bilingual art history database; proprietary database design; relational database design; in-house databases;…

Database resources of the National Center for Biotechnology Information

PubMed Central

2015-01-01

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (Bookshelf, PubMed Central (PMC) and PubReader); medical genetics (ClinVar, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen); genes and genomics (BioProject, BioSample, dbSNP, dbVar, Epigenomics, Gene, Gene Expression Omnibus (GEO), Genome, HomoloGene, the Map Viewer, Nucleotide, PopSet, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser, Trace Archive and UniGene); and proteins and chemicals (Biosystems, COBALT, the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB), Protein Clusters, Protein and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for many of these databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov. PMID:25398906

Database resources of the National Center for Biotechnology Information

PubMed Central

2016-01-01

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (PubMed Central (PMC), Bookshelf and PubReader), health (ClinVar, dbGaP, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen), genomes (BioProject, Assembly, Genome, BioSample, dbSNP, dbVar, Epigenomics, the Map Viewer, Nucleotide, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser and the Trace Archive), genes (Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and chemicals (Biosystems and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for most of these databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:26615191

Integrative medicine for managing the symptoms of lupus nephritis

PubMed Central

Choi, Tae-Young; Jun, Ji Hee; Lee, Myeong Soo

2018-01-01

Abstract Background: Integrative medicine is claimed to improve symptoms of lupus nephritis. No systematic reviews have been performed for the application of integrative medicine for lupus nephritis on patients with systemic lupus erythematosus (SLE). Thus, this review will aim to evaluate the current evidence on the efficacy of integrative medicine for the management of lupus nephritis in patients with SLE. Methods and analyses: The following electronic databases will be searched for studies published from their dates of inception February 2018: Medline, EMBASE and the Cochrane Central Register of Controlled Trials (CENTRAL), as well as 6 Korean medical databases (Korea Med, the Oriental Medicine Advanced Search Integrated System [OASIS], DBpia, the Korean Medical Database [KM base], the Research Information Service System [RISS], and the Korean Studies Information Services System [KISS]), and 1 Chinese medical database (the China National Knowledge Infrastructure [CNKI]). Study selection, data extraction, and assessment will be performed independently by 2 researchers. The risk of bias (ROB) will be assessed using the Cochrane ROB tool. Dissemination: This systematic review will be published in a peer-reviewed journal and disseminated both electronically and in print. The review will be updated to inform and guide healthcare practice and policy. Trial registration number: PROSPERO 2018 CRD42018085205 PMID:29595669

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

PubMed Central

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

1993-01-01

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

miRwayDB: a database for experimentally validated microRNA-pathway associations in pathophysiological conditions

PubMed Central

Das, Sankha Subhra; Saha, Pritam

2018-01-01

Abstract MicroRNAs (miRNAs) are well-known as key regulators of diverse biological pathways. A series of experimental evidences have shown that abnormal miRNA expression profiles are responsible for various pathophysiological conditions by modulating genes in disease associated pathways. In spite of the rapid increase in research data confirming such associations, scientists still do not have access to a consolidated database offering these miRNA-pathway association details for critical diseases. We have developed miRwayDB, a database providing comprehensive information of experimentally validated miRNA-pathway associations in various pathophysiological conditions utilizing data collected from published literature. To the best of our knowledge, it is the first database that provides information about experimentally validated miRNA mediated pathway dysregulation as seen specifically in critical human diseases and hence indicative of a cause-and-effect relationship in most cases. The current version of miRwayDB collects an exhaustive list of miRNA-pathway association entries for 76 critical disease conditions by reviewing 663 published articles. Each database entry contains complete information on the name of the pathophysiological condition, associated miRNA(s), experimental sample type(s), regulation pattern (up/down) of miRNA, pathway association(s), targeted member of dysregulated pathway(s) and a brief description. In addition, miRwayDB provides miRNA, gene and pathway score to evaluate the role of a miRNA regulated pathways in various pathophysiological conditions. The database can also be used for other biomedical approaches such as validation of computational analysis, integrated analysis and prediction of computational model. It also offers a submission page to submit novel data from recently published studies. We believe that miRwayDB will be a useful tool for miRNA research community. Database URL: http://www.mirway.iitkgp.ac.in PMID:29688364

Assessing the Eventual Publication of Clinical Trial Abstracts Submitted to a Large Annual Oncology Meeting

PubMed Central

Wang, Ruibin; Prasad, Vinay; Bates, Susan E.; Fojo, Tito

2016-01-01

Background. Despite the ethical imperative to publish clinical trials when human subjects are involved, such data frequently remain unpublished. The objectives were to tabulate the rate and ascertain factors associated with eventual publication of clinical trial results reported as abstracts in the Proceedings of the American Society of Clinical Oncology (American Society of Clinical Oncology). Materials and Methods. Abstracts describing clinical trials for patients with breast, lung, colorectal, ovarian, and prostate cancer from 2009 to 2011 were identified by using a comprehensive online database (http://meetinglibrary.asco.org/abstracts). Abstracts included reported results of a treatment or intervention assessed in a discrete, prospective clinical trial. Publication status at 4−6 years was determined by using a standardized search of PubMed. Primary outcomes were the rate of publication for abstracts of randomized and nonrandomized clinical trials. Secondary outcomes included factors influencing the publication of results. Results. A total of 1,075 abstracts describing 378 randomized and 697 nonrandomized clinical trials were evaluated. Across all years, 75% of randomized and 54% of nonrandomized trials were published, with an overall publication rate of 61%. Sample size was a statistically significant predictor of publication for both randomized and nonrandomized trials (odds ratio [OR] per increase of 100 participants = 1.23 [1.11–1.36], p < .001; and 1.64 [1.15–2.34], p = .006, respectively). Among randomized studies, an industry coauthor or involvement of a cooperative group increased the likelihood of publication (OR 2.37, p = .013; and 2.21, p = .01, respectively). Among nonrandomized studies, phase II trials were more likely to be published than phase I (p < .001). Use of an experimental agent was not a predictor of publication in randomized (OR 0.76 [0.38–1.52]; p = .441) or nonrandomized trials (OR 0.89 [0.61–1.29]; p = .532). Conclusion. This is the largest reported study examining why oncology trials are not published. The data show that 4−6 years after appearing as abstracts, 39% of oncology clinical trials remain unpublished. Larger sample size and advanced trial phase were associated with eventual publication; among randomized trials, an industry-affiliated author or a cooperative group increased likelihood of publication. Unfortunately, we found that, despite widespread recognition of the problem and the creation of central data repositories, timely publishing of oncology clinical trials results remains unsatisfactory. Implications for Practice: The Declaration of Helsinki Ethical Principles for Medical Research Involving Human Subjects notes the ethical obligation to report clinical trial data, whether positive or negative. This obligation is listed alongside requirements for risk minimization, access, confidentiality, and informed consent, all bedrocks of the clinical trial system, yet clinical trials are often not published, particularly if negative or difficult to complete. This study found that among American Society for Clinical Oncology (ASCO) Annual Meeting abstracts, 2009–2011, only 61% were published 4–6 years later: 75% of randomized trials and 54% of nonrandomized trials. Clinicians need to insist that every study in which they participate is published. PMID:26888691

Bioindicators of marine pollution. (Latest citations from Oceanic Abstracts database). Published Search

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

Not Available

1993-09-01

The bibliography contains citations concerning the use of marine plants and animals as indicators of organic and inorganic pollutant distribution. Topics include descriptions of specific species and assemblages, regional and local monitoring studies, and analyses of the soft and hard parts of marine animals. Studies of algae, bivalves, corals, crustaceans, bacterial counts, and seagrasses in estuaries and benthic areas are included. (Contains 250 citations and includes a subject term index and title list.)

Sunshine Act: shedding light on inaccurate disclosures at a gynecologic annual meeting.

PubMed

Thompson, Jennifer C; Volpe, Katherine A; Bridgewater, Lindsay K; Qeadan, Fares; Dunivan, Gena C; Komesu, Yuko M; Cichowski, Sara B; Jeppson, Peter C; Rogers, Rebecca G

2016-11-01

Physicians and hospital systems often have relationships with biomedical manufacturers to develop new ideas, products, and further education. Because this relationship can influence medical research and practice, reporting disclosures are necessary to reveal any potential bias and inform consumers. The Sunshine Act was created to develop a new reporting system of these financial relationships called the Open Payments database. Currently all disclosures submitted with research to scientific meetings are at the discretion of the physician. We hypothesized that financial relationships between authors and the medical industry are underreported. We aimed to describe concordance between physicians' financial disclosures listed in the abstract book from the 41st annual scientific meeting of the Society of Gynecologic Surgeons to physician payments reported to the Center for Medicaid and Medicare Services Open Payments database for the same year. Authors and scientific committee members responsible for the content of the 41st annual scientific meeting of the Society of Gynecologic Surgeons were identified from the published abstract book; each abstract listed disclosures for each author. Abstract disclosures were compared with the transactions recorded on the Center for Medicaid and Medicare Services Open Payments database for concordance. Two authors reviewed each nondisclosed Center for Medicaid and Medicare Services listing to determine the relatedness between the company listed on the Center for Medicaid and Medicare Services and abstract content. Abstracts and disclosures of 335 physicians meeting inclusion criteria were reviewed. A total of 209 of 335 physicians (62%) had transactions reported in the Center for Medicaid and Medicare Services, which totaled $1.99 million. Twenty-four of 335 physicians (7%) listed companies with their abstracts; 5 of those 24 physicians were concordant with the Center for Medicaid and Medicare Services. The total amount of all nondisclosed transactions was $1.3 million. Transactions reported in the Center for Medicaid and Medicare Services associated with a single physician ranged from $11.72 to $405,903.36. Of the 209 physicians with Center for Medicaid and Medicare Services transactions that were not disclosed, the majority (68%) had at least 1 company listed in the Center for Medicaid and Medicare Services that was determined after review to be related to the subject of their abstract. Voluntary disclosure of financial relationships was poor, and the majority of unlisted disclosures in the abstract book were companies related to the scientific content of the abstract. Better transparency is needed by physicians responsible for the content presented at gynecological scientific meetings. Copyright © 2016 Elsevier Inc. All rights reserved.

Clinical Effectiveness of Aloe Vera in the Management of Oral Mucosal Diseases- A Systematic Review

PubMed Central

Nair, Gopakumar Ramachandran; Naidu, Giridhar Seetharam; Jain, Supreet; Makkad, Ramanpal Singh; Jha, Abhishek

2016-01-01

Introduction Aloe vera is well known for its medicinal properties which lead to its application in treating various diseases. Its use in treating oral lesions has not been much documented in literature. Aim Although, systematic reviews on aloe vera and its extracts have been done earlier, but in relation to oral diseases this is the first systematic review. The aim of the present systematic review was to compile evidence based studies on the effectiveness of Aloe vera in treatment of various oral diseases. Materials and Methods Computerized literature searches were performed to identify all published articles in the subject. The following databases were used: PUBMED [MEDLINE], SCOPUS, COCHRANE DATABASE, EMBASE and SCIENCE DIRECT using specific keywords. The search was limited to articles published in English or with an English Abstract. All articles (or abstracts if available as abstracts) were read in full. Data were extracted in a predefined fashion. Assessment was done using Jadad score. Results Fifteen studies satisfied the inclusion criteria. Population of sample study ranged from 20 patients to 110 patients with clinically diagnosed oral mucosal lesions. Out of 15 studies, five were on patients with oral lichen planus, two on patients with oral submucous fibrosis, other studies were carried on patients with burning mouth syndrome, radiation induced mucositis, candida associated denture stomatitis, xerostomic patients and four were on minor recurrent apthous stomatitis. Most studies showed statistically significant result demonstrating the effectiveness of Aloe vera in treatment of oral diseases. Conclusion Although there are promising results but in future, more controlled clinical trials are required to prove the effectiveness of Aloe vera for management of oral diseases. PMID:27656587

Stress and well-being at work: A century of empirical trends reflecting theoretical and societal influences.

PubMed

Bliese, Paul D; Edwards, Jeffrey R; Sonnentag, Sabine

2017-03-01

In various forms, research on stress and well-being has been a part of the Journal of Applied Psychology ( JAP ) since its inception. In this review, we examine the history of stress research in JAP by tracking word frequencies from 606 abstracts of published articles in the journal. From these abstracts, we define 3 eras: a 50 year-era from 1917 to 1966, a 30-year era from 1967 to 1996, and a 20-year era from 1997 to the present. Each era is distinct in terms of the number of articles published and the general themes of the topic areas examined. We show that advances in theory are a major impetus underlying research topics and the number of publications. Our review also suggests that articles have increasingly tended to reflect broader events occurring in society such as recessions and workforce changes. We conclude by offering ideas about the future of stress and well-being research. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

NASA Patent Abstracts Bibliography: A Continuing Bibliography. Supplement 58

NASA Technical Reports Server (NTRS)

2001-01-01

This report lists reports, articles and other documents recently announced in the NASA STI Database. Several thousand inventions result each year from the aeronautical and space research supported by the National Aeronautics and Space Administration. The inventions having important use in government programs or significant commercial potential are usually patented by NASA. These inventions cover practically all fields of technology and include many that have useful and valuable commercial application. NASA inventions best serve the interests of the United States when their benefits are available to the public. In many instances, the granting of nonexclusive or exclusive licenses for the practice of these inventions may assist in the accomplishment of this objective. This bibliography is published as a service to companies, firms, and individuals seeking new, licensable products for the commercial market. The NASA Patent Abstracts Bibliography is a semiannual NASA publication containing comprehensive abstracts of NASA owned inventions covered by U.S. patents. The citations included in the bibliography arrangement of citations were originally published in NASA's Scientific and Technical Aerospace Reports (STAR) and cover STAR announcements made since May 1969. The citations published in this issue cover the period July 2000 through December 2000. This issue includes 10 major subject divisions separated into 76 specific categories and one general category/division. This scheme was devised in 1975 and revised in 1987 in lieu of the 34 category divisions which were utilized in supplements (01) through (06) covering STAR abstracts from May 1969 through January 1974. Each entry consists of a STAR citation accompanied by an abstract and, when appropriate, a key illustration taken from the patent or application for patent. Entries are arranged by subject category in ascending order. A typical citation and abstract presents the various data elements included in most records cited. This appears after the table of contents.

Searching fee and non-fee toxicology information resources: an overview of selected databases.

PubMed

Wright, L L

2001-01-12

Toxicology profiles organize information by broad subjects, the first of which affirms identity of the agent studied. Studies here show two non-fee databases (ChemFinder and ChemIDplus) verify the identity of compounds with high efficiency (63% and 73% respectively) with the fee-based Chemical Abstracts Registry file serving well to fill data gaps (100%). Continued searching proceeds using knowledge of structure, scope and content to select databases. Valuable sources for information are factual databases that collect data and facts in special subject areas organized in formats available for analysis or use. Some sources representative of factual files are RTECS, CCRIS, HSDB, GENE-TOX and IRIS. Numerous factual databases offer a wealth of reliable information; however, exhaustive searches probe information published in journal articles and/or technical reports with records residing in bibliographic databases such as BIOSIS, EMBASE, MEDLINE, TOXLINE and Web of Science. Listed with descriptions are numerous factual and bibliographic databases supplied by 11 producers. Given the multitude of options and resources, it is often necessary to seek service desk assistance. Questions were posed by telephone and e-mail to service desks at DIALOG, ISI, MEDLARS, Micromedex and STN International. Results of the survey are reported.

ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining.

PubMed

Lee, Myunggyo; Lee, Kyubum; Yu, Namhee; Jang, Insu; Choi, Ikjung; Kim, Pora; Jang, Ye Eun; Kim, Byounggun; Kim, Sunkyu; Lee, Byungwook; Kang, Jaewoo; Lee, Sanghyuk

2017-01-04

Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. Importantly, we have analyzed RNA-Seq data of the TCGA project covering 4569 patients in 23 cancer types using two reliable programs of FusionScan and TopHat-Fusion. The new user interface supports diverse search options and graphic representation of fusion gene structure. ChimerDB 3.0 is available at http://ercsb.ewha.ac.kr/fusiongene/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Review of HaNDLE-on-QoL: a database of published papers that use questionnaires to report quality of life in patients with cancer of the head and neck.

PubMed

Wotherspoon, R J; Kanatas, A N; Rogers, S N

2018-02-01

HaNDLE-on-QoL (Head And Neck Database Listing Evidence on QoL) is a searchable database that comprises abstracts of papers that have used questionnaires to report on quality of life (QoL) in patients with cancer of the head and neck. It can be searched by title, first author, year of publication, words used in the abstract, site of cancer, study design, and questionnaires used. The aim of this paper was to summarise its contents. In May 2017 we searched the website using the criteria above. It contained 1498 papers (including 149 reviews), and the number is increasing each year. Most studies concerned a combination of subsites in the head and neck (n=871); 180 focused specifically on oral sites, and 109 on the larynx. The commonest topics were swallowing (n=353), speech (n=299), pain (n=292), emotions (n=226), and depression (n=193). Nearly all the papers concerned function or predictors of health-related QoL (HRQoL), but 98 were clinical or randomised controlled trials. The site included over 250 questionnaires of which the most common were the European Organisation for Research and Treatment of Cancer C30 (EORTC-C30, n=369), the EORTC-head and neck 35 (EORTC H&N35, n=353), and the University of Washington Quality of Life (UWQoL) (n=276). HaNDLE-on-QoL highlights the complexity of QoL after treatment and the diversity and range of the studies. It is a useful point of reference for those involved in clinical practice or research. Copyright © 2017 The British Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Barriers related to prenatal care utilization among women

PubMed Central

Roozbeh, Nasibeh; Nahidi, Fatemeh; Hajiyan, Sepideh

2016-01-01

Objectives To investigate barriers related to prenatal care utilization among women. Methods Data was collected in both English and Persian databases. English databases included: the International Medical Sciences, Medline, Web of Science, Scopus, Google Scholar. The Persian databases included: the Iranmedex, the State Inpatient Databases (SID) with the use of related keywords, and on the basis of inclusion-exclusion criteria. The keywords included are barrier, prenatal care, women, access, and preventive factors. OR and AND were Boolean operators. After the study, articles were summarized, unrelated articles were rejected, and related articles were identified. Inclusion criteria were all published articles from 1990 to 2015, written in English and Persian languages. The titles and abstracts are related, and addressed all subjects about barriers related to prenatal care utilization. At the end, all duplicated articles were excluded. There were no restrictions for exclusion or inclusion of articles. Exclusion criteria were failure in reporting in studies, case studies, and lack of access to the full text. Results After searching various databases, 112 related articles were included. After reviewing articles’ titles, 67 unrelated articles and abstracts were rejected, 45 articles were evaluated, 20 of them were duplicated. Then, the qualities of 25 articles were analyzed. Therefore, 5 articles were excluded due to not mentioning the sample size, mismatches between method and data, or results. Total of 20 articles were selected for final analysis. Prenatal care utilization barrier can be divided into various domains such as individual barriers, financial barriers, organizational barriers, social, and cultural barriers. Conclusion To increase prenatal care coverage, it is necessary to pay attention to all domains, especially individual and financial barriers.

Saccharomyces genome database informs human biology

PubMed Central

Skrzypek, Marek S; Nash, Robert S; Wong, Edith D; MacPherson, Kevin A; Karra, Kalpana; Binkley, Gail; Simison, Matt; Miyasato, Stuart R

2018-01-01

Abstract The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existing data, and to organize them into a comprehensive and up-to-date information resource. The primary mission of SGD is to facilitate research into the biology of yeast and to provide this wealth of information to advance, in many ways, research on other organisms, even those as evolutionarily distant as humans. To build such a bridge between biological kingdoms, SGD is curating data regarding yeast-human complementation, in which a human gene can successfully replace the function of a yeast gene, and/or vice versa. These data are manually curated from published literature, made available for download, and incorporated into a variety of analysis tools provided by SGD. PMID:29140510

Digital database architecture and delineation methodology for deriving drainage basins, and a comparison of digitally and non-digitally derived numeric drainage areas

USGS Publications Warehouse

Dupree, Jean A.; Crowfoot, Richard M.

2012-01-01

The drainage basin is a fundamental hydrologic entity used for studies of surface-water resources and during planning of water-related projects. Numeric drainage areas published by the U.S. Geological Survey water science centers in Annual Water Data Reports and on the National Water Information Systems (NWIS) Web site are still primarily derived from hard-copy sources and by manual delineation of polygonal basin areas on paper topographic map sheets. To expedite numeric drainage area determinations, the Colorado Water Science Center developed a digital database structure and a delineation methodology based on the hydrologic unit boundaries in the National Watershed Boundary Dataset. This report describes the digital database architecture and delineation methodology and also presents the results of a comparison of the numeric drainage areas derived using this digital methodology with those derived using traditional, non-digital methods. (Please see report for full Abstract)

Scientometrics of zoonoses transmitted by the giant African snail Achatina fulica Bowdich, 1822

PubMed Central

Pavanelli, Gilberto Cezar; Yamaguchi, Mirian Ueda; Calaça, Elaine Alves; Oda, Fabrício Hiroiuki

2017-01-01

ABSTRACT The dissemination of the giant African snail Achatina fulica in several countries has triggered a great number of studies on the mollusk, including those on zoonoses related to health in humans. The current research is a scientific survey on articles published in four databases, namely, PubMed, Bireme, Scielo and Lilacs. Results indicate that Brazil has a prominent position in international scientific production on this subject, with focus on Angiostrongylus cantonensis occurrences. PMID:28423090

Multi-Database Searching in the Behavioral Sciences--Part I: Basic Techniques and Core Databases.

ERIC Educational Resources Information Center

Angier, Jennifer J.; Epstein, Barbara A.

1980-01-01

Outlines practical searching techniques in seven core behavioral science databases accessing psychological literature: Psychological Abstracts, Social Science Citation Index, Biosis, Medline, Excerpta Medica, Sociological Abstracts, ERIC. Use of individual files is discussed and their relative strengths/weaknesses are compared. Appended is a list…

Where Full-Text Is Viable.

ERIC Educational Resources Information Center

Cotton, P. L.

1987-01-01

Defines two types of online databases: source, referring to those intended to be complete in themselves, whether full-text or abstracts; and bibliographic, meaning those that are not complete. Predictions are made about the future growth rate of these two types of databases, as well as full-text versus abstract databases. (EM)

Protocol for a systematic review of screening tools for fear of recurrent illness in common life-threatening diseases.

PubMed

Jones, Jenny; Kane, Paul; Polson, Rob; Leslie, Stephen J; Hulbert-Williams, Nicholas J; Simard, Sébastien; Ozakinci, Gozde; Hubbard, Gill

2015-03-19

A myocardial infarction (MI) ('heart attack') can be intensely stressful, and the impact of this event can leave patients with clinically significant post-MI stress symptoms. Untreated stress can make heart disease worse. Few tools are available that screen for specific thoughts or beliefs that can trigger post-MI stress responses. In other life-threatening illnesses, fear of recurrence (FoR) of illness has been identified as a key stressor, and screening tools have been developed to identify this. The aim of this review is to identify FoR screening tools used in other common life-threatening diseases that report on the development of the tool, to assess if there are any that can be adapted for use in MI survivors so that those with high levels of FoR can be identified and helped. The review will evaluate full FoR screening tools and methods of measurement used in common life-threatening disease clinical populations. The Campbell and Cochrane Libraries, Cumulative Index of Nursing and Allied Health Literature (CINAHL), PsycINFO, MEDLINE, Embase, Applied Social Sciences Index and Abstracts (ASSIA), Published International Literature on Traumatic Stress (PILOTS), Social Services Abstracts, Sociological Abstracts, Web of Knowledge, Health and Psychosocial Instruments and SCOPUS databases will be searched for relevant studies published from database inception. Reference lists and published reviews/meta-analyses will also be searched. All titles and abstracts will be screened and relevant full-text versions retrieved by two reviewers, who will then extract all the data. Each will independently review all data extracted by the other. Selected studies will also be assessed by two independent researchers using the COnsensus-based standards for the Selection of health status measurement INstruments (COSMIN) checklist and other quality criteria. This will be done to evaluate the degree to which their measurement properties meet the standards for good methodological quality. Disagreement will be resolved through consensus. Untreated post-MI stress has a considerable psychological and physical impact on MI survivors. Therefore, there is a critical need to develop a screening tool to identify fear of recurrent MI so that those affected can be identified and directed to appropriate support interventions. This proposed research will enable a tool to be developed and adapted for use in the MI survivor patient population. CRD42014010500.

Validation of chronic obstructive pulmonary disease (COPD) diagnoses in healthcare databases: a systematic review protocol.

PubMed

Rimland, Joseph M; Abraha, Iosief; Luchetta, Maria Laura; Cozzolino, Francesco; Orso, Massimiliano; Cherubini, Antonio; Dell'Aquila, Giuseppina; Chiatti, Carlos; Ambrosio, Giuseppe; Montedori, Alessandro

2016-06-01

Healthcare databases are useful sources to investigate the epidemiology of chronic obstructive pulmonary disease (COPD), to assess longitudinal outcomes in patients with COPD, and to develop disease management strategies. However, in order to constitute a reliable source for research, healthcare databases need to be validated. The aim of this protocol is to perform the first systematic review of studies reporting the validation of codes related to COPD diagnoses in healthcare databases. MEDLINE, EMBASE, Web of Science and the Cochrane Library databases will be searched using appropriate search strategies. Studies that evaluated the validity of COPD codes (such as the International Classification of Diseases 9th Revision and 10th Revision system; the Real codes system or the International Classification of Primary Care) in healthcare databases will be included. Inclusion criteria will be: (1) the presence of a reference standard case definition for COPD; (2) the presence of at least one test measure (eg, sensitivity, positive predictive values, etc); and (3) the use of a healthcare database (including administrative claims databases, electronic healthcare databases or COPD registries) as a data source. Pairs of reviewers will independently abstract data using standardised forms and will assess quality using a checklist based on the Standards for Reporting of Diagnostic accuracy (STARD) criteria. This systematic review protocol has been produced in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocol (PRISMA-P) 2015 statement. Ethics approval is not required. Results of this study will be submitted to a peer-reviewed journal for publication. The results from this systematic review will be used for outcome research on COPD and will serve as a guide to identify appropriate case definitions of COPD, and reference standards, for researchers involved in validating healthcare databases. CRD42015029204. 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/

Athletic groin pain: a systematic review of surgical diagnoses, investigations and treatment.

PubMed

de Sa, Darren; Hölmich, Per; Phillips, Mark; Heaven, Sebastian; Simunovic, Nicole; Philippon, Marc J; Ayeni, Olufemi R

2016-10-01

Athletic groin pain requiring surgery remains a diagnostic and therapeutic challenge. This systematic review aims to identify the most common causes of groin pain in athletes requiring surgery. Additionally, it aims to further characterise their susceptible athlete profiles, common physical examination and imaging techniques, and surgical procedures performed. This will enable the orthopaedic sports medicine clinician/surgeon to best treat these patients. The electronic databases MEDLINE, PubMed and EMBASE were searched from database inception to 13 August 2014 for studies in the English language that addressed athletic groin pain necessitating surgery. The search was updated on 4 August 2015 to find any articles published after the original search. The studies were systematically screened and data were abstracted in duplicate, with descriptive data presented. A total of 73 articles were included within our study, with data from 4655 patients abstracted. Overall, intra-articular and extra-articular causes of groin pain in athletes requiring surgery were equal. The top five causes for pain were: femoroacetabular impingement (FAI) (32%), athletic pubalgia (24%), adductor-related pathology (12%), inguinal pathology (10%) and labral pathology (5%), with 35% of this labral pathology specifically attributed to FAI. Given the complex anatomy, equal intra-articular and extra-articular contribution, and potential for overlap of clinical entities causing groin pain leading to surgery in athletes, further studies are required to ascertain the finer details regarding specific exam manoeuvres, imaging views and surgical outcomes to best treat this patient population. 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/

Occupational dose reduction at Department of Energy contractor facilities: Bibliography of selected readings in radiation protection and ALARA; Volume 5

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

Dionne, B.J.; Sullivan, S.G.; Baum, J.W.

1994-01-01

Promoting the exchange of information related to implementation of the As Low as Reasonably Achievable (ALARA) philosophy is a continuing objective for the Department of Energy (DOE). This report was prepared by the Brookhaven National Laboratory (BNL) ALARA Center for the DOE Office of Health. It contains the fifth in a series of bibliographies on dose reduction at DOE facilities. The BNL ALARA Center was originally established in 1983 under the sponsorship of the Nuclear Regulatory Commission to monitor dose-reduction research and ALARA activities at nuclear power plants. This effort was expanded in 1988 by the DOE`s Office of Environment,more » Safety and Health, to include DOE nuclear facilities. This bibliography contains abstracts relating to various aspects of ALARA program implementation and dose-reduction activities, with a specific focus on DOE facilities. Abstracts included in this bibliography were selected from proceedings of technical meetings, journals, research reports, searches of the DOE Energy, Science and Technology Database (in general, the citation and abstract information is presented as obtained from this database), and reprints of published articles provided by the authors. Facility types and activities covered in the scope of this report include: radioactive waste, uranium enrichment, fuel fabrication, spent fuel storage and reprocessing, facility decommissioning, hot laboratories, tritium production, research, test and production reactors, weapons fabrication and testing, fusion, uranium and plutonium processing, radiography, and accelerators. Information on improved shielding design, decontamination, containments, robotics, source prevention and control, job planning, improved operational and design techniques, as well as on other topics, has been included. In addition, DOE/EH reports not included in previous volumes of the bibliography are in this volume (abstracts 611 to 684). This volume (Volume 5 of the series) contains 217 abstracts.« less

Analysis of conference abstract-to-publication rate in UK orthopaedic research.

PubMed

Collier, Thomas; Roadley-Battin, Michelle; Darlow, Chloe; Chant, Philip; Hing, Caroline B; Smith, Toby O

2018-02-01

Presentation of research at orthopaedic conferences is an important component for surgical evidence-based practice. However, there remains uncertainty as to how many conference abstracts proceed to achieve full-text publication (FTP) for wider dissemination. This study aimed to determine the abstract-to-publication rate (APR) of research presented in the largest hip and knee orthopaedic meetings in the UK, and to identify predictive factors which influence the APR. All published abstracts (n=744) from the 2006, 2008, 2009 and 2010 British Hip Society (BHS) and the 2007, 2009, 2010 and 2011 British Association for Surgery of the Knee (BASK) annual conference meetings were examined by four researchers independently. To determine whether abstracts had been published in full-text form, Google Scholar, Medline and EMBASE evidence databases were used to verify FTP status. Variables including sample size, statistical significance, grade of the first author, research affiliated institution and research design were extracted and analysed to identify whether these were associated with FTP. 176 out of 744 abstracts achieved FTP status (APR: 23.7%). Factors associated with FTP status included statistically significant results (P<0.01) and research design (P=0.02). Factors not associated included sample size, grade of the first author and research affiliated institution (P>0.05). APRs of the assessed BHS and BASK annual conference presentations are low in comparison to other scientific meetings. Encouragement should be provided to clinicians and academics to submit their work for publication to address this short fall, thereby enhancing the potential for full-text research publications to inform evidence-based orthopaedics. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Traditional Chinese Medical Journals currently published in mainland China.

PubMed

Fan, Wei-Yu; Tong, Yuan-Yuan; Pan, Yan-Li; Shang, Wen-Ling; Shen, Jia-Yi; Li, Wei; Li, Li-Jun

2008-06-01

Traditional Chinese Medical (TCM) journals have been playing an important role in scholarly communication in China. However, the information in those periodicals was not enough for international readers. This study aims to provide an overview of TCM journals in China. TCM journals currently published in mainland China were identified from Chinese databases and journal subscription catalogs. Data on publication start year, publishing region, language, whether core journals, whether indexed in famous international databases, with/without accessible URL were investigated, and subjects of journals were categorized. One hundred and forty-nine (149) TCM journals are currently published in mainland China; 88.59% of them are academic journals. The subjects of those journals are various, ranging from the general TCM, integrative medicine, herbal medicines, to veterinary TCM. The publishing areas are distributed in 27 regions, with Beijing having the most TCM journals published. One hundred and forty-two (142) of those periodicals are in Chinese, while 4 are also in English, and 3 in other languages. Only 8 TCM journals were recognized as core journals, and 5 were identified as both core journals and journals with high impacted articles by all evaluation systems in China. A few of the TCM journals from mainland China are indexed in PubMed/MEDLINE (10), EMBASE (5), Biological Abstracts (2), or AMED (1). Online full-text Chinese databases CJFD, COJ, and CSTPD cover most of TCM the journals published in the country. One hundred (100) TCM journals have accessible URLs, but only 3 are open access with free full texts. Publication of TCM journals in China has been active in academic communication in the past 20 years. However, only a few of them received recognized high evaluation. English information from them is not sufficient. Open access is not extensively acceptable. The accessibility of those journals to international readers needs to be improved.

Nuclear science abstracts (NSA) database 1948--1974 (on the Internet)

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

NONE

Nuclear Science Abstracts (NSA) is a comprehensive abstract and index collection of the International Nuclear Science and Technology literature for the period 1948 through 1976. Included are scientific and technical reports of the US Atomic Energy Commission, US Energy Research and Development Administration and its contractors, other agencies, universities, and industrial and research organizations. Coverage of the literature since 1976 is provided by Energy Science and Technology Database. Approximately 25% of the records in the file contain abstracts. These are from the following volumes of the print Nuclear Science Abstracts: Volumes 12--18, Volume 29, and Volume 33. The database containsmore » over 900,000 bibliographic records. All aspects of nuclear science and technology are covered, including: Biomedical Sciences; Metals, Ceramics, and Other Materials; Chemistry; Nuclear Materials and Waste Management; Environmental and Earth Sciences; Particle Accelerators; Engineering; Physics; Fusion Energy; Radiation Effects; Instrumentation; Reactor Technology; Isotope and Radiation Source Technology. The database includes all records contained in Volume 1 (1948) through Volume 33 (1976) of the printed version of Nuclear Science Abstracts (NSA). This worldwide coverage includes books, conference proceedings, papers, patents, dissertations, engineering drawings, and journal literature. This database is now available for searching through the GOV. Research Center (GRC) service. GRC is a single online web-based search service to well known Government databases. Featuring powerful search and retrieval software, GRC is an important research tool. The GRC web site is at http://grc.ntis.gov.« less

An automated procedure to identify biomedical articles that contain cancer-associated gene variants.

PubMed

McDonald, Ryan; Scott Winters, R; Ankuda, Claire K; Murphy, Joan A; Rogers, Amy E; Pereira, Fernando; Greenblatt, Marc S; White, Peter S

2006-09-01

The proliferation of biomedical literature makes it increasingly difficult for researchers to find and manage relevant information. However, identifying research articles containing mutation data, a requisite first step in integrating large and complex mutation data sets, is currently tedious, time-consuming and imprecise. More effective mechanisms for identifying articles containing mutation information would be beneficial both for the curation of mutation databases and for individual researchers. We developed an automated method that uses information extraction, classifier, and relevance ranking techniques to determine the likelihood of MEDLINE abstracts containing information regarding genomic variation data suitable for inclusion in mutation databases. We targeted the CDKN2A (p16) gene and the procedure for document identification currently used by CDKN2A Database curators as a measure of feasibility. A set of abstracts was manually identified from a MEDLINE search as potentially containing specific CDKN2A mutation events. A subset of these abstracts was used as a training set for a maximum entropy classifier to identify text features distinguishing "relevant" from "not relevant" abstracts. Each document was represented as a set of indicative word, word pair, and entity tagger-derived genomic variation features. When applied to a test set of 200 candidate abstracts, the classifier predicted 88 articles as being relevant; of these, 29 of 32 manuscripts in which manual curation found CDKN2A sequence variants were positively predicted. Thus, the set of potentially useful articles that a manual curator would have to review was reduced by 56%, maintaining 91% recall (sensitivity) and more than doubling precision (positive predictive value). Subsequent expansion of the training set to 494 articles yielded similar precision and recall rates, and comparison of the original and expanded trials demonstrated that the average precision improved with the larger data set. Our results show that automated systems can effectively identify article subsets relevant to a given task and may prove to be powerful tools for the broader research community. This procedure can be readily adapted to any or all genes, organisms, or sets of documents. Published 2006 Wiley-Liss, Inc.

Using multi-criteria decision analysis to appraise orphan drugs: a systematic review.

PubMed

Friedmann, Carlotta; Levy, Pierre; Hensel, Paul; Hiligsmann, Mickaël

2018-04-01

Multi-criteria decision analysis (MCDA) could potentially solve current methodological difficulties in the appraisal of orphan drugs. Areas covered: We provide an overview of the existing evidence regarding the use of MCDA in the appraisal of orphan drugs worldwide. Three databases (Pubmed, Embase, Web of Science) were searched for English, French and German literature published between January 2000 and April 2017. Full-text articles were supplemented with conference abstracts. A total of seven articles and six abstracts were identified. Expert commentary: The literature suggests that MCDA is increasingly being used in the context of appraising orphan drugs. It has shown itself to be a flexible approach with the potential to assist in decision-making regarding reimbursement for orphan drugs. However, further research regarding its application must be conducted.

Database Overlap vs. Complementary Coverage in Forestry and Forest Products: Factors in Database Acquisition.

ERIC Educational Resources Information Center

Hoover, Ryan E.

This study examines (1) subject content, (2) file size, (3) types of documents indexed, (4) range of years spanned, and (5) level of indexing and abstracting in five databases which collectively provide extensive coverage of the forestry and forest products industries: AGRICOLA, CAB ABSTRACTS, FOREST PRODUCTS (AIDS), PAPERCHEM, and PIRA. The…

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.

[Application of ultrasound counter currentextraction in patent of traditional Chinese medicine].

PubMed

Miao, Yan-ni; Wu, Bin; Yue, Xue-lian

2015-07-01

The patent information of ultrasound countercurrent extraction used in traditional Chinese medicine was analyzed in this paper by the samples from Derwent World Patent Database (DWPI) and the Chinese Patent Abstracts Database (CNABS). The application of ultrasound countercurrent was discussed with the patent applicant,the amount of the annual distribution, and the pharmaceutical raw materials and other aspects. While the technical parameters published in the patent was deeply analyzed, such as material crushing, extraction solvent, extraction time and temperature, extraction equipment and ultrasonic frequency. Thought above research, various technical parameters of ultrasound countercurrent extraction used in traditional Chinese was summarize. The analysis conclusion of the paper can be used in discovering the technical advantages, optimizing extraction conditions, and providing a reference to extraction technological innovation of traditional Chinese medicine.

Emotional intelligence education in pre-registration nursing programmes: an integrative review.

PubMed

Foster, Kim; McCloughen, Andrea; Delgado, Cynthia; Kefalas, Claudia; Harkness, Emily

2015-03-01

To investigate the state of knowledge on emotional intelligence (EI) education in pre-registration nursing programmes. Integrative literature review. CINAHL, Medline, Scopus, ERIC, and Web of Knowledge electronic databases were searched for abstracts published in English between 1992-2014. Data extraction and constant comparative analysis of 17 articles. Three categories were identified: Constructs of emotional intelligence; emotional intelligence curricula components; and strategies for emotional intelligence education. A wide range of emotional intelligence constructs were found, with a predominance of trait-based constructs. A variety of strategies to enhance students' emotional intelligence skills were identified, but limited curricula components and frameworks reported in the literature. An ability-based model for curricula and learning and teaching approaches is recommended. Copyright © 2014. Published by Elsevier Ltd.

Tools for evaluation of restriction on auditory participation: systematic review of the literature.

PubMed

Souza, Valquíria Conceição; Lemos, Stela Maris Aguiar

2015-01-01

To systematically review studies that used questionnaires for the evaluation of restriction on auditory participation in adults and the elderly. Studies from the last five years were selected through a bibliographic collection of data in national and international journals in the following electronic databases: ISI Web of Science and Virtual Health Library - BIREME, which includes the LILACS and MEDLINE databases. Studies available fully; published in Portuguese, English, or Spanish; whose participants were adults and/or the elderly and that used questionnaires for the evaluation of restriction on auditory participation. Initially, the studies were selected based on the reading of titles and abstracts. Then, the articles were fully and the information was included in the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) checklist. Three-hundred seventy studies were found in the researched databases; 14 of these studies were excluded because they were found in more than one database. The titles and abstracts of 356 articles were analyzed; 40 of them were selected for full reading, of which 26 articles were finally selected. In the present review, nine instruments were found for the evaluation of restriction on auditory participation. The most used questionnaires for the assessment of the restriction on auditory participation were the Hearing Handicap Inventory for the Elderly (HHIE), Hearing Handicap Inventory for Adults (HHIA), and Hearing Handicap Inventory for the Elderly - Screening (HHIE-S). The use of restriction on auditory participation questionnaires can assist in validating decisions in audiology practices and be useful in the fitting of hearing aids and results of aural rehabilitation.

MGDB: a comprehensive database of genes involved in melanoma.

PubMed

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

2015-01-01

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

Biomedical journals and databases in Russia and Russian language in the former Soviet Union and beyond

PubMed Central

Vlassov, Vasiliy V; Danishevskiy, Kirill D

2008-01-01

In the 20th century, Russian biomedical science experienced a decline from the blossom of the early years to a drastic state. Through the first decades of the USSR, it was transformed to suit the ideological requirements of a totalitarian state and biased directives of communist leaders. Later, depressing economic conditions and isolation from the international research community further impeded its development. Contemporary Russia has inherited a system of medical education quite different from the west as well as counterproductive regulations for the allocation of research funding. The methodology of medical and epidemiological research in Russia is largely outdated. Epidemiology continues to focus on infectious disease and results of the best studies tend to be published in international periodicals. MEDLINE continues to be the best database to search for Russian biomedical publications, despite only a small proportion being indexed. The database of the Moscow Central Medical Library is the largest national database of medical periodicals, but does not provide abstracts and full subject heading codes, and it does not cover even the entire collection of the Library. New databases and catalogs (e.g. Panteleimon) that have appeared recently are incomplete and do not enable effective searching. PMID:18826569

Viral taxonomy needs a spring clean; its exploration era is over.

PubMed

Gibbs, Adrian J

2013-08-09

The International Committee on Taxonomy of Viruses has recently changed its approved definition of a viral species, and also discontinued work on its database of virus descriptions. These events indicate that the exploration era of viral taxonomy has ended; over the past century the principles of viral taxonomy have been established, the tools for phylogenetic inference invented, and the ultimate discriminatory data required for taxonomy, namely gene sequences, are now readily available. Further changes would make viral taxonomy more informative. First, the status of a 'taxonomic species' with an italicized name should only be given to viruses that are specifically linked with a single 'type genomic sequence' like those in the NCBI Reference Sequence Database. Secondly all approved taxa should be predominately monophyletic, and uninformative higher taxa disendorsed. These are 'quality assurance' measures and would improve the value of viral nomenclature to its users. The ICTV should also promote the use of a public database, such as Wikipedia, to replace the ICTV database as a store of the primary metadata of individual viruses, and should publish abstracts of the ICTV Reports in that database, so that they are 'Open Access'.

Biomedical journals and databases in Russia and Russian language in the former Soviet Union and beyond.

PubMed

Vlassov, Vasiliy V; Danishevskiy, Kirill D

2008-09-30

In the 20th century, Russian biomedical science experienced a decline from the blossom of the early years to a drastic state. Through the first decades of the USSR, it was transformed to suit the ideological requirements of a totalitarian state and biased directives of communist leaders. Later, depressing economic conditions and isolation from the international research community further impeded its development. Contemporary Russia has inherited a system of medical education quite different from the west as well as counterproductive regulations for the allocation of research funding. The methodology of medical and epidemiological research in Russia is largely outdated. Epidemiology continues to focus on infectious disease and results of the best studies tend to be published in international periodicals. MEDLINE continues to be the best database to search for Russian biomedical publications, despite only a small proportion being indexed. The database of the Moscow Central Medical Library is the largest national database of medical periodicals, but does not provide abstracts and full subject heading codes, and it does not cover even the entire collection of the Library. New databases and catalogs (e.g. Panteleimon) that have appeared recently are incomplete and do not enable effective searching.

Economic evaluation of manual therapy for musculoskeletal diseases: a protocol for a systematic review and narrative synthesis of evidence.

PubMed

Kim, Chang-Gon; Mun, Su-Jeong; Kim, Ka-Na; Shin, Byung-Cheul; Kim, Nam-Kwen; Lee, Dong-Hyo; Lee, Jung-Han

2016-05-13

Manual therapy is the non-surgical conservative management of musculoskeletal disorders using the practitioner's hands on the patient's body for diagnosing and treating disease. The aim of this study is to systematically review trial-based economic evaluations of manual therapy relative to other interventions used for the management of musculoskeletal diseases. Randomised clinical trials (RCTs) on the economic evaluation of manual therapy for musculoskeletal diseases will be included in the review. The following databases will be searched from their inception: Medline, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), Cumulative Index to Nursing and Allied Health Literature (CINAHL), Econlit, Mantis, Index to Chiropractic Literature, Science Citation Index, Social Science Citation Index, Allied and Complementary Medicine Database (AMED), Cochrane Database of Systematic Reviews (CDSR), National Health Service Database of Abstracts of Reviews of Effects (NHS DARE), National Health Service Health Technology Assessment Database (NHS HTA), National Health Service Economic Evaluation Database (NHS EED), CENTRAL, five Korean medical databases (Oriental Medicine Advanced Searching Integrated System (OASIS), Research Information Service System (RISS), DBPIA, Korean Traditional Knowledge Portal (KTKP) and KoreaMed) and three Chinese databases (China National Knowledge Infrastructure (CNKI), VIP and Wanfang). The evidence for the cost-effectiveness, cost-utility and cost-benefit of manual therapy for musculoskeletal diseases will be assessed as the primary outcome. Health-related quality of life and adverse effects will be assessed as secondary outcomes. We will critically appraise the included studies using the Cochrane risk of bias tool and the Drummond checklist. Results will be summarised using Slavin's qualitative best-evidence synthesis approach. The results of the study will be disseminated via a peer-reviewed journal and/or conference presentations. PROSPERO CRD42015026757. 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/

Validity of breast, lung and colorectal cancer diagnoses in administrative databases: a systematic review protocol.

PubMed

Abraha, Iosief; Giovannini, Gianni; Serraino, Diego; Fusco, Mario; Montedori, Alessandro

2016-03-18

Breast, lung and colorectal cancers constitute the most common cancers worldwide and their epidemiology, related health outcomes and quality indicators can be studied using administrative healthcare databases. To constitute a reliable source for research, administrative healthcare databases need to be validated. The aim of this protocol is to perform the first systematic review of studies reporting the validation of International Classification of Diseases 9th and 10th revision codes to identify breast, lung and colorectal cancer diagnoses in administrative healthcare databases. This review protocol has been developed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocol (PRISMA-P) 2015 statement. We will search the following databases: MEDLINE, EMBASE, Web of Science and the Cochrane Library, using appropriate search strategies. We will include validation studies that used administrative data to identify breast, lung and colorectal cancer diagnoses or studies that evaluated the validity of breast, lung and colorectal cancer codes in administrative data. The following inclusion criteria will be used: (1) the presence of a reference standard case definition for the disease of interest; (2) the presence of at least one test measure (eg, sensitivity, positive predictive values, etc) and (3) the use of data source from an administrative database. Pairs of reviewers will independently abstract data using standardised forms and will assess quality using a checklist based on the Standards for Reporting of Diagnostic accuracy (STARD) criteria. Ethics approval is not required. We will submit results of this study to a peer-reviewed journal for publication. The results will serve as a guide to identify appropriate case definitions and algorithms of breast, lung and colorectal cancers for researchers involved in validating administrative healthcare databases as well as for outcome research on these conditions that used administrative healthcare databases. CRD42015026881. 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/

Does providing dental services reduce overall health care costs?: A systematic review of the literature.

PubMed

Elani, Hawazin W; Simon, Lisa; Ticku, Shenam; Bain, Paul A; Barrow, Jane; Riedy, Christine A

2018-06-01

The authors conducted a systematic review of the literature to assess the impact of dental treatment on overall health care costs for patients with chronic health conditions and patients who were pregnant. The authors searched multiple databases including MEDLINE, Embase, Web of Science, and Dentistry & Oral Sciences Source from the earliest date available through May 2017. Two reviewers conducted the initial screening of all retrieved titles and abstracts, read the full text of the eligible studies, and conducted data extraction and quality assessment of included studies. The authors found only 3 published studies that examined the effect of periodontal treatment on health care costs using medical and dental claims data from different insurance databases. Findings from the qualitative synthesis of those studies were inconclusive as 1 of the 3 studies showed a cost increase, whereas 2 studies showed a decrease. The small number of studies and their mixed outcomes demonstrate the need for high-quality studies to evaluate the effect of periodontal intervention on overall health care costs. Copyright © 2018 American Dental Association. Published by Elsevier Inc. All rights reserved.

Ten-year analysis of hepatitis-related papers in the Middle East: a web of science-based scientometric study.

PubMed

Rezaee Zavareh, Mohammad Saeid; Alavian, Seyed Moayed

2017-01-01

In the Middle East (ME), the proper understanding of hepatitis, especially viral hepatitis, is considered to be extremely important. However, no published paper has investigated the status of hepatitis-related research in the ME. A scientometric analysis based on the Web of Science database was conducted on hepatitis-related papers in the ME to determine the current status of research on this topic. A scientometric analysis using the Web of Science database, specifically articles from the Expanded Science Citation Index and Social Sciences Citation Index, was conducted on work published between 2005 and 2014 using the keyword "hepatitis" in conjunction with the names of countries in the ME. Of 103,096 papers that used the word "hepatitis" in their title, abstract, or keywords, only 6,540 papers (6.34%) were associated with countries in the ME. Turkey, Iran, Egypt, Israel, and Saudi Arabia were the top five countries in which hepatitis-related papers were published. Most papers on hepatitis A, B, and D and autoimmune hepatitis were published in Turkey, and most papers on hepatitis C were published in Egypt. We believe that both the quantity and the quality of hepatitis-related papers in this region should be improved. Implementing multicenter and international research projects, holding conferences and congress meetings, conducting educational workshops, and establishing high-quality medical research journals in the region will help countries in the ME address this issue effectively.

Harnessing the wealth of Chinese scientific literature: schistosomiasis research and control in China

PubMed Central

Liu, Qin; Tian, Li-Guang; Xiao, Shu-Hua; Qi, Zhen; Steinmann, Peter; Mak, Tippi K; Utzinger, Jürg; Zhou, Xiao-Nong

2008-01-01

The economy of China continues to boom and so have its biomedical research and related publishing activities. Several so-called neglected tropical diseases that are most common in the developing world are still rampant or even emerging in some parts of China. The purpose of this article is to document the significant research potential from the Chinese biomedical bibliographic databases. The research contributions from China in the epidemiology and control of schistosomiasis provide an excellent illustration. We searched two widely used databases, namely China National Knowledge Infrastructure (CNKI) and VIP Information (VIP). Employing the keyword "Schistosoma" () and covering the period 1990–2006, we obtained 10,244 hits in the CNKI database and 5,975 in VIP. We examined 10 Chinese biomedical journals that published the highest number of original research articles on schistosomiasis for issues including languages and open access. Although most of the journals are published in Chinese, English abstracts are usually available. Open access to full articles was available in China Tropical Medicine in 2005/2006 and is granted by the Chinese Journal of Parasitology and Parasitic Diseases since 2003; none of the other journals examined offered open access. We reviewed (i) the discovery and development of antischistosomal drugs, (ii) the progress made with molluscicides and (iii) environmental management for schistosomiasis control in China over the past 20 years. In conclusion, significant research is published in the Chinese literature, which is relevant for local control measures and global scientific knowledge. Open access should be encouraged and language barriers removed so the wealth of Chinese research can be more fully appreciated by the scientific community. PMID:18826598

The Eclipsing Binary On-Line Atlas (EBOLA)

NASA Astrophysics Data System (ADS)

Bradstreet, D. H.; Steelman, D. P.; Sanders, S. J.; Hargis, J. R.

2004-05-01

In conjunction with the upcoming release of \\it Binary Maker 3.0, an extensive on-line database of eclipsing binaries is being made available. The purposes of the atlas are: \\begin {enumerate} Allow quick and easy access to information on published eclipsing binaries. Amass a consistent database of light and radial velocity curve solutions to aid in solving new systems. Provide invaluable querying capabilities on all of the parameters of the systems so that informative research can be quickly accomplished on a multitude of published results. Aid observers in establishing new observing programs based upon stars needing new light and/or radial velocity curves. Encourage workers to submit their published results so that others may have easy access to their work. Provide a vast but easily accessible storehouse of information on eclipsing binaries to accelerate the process of understanding analysis techniques and current work in the field. \\end {enumerate} The database will eventually consist of all published eclipsing binaries with light curve solutions. The following information and data will be supplied whenever available for each binary: original light curves in all bandpasses, original radial velocity observations, light curve parameters, RA and Dec, V-magnitudes, spectral types, color indices, periods, binary type, 3D representation of the system near quadrature, plots of the original light curves and synthetic models, plots of the radial velocity observations with theoretical models, and \\it Binary Maker 3.0 data files (parameter, light curve, radial velocity). The pertinent references for each star are also given with hyperlinks directly to the papers via the NASA Abstract website for downloading, if available. In addition the Atlas has extensive searching options so that workers can specifically search for binaries with specific characteristics. The website has more than 150 systems already uploaded. The URL for the site is http://ebola.eastern.edu/.

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

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

NONE

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

Process improvement: a multi-registry database abstraction success story.

PubMed

Abrich, Victor; Rokey, Roxann; Devadas, Christopher; Uebel, Julie

2014-01-01

The St. Joseph Hospital/Marshfield Clinic Cardiac Database Registry submits data to the National Cardiovascular Data Registry (NCDR) and to the Society of Thoracic Surgeons (STS) National Database. Delayed chart abstraction is problematic, since hospital policy prohibits patient care clarifications made to the medical record more than 1 month after hospital discharge. This can also lead to late identification of missed care opportunities and untimely notification to providers. Our institution was 3.5 months behind in retrospective postdischarge case abstraction. A process improvement plan was implemented to shorten this delay to 1 month postdischarge. Daily demand of incoming cases and abstraction capacity were determined for 4 employees. Demand was matched to capacity, with the remaining time allocated to reducing backlog. Daily demand of new cases was 17.1 hours. Daily abstraction capacity was 24 hours, assuming 6 hours of effective daily abstraction time per employee, leaving 7 hours per day for backlogged case abstraction. The predicted time to reach abstraction target was 10 weeks. This was accomplished after 10 weeks, as predicted, leading to a 60% reduction of backlogged cases. The delay of postdischarge chart abstraction was successfully shortened from 3.5 months to 1 month. We intend to maintain same-day abstraction efficiency without reaccumulating substantial backlog.

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

PubMed

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

2011-05-01

This communication analyzed research publications in dentistry in the Institute of Scientific Information Web of Science databases of 10 dental faculties in the Association of South-East Asian Nations (ASEAN) from 2000 to 2009. The term used for the "all-document types" search was "Faculty of Dentistry/College of Dentistry." Abstracts presented at regional meetings were also included in the analysis. The Times Higher Education System QS World University Rankings showed that universities in the region fare poorly in world university rankings. Only the National University of Singapore and Nanyang Technological University appeared in the top 100 in 2009; 19 universities in the region, including Indonesia, Malaysia, the Philippines, Singapore, and Thailand, appeared in the top 500. Data from the databases showed that research publications by dental institutes in the region fall short of their Asian counterparts. Singapore and Thailand are the most active in dental research of the ASEAN countries. © 2011 Blackwell Publishing Asia Pty Ltd.

A bibliography of IRIS-related publications, 2000-2011

NASA Astrophysics Data System (ADS)

Muco, B.

2012-12-01

Citations and acknowledgements in scientific journals can be an indicator of the role an organization has on the research of that field. Since its formation and incorporation in May 1984, the IRIS Consortium (Incorporated Research Institutions for Seismology) is mentioned more and more as a valuable source of data, instruments and programs in the literature of earth sciences. As a large organization with more than 100 member domestic institutes and about 40 international affiliates, obviously IRIS has a direct impact on the earth sciences through all its programs, projects, workshops, symposia, and news¬letters and as a lively forum for exchanging ideas. In order to maintain support from National Science Foundation (NSF) and the research community, it is important to document the continued use of IRIS facilities in basic research programs. IRIS maintains a database of articles that are based on the use of IRIS facilities or which reference use of IRIS data and resources. Articles in this database have been either been provided to IRIS by the authors or selected through an annual search of a number of prominent journals. A text version of the full bibliographic database is available on the IRIS website and a version in EndNote format is also provided. To provide a more complete bibliography and a consistent evaluation of temporal tends in publications, a special annual search began in 2000 which focused on a subset of key seismology and Earth science journals: Bulletin of Seismological Society of America, Journal of Geophysical Research, Seismological Research Letters, Geophysical Research Letters, Earth and Planetary Science Letters, Physics of the Earth and Planetary Interiors, Tectonophysics, Geophysical Journal International, Nature, Science, Geology and EOS. Using different search engines as Scirus, ScienceDirect, GeoRef, OCLC First Search, EASI Search, NASA Abstract Service etc. for online journals and publishers' databases, we searched for key words (IRIS, GSN, DMS, PASSCAL, USArray etc) in titles, abstracts and text. Most of the selections found by this method were confirmed by reading through online texts or original journals. This bibliography of peer-reviewed articles (excluding abstracts) identified in these key journals for 2000-2011 includes approximately 1800 entries. As for American Geophysical Union (AGU) transaction, the bibliography of IRIS-related abstracts for the abovementioned period includes approximately 1400 abstracts. This study is a clear indicator of making intensive use by the seismological community of the resources that IRIS provides and of the paramount importance this organization has in advancement of seismological research worldwide.

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

PubMed

Lin, Ming-Hwai; Hwang, Shinn-Jang; Hwang, I-Hsuan; Chen, Yu-Chun

2014-11-01

Academic publications are important for developing a medical specialty or discipline. Since family medicine is a rapidly growing medical specialty in Taiwan, this study aimed to analyze family medicine publications from 1993 to 2012 in Taiwan using the Web of Science database. Published academic articles submitted from departments/institutes of family medicine were retrieved and analyzed from the Web of Science database, which includes articles published in the Science Citation Index-Expanded and Social Science Citation Indexed journals from 1993 to 2012. Among 33,073 published articles submitted from the departments/institutes of family medicine worldwide during the years 1993-2012, 1552 articles (4.69%) were submitted from Taiwan, ranking fourth in the world after the USA, Canada, and Sweden. In total, 1409 articles from Taiwan, excluding meeting abstracts and corrections, were selected for further analyses. During these two decades, family medicine publications increased rapidly. There were 60 articles published during 1993-1997, 180 articles during 1998-2002, 334 articles during 2003-2007, and up to 836 articles during 2008-2012. However, the mean citation number of articles decreased from 19.0 to 17.7, 15.1, and 3.8, and the mean impact factor of published journals decreased from 3.41 to 3.15, 2.78 and 2.82 during the periods 1993-1997, 1998-2002, 2003-2007, and 2008-2012, respectively. Most articles belonged to the subject category of the Medicine, General and Internal category (194 articles, 13.8%), followed by Public Environmental Occupational Health (144 articles, 10.2%), Oncology (126 articles, 9.2%), Endocrinology Metabolism (111 articles, 7.9%), Geriatrics Gerontology (99 articles, 7.0%), and the Gastroenterology Hepatology category (85 articles, 6.0%). However, only six articles (0.4%) were published in the Primary Health Care category. Publications from departments/institutes of family medicine in Taiwan increased rapidly from 1993 to 2012. However, the trends of decreased citation number of articles and journal impact factor, as well as the small amount of articles published in the Primary Health Care Category, deserve further attention and effort. Copyright © 2014. Published by Elsevier Taiwan.

Utilisation of the c-fos immunohistochemical method: a 2004 quantitative study.

PubMed

Robert, C; Arreto, C D; Gaudy, J F; Wilson, C S

2007-10-01

The aim of this study was to provide a quantitative view of the utilisation of the c-fos immunohistochemical method. Articles including the term "c-fos" in their title, abstract or keywords and published in 2004 were retrieved from the Current Content/Life Sciences or Current Content/Clinical Medicine collection of the SCI database. The 933 article-type documents retained were distributed in almost all the sub-disciplines of the Life Sciences and Clinical Medicine, but were principally published in the field of neuroscience. They were authored by researchers from 44 countries - the most prolific were the USA (435 articles), Japan (135) and the UK (55). The 933 articles were published in 283 different journals; all but one of the top-20 most prolific journals are in the Life Sciences discipline, and their Impact Factors ranged from 2.0 to 7.9. A comparison of the USA and the European Union scientific profiles is also made.

The academic value of rehabilitation medicine meetings.

PubMed

Sivan, Manoj; Smith, Matthew; Bavikatte, Ganesh; Bradley, Lloyd

2010-01-01

Twice-yearly meetings of The British Society of Rehabilitation Medicine (BSRM) take place at which posters and free papers are generated, as abstracts, to present novel research findings, audits and case reports. The aim of this study was to evaluate the academic value of these meetings, by determining the subsequent rate of publication in peer-reviewed journals of abstracts presented. This was compared to the publication rate of other European medical specialist society meetings. The authors used MEDLINE, PubMed and Google Scholar search engines to look for publication of abstracts presented at BSRM meetings within peer-reviewed journals over a 7-year period (2000-2006). The abstracts were categorised into sub-groups (original study, audit, review, case report and service description) to determine which type was more likely to be published. The above databases were used also to extract studies on publication rate of other medical specialties in Europe. In 7 years, a total of 251 abstracts (of which 152 are original studies) have been presented as free papers or posters in a total of 13 meetings. The publication rate for the described study categories were: total 34%, original study 52%, review 50%, case report 5%, audit 0% and service description 0%. Publication rates from other specialist meetings in Europe range from 10% to 70%. The average publication rate for an abstract submitted to a BSRM meeting is 34% for any abstract and 52% for an original study suggesting that the meeting is generating abstracts of comparable academic interest to other specialist societies.

Bibliometric analysis of poison center-related research published in peer-review journals.

PubMed

Forrester, M B

2016-07-01

Poison centers advance knowledge in the field of toxicology through publication in peer-review journals. This investigation describes the pattern of poison center-related publications. Cases were poison center-related research published in peer-review journals during 1995-2014. These were identified through searching the PubMed database, reviewing the tables of contents of selected toxicology journals, and reviewing abstracts of various national and international meetings. The following variables for each publication were identified: year of publication, journal, type of publication (meeting abstract vs. other, i.e. full article or letter to the editor), and the country(ies) of the poison center(s) included in the research. Of the 3147 total publications, 62.1% were meeting abstracts. There were 263 publications in 1995-1999, 536 in 2000-2004, 999 in 2005-2009, and 1349 in 2010-2014. The publications were in 234 different journals. The journals in which the highest number of research was published were Clinical Toxicology (69.7%), Journal of Medical Toxicology (2.2%), and Veterinary and Human Toxicology (2.1%). The research was reported from 62 different countries. The countries with the highest number of publications were the United States (67.9%), United Kingdom (6.5%), Germany (3.9%), France (2.5%), and Italy (2.4%). The number of publications increased greatly over the 20 years. Although the publications were in a large number of journals, a high proportion of the publications were in one journal. While the research came from a large number of countries, the preponderance came from the United States. © The Author(s) 2015.

Interventions to increase HPV vaccination coverage: A systematic review

PubMed Central

Smulian, Elizabeth A.; Mitchell, Krista R.; Stokley, Shannon

2016-01-01

ABSTRACT We reviewed intervention studies designed to increase human papillomavirus (HPV) vaccination coverage to further understand the impact interventions can have on HPV vaccination coverage. We searched 5 databases for intervention studies published from June 2006 to May 2015. Studies were included if they quantitatively measured HPV vaccination coverage as an outcome and were conducted in the United States. We abstracted outcomes, methods, and results from each study and classified by type of intervention conducted. Findings from 34 studies suggest many types of intervention strategies can increase HPV vaccination coverage in different settings, and with modest cost. Interventions were effective especially when implemented in combination at both provider and community levels. However, not all interventions showed significant effects on coverage. More research is needed to identify the best methods for widespread implementation of effective strategies. PMID:26838959

Abstraction of the Relational Model from a Department of Veterans Affairs DHCP Database: Bridging Theory and Working Application

PubMed Central

Levy, C.; Beauchamp, C.

1996-01-01

This poster describes the methods used and working prototype that was developed from an abstraction of the relational model from the VA's hierarchical DHCP database. Overlaying the relational model on DHCP permits multiple user views of the physical data structure, enhances access to the database by providing a link to commercial (SQL based) software, and supports a conceptual managed care data model based on primary and longitudinal patient care. The goal of this work was to create a relational abstraction of the existing hierarchical database; to construct, using SQL data definition language, user views of the database which reflect the clinical conceptual view of DHCP, and to allow the user to work directly with the logical view of the data using GUI based commercial software of their choosing. The workstation is intended to serve as a platform from which a managed care information model could be implemented and evaluated.

A systematic review of factors influencing older adults' decision to accept or decline cancer treatment.

PubMed

Puts, Martine T E; Tapscott, Brianne; Fitch, Margaret; Howell, Doris; Monette, Johanne; Wan-Chow-Wah, Doreen; Krzyzanowska, Monika; Leighl, Nathasha B; Springall, Elena; Alibhai, Shabbir M

2015-02-01

Cancer is a disease that affects mostly older adults. Older adults often have other chronic health conditions in addition to cancer and may have different health priorities, both of which can impact cancer treatment decision-making. However, no systematic review of factors that influence an older cancer patient's decision to accept or decline cancer treatment has been conducted. Systematic review of the literature published between inception of the databases and February 2013. Dutch, English, French or German articles reporting on qualitative studies, cross-sectional, longitudinal observational or intervention studies describing factors why older adults accepted or declined cancer treatment examining actual treatment decisions were included. Ten databases were used. Two independent reviewers reviewed manuscripts and performed data abstraction using a standardized form and the quality of studies was assessed with the Mixed Methods Appraisal Tool. Of 17,343 abstracts reviewed, a total of 38 studies were included. The majority focused on breast and prostate cancer treatment decisions and most studies used a qualitative design. Important factors for accepting treatment were convenience and success rate of treatment, seeing necessity of treatment, trust in the physician and following the physician's recommendation. Factors important for declining cancer treatment included concerns about the discomfort of the treatments, fear of side effects and transportation difficulties. Although the reasons why older adults with cancer accepted or declined treatment varied considerably, the most consistent determinant was physician recommendation. Further studies using large, representative samples and exploring decision-making incorporating health literacy and comorbidity are needed. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Electronic cigarette devices and oro-facial trauma (Literature review)

NASA Astrophysics Data System (ADS)

Ghazali, A. F.; Ismail, A. F.; Daud, A.

2017-08-01

Detrimental effects of cigarette smoking have been well described and recognized globally. With recent advancement of technology, electronic cigarette has been introduced and gained its popularity and became a global trend, especially among young adults. However, the safety of the electronic devices remains debatable. This paper aimed to compile and review the reported cases of oro-facial trauma related to the usage of electronic cigarette devices. A literature search was conducted using PubMed/Medline in December 2016. The search terms used were a combination of “oral trauma”, “dental trauma”, “oral injury” and “electronic cigarette”. The search included all abstract published from the inception of the database until December 2016. Abstract that was written in English, case report, letter to editors, clinical and human studies were included for analysis. All selected abstract were searched for full articles. A total of 8 articles were included for review. All of the articles were published in 2016 with mostly case reports. The sample size of the studies ranged from 1 to 15 patients. Seven of the included articles are from United States of America and one from Mexico. Our review concluded that the use of electronic cigarette devices posed not only a safety concern but also that the devices were mostly unregulated. There should be a recognized authority body to regulate the safety and standard of the electronic devices.

Publication Rates of Studies Presented at the International Society of Craniofacial Surgery Congress.

PubMed

Dobson, Hannah; Wall, Steven

2016-11-01

The proportion of presentations achieving publication in a peer-review journal has been suggested to demonstrate the quality of research presented at a conference. No data is available examining the publication rate of research presented at Craniofacial Surgery meetings. The aim of the study was to examine the publication rate of abstracts presented at the International Society of Craniofacial Surgery Biennial Congresses from 2003 to 2011. A search was made of the PubMed database for publication of podium presentations of International Society of Craniofacial Surgery Congresses between 2003 and 2011. Thirty-five percent of podium presentations were published in a peer-reviewed journal. Thirty-one percent of presentations were published within 4 years, and the rate of publication decreased 2 years following presentation.

"Balkan journal of medical genetics"--facts, editorial policies, practices and challenges.

PubMed

Plaseska Karanfilska, Dijana; Sukarova Stefanovska, Emilija

2014-01-01

The Balkan Journal of Medical Genetics (BJMG) is an international, open access journal that publishes scientific papers covering different aspects of medical genetics. It is published by the Macedonian Academy of Sciences and Arts twice a year in both printed and electronic versions. BJMG is covered by many abstracting and indexing databases, including PubMed Central and Thomson Reuters. Although there are many journals in the field of medical genetics, only a few come from regions outside Western Europe and North America. Being one of these few journals, BJMG aims to promote genetics and research on this topic in the Balkan countries and beyond. BJMG's ultimate goal is to raise the scientific quality and metrics of the journal and provide a better place for BJMG in the community of scientific journals.

An Analysis of Factors Predicting Successful Transition From Pancreatology Abstracts to Full Publications.

PubMed

Grunwald, Douglas; Feuerstein, Joseph D; Maier, Irena Maria; Sheth, Sunil G

2017-01-01

Historically, less than half of peer-reviewed abstracts are published. We set out to determine how many pancreas-related abstracts are published within 5 years of presentation at gastroenterology conferences and to determine a model that predicts successful transition from abstract to journal publication. We collected data on study design from all pancreas-related abstracts at the 2010 Digestive Disease Week (DDW), American College of Gastroenterology, and American Pancreatic Association conferences. We then determined whether an abstract was published by October 2015 using a standardized search algorithm. Of 412 abstracts, 39.8% were published. Studies that were of basic science or translational design (P = 0.02, 0.01, respectively); had more listed authors (P = 0.05); employed randomized, prospective, and multicenter methodology (P = 0.02); and were accepted to DDW (P = 0.02) were more likely to be published. After regression, basic/translational studies (P = 0.002, 0.02, respectively) and DDW-accepted abstracts (P = 0.004) continued to predict successful publication. It is not clear why only 40% of the pancreas abstracts from 2010 were published 5 years later. Some abstracts may go unpublished because of methodological flaws that escape detection during abstract peer review. Therefore, physicians should use caution when applying abstract data to their clinical decision making.

Assessing telemedicine: a systematic review of the literature.

PubMed

Roine, R; Ohinmaa, A; Hailey, D

2001-09-18

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

The Efficacy of Multidimensional Constraint Keys in Database Query Performance

ERIC Educational Resources Information Center

Cardwell, Leslie K.

2012-01-01

This work is intended to introduce a database design method to resolve the two-dimensional complexities inherent in the relational data model and its resulting performance challenges through abstract multidimensional constructs. A multidimensional constraint is derived and utilized to implement an indexed Multidimensional Key (MK) to abstract a…

Effective knowledge translation approaches and practices in Indigenous health research: a systematic review protocol.

PubMed

Morton Ninomiya, Melody E; Atkinson, Donna; Brascoupé, Simon; Firestone, Michelle; Robinson, Nicole; Reading, Jeff; Ziegler, Carolyn P; Maddox, Raglan; Smylie, Janet K

2017-02-20

Effective knowledge translation (KT) is critical to implementing program and policy changes that require shared understandings of knowledge systems, assumptions, and practices. Within mainstream research institutions and funding agencies, systemic and insidious inequities, privileges, and power relationships inhibit Indigenous peoples' control, input, and benefits over research. This systematic review will examine literature on KT initiatives in Indigenous health research to help identify wise and promising Indigenous KT practices and language in Canada and abroad. Indexed databases including Aboriginal Health Abstract Database, Bibliography of Native North Americans, CINAHL, Circumpolar Health Bibliographic Database, Dissertation Abstracts, First Nations Periodical Index, Medline, National Indigenous Studies Portal, ProQuest Conference Papers Index, PsycInfo, Social Services Abstracts, Social Work Abstracts, and Web of Science will be searched. A comprehensive list of non-indexed and grey literature sources will also be searched. For inclusion, documents must be published in English; linked to Indigenous health and wellbeing; focused on Indigenous people; document KT goals, activities, and rationale; and include an evaluation of their KT strategy. Identified quantitative, qualitative, and mixed methods' studies that meet the inclusion criteria will then be appraised using a quality appraisal tool for research with Indigenous people. Studies that score 6 or higher on the quality appraisal tool will be included for analysis. This unique systematic review involves robust Indigenous community engagement strategies throughout the life of the project, starting with the development of the review protocol. The review is being guided by senior Indigenous researchers who will purposefully include literature sources characterized by Indigenous authorship, community engagement, and representation; screen and appraise sources that meet Indigenous health research principles; and discuss the project with the Indigenous Elders to further explore the hazards, wisdom, and processes of sharing knowledge in research contexts. The overall aim of this review is to provide the evidence and basis for recommendations on wise practices for KT terminology and research that improves Indigenous health and wellbeing and/or access to services, programs, or policies that will lead to improved health and wellbeing. PROSPERO CRD42016049787 .

Drinking water quality standards and standard tests: Worldwide. (Latest citations from the Food Science and Technology Abstracts database). Published Search

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

Not Available

1993-06-01

The bibliography contains citations concerning standards and standard tests for water quality in drinking water sources, reservoirs, and distribution systems. Standards from domestic and international sources are presented. Glossaries and vocabularies that concern water quality analysis, testing, and evaluation are included. Standard test methods for individual elements, selected chemicals, sensory properties, radioactivity, and other chemical and physical properties are described. Discussions for proposed standards on new pollutant materials are briefly considered. (Contains a minimum of 203 citations and includes a subject term index and title list.)

Fire-induced water-repellent soils, an annotated bibliography

USGS Publications Warehouse

Kalendovsky, M.A.; Cannon, S.H.

1997-01-01

The development and nature of water-repellent, or hydrophobic, soils are important issues in evaluating hillslope response to fire. The following annotated bibliography was compiled to consolidate existing published research on the topic. Emphasis was placed on the types, causes, effects and measurement techniques of water repellency, particularly with respect to wildfires and prescribed burns. Each annotation includes a general summary of the respective publication, as well as highlights of interest to this focus. Although some references on the development of water repellency without fires, the chemistry of hydrophobic substances, and remediation of water-repellent conditions are included, coverage of these topics is not intended to be comprehensive. To develop this database, the GeoRef, Agricola, and Water Resources Abstracts databases were searched for appropriate references, and the bibliographies of each reference were then reviewed for additional entries. Additional references will be added to this bibliography as they become available. The annotated bibliography can be accessed on the Web at http://geohazards.cr.usgs.gov/html_files/landslides/ofr97-720/biblio.html. A database consisting of the references and keywords is available through a link at the above address. This database was compiled using EndNote2 plus software by Niles and Associates, and is necessary to search the database.

Yellow fever vaccine-associated viscerotropic disease: current perspectives.

PubMed

Thomas, Roger E

2016-01-01

To assess those published cases of yellow fever (YF) vaccine-associated viscerotropic disease that meet the Brighton Collaboration criteria and to assess the safety of YF vaccine with respect to viscerotropic disease. Ten electronic databases were searched with no restriction of date or language and reference lists of retrieved articles. All abstracts and titles were independently read by two reviewers and data independently entered by two reviewers. All serious adverse events that met the Brighton Classification criteria were associated with first YF vaccinations. Sixty-two published cases (35 died) met the Brighton Collaboration viscerotropic criteria, with 32 from the US, six from Brazil, five from Peru, three from Spain, two from the People's Republic of China, one each from Argentina, Australia, Belgium, Ecuador, France, Germany, Ireland, New Zealand, Portugal, and the UK, and four with no country stated. Two cases met both the viscerotropic and YF vaccine-associated neurologic disease criteria. Seventy cases proposed by authors as viscerotropic disease did not meet any Brighton Collaboration viscerotropic level of diagnostic certainty or any YF vaccine-associated viscerotropic disease causality criteria (37 died). Viscerotropic disease is rare in the published literature and in pharmacovigilance databases. All published cases were from developing countries. Because the symptoms are usually very severe and life threatening, it is unlikely that cases would not come to medical attention (but might not be published). Because viscerotropic disease has a highly predictable pathologic course, it is likely that viscerotropic disease post-YF vaccine occurs in low-income countries with the same incidence as in developing countries. YF vaccine is a very safe vaccine that likely confers lifelong immunity.

Effectiveness of pelvic floor muscle training in treating urinary incontinence in women: A current review.

PubMed

García-Sánchez, E; Rubio-Arias, J A; Ávila-Gandía, V; Ramos-Campo, D J; López-Román, J

2016-06-01

To analyse the content of various published studies related to physical exercise and its effects on urinary incontinence and to determine the effectiveness of pelvic floor training programmes. We conducted a search in the databases of PubMed, CINAHL, the Cochrane Plus Library, The Cochrane Library, WOS and SPORTDiscus and a manual search in the Google Scholar metasearcher using the search descriptors for documents published in the last 10 years in Spanish or English. The documents needed to have an abstract or complete text on the treatment of urinary incontinence in female athletes and in women in general. We selected 3 full-text articles on treating urinary incontinence in female athletes and 6 full-text articles and 1 abstract on treating urinary incontinence in women in general. The 9 studies included in the review achieved positive results, i.e., there was improvement in the disease in all of the studies. Physical exercise, specifically pelvic floor muscle training programmes, has positive effects on urinary incontinence. This type of training has been shown to be an effective programme for treating urinary incontinence, especially stress urinary incontinence. Copyright © 2015 AEU. Publicado por Elsevier España, S.L.U. All rights reserved.

Inventory of U.S. Health Care Data Bases, 1976-1987.

ERIC Educational Resources Information Center

Kralovec, Peter D.; Andes, Steven M.

This inventory contains summary abstracts of 305 current (1976-1987) non-bibliographic machine-readable databases and national health care data that have been created by public and private organizations throughout the United States. Each of the abstracts contains pertinent information on the sponsor or database, a description of the purpose and…

Subsequent publication of oral and maxillofacial surgery meeting abstracts.

PubMed

Rodriguez, Joseph L; Laskin, Daniel M

2012-05-01

Previous studies in various medical specialties have shown that fewer than 50% of abstracts presented at meetings are subsequently published. The purpose of the present study was to determine the publication rate of abstracts presented at the annual meetings of the American Association of Oral and Maxillofacial Surgeons. The titles and authors of the abstracts from all oral abstract session presentations and posters by American contributors were collected from the Final Programs of the American Association of Oral and Maxillofacial Surgeons annual meetings for 2006 to 2009. A PubMed search for published articles through December 2010 was then performed using the authors' names, abstract titles, and key words. A total of 311 abstract presentations were done at the 4 annual meetings. Of these, only 85 (24%) were subsequently published. No difference was found between abstracts from oral or poster presentations. Most of the articles were published in the Journal of Oral and Maxillofacial Surgery. Because of deficiencies that can occur in abstracts and the need to disseminate the information they contain, it is important to take the appropriate measures to ensure that full articles are subsequently published. Copyright © 2012 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

Hawaii bibliographic database

USGS Publications Warehouse

Wright, T.L.; Takahashi, T.J.

1998-01-01

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

Publication rates of the abstracts presented at the annual meeting of International Society for Pediatric Neurosurgery.

PubMed

Ekşi, Murat Şakir; Özcan-Ekşi, Emel Ece

2018-01-19

Publication of a study is the end point of the process to contribute to the literature and confirm the scientific value of the study. Publication rates of the abstracts presented at the annual meetings of neurosurgery have been studied, previously. However, publication rates of the abstracts presented at the annual meetings of pediatric neurosurgery have not been reported, yet. We evaluated abstracts presented at the 38th annual meeting of the International Society for Pediatric Neurosurgery (ISPN) held in South Korea, 2010. We conducted this cross-sectional study by reviewing the abstracts presented at the annual meeting of the ISPN, 2010. Titles and authors of the abstracts were surveyed using Google Scholar and PubMed/MEDLINE. Time to publication, origin of the study, journal name in which the study has been accepted and published, and type of study has been analyzed for each abstract. The abstract booklet included 235 abstracts, consisted of 128 oral presentations (54%) and 107 electronic posters (46%). Fifty-nine (46%) of the oral presentations were published in a peer-reviewed journal. Laboratory studies were more likely to be published when compared to the clinical studies (72 vs. 39%). Thirty-two (30%) of the electronic posters were published in peer-reviewed journals. Most of the published abstracts were from Asia and Europe. Most of the abstracts were published in Child's Nervous System and Journal of Neurosurgery: Pediatrics. Publication rates of the abstracts presented at annual meeting of the ISPN were comparable to the other similar congresses. Oral presentations were more likely to be published. High publication rates of the abstracts presented at the annual meeting of the ISPN suggested that the meeting had a high scientific value.

High-Level Data-Abstraction System

NASA Technical Reports Server (NTRS)

Fishwick, P. A.

1986-01-01

Communication with data-base processor flexible and efficient. High Level Data Abstraction (HILDA) system is three-layer system supporting data-abstraction features of Intel data-base processor (DBP). Purpose of HILDA establishment of flexible method of efficiently communicating with DBP. Power of HILDA lies in its extensibility with regard to syntax and semantic changes. HILDA's high-level query language readily modified. Offers powerful potential to computer sites where DBP attached to DEC VAX-series computer. HILDA system written in Pascal and FORTRAN 77 for interactive execution.

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

PubMed

Shi, Lei; Campagne, Fabien

2005-04-07

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

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

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

PubMed Central

Shi, Lei; Campagne, Fabien

2005-01-01

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

A systematic review of the evidence on clitoral reconstruction after female genital mutilation/cutting.

PubMed

Abdulcadir, Jasmine; Rodriguez, Maria I; Say, Lale

2015-05-01

Clitoral reconstruction is a new surgical technique for women who have undergone female genital mutilation/cutting (FGM/C). To review evidence on the safety and efficacy of clitoral reconstruction. PubMed and Cochrane databases were searched for articles published in any language from database inception until May 2014. Search terms related to FGM/C and clitoral reconstruction were used in various combinations. Studies of any design that reported on safety or clinical outcomes (e.g. appearance, pain, sexual response, or patient satisfaction) associated with clitoral reconstruction after FGM/C were included. Evidence was summarized and systematically assessed via a standard data abstraction form. Four of 269 identified articles were included. They were fair to poor in quality. Summary measures could not be computed owing to heterogeneity. The studies reported on immediate surgical complications, clitoral appearance, dyspareunia or chronic pain, and clitoral function postoperatively via non-standardized scales. Women who request clitoral reconstruction should be informed about the scarcity of evidence available. Additional research is needed on the safety and efficacy of the procedure to identify both long-term outcomes and which women might benefit. Copyright © 2015 International Federation of Gynecology and Obstetrics. Published by Elsevier Ireland Ltd. All rights reserved.

Lack of Cost-Effectiveness Analyses to Address Healthy People 2020 Priority Areas.

PubMed

Neumann, Peter J; Farquhar, Megan; Wilkinson, Colby L; Lowry, Mackenzie; Gold, Marthe

2016-12-01

To examine the extent to which recently published cost-utility analyses (cost-effectiveness analyses using quality-adjusted life-years to measure health benefits) have covered the leading health concerns in the US Department of Health and Human Services Healthy People 2020 report. We examined data in the Tufts Medical Center Cost-Effectiveness Analysis Registry, a database containing 5000 published cost-utility analyses published in the MEDLINE literature through 2014. We focused on US-based cost-utility analyses published from 2011 through 2014 (n = 687). Two reviewers scanned abstracts and met for a consensus on categorization of cost-utility analyses that addressed the specific priorities listed in the 12 Healthy People 2020 areas (n = 120). Although 7.3% of recently published cost-utility analyses addressed key clinical preventive services, only about 2% of recently published cost-utility analyses covered each of the following Healthy People 2020 topics: reproductive and sexual health, nutrition/physical activity/obesity, maternal and infant health, and tobacco. Fewer than 1% addressed priorities such as injuries and violence, mental health or substance abuse, environmental quality, and oral health. Few cost-utility analyses have addressed Healthy People 2020 priority areas.

Safety and Procedural Success of Left Atrial Appendage Exclusion With the Lariat Device: A Systematic Review of Published Reports and Analytic Review of the FDA MAUDE Database.

PubMed

Chatterjee, Saurav; Herrmann, Howard C; Wilensky, Robert L; Hirshfeld, John; McCormick, Daniel; Frankel, David S; Yeh, Robert W; Armstrong, Ehrin J; Kumbhani, Dharam J; Giri, Jay

2015-07-01

The Lariat device has received US Food and Drug Administration (FDA) 510(k) clearance for soft-tissue approximation and is being widely used off-label for left atrial appendage (LAA) exclusion. A comprehensive analysis of safety and effectiveness has not been reported. To perform a systematic review of published literature to assess safety and procedural success, defined as successful closure of the LAA during the index procedure, of the Lariat device. We performed a formal analytic review of the FDA MAUDE (Manufacturer and User Facility Device Experience) database to compile adverse event reports from real-world practice with the Lariat. For the systematic review, PubMed, EMBASE, CINAHL, and the Cochrane Library were searched from January 2007 through August 2014 to identify all studies reporting use of the Lariat device in 3 or more patients. The FDA MAUDE database was queried for adverse events reports related to Lariat use. Data were abstracted in duplicate by 2 physician reviewers. Events from published literature were pooled using a generic inverse variance weighting with a random effects model. Cumulative and individual adverse events were also reported using the FDA MAUDE data set. Procedural adverse events and procedural success. In the systematic review, 5 reports of Lariat device use in 309 participants were identified. Specific complications weighted for inverse of variance of individual studies were urgent need for cardiac surgery (2.3%; 7 of 309 procedures) and death (0.3%; 1 of 309 procedures). Procedural success was 90.3% (279 of 309 procedures). In the FDA MAUDE database, there were 35 unique reports of adverse events with use of the Lariat device. Among these, we identified 5 adverse event reports that noted pericardial effusion and death and an additional 23 reported urgent cardiac surgery without mention of death. This review of published reports and case reports identified risks of adverse events with off-label use of the Lariat device for LAA exclusion. Formal, controlled investigations into the safety and efficacy of the device for this indication are warranted.

State of reporting of primary biomedical research: a scoping review protocol

PubMed Central

Mbuagbaw, Lawrence; Samaan, Zainab; Jin, Yanling; Nwosu, Ikunna; Levine, Mitchell A H; Adachi, Jonathan D; Thabane, Lehana

2017-01-01

Introduction Incomplete or inconsistent reporting remains a major concern in the biomedical literature. Incomplete or inconsistent reporting may yield the published findings unreliable, irreproducible or sometimes misleading. In this study based on evidence from systematic reviews and surveys that have evaluated the reporting issues in primary biomedical studies, we aim to conduct a scoping review with focuses on (1) the state-of-the-art extent of adherence to the emerging reporting guidelines in primary biomedical research, (2) the inconsistency between protocols or registrations and full reports and (3) the disagreement between abstracts and full-text articles. Methods and analyses We will use a comprehensive search strategy to retrieve all available and eligible systematic reviews and surveys in the literature. We will search the following electronic databases: Web of Science, Excerpta Medica Database (EMBASE), MEDLINE and Cumulative Index to Nursing and Allied Health Literature (CINAHL). Our outcomes are levels of adherence to reporting guidelines, levels of consistency between protocols or registrations and full reports and the agreement between abstracts and full reports, all of which will be expressed as percentages, quality scores or categorised rating (such as high, medium and low). No pooled analyses will be performed quantitatively given the heterogeneity of the included systematic reviews and surveys. Likewise, factors associated with improved completeness and consistency of reporting will be summarised qualitatively. The quality of the included systematic reviews will be evaluated using AMSTAR (a measurement tool to assess systematic reviews). Ethics and dissemination All findings will be published in peer-reviewed journals and relevant conferences. These results may advance our understanding of the extent of incomplete and inconsistent reporting, factors related to improved completeness and consistency of reporting and potential recommendations for various stakeholders in the biomedical community. PMID:28360252

NATIVE HEALTH DATABASES: NATIVE HEALTH RESEARCH DATABASE (NHRD)

EPA Science Inventory

The Native Health Databases contain bibliographic information and abstracts of health-related articles, reports, surveys, and other resource documents pertaining to the health and health care of American Indians, Alaska Natives, and Canadian First Nations. The databases provide i...

Preference vs. Authority: A Comparison of Student Searching in a Subject-Specific Indexing and Abstracting Database and a Customized Discovery Layer

ERIC Educational Resources Information Center

Dahlen, Sarah P. C.; Hanson, Kathlene

2017-01-01

Discovery layers provide a simplified interface for searching library resources. Libraries with limited finances make decisions about retaining indexing and abstracting databases when similar information is available in discovery layers. These decisions should be informed by student success at finding quality information as well as satisfaction…

SERS internship fall 1995 abstracts and research papers

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

Davis, Beverly

1996-05-01

This report is a compilation of twenty abstracts and their corresponding full papers of research projects done under the US Department of Energy Science and Engineering Research Semester (SERS) program. Papers cover a broad range of topics, for example, environmental transport, supercomputers, databases, biology. Selected papers were indexed separately for inclusion the the Energy Science and Technology Database.

The distribution of probability values in medical abstracts: an observational study.

PubMed

Ginsel, Bastiaan; Aggarwal, Abhinav; Xuan, Wei; Harris, Ian

2015-11-26

A relatively high incidence of p values immediately below 0.05 (such as 0.047 or 0.04) compared to p values immediately above 0.05 (such as 0.051 or 0.06) has been noticed anecdotally in published medical abstracts. If p values immediately below 0.05 are over-represented, such a distribution may reflect the true underlying distribution of p values or may be due to error (a false distribution). If due to error, a consistent over-representation of p values immediately below 0.05 would be a systematic error due either to publication bias or (overt or inadvertent) bias within studies. We searched the Medline 2012 database to identify abstracts containing a p value. Two thousand abstracts out of 80,649 abstracts were randomly selected. Two independent researchers extracted all p values. The p values were plotted and compared to a predicted curve. Chi square test was used to test assumptions and significance was set at 0.05. 2798 p value ranges and 3236 exact p values were reported. 4973 of these (82%) were significant (<0.05). There was an over-representation of p values immediately below 0.05 (between 0.01 and 0.049) compared to those immediately above 0.05 (between 0.05 and 0.1) (p = 0.001). The distribution of p values in reported medical abstracts provides evidence for systematic error in the reporting of p values. This may be due to publication bias, methodological errors (underpowering, selective reporting and selective analyses) or fraud.

Innovative patient care practices using social media.

PubMed

Mattingly, T Joseph

2015-01-01

To characterize the literature on social media applications used to deliver patient care. A search of the literature was conducted on June 11, 2014, using PubMed, MEDLINE, CINAHL, and Communication Abstracts databases for clinical studies between 2004 and 2014. A combination of the search terms "social media" or "Web 2.0" or "online social networking" or "Facebook" or "Twitter" AND "patient care" or "health care" was used. In addition, 42 additional abstracts were retrieved from www.patientslikeme.com for review. Only published, peer-reviewed journal articles were considered and only publications in English were included. The abstracts from this search were reviewed for relevance to Web-based social media platforms being used in patient care activities. A total of 35 articles were included in the review. A majority of the studies published on social media and patient care used cross-sectional designs and were conducted in the United States. Multiple social media applications were studied, but Facebook was the predominant social media tool found. Patient care opportunities for various diseases with social media have been studied. Recurring themes included overcoming barriers, engaging and empowering patients, enhancing research, providing information for health promotion, scratching the surface, and potential pitfalls. Social media have the potential to help patients and practitioners overcome multiple barriers in the delivery of health care. Maintaining patient privacy, security of information shared in the platform, and integrity of information shared are all concerns when using this type of Web application.

Type 2 Diabetes Research Yield, 1951-2012: Bibliometrics Analysis and Density-Equalizing Mapping

PubMed Central

Geaney, Fiona; Scutaru, Cristian; Kelly, Clare; Glynn, Ronan W.; Perry, Ivan J.

2015-01-01

The objective of this paper is to provide a detailed evaluation of type 2 diabetes mellitus research output from 1951-2012, using large-scale data analysis, bibliometric indicators and density-equalizing mapping. Data were retrieved from the Science Citation Index Expanded database, one of the seven curated databases within Web of Science. Using Boolean operators "OR", "AND" and "NOT", a search strategy was developed to estimate the total number of published items. Only studies with an English abstract were eligible. Type 1 diabetes and gestational diabetes items were excluded. Specific software developed for the database analysed the data. Information including titles, authors’ affiliations and publication years were extracted from all files and exported to excel. Density-equalizing mapping was conducted as described by Groenberg-Kloft et al, 2008. A total of 24,783 items were published and cited 476,002 times. The greatest number of outputs were published in 2010 (n=2,139). The United States contributed 28.8% to the overall output, followed by the United Kingdom (8.2%) and Japan (7.7%). Bilateral cooperation was most common between the United States and United Kingdom (n=237). Harvard University produced 2% of all publications, followed by the University of California (1.1%). The leading journals were Diabetes, Diabetologia and Diabetes Care and they contributed 9.3%, 7.3% and 4.0% of the research yield, respectively. In conclusion, the volume of research is rising in parallel with the increasing global burden of disease due to type 2 diabetes mellitus. Bibliometrics analysis provides useful information to scientists and funding agencies involved in the development and implementation of research strategies to address global health issues. PMID:26208117

Ioss IO Subsystem

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

Sjaardema, Gregory; Bauer, David; Erik, & Illescas

2017-01-06

The Ioss is a database-independent package for providing an object-oriented, abstract interface to IO capabilities for a finite element application; and concrete database interfaces which provided input and/or output to exodusII, xdmf, generated, and heartbeat database formats. The Ioss provides an object-oriented C++-based IO interface for a finite element application code. The application code can perform all IO operations through the Ioss interface which is typically at a higher abstraction level than the concrete database formats. The Ioss then performs the needed operations to translate the finite element data to the specific format required by the concrete database implementations. Themore » Ioss currently supports interfaces to exodusII, xdmf, generated, and heartbeat formats, but additional formats can be easily added.« less

DiMeX: A Text Mining System for Mutation-Disease Association Extraction.

PubMed

Mahmood, A S M Ashique; Wu, Tsung-Jung; Mazumder, Raja; Vijay-Shanker, K

2016-01-01

The number of published articles describing associations between mutations and diseases is increasing at a fast pace. There is a pressing need to gather such mutation-disease associations into public knowledge bases, but manual curation slows down the growth of such databases. We have addressed this problem by developing a text-mining system (DiMeX) to extract mutation to disease associations from publication abstracts. DiMeX consists of a series of natural language processing modules that preprocess input text and apply syntactic and semantic patterns to extract mutation-disease associations. DiMeX achieves high precision and recall with F-scores of 0.88, 0.91 and 0.89 when evaluated on three different datasets for mutation-disease associations. DiMeX includes a separate component that extracts mutation mentions in text and associates them with genes. This component has been also evaluated on different datasets and shown to achieve state-of-the-art performance. The results indicate that our system outperforms the existing mutation-disease association tools, addressing the low precision problems suffered by most approaches. DiMeX was applied on a large set of abstracts from Medline to extract mutation-disease associations, as well as other relevant information including patient/cohort size and population data. The results are stored in a database that can be queried and downloaded at http://biotm.cis.udel.edu/dimex/. We conclude that this high-throughput text-mining approach has the potential to significantly assist researchers and curators to enrich mutation databases.

DiMeX: A Text Mining System for Mutation-Disease Association Extraction

PubMed Central

Mahmood, A. S. M. Ashique; Wu, Tsung-Jung; Mazumder, Raja; Vijay-Shanker, K.

2016-01-01

The number of published articles describing associations between mutations and diseases is increasing at a fast pace. There is a pressing need to gather such mutation-disease associations into public knowledge bases, but manual curation slows down the growth of such databases. We have addressed this problem by developing a text-mining system (DiMeX) to extract mutation to disease associations from publication abstracts. DiMeX consists of a series of natural language processing modules that preprocess input text and apply syntactic and semantic patterns to extract mutation-disease associations. DiMeX achieves high precision and recall with F-scores of 0.88, 0.91 and 0.89 when evaluated on three different datasets for mutation-disease associations. DiMeX includes a separate component that extracts mutation mentions in text and associates them with genes. This component has been also evaluated on different datasets and shown to achieve state-of-the-art performance. The results indicate that our system outperforms the existing mutation-disease association tools, addressing the low precision problems suffered by most approaches. DiMeX was applied on a large set of abstracts from Medline to extract mutation-disease associations, as well as other relevant information including patient/cohort size and population data. The results are stored in a database that can be queried and downloaded at http://biotm.cis.udel.edu/dimex/. We conclude that this high-throughput text-mining approach has the potential to significantly assist researchers and curators to enrich mutation databases. PMID:27073839

How much importance do we give to target audiences in article writing?

PubMed

Nedjat, Sima; Nedjat, Saharnaz; Gholami, Jaleh; Ashoorkhani, Mahnaz; Maleki, Katayoun; Hejrie, Soroush Mortaz; Majdzadeh, Reza

2010-01-01

Writing papers can be used as a means to convey a message. Knowledge transfer is also about conveying the right message to the right target audience. The aim of this study was to determine the proportion of articles that had mentioned a clear message and the target audience in the abstract and the article as a whole, and also to examine their association with different determinant factors. Articles published from 2001 to 2006 that were based on clinical and health system research conducted on Iranian populations and on maternal care, diabetes and tuberculosis were searched systematically in domestic and international databases. Eventually checklists (Additional file 1) were completed for 795 articles. Overall, 98.5% of articles had a clear message, whereas 12.5% had addressed the direct target audience. Presence of a clear message in formatted abstracts were seen 3.6 times more (CI95%: 1.5-8.7) than in articles without formatted abstracts (p = 0.005). Addressing of the direct target audience was seen twice as much in health system research articles as compared to clinical studies, odds ratio was 2.3 (CI95%: 1.47-3.48, p<0.001). Creating a format for journal abstracts seems to be an effective intervention for presenting the message in articles.

Publication rates of podium and poster abstract presentations at the 2010 and 2011 society of gynecologic oncology conferences.

PubMed

Imani, Saba; Moore, Gretchan; Nelson, Nathan; Scott, Jared; Vassar, Matt

2018-05-01

This study aimed to determine the publication rate of oral and poster abstracts presented at the 2010 and 2011 Society of Gynecologic Oncology (SGO) conferences as well as the journals that most commonly published these studies, their 5-year impact factor, the time to publication, and the reasons for nonpublication. Abstracts presented at the 2010-2011 SGO conferences were included in this study. We searched Google, Google Scholar, and PubMed to locate published reports of these abstracts. If an abstract's full-text manuscript could not be located, an author of the conference abstract was contacted via email to inquire whether the research was published. If the research was unpublished, the authors were asked to provide the reason for nonpublication. The time to publication, journal, and journal impact factor were noted for abstracts that reached full-text publication. A total of 725 abstracts were identified, of which 386 (53%) reached publication in a peer-reviewed journal. Oral presentations were published at a higher rate than poster presentations. Most (70%) reached publication within 2 years of abstract presentation. Abstracts were published in 89 journals, but most (39%) were published in Gynecologic Oncology. The mean time to publication was 15.7 months, with a mean 5-year impact factor of 4.956. A 53% publication rate indicates that the SGO conference selection process favors research likely to be published and, thus, presumably of high quality. The overall publication rate is higher than that reported for many other biomedical conferences.

Conference presentation to publication: a retrospective study evaluating quality of abstracts and journal articles in medical education research.

PubMed

Stephenson, Christopher R; Vaa, Brianna E; Wang, Amy T; Schroeder, Darrell R; Beckman, Thomas J; Reed, Darcy A; Sawatsky, Adam P

2017-11-09

There is little evidence regarding the comparative quality of abstracts and articles in medical education research. The Medical Education Research Study Quality Instrument (MERSQI), which was developed to evaluate the quality of reporting in medical education, has strong validity evidence for content, internal structure, and relationships to other variables. We used the MERSQI to compare the quality of reporting for conference abstracts, journal abstracts, and published articles. This is a retrospective study of all 46 medical education research abstracts submitted to the Society of General Internal Medicine 2009 Annual Meeting that were subsequently published in a peer-reviewed journal. We compared MERSQI scores of the abstracts with scores for their corresponding published journal abstracts and articles. Comparisons were performed using the signed rank test. Overall MERSQI scores increased significantly for published articles compared with conference abstracts (11.33 vs 9.67; P < .001) and journal abstracts (11.33 vs 9.96; P < .001). Regarding MERSQI subscales, published articles had higher MERSQI scores than conference abstracts in the domains of sampling (1.59 vs 1.34; P = .006), data analysis (3.00 vs 2.43; P < .001), and validity of evaluation instrument (1.04 vs 0.28; P < .001). Published articles also had higher MERSQI scores than journal abstracts in the domains of data analysis (3.00 vs 2.70; P = .004) and validity of evaluation instrument (1.04 vs 0.26; P < .001). To our knowledge, this is the first study to compare the quality of medical education abstracts and journal articles using the MERSQI. Overall, the quality of articles was greater than that of abstracts. However, there were no significant differences between abstracts and articles for the domains of study design and outcomes, which indicates that these MERSQI elements may be applicable to abstracts. Findings also suggest that abstract quality is generally preserved from original presentation to publication.

Trends in the Scholarship on Teachers of Color for Diverse Populations: Implications for Multicultural Education.

ERIC Educational Resources Information Center

Sheets, Rosa Hernandez

This paper reviews patterns in the literature on minority teachers and teacher preparation. The study involved an extensive literature search using the following database selections: Books in Print A-Z; ERIC Database 1966-2000; Education Abstracts FTX 6/83-12/99; PsycINFO 1984-2000/02; Sociological Abstracts 1963-1999/12; and Social Sciences Abst…

Erratum:Quality of life in long-term premenopausal early-stage breast cancer survivors from Spain. Effects of surgery and time since surgery.

PubMed

Arraras, J I; Illarramendi, J J; de la Cruz, S; Asin, G; Manterola, A; Ibanez, B; Salgado, E; Cambra, K; Zarandona, U; Dominguez, M A; Vera, R

2016-01-01

In this article published in Volume 21, issue 5, the authors' names were incorrectly stated in the Pubmed abstract as: "Ignacio Arraras J(1), Juan Illarramendi J, de la Cruz S, Asin G, Manterola A, Ibanez B, Salgado E, Cambra K, Zarandona U, Angel Dominguez M, Vera R.". The correct authors' names are: "Arraras JI(1), Illarramendi JJ, de la Cruz S, Asin G, Manterola A, Ibanez B, Salgado E, Cambra K, Zarandona U, Dominguez MA, Vera R.". This error appeared only in the PubMed database and not in the print form of the Journal.

The psychosocial impact of natural disasters among adult survivors: an integrative review.

PubMed

Warsini, Sri; West, Caryn; Ed Tt, Grad Dip; Res Meth, Grad Cert; Mills, Jane; Usher, Kim

2014-06-01

The aim of this review was to identify the psychosocial impact of natural disasters on adult (over the age of 18 years) survivors. Databases searched included PsycInfo, CINAHL, Proquest, Ovid SP, Scopus, and Science Direct. The search was limited to articles written in English and published between 2002 and 2012. A total of 1,642 abstracts and articles were obtained during the first search; 39 articles were retained. The results indicate that PTSD is the most-studied psychosocial impact after a disaster. Mental health nurses have a significant role to play in supporting survivors and can assist with the development of resilience in community members.

Yellow fever vaccine-associated viscerotropic disease: current perspectives

PubMed Central

Thomas, Roger E

2016-01-01

Purpose To assess those published cases of yellow fever (YF) vaccine-associated viscerotropic disease that meet the Brighton Collaboration criteria and to assess the safety of YF vaccine with respect to viscerotropic disease. Literature search Ten electronic databases were searched with no restriction of date or language and reference lists of retrieved articles. Methods All abstracts and titles were independently read by two reviewers and data independently entered by two reviewers. Results All serious adverse events that met the Brighton Classification criteria were associated with first YF vaccinations. Sixty-two published cases (35 died) met the Brighton Collaboration viscerotropic criteria, with 32 from the US, six from Brazil, five from Peru, three from Spain, two from the People’s Republic of China, one each from Argentina, Australia, Belgium, Ecuador, France, Germany, Ireland, New Zealand, Portugal, and the UK, and four with no country stated. Two cases met both the viscerotropic and YF vaccine-associated neurologic disease criteria. Seventy cases proposed by authors as viscerotropic disease did not meet any Brighton Collaboration viscerotropic level of diagnostic certainty or any YF vaccine-associated viscerotropic disease causality criteria (37 died). Conclusion Viscerotropic disease is rare in the published literature and in pharmacovigilance databases. All published cases were from developing countries. Because the symptoms are usually very severe and life threatening, it is unlikely that cases would not come to medical attention (but might not be published). Because viscerotropic disease has a highly predictable pathologic course, it is likely that viscerotropic disease post-YF vaccine occurs in low-income countries with the same incidence as in developing countries. YF vaccine is a very safe vaccine that likely confers lifelong immunity. PMID:27784992

The value of protein structure classification information—Surveying the scientific literature

PubMed Central

Fox, Naomi K.; Brenner, Steven E.

2015-01-01

ABSTRACT The Structural Classification of Proteins (SCOP) and Class, Architecture, Topology, Homology (CATH) databases have been valuable resources for protein structure classification for over 20 years. Development of SCOP (version 1) concluded in June 2009 with SCOP 1.75. The SCOPe (SCOP–extended) database offers continued development of the classic SCOP hierarchy, adding over 33,000 structures. We have attempted to assess the impact of these two decade old resources and guide future development. To this end, we surveyed recent articles to learn how structure classification data are used. Of 571 articles published in 2012–2013 that cite SCOP, 439 actually use data from the resource. We found that the type of use was fairly evenly distributed among four top categories: A) study protein structure or evolution (27% of articles), B) train and/or benchmark algorithms (28% of articles), C) augment non‐SCOP datasets with SCOP classification (21% of articles), and D) examine the classification of one protein/a small set of proteins (22% of articles). Most articles described computational research, although 11% described purely experimental research, and a further 9% included both. We examined how CATH and SCOP were used in 158 articles that cited both databases: while some studies used only one dataset, the majority used data from both resources. Protein structure classification remains highly relevant for a diverse range of problems and settings. Proteins 2015; 83:2025–2038. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:26313554

Problems experienced by informal caregivers of individuals with heart failure: An integrative review.

PubMed

Grant, Joan S; Graven, Lucinda J

2018-04-01

The purpose of this review was to examine and synthesize recent literature regarding problems experienced by informal caregivers when providing care for individuals with heart failure in the home. Integrative literature review. A review of current empirical literature was conducted utilizing PubMed, CINAHL, Embase, Sociological Abstracts, Social Sciences Full Text, PsycARTICLES, PsycINFO, Health Source: Nursing/Academic Edition, and Cochrane computerized databases. 19 qualitative, 16 quantitative, and 2 mixed methods studies met the inclusion criteria for review. Computerized databases were searched for a combination of subject terms (i.e., MeSH) and keywords related to informal caregivers, problems, and heart failure. The title and abstract of identified articles and reference lists were reviewed. Studies were included if they were published in English between January 2000 and December 2016 and examined problems experienced by informal caregivers in providing care for individuals with heart failure in the home. Studies were excluded if not written in English or if elements of caregiving in heart failure were not present in the title, abstract, or text. Unpublished and duplicate empirical literature as well as articles related to specific end-stage heart failure populations also were excluded. Methodology described by Cooper and others for integrative reviews of quantitative and qualitative research was used. Quality appraisal of the included studies was evaluated using the Joanna Briggs Institute critical appraisal tools for cross-sectional quantitative and qualitative studies. Informal caregivers experienced four key problems when providing care for individuals with heart failure in the home, including performing multifaceted activities and roles that evolve around daily heart failure demands; maintaining caregiver physical, emotional, social, spiritual, and financial well-being; having insufficient caregiver support; and performing caregiving with uncertainty and inadequate knowledge. Informal caregivers of individuals with heart failure experience complex problems in the home when providing care which impact all aspects of their lives. Incorporating advice from informal caregivers of individuals with heart failure will assist in the development of interventions to reduce negative caregiver outcomes. Given the complex roles in caring for individuals with heart failure, multicomponent interventions are potentially promising in assisting informal caregivers in performing these roles. Published by Elsevier Ltd.

Abstracting/Annotating. ERIC Processing Manual, Section VI.

ERIC Educational Resources Information Center

Brandhorst, Ted, Ed.

Rules and guidelines are provided for the preparation of abstracts and annotations for documents and journal articles entering the ERIC database. Various types of abstracts are defined, including the Informative, Indicative, and mixed Informative-Indicative. Advice is given on how to select the abstract type appropriate for the particular…

Large-scale extraction of accurate drug-disease treatment pairs from biomedical literature for drug repurposing

PubMed Central

2013-01-01

Background A large-scale, highly accurate, machine-understandable drug-disease treatment relationship knowledge base is important for computational approaches to drug repurposing. The large body of published biomedical research articles and clinical case reports available on MEDLINE is a rich source of FDA-approved drug-disease indication as well as drug-repurposing knowledge that is crucial for applying FDA-approved drugs for new diseases. However, much of this information is buried in free text and not captured in any existing databases. The goal of this study is to extract a large number of accurate drug-disease treatment pairs from published literature. Results In this study, we developed a simple but highly accurate pattern-learning approach to extract treatment-specific drug-disease pairs from 20 million biomedical abstracts available on MEDLINE. We extracted a total of 34,305 unique drug-disease treatment pairs, the majority of which are not included in existing structured databases. Our algorithm achieved a precision of 0.904 and a recall of 0.131 in extracting all pairs, and a precision of 0.904 and a recall of 0.842 in extracting frequent pairs. In addition, we have shown that the extracted pairs strongly correlate with both drug target genes and therapeutic classes, therefore may have high potential in drug discovery. Conclusions We demonstrated that our simple pattern-learning relationship extraction algorithm is able to accurately extract many drug-disease pairs from the free text of biomedical literature that are not captured in structured databases. The large-scale, accurate, machine-understandable drug-disease treatment knowledge base that is resultant of our study, in combination with pairs from structured databases, will have high potential in computational drug repurposing tasks. PMID:23742147

Regular Consumption of Sauerkraut and Its Effect on Human Health: A Bibliometric Analysis

PubMed Central

Ostermann, Thomas; Boehm, Katja; Molsberger, Friedrich

2014-01-01

Background: Sauerkraut is one of the most common and oldest forms of preserving cabbage and can be traced back as a food source to the 4th century BC. It contains a large quantity of lactic acid and tyramines, as well as vitamins and minerals, and has few calories. Objective: We aimed to provide an overview regarding the evidence of the effects of sauerkraut on human health by means of a bibliometric analysis. Methodology: Electronic databases (Medline, AMED, CamBase, CamQuest, the Cochrane Central Register of Controlled Trials, the Database of Abstracts of Reviews of Effects, the Cochrane Database of Systematic Reviews, EMBASE, the Karger-Publisher and the Thieme-Publisher databases) were searched from their inception until September 2012. Results: The search revealed 139 publications ranging over a 90-year period from 1921 to 2012. The majority of publications originated from Europe (48.6%), followed by the United States (30.7%) and Asia (10%). More than half of the research (56.8%) focused on food analysis, and 23.7% evaluated the impact of sauerkraut on health, including risk factors or digestive well-being. Direct research in humans was almost constant over time at about 11.5%. The studies found that sauerkraut induced inflammation locally, but repeated intake may result in diarrhea. Some studies pointed out anticarcinogenic effects of sauerkraut, while others concentrated on the interaction with monoamine oxidase inhibitors (MAOIs). Discussion: Sauerkraut, one of the oldest traditional foods, has a variety of beneficial effects on human health. However, unwanted effects such as intolerance reactions must be considered when dealing with sauerkraut as a functional food. PMID:25568828

MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups

PubMed Central

McIlroy, Simon Jon; Kirkegaard, Rasmus Hansen; McIlroy, Bianca; Nierychlo, Marta; Kristensen, Jannie Munk; Karst, Søren Michael; Albertsen, Mads

2017-01-01

Abstract Wastewater is increasingly viewed as a resource, with anaerobic digester technology being routinely implemented for biogas production. Characterising the microbial communities involved in wastewater treatment facilities and their anaerobic digesters is considered key to their optimal design and operation. Amplicon sequencing of the 16S rRNA gene allows high-throughput monitoring of these systems. The MiDAS field guide is a public resource providing amplicon sequencing protocols and an ecosystem-specific taxonomic database optimized for use with wastewater treatment facility samples. The curated taxonomy endeavours to provide a genus-level-classification for abundant phylotypes and the online field guide links this identity to published information regarding their ecology, function and distribution. This article describes the expansion of the database resources to cover the organisms of the anaerobic digester systems fed primary sludge and surplus activated sludge. The updated database includes descriptions of the abundant genus-level-taxa in influent wastewater, activated sludge and anaerobic digesters. Abundance information is also included to allow assessment of the role of emigration in the ecology of each phylotype. MiDAS is intended as a collaborative resource for the progression of research into the ecology of wastewater treatment, by providing a public repository for knowledge that is accessible to all interested in these biotechnologically important systems. Database URL: http://www.midasfieldguide.org PMID:28365734

Full Text Searching and Customization in the NASA ADS Abstract Service

NASA Technical Reports Server (NTRS)

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

2004-01-01

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

Validity of peptic ulcer disease and upper gastrointestinal bleeding diagnoses in administrative databases: a systematic review protocol.

PubMed

Montedori, Alessandro; Abraha, Iosief; Chiatti, Carlos; Cozzolino, Francesco; Orso, Massimiliano; Luchetta, Maria Laura; Rimland, Joseph M; Ambrosio, Giuseppe

2016-09-15

Administrative healthcare databases are useful to investigate the epidemiology, health outcomes, quality indicators and healthcare utilisation concerning peptic ulcers and gastrointestinal bleeding, but the databases need to be validated in order to be a reliable source for research. The aim of this protocol is to perform the first systematic review of studies reporting the validation of International Classification of Diseases, 9th Revision and 10th version (ICD-9 and ICD-10) codes for peptic ulcer and upper gastrointestinal bleeding diagnoses. MEDLINE, EMBASE, Web of Science and the Cochrane Library databases will be searched, using appropriate search strategies. We will include validation studies that used administrative data to identify peptic ulcer disease and upper gastrointestinal bleeding diagnoses or studies that evaluated the validity of peptic ulcer and upper gastrointestinal bleeding codes in administrative data. The following inclusion criteria will be used: (a) the presence of a reference standard case definition for the diseases of interest; (b) the presence of at least one test measure (eg, sensitivity, etc) and (c) the use of an administrative database as a source of data. Pairs of reviewers will independently abstract data using standardised forms and will evaluate quality using the checklist of the Standards for Reporting of Diagnostic Accuracy (STARD) criteria. This systematic review protocol has been produced in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocol (PRISMA-P) 2015 statement. Ethics approval is not required given that this is a protocol for a systematic review. We will submit results of this study to a peer-reviewed journal for publication. The results will serve as a guide for researchers validating administrative healthcare databases to determine appropriate case definitions for peptic ulcer disease and upper gastrointestinal bleeding, as well as to perform outcome research using administrative healthcare databases of these conditions. CRD42015029216. 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/

The method of abstraction in the design of databases and the interoperability

NASA Astrophysics Data System (ADS)

Yakovlev, Nikolay

2018-03-01

When designing the database structure oriented to the contents of indicators presented in the documents and communications subject area. First, the method of abstraction is applied by expansion of the indices of new, artificially constructed abstract concepts. The use of abstract concepts allows to avoid registration of relations many-to-many. For this reason, when built using abstract concepts, demonstrate greater stability in the processes. The example abstract concepts to address structure - a unique house number. Second, the method of abstraction can be used in the transformation of concepts by omitting some attributes that are unnecessary for solving certain classes of problems. Data processing associated with the amended concepts is more simple without losing the possibility of solving the considered classes of problems. For example, the concept "street" loses the binding to the land. The content of the modified concept of "street" are only the relations of the houses to the declared name. For most accounting tasks and ensure communication is enough.

CardioTF, a database of deconstructing transcriptional circuits in the heart system

PubMed Central

2016-01-01

Background: Information on cardiovascular gene transcription is fragmented and far behind the present requirements of the systems biology field. To create a comprehensive source of data for cardiovascular gene regulation and to facilitate a deeper understanding of genomic data, the CardioTF database was constructed. The purpose of this database is to collate information on cardiovascular transcription factors (TFs), position weight matrices (PWMs), and enhancer sequences discovered using the ChIP-seq method. Methods: The Naïve-Bayes algorithm was used to classify literature and identify all PubMed abstracts on cardiovascular development. The natural language learning tool GNAT was then used to identify corresponding gene names embedded within these abstracts. Local Perl scripts were used to integrate and dump data from public databases into the MariaDB management system (MySQL). In-house R scripts were written to analyze and visualize the results. Results: Known cardiovascular TFs from humans and human homologs from fly, Ciona, zebrafish, frog, chicken, and mouse were identified and deposited in the database. PWMs from Jaspar, hPDI, and UniPROBE databases were deposited in the database and can be retrieved using their corresponding TF names. Gene enhancer regions from various sources of ChIP-seq data were deposited into the database and were able to be visualized by graphical output. Besides biocuration, mouse homologs of the 81 core cardiac TFs were selected using a Naïve-Bayes approach and then by intersecting four independent data sources: RNA profiling, expert annotation, PubMed abstracts and phenotype. Discussion: The CardioTF database can be used as a portal to construct transcriptional network of cardiac development. Availability and Implementation: Database URL: http://www.cardiosignal.org/database/cardiotf.html. PMID:27635320

CardioTF, a database of deconstructing transcriptional circuits in the heart system.

PubMed

Zhen, Yisong

2016-01-01

Information on cardiovascular gene transcription is fragmented and far behind the present requirements of the systems biology field. To create a comprehensive source of data for cardiovascular gene regulation and to facilitate a deeper understanding of genomic data, the CardioTF database was constructed. The purpose of this database is to collate information on cardiovascular transcription factors (TFs), position weight matrices (PWMs), and enhancer sequences discovered using the ChIP-seq method. The Naïve-Bayes algorithm was used to classify literature and identify all PubMed abstracts on cardiovascular development. The natural language learning tool GNAT was then used to identify corresponding gene names embedded within these abstracts. Local Perl scripts were used to integrate and dump data from public databases into the MariaDB management system (MySQL). In-house R scripts were written to analyze and visualize the results. Known cardiovascular TFs from humans and human homologs from fly, Ciona, zebrafish, frog, chicken, and mouse were identified and deposited in the database. PWMs from Jaspar, hPDI, and UniPROBE databases were deposited in the database and can be retrieved using their corresponding TF names. Gene enhancer regions from various sources of ChIP-seq data were deposited into the database and were able to be visualized by graphical output. Besides biocuration, mouse homologs of the 81 core cardiac TFs were selected using a Naïve-Bayes approach and then by intersecting four independent data sources: RNA profiling, expert annotation, PubMed abstracts and phenotype. The CardioTF database can be used as a portal to construct transcriptional network of cardiac development. Database URL: http://www.cardiosignal.org/database/cardiotf.html.

Three Library and Information Science Databases Revisited: Currency, Coverage and Overlap, Interindexing Consistency.

ERIC Educational Resources Information Center

Blackwell, Michael Lind

This study evaluates the "Education Resources Information Center" (ERIC), "Library and Information Science Abstracts" (LISA), and "Library Literature" (LL) databases, determining how long the databases take to enter records (indexing delay), how much duplication of effort exists among the three databases (indexing…

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.

CANCER PREVENTION AND CONTROL (CP) DATABASE

EPA Science Inventory

This database focuses on breast, cervical, skin, and colorectal cancer emphasizing the application of early detection and control program activities and risk reduction efforts. The database provides bibliographic citations and abstracts of various types of materials including jou...

Impact of late radiation effects on cancer survivor children: an integrative review

PubMed Central

Coura, Cibeli Fernandes; Modesto, Patrícia Cláudia

2016-01-01

ABSTRACT We aimed to identify the late effects of radiation exposure in pediatric cancer survivors. An integrated literature review was performed in the databases MEDLINE and LILACS and SciELO. Included were articles in Portuguese and English, published over the past 10 years, using the following keywords: “neoplasias/neoplasms” AND “radioterapia/radiotherapy” AND “radiação/radiation”. After analysis, 14 articles - published in nine well-known journals - met the inclusion criteria. The publications were divided into two categories: “Late endocrine effects” and “Late non-endocrine effects”. Considering the increased survival rates in children who had cancer, the impact of late effects of exposure to radiation during radiological examinations for diagnosis and treatment was analyzed. Childhood cancer survivors were exposed to several late effects and should be early and regularly followed up, even when exposed to low radiation doses. PMID:26313432

[Medycyna Pracy: the scopus-based analysis of citations].

PubMed

Przyłuska, Jolanta

2006-01-01

Medycyna Pracy, a Polish bimonthly published since 1950, forms a long-standing documentation of studies carried out in the area of workers' health protection. The journal is primarily addressed to occupational health physicians and work hygiene specialists in Poland. It is indexed by numerous foreign information services (e.g., MEDLINE, EMBASE, BIOSIS PREVIEWS, BIOLOGICAL ABSTRACTS, SCOPUS) and thus promotes Polish research in occupational medicine throughout the world. The quantitative analysis for the years 1996-2005, grounded on the SCOPUS database, presents an average number of citations concerning a given volume, frequency of citations, articles most frequently cited, and countries, in which articles published in Medycyna Pracy have been referred to. A growing number of citations observed in the recent years signify the importance of issues investigated and discussed in the journal as well as its role in the world-wide circulation of scientific information.

A literature review of quantitative indicators to measure the quality of labor and delivery care.

PubMed

Tripathi, Vandana

2016-02-01

Strengthening measurement of the quality of labor and delivery (L&D) care in low-resource countries requires an understanding of existing approaches. To identify quantitative indicators of L&D care quality and assess gaps in indicators. PubMed, CINAHL Plus, and Embase databases were searched for research published in English between January 1, 1990, and October 31, 2013, using structured terms. Studies describing indicators for L&D care quality assessment were included. Those whose abstracts contained inclusion criteria underwent full-text review. Study characteristics, including indicator selection and data sources, were extracted via a standard spreadsheet. The structured search identified 1224 studies. After abstract and full-text review, 477 were included in the analysis. Most studies selected indicators by using literature review, clinical guidelines, or expert panels. Few indicators were empirically validated; most studies relied on medical record review to measure indicators. Many quantitative indicators have been used to measure L&D care quality, but few have been validated beyond expert opinion. There has been limited use of clinical observation in quality assessment of care processes. The findings suggest the need for validated, efficient consensus indicators of the quality of L&D care processes, particularly in low-resource countries. Copyright © 2015 International Federation of Gynecology and Obstetrics. Published by Elsevier Ireland Ltd. All rights reserved.

Drowning in Data: Sorting through CD ROM and Computer Databases.

ERIC Educational Resources Information Center

Cates, Carl M.; Kaye, Barbara K.

This paper identifies the bibliographic and numeric databases on CD-ROM and computer diskette that should be most useful for investigators in communication, marketing, and communication education. Bibliographic databases are usually found in three formats: citations only, citations and abstracts, and full-text articles. Numeric databases are…

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.

Which DSM validated tools for diagnosing depression are usable in primary care research? A systematic literature review.

PubMed

Nabbe, P; Le Reste, J Y; Guillou-Landreat, M; Munoz Perez, M A; Argyriadou, S; Claveria, A; Fernández San Martín, M I; Czachowski, S; Lingner, H; Lygidakis, C; Sowinska, A; Chiron, B; Derriennic, J; Le Prielec, A; Le Floch, B; Montier, T; Van Marwijk, H; Van Royen, P

2017-01-01

Depression occurs frequently in primary care. Its broad clinical variability makes it difficult to diagnose. This makes it essential that family practitioner (FP) researchers have validated tools to minimize bias in studies of everyday practice. Which tools validated against psychiatric examination, according to the major depression criteria of DSM-IV or 5, can be used for research purposes? An international FP team conducted a systematic review using the following databases: Pubmed, Cochrane and Embase, from 2000/01/01 to 2015/10/01. The three databases search identified 770 abstracts: 546 abstracts were analyzed after duplicates had been removed (224 duplicates); 50 of the validity studies were eligible and 4 studies were included. In 4 studies, the following tools were found: GDS-5, GDS-15, GDS-30, CESD-R, HADS, PSC-51 and HSCL-25. Sensitivity, Specificity, Positive Predictive Value, Negative Predictive Value were collected. The Youden index was calculated. Using efficiency data alone to compare these studies could be misleading. Additional reliability, reproducibility and ergonomic data will be essential for making comparisons. This study selected seven tools, usable in primary care research, for the diagnosis of depression. In order to define the best tools in terms of efficiency, reproducibility, reliability and ergonomics for research in primary care, and for care itself, further research will be essential. Copyright © 2016. Published by Elsevier Masson SAS.

Systematic review of qualitative evaluations of reentry programs addressing problematic drug use and mental health disorders amongst people transitioning from prison to communities.

PubMed

Kendall, Sacha; Redshaw, Sarah; Ward, Stephen; Wayland, Sarah; Sullivan, Elizabeth

2018-03-02

The paper presents a systematic review and metasynthesis of findings from qualitative evaluations of community reentry programs. The programs sought to engage recently released adult prison inmates with either problematic drug use or a mental health disorder. Seven biomedical and social science databases, Cinahl, Pubmed, Scopus, Proquest, Medline, Sociological abstracts and Web of Science and publisher database Taylor and Francis were searched in 2016 resulting in 2373 potential papers. Abstract reviews left 140 papers of which 8 were included after detailed review. Major themes and subthemes were identified through grounded theory inductive analysis of results from the eight papers. Of the final eight papers the majority (6) were from the United States. In total, the papers covered 405 interviews and included 121 (30%) females and 284 (70%) males. Findings suggest that the interpersonal skills of case workers; access to social support and housing; and continuity of case worker relationships throughout the pre-release and post-release period are key social and structural factors in program success. Evaluation of community reentry programs requires qualitative data to contextualize statistical findings and identify social and structural factors that impact on reducing incarceration and improving participant health. These aspects of program efficacy have implications for reentry program development and staff training and broader social and health policy and services.

The travesty of choosing after positive prenatal diagnosis.

PubMed

Sandelowski, Margarete; Barroso, Julie

2005-01-01

To integrate the findings of qualitative studies of expectant parents receiving positive prenatal diagnosis. Seventeen published and unpublished reports appearing between 1984 and 2001 and retrieved between December of 2002 and March of 2003. The electronic databases searched include Academic Search Elite, AIDS Information Online (AIDSLINE), Anthropological Index Online, Anthropological Literature, Black Studies, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Digital Dissertations, Dissertation Abstracts Index (DAI), Educational Resource Information Center (ERIC), MEDLINE, PsycInfo, Public Affairs Information Service (PAIS), PubMed, Social Science Abstracts (SocSci Abstracts), Social Science Citation Index, Social Work Abstracts, Sociological Abstracts (Sociofile), Women's Resources International, and Women's Studies. Qualitative studies involving expectant parents living in the United States of any race, ethnicity, nationality, or class who learned during any time in pregnancy of any fetal impairment by any means of diagnosis were eligible for inclusion. Metasummary techniques, including the calculation of frequency effect sizes, were used to aggregate the findings. Metasynthesis techniques, including constant comparison analysis and the reciprocal translation of concepts, were used to interpret the findings. The topical emphasis in the findings is on the termination of pregnancy following positive diagnosis. The thematic emphasis is on the dilemmas of choice and decision making. Positive prenatal diagnosis was for couples an experience of chosen losses and lost choices. Couples managed information to minimize stigmatization and cognitive dissonance. Existing guidelines for caring for couples after perinatal losses must accommodate the chosen loss experientially defining positive prenatal diagnosis.

Complementary and Alternative Medicine for Chronic Prostatitis/Chronic Pelvic Pain Syndrome

PubMed Central

2005-01-01

To discuss challenges concerning treatment for chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) and review complementary and alternative medical (CAM) therapies being evaluated for this condition, we performed a comprehensive search of articles published from 1990–2005 using the PubMed, Medline databases. Data from the articles were abstracted and pooled by subject. Keywords cross-searched with CP/CPPS included: complementary, alternative, integrative, therapies, interventions, nutrition, antioxidants, herbs, supplements, biofeedback and acupuncture. Listed articles with no abstracts were not included. Various CAM therapies for CP/CPPS exist including biofeedback, acupuncture, hyperthermia and electrostimulation. Additionally, a variety of in vitro and in vivo studies testing herbal and nutritional supplements were found. Saw palmetto, cernilton and quercetin were the most frequently tested supplements for CP/CPPS. Although many CAM therapies demonstrate positive preliminary observations as prospective treatments for CP/CPPS, further exploratory studies including more randomized, controlled trials are necessary for significant validation as treatment options for this complex disorder. PMID:16322807

Factors influencing adherence to cancer treatment in older adults with cancer: a systematic review.

PubMed

Puts, M T E; Tu, H A; Tourangeau, A; Howell, D; Fitch, M; Springall, E; Alibhai, S M H

2014-03-01

Cancer is a disease that mostly affects older adults. Treatment adherence is crucial to obtain optimal outcomes such as cure or improvement in quality of life. Older adults have numerous comorbidites as well as cognitive and sensory impairments that may affect adherence. The aim of this systematic review was to examine factors that influence adherence to cancer treatment in older adults with cancer. Systematic review of the literature published between inception of the databases and February 2013. English, Dutch, French and German-language articles reporting cross-sectional or longitudinal, intervention or observational studies of cancer treatment adherence were included. Data sources included MEDLINE, EMBASE, PsychINFO, Cumulative Index to Nursing and Allied Health (CINAHL), Web of Science, ASSIA, Ageline, Allied and Complementary Medicine (AMED), SocAbstracts and the Cochrane Library. Two reviewers reviewed abstracts and abstracted data using standardized forms. Study quality was assessed using the Mixed Methods Appraisal Tool 2011. Twenty-two manuscripts were identified reporting on 18 unique studies. The quality of most studies was good. Most studies focused on women with breast cancer and adherence to adjuvant hormonal therapy. More than half of the studies used data from administrative or clinical databases or chart reviews. The adherence rate varied from 52% to 100%. Only one qualitative study asked older adults about reasons for non-adherence. Factors associated with non-adherence varied widely across studies. Non-adherence was common across studies but little is known about the factors influencing non-adherence. More research is needed to investigate why older adults choose to adhere or not adhere to their treatment regimens taking into account their multimorbidity.

GAPscreener: an automatic tool for screening human genetic association literature in PubMed using the support vector machine technique.

PubMed

Yu, Wei; Clyne, Melinda; Dolan, Siobhan M; Yesupriya, Ajay; Wulf, Anja; Liu, Tiebin; Khoury, Muin J; Gwinn, Marta

2008-04-22

Synthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into health applications. Although genetic association studies account for a substantial proportion of the abstracts in PubMed, identifying them with standard queries is not always accurate or efficient. Further automating the literature-screening process can reduce the burden of a labor-intensive and time-consuming traditional literature search. The Support Vector Machine (SVM), a well-established machine learning technique, has been successful in classifying text, including biomedical literature. The GAPscreener, a free SVM-based software tool, can be used to assist in screening PubMed abstracts for human genetic association studies. The data source for this research was the HuGE Navigator, formerly known as the HuGE Pub Lit database. Weighted SVM feature selection based on a keyword list obtained by the two-way z score method demonstrated the best screening performance, achieving 97.5% recall, 98.3% specificity and 31.9% precision in performance testing. Compared with the traditional screening process based on a complex PubMed query, the SVM tool reduced by about 90% the number of abstracts requiring individual review by the database curator. The tool also ascertained 47 articles that were missed by the traditional literature screening process during the 4-week test period. We examined the literature on genetic associations with preterm birth as an example. Compared with the traditional, manual process, the GAPscreener both reduced effort and improved accuracy. GAPscreener is the first free SVM-based application available for screening the human genetic association literature in PubMed with high recall and specificity. The user-friendly graphical user interface makes this a practical, stand-alone application. The software can be downloaded at no charge.

Overweight and obesity management strategies in survivors of paediatric acute lymphoblastic leukaemia: a systematic review protocol.

PubMed

Ladhani, Salma; Empringham, Brianna; Wang, Kuan-Wen; Portwine, Carol; Banfield, Laura; de Souza, Russell J; Thabane, Lehana; Samaan, M Constantine

2018-06-22

Acute lymphoblastic leukaemia is the most common paediatric cancer. Survivors of childhood acute lymphoblastic leukaemia (SALL) are at risk of obesity and related cardiometabolic diseases including type 2 diabetes, hypertension, stroke and cardiovascular events. Therefore, it is important to address obesity in this population as this may help mitigate future cardiometabolic comorbidities. In this systematic review, we aim to assess current treatment strategies including lifestyle interventions, pharmacotherapy and bariatric surgery to manage overweight and obesity in SALL. We will search the following databases for primary studies: CINAHL, SPORTDiscus, EMBASE, MEDLINE, PsycINFO, Cochrane Central Register of Controlled Trials, and Cochrane Database of Systematic Reviews. In addition, unpublished primary studies will be searched in ClinicalTrials.gov as well as conference proceedings, presentations, abstracts, editorials and ProQuest Dissertations and Theses A&I. Reviewers will perform title, abstract, and full-text screening as well as data abstraction and risk of bias assessment independently with a third reviewer to be consulted to resolve disagreements. Searches will be run and updated through May 1st, 2018. The overall quality of the evidence will be determined using the Grading of Recommendations, Assessment, Development, and Evaluation criteria for each outcome. A meta-analysis will be performed if two studies deploying similar interventions, populations, and design and outcomes are identified. As individual patient data will not be included, we do not require ethics approval. This review will be published in a peer-reviewed journal. CRD42016051031. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

CE: Original Research: End-of-Life Care Behind Bars: A Systematic Review.

PubMed

Wion, Rachel K; Loeb, Susan J

2016-03-01

: To conduct a systematic review of the published research literature on end-of-life (EOL) care in prisons in order to determine the current state of the science and suggest implications for nursing practice and areas for future research.Applying the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we performed a comprehensive search of the literature using the following databases: CINAHL, Criminal Justice Abstracts, the National Criminal Justice Reference Service, PsycINFO, PubMed, and Sociological Abstracts. All databases were searched from the time of their inception through June 2014. All English-language articles that reported on original quantitative and qualitative research involving EOL or palliative care delivered to prisoners were included. We abstracted data, using the matrix method, and independently reviewed and graded the evidence on its level of strength and quality in accordance with the Johns Hopkins Nursing Evidence-Based Practice rating scales.Nineteen articles, all published between 2002 and 2014, met the inclusion criteria. Of these, 53% were published between 2009 and 2014, and 58% reported findings from qualitative research. One article reported on research conducted in the United Kingdom; the remaining 18 reported on research conducted in the United States. Capacity (that is, the number of prisoners requiring EOL care and the ability of the prison to accommodate them) and the site of EOL care delivery varied across studies, as did the criteria for admission to EOL or hospice services. Care was provided by prison health care staff, which variously included numerous professional disciplines, corrections officers, and inmate caregivers. The inmate caregivers, in particular, provided a wide array of services and were viewed positively by both EOL patients and health care staff. There are insufficient data to characterize the patients' and inmate caregivers' perceptions of the EOL care staff and the quality of care they provided. The screening criteria applied to inmate caregivers and the training they received varied widely among care programs. Inmates providing EOL care viewed caregiving as a transformational experience. Likewise, prison administrators and health care staff viewed inmate participation positively.This literature review reveals the challenges of providing EOL care to prisoners and may inspire nurses to consider steps they can take individually or within nursing organizations to improve this care and address the unique challenges faced by dying inmates. By being aware of these issues and advocating for best practices, nurses can help inmates at the end of life to have a dignified death.

Development of an Online Library of Patient-Reported Outcome Measures in Gastroenterology: The GI-PRO Database

PubMed Central

Khanna, Puja; Agarwal, Nikhil; Khanna, Dinesh; Hays, Ron D.; Chang, Lin; Bolus, Roger; Melmed, Gil; Whitman, Cynthia B.; Kaplan, Robert M.; Ogawa, Rikke; Snyder, Bradley; Spiegel, Brennan M.R.

2014-01-01

OBJECTIVES Because gastrointestinal (GI) illnesses can cause physical, emotional, and social distress, patient-reported outcomes (PROs) are used to guide clinical decision making, conduct research, and seek drug approval. It is important to develop a mechanism for identifying, categorizing, and evaluating the over 100 GI PROs that exist. Here we describe a new, National Institutes of Health (NIH)-supported, online PRO clearinghouse—the GI-PRO database. METHODS Using a protocol developed by the NIH Patient-Reported Outcome Measurement Information System (PROMIS®), we performed a systematic review to identify English-language GI PROs. We abstracted PRO items and developed an online searchable item database. We categorized symptoms into content “bins” to evaluate a framework for GI symptom reporting. Finally, we assigned a score for the methodological quality of each PRO represented in the published literature (0–20 range; higher indicates better). RESULTS We reviewed 15,697 titles (κ > 0.6 for title and abstract selection), from which we identified 126 PROs. Review of the PROs revealed eight GI symptom “bins”: (i) abdominal pain, (ii) bloat/gas, (iii) diarrhea, (iv) constipation, (v) bowel incontinence/soilage, (vi) heartburn/reflux, (vii) swallowing, and (viii) nausea/vomiting. In addition to these symptoms, the PROs covered four psychosocial domains: (i) behaviors, (ii) cognitions, (iii) emotions, and (iv) psychosocial impact. The quality scores were generally low (mean 8.88±4.19; 0 (min)−20 (max)). In addition, 51% did not include patient input in developing the PRO, and 41% provided no information on score interpretation. CONCLUSIONS GI PROs cover a wide range of biopsychosocial symptoms. Although plentiful, GI PROs are limited by low methodological quality. Our online PRO library (www.researchcore.org/gipro/) can help in selecting PROs for clinical and research purposes. PMID:24343547

International Early Childhood Resources from Educational Research Abstracts Online (ERA)

ERIC Educational Resources Information Center

International Journal of Early Years Education, 2004

2004-01-01

This annotated bibliography provides abstracts for 14 resources relating to early childhood around the world. Each annotation contains: title; author name(s); Educational Research Abstract; Abstract number; Source (name of journal in which the resource was published); ISSN of the journal in which the resource was published; and Issue (journal…

REMOVED: Neuropsychological profile of children aged 5-7 years with Traumatic Brain Injury.

PubMed

Bolaños, Maria Jimena Sarmiento; Solovieva, Yulia; Quintanar-Rojas, Luis

2015-12-01

This article has been removed: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal) This meeting abstract has been removed by the Publisher. Due to an administrative error, abstracts that were not presented at the ISDN 2014 meeting were inadvertently published in the meeting's abstract supplement. The Publisher apologizes to the authors and readers for this error. Copyright © 2015. Published by Elsevier Ltd.

REMOVED: Reproducibility in science: How video journals increase research validity and productivity.

PubMed

Henderson, Kira M

2015-12-01

This article has been removed: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal) This meeting abstract has been removed by the Publisher. Due to an administrative error, abstracts that were not presented at the ISDN 2014 meeting were inadvertently published in the meeting's abstract supplement. The Publisher apologizes to the authors and readers for this error. Copyright © 2015. Published by Elsevier Ltd.

When will I see you again? The fate of research findings from international wound care conferences*.

PubMed

Dumville, Jo C; Petherick, Emily S; Cullum, Nicky

2008-03-01

Medical conferences provide a forum for the rapid dissemination of research directly to health professionals and academics. However, the published record of poster and oral presentations from these meetings is usually limited to abstracts. We aimed to assess how many wound studies presented as conference abstracts were eventually published in journals and to identify the factors that predicted publication. The study was a retrospective review. We identified abstracts relating to oral and poster presentation from two large wound conferences. Following data extraction from the abstracts, a systematic search was conducted to examine if the research was subsequently published as a journal article. A time-to-event analysis was conducted to assess predictive associations between features of the research reported in the conference abstracts and time to full publication. In total, 492 abstracts from two European wound care conferences were identified (467 after exclusions). Of the abstracts included, 60% (279) were for posters and 40% (188) were for oral presentations. Over half of the abstracts (53%) reported results from case studies or case series design. In total, only 57 (12%) of the abstracts included resulted in a related publication. Analysis suggested that those studies reporting positive findings were significantly more likely to be published (hazard ratio 1.79, P= 0.001, 95% CIs 1.26-2.55). Few studies presented as conference abstracts at these two wounds conferences were subsequently published. This may be because of the low methodological quality of studies accepted for poster or oral presentation.

PedAM: a database for Pediatric Disease Annotation and Medicine.

PubMed

Jia, Jinmeng; An, Zhongxin; Ming, Yue; Guo, Yongli; Li, Wei; Li, Xin; Liang, Yunxiang; Guo, Dongming; Tai, Jun; Chen, Geng; Jin, Yaqiong; Liu, Zhimei; Ni, Xin; Shi, Tieliu

2018-01-04

There is a significant number of children around the world suffering from the consequence of the misdiagnosis and ineffective treatment for various diseases. To facilitate the precision medicine in pediatrics, a database namely the Pediatric Disease Annotations & Medicines (PedAM) has been built to standardize and classify pediatric diseases. The PedAM integrates both biomedical resources and clinical data from Electronic Medical Records to support the development of computational tools, by which enables robust data analysis and integration. It also uses disease-manifestation (D-M) integrated from existing biomedical ontologies as prior knowledge to automatically recognize text-mined, D-M-specific syntactic patterns from 774 514 full-text articles and 8 848 796 abstracts in MEDLINE. Additionally, disease connections based on phenotypes or genes can be visualized on the web page of PedAM. Currently, the PedAM contains standardized 8528 pediatric disease terms (4542 unique disease concepts and 3986 synonyms) with eight annotation fields for each disease, including definition synonyms, gene, symptom, cross-reference (Xref), human phenotypes and its corresponding phenotypes in the mouse. The database PedAM is freely accessible at http://www.unimd.org/pedam/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Electronic nicotine delivery system (electronic cigarette) awareness, use, reactions and beliefs: a systematic review.

PubMed

Pepper, Jessica K; Brewer, Noel T

2014-09-01

We sought to systematically review the literature on electronic nicotine delivery systems (ENDS, also called electronic cigarettes) awareness, use, reactions and beliefs. We searched five databases for articles published between 2006 and 1 July 2013 that contained variations of the phrases 'electronic cigarette', 'e-cigarette' and 'electronic nicotine delivery'. Of the 244 abstracts identified, we excluded articles not published in English, articles unrelated to ENDS, dissertation abstracts and articles without original data on prespecified outcomes. Two reviewers coded each article for ENDS awareness, use, reactions and beliefs. 49 studies met inclusion criteria. ENDS awareness increased from 16% to 58% from 2009 to 2011, and use increased from 1% to 6%. The majority of users were current or former smokers. Many users found ENDS satisfying, and some engaged in dual use of ENDS and other tobacco. No longitudinal studies examined whether ENDS serve as 'gateways' to future tobacco use. Common reasons for using ENDS were quitting smoking and using a product that is healthier than cigarettes. Self-reported survey data and prospective trials suggest that ENDS might help cigarette smokers quit, but no randomised controlled trials with probability samples compared ENDS with other cessation tools. Some individuals used ENDS to avoid smoking restrictions. ENDS use is expanding rapidly despite experts' concerns about safety, dual use and possible 'gateway' effects. More research is needed on effective public health messages, perceived health risks, validity of self-reports of smoking cessation and the use of different kinds of ENDS. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

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.

Virtualization of open-source secure web services to support data exchange in a pediatric critical care research network.

PubMed

Frey, Lewis J; Sward, Katherine A; Newth, Christopher J L; Khemani, Robinder G; Cryer, Martin E; Thelen, Julie L; Enriquez, Rene; Shaoyu, Su; Pollack, Murray M; Harrison, Rick E; Meert, Kathleen L; Berg, Robert A; Wessel, David L; Shanley, Thomas P; Dalton, Heidi; Carcillo, Joseph; Jenkins, Tammara L; Dean, J Michael

2015-11-01

To examine the feasibility of deploying a virtual web service for sharing data within a research network, and to evaluate the impact on data consistency and quality. Virtual machines (VMs) encapsulated an open-source, semantically and syntactically interoperable secure web service infrastructure along with a shadow database. The VMs were deployed to 8 Collaborative Pediatric Critical Care Research Network Clinical Centers. Virtual web services could be deployed in hours. The interoperability of the web services reduced format misalignment from 56% to 1% and demonstrated that 99% of the data consistently transferred using the data dictionary and 1% needed human curation. Use of virtualized open-source secure web service technology could enable direct electronic abstraction of data from hospital databases for research purposes. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability

PubMed Central

Vita, Randi; Overton, James A; Mungall, Christopher J; Sette, Alessandro

2018-01-01

Abstract The Immune Epitope Database (IEDB), at www.iedb.org, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public. By presenting curated data in a searchable database, we have liberated it from the tables and figures of journal articles, making it more accessible and usable by immunologists. Recently, the principles of Findability, Accessibility, Interoperability and Reusability have been formulated as goals that data repositories should meet to enhance the usefulness of their data holdings. We here examine how the IEDB complies with these principles and identify broad areas of success, but also areas for improvement. We describe short-term improvements to the IEDB that are being implemented now, as well as a long-term vision of true ‘machine-actionable interoperability’, which we believe will require community agreement on standardization of knowledge representation that can be built on top of the shared use of ontologies. PMID:29688354

Mathematical Notation in Bibliographic Databases.

ERIC Educational Resources Information Center

Pasterczyk, Catherine E.

1990-01-01

Discusses ways in which using mathematical symbols to search online bibliographic databases in scientific and technical areas can improve search results. The representations used for Greek letters, relations, binary operators, arrows, and miscellaneous special symbols in the MathSci, Inspec, Compendex, and Chemical Abstracts databases are…

Current Abstracts Nuclear Reactors and Technology

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

Bales, J.D.; Hicks, S.C.

1993-01-01

This publication Nuclear Reactors and Technology (NRT) announces on a monthly basis the current worldwide information available from the open literature on nuclear reactors and technology, including all aspects of power reactors, components and accessories, fuel elements, control systems, and materials. This publication contains the abstracts of DOE reports, journal articles, conference papers, patents, theses, and monographs added to the Energy Science and Technology Database during the past month. Also included are US information obtained through acquisition programs or interagency agreements and international information obtained through acquisition programs or interagency agreements and international information obtained through the International Energy Agency`smore » Energy Technology Data Exchange or government-to-government agreements. The digests in NRT and other citations to information on nuclear reactors back to 1948 are available for online searching and retrieval on the Energy Science and Technology Database and Nuclear Science Abstracts (NSA) database. Current information, added daily to the Energy Science and Technology Database, is available to DOE and its contractors through the DOE Integrated Technical Information System. Customized profiles can be developed to provide current information to meet each user`s needs.« less

The immune epitope database: a historical retrospective of the first decade.

PubMed

Salimi, Nima; Fleri, Ward; Peters, Bjoern; Sette, Alessandro

2012-10-01

As the amount of biomedical information available in the literature continues to increase, databases that aggregate this information continue to grow in importance and scope. The population of databases can occur either through fully automated text mining approaches or through manual curation by human subject experts. We here report our experiences in populating the National Institute of Allergy and Infectious Diseases sponsored Immune Epitope Database and Analysis Resource (IEDB, http://iedb.org), which was created in 2003, and as of 2012 captures the epitope information from approximately 99% of all papers published to date that describe immune epitopes (with the exception of cancer and HIV data). This was achieved using a hybrid model based on automated document categorization and extensive human expert involvement. This task required automated scanning of over 22 million PubMed abstracts followed by classification and curation of over 13 000 references, including over 7000 infectious disease-related manuscripts, over 1000 allergy-related manuscripts, roughly 4000 related to autoimmunity, and 1000 transplant/alloantigen-related manuscripts. The IEDB curation involves an unprecedented level of detail, capturing for each paper the actual experiments performed for each different epitope structure. Key to enabling this process was the extensive use of ontologies to ensure rigorous and consistent data representation as well as interoperability with other bioinformatics resources, including the Protein Data Bank, Chemical Entities of Biological Interest, and the NIAID Bioinformatics Resource Centers. A growing fraction of the IEDB data derives from direct submissions by research groups engaged in epitope discovery, and is being facilitated by the implementation of novel data submission tools. The present explosion of information contained in biological databases demands effective query and display capabilities to optimize the user experience. Accordingly, the development of original ways to query the database, on the basis of ontologically driven hierarchical trees, and display of epitope data in aggregate in a biologically intuitive yet rigorous fashion is now at the forefront of the IEDB efforts. We also highlight advances made in the realm of epitope analysis and predictive tools available in the IEDB. © 2012 The Authors. Immunology © 2012 Blackwell Publishing Ltd.

REMOVED: Risk-taking and self-regulation: A systematic review of the analysis of delinquency outcomes in the juvenile justice intervention literature 1996-2009.

PubMed

Evans-Chase, Michelle; Kim, Minseop; Zhou, Huiquan

2015-12-01

This article has been removed: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal) This meeting abstract has been removed by the Publisher. Due to an administrative error, abstracts that were not presented at the ISDN 2014 meeting were inadvertently published in the meeting's abstract supplement. The Publisher apologizes to the authors and readers for this error. Copyright © 2015. Published by Elsevier Ltd.

REMOVED: Reversal of immobilization stress-induced anorexia and endogenous leptin levels by Rauwolfia serpentina in rats: Relationship with adaptation to stress.

PubMed

Shireen, Erum; Bint-E-Ali, Wafa; Shafaq, Sania; Majeed, Azka; Fatima, Rija; Masroor, Maria; Haleem, Darakshan J

2015-12-01

This article has been removed: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal) This meeting abstract has been removed by the Publisher. Due to an administrative error, abstracts that were not presented at the ISDN 2014 meeting were inadvertently published in the meeting's abstract supplement. The Publisher apologizes to the authors and readers for this error. Copyright © 2015. Published by Elsevier Ltd.

REMOVED: Mindfulness meditation with incarcerated youth: A randomized controlled trial informed by neuropsychosocial theories of adolescence.

PubMed

Evans-Chase, Michelle

2015-12-01

This article has been removed: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal) This meeting abstract has been removed by the Publisher. Due to an administrative error, abstracts that were not presented at the ISDN 2014 meeting were inadvertently published in the meeting's abstract supplement. The Publisher apologizes to the authors and readers for this error. Copyright © 2015. Published by Elsevier Ltd.

Extracellular vesicles: the growth as diagnostics and therapeutics; a survey

PubMed Central

Roy, Sabrina; Hochberg, Fred H.; Jones, Pamela S.

2018-01-01

ABSTRACT This article aims to document the growth in extracellular vesicle (EV) research. Here, we report the growth in EV-related studies, patents, and grants as well as emerging companies with major intent on exosomes. Four different databases were utilized for electronic searches of published literature: two general databases – Scopus/Elsevier and Web of Science (WoS), as well as two specialized US government databases – the USA Patent and Trademark Office and National Institutes of Health (NIH) of the Department of Health and Human Services. The applied combination of key words was carefully chosen to cover the most commonly used terms in titles of publications, patents and grants dealing with conceptual areas of EVs. Within the time frame from 1 January 2000 to 31 December 2016, limited to articles published in English, we identified output using search strategies based upon Scopus/Elsevier and WoS, patent filings and NIH Federal Reports of funded grants. Consistently, USA and UK universities are the most frequent among the top 15 affiliations/organizations of the authors of the identified records. There is clear evidence of upward streaming of EV-related publications. By documenting the growth of the EV field, we hope to encourage a roster of independent authorities skilled to provide peer review of manuscripts, evaluation of grant applications, support of foundation initiatives and corporate long-term planning. It is important to encourage EV research to further identify biomarkers in diseases and allow for the development of adequate diagnostic tools that could distinguish disease subpopulations and enable personalized treatment of patients. PMID:29511461

Preliminary geologic map of the eastern Willapa Hills, Cowlitz, Lewis, and Wahkiakum Counties, Washington

USGS Publications Warehouse

Wells, Ray E.; Sawlan, Michael G.

2014-01-01

This digital map database and the PDF derived from the database were created from the analog geologic map: Wells, R.E. (1981), “Geologic map of the eastern Willapa Hills, Cowlitz, Lewis, and Wahkiakum Counties, Washington.” The geodatabase replicates the geologic mapping of the 1981 report with minor exceptions along water boundaries and also along the north and south map boundaries. Slight adjustments to contacts along water boundaries were made to correct differences between the topographic base map used in the 1981 compilation (analog USGS 15-minute series quadrangle maps at 1:62,500 scale) and the base map used for this digital compilation (scanned USGS 7.5-minute series quadrangle maps at 1:24,000 scale). These minor adjustments, however, did not materially alter the geologic map. No new field mapping was performed to create this digital map database, and no attempt was made to fit geologic contacts to the new 1:24,000 topographic base, except as noted above. We corrected typographical errors, formatting errors, and attribution errors (for example, the name change of Goble Volcanics to Grays River Volcanics following current State of Washington usage; Walsh and others, 1987). We also updated selected references, substituted published papers for abstracts, and cited published radiometric ages for the volcanic and plutonic rocks. The reader is referred to Magill and others (1982), Wells and Coe (1985), Walsh and others (1987), Moothart (1993), Payne (1998), Kleibacker (2001), McCutcheon (2003), Wells and others (2009), Chan and others (2012), and Wells and others (in press) for subsequent interpretations of the Willapa Hills geology.

Demonstrating the Open Data Repository's Data Publisher: The CheMin Database

NASA Astrophysics Data System (ADS)

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

2018-04-01

The Open Data Repository's Data Publisher aims to provide an easy-to-use software tool that will allow researchers to create and publish database templates and related data. The CheMin Database developed using this framework is shown as an example.

Yoga as a Therapeutic Intervention: A Bibliometric Analysis of Published Research Studies from 1967 to 2013

PubMed Central

Slutsky, Jeremiah; Singh, Nilkamal; Khalsa, Sat Bir S.

2015-01-01

Abstract Objective: A comprehensive bibliometric analysis was conducted on publications for yoga therapy research in clinical populations. Methods: Major electronic databases were searched for articles in all languages published between 1967 and 2013. Databases included PubMed, PsychInfo, MEDLINE, IndMed, Indian Citation Index, Index Medicus for South-East Asia Region, Web of Knowledge, Embase, EBSCO, and Google Scholar. Nonindexed journals were searched manually. Key search words included yoga, yoga therapy, pranayama, asana. All studies met the definition of a clinical trial. All styles of yoga were included. The authors extracted the data. Results: A total of 486 articles met the inclusion criteria and were published in 217 different peer-reviewed journals from 29 different countries on 28,080 study participants. The primary result observed is the three-fold increase in number of publications seen in the last 10 years, inclusive of all study designs. Overall, 45% of the studies published were randomized controlled trials, 18% were controlled studies, and 37% were uncontrolled studies. Most publications originated from India (n=258), followed by the United States (n=122) and Canada (n=13). The top three disorders addressed by yoga interventions were mental health, cardiovascular disease, and respiratory disease. Conclusion: A surge in publications on yoga to mitigate disease-related symptoms in clinical populations has occurred despite challenges facing the field of yoga research, which include standardization and limitations in funding, time, and resources. The population at large has observed a parallel surge in the use of yoga outside of clinical practice. The use of yoga as a complementary therapy in clinical practice may lead to health benefits beyond traditional treatment alone; however, to effect changes in health care policy, more high-quality, evidence-based research is needed. PMID:26196166

Comparison of conference abstracts and presentations with full-text articles in the health technology assessments of rapidly evolving technologies.

PubMed

Dundar, Y; Dodd, S; Dickson, R; Walley, T; Haycox, A; Williamson, P R

2006-02-01

To assess the extent of use of data from conference abstracts and presentations in health technology assessments (HTAs) provided as part of the National Institute for Health and Clinical Excellence (NICE) appraisal process. Also to assess the methodological quality of trials from conference abstracts and presentations, the consistency of reporting major outcomes between these sources and subsequent full-length publications, the effect of inclusion or exclusion of data from these sources on the meta-analysis pooled effect estimates, and the timeliness of availability of data from these sources and full articles in relation to the development of technology assessment reviews (TARs). A survey of seven TAR groups. An audit of published TARs: included all NICE TARs published between January 2000 and October 2004. Case studies of selected TARs. Analyses of the results of the survey and audit were presented as a descriptive summary and in a tabular format. Sensitivity analyses were carried out to compare the effect of inclusion of data from abstracts and presentations on the meta-analysis pooled effect estimates by including data from both abstracts/presentations and full papers, and data from only full publications, included in the original TAR. These analyses were then compared with meta-analysis of data from trials that have subsequently been published in full. All seven TAR groups completed and returned the survey. Five out of seven groups reported a general policy that included searching for and including studies available as conference abstracts/presentations. Five groups responded that if they included data from these sources they would carry out methodological quality assessment of studies from these sources using the same assessment tools as for full publications, and manage the data from these sources in the same way as fully published reports. All groups reported that if relevant outcome data were reported in both an abstract/presentation and a full publication, they would only consider the data in the full publication. Conversely, if data were only available in conference abstract/presentation, all but two groups reported that they would extract and use the data from the abstract/presentation. In total, 63 HTA reports for NICE were identified. In 20 of 63 TARs (32%) explicit statements were made with regards to inclusion and assessment of data from abstracts/presentations. Thirty-eight (60%) identified at least one randomised controlled trial (RCT) available as a conference abstract or presentation. Of these, 26 (68%) included trials available as abstracts/presentations. About 80% (20/26) of the 26 TARs that included RCTs in abstract/presentation form carried out an assessment of the methodological quality of such trials. In 16 TARs full reports of these trials were used for quality assessment where both abstracts/presentations and subsequent full publications were available. Twenty-three of 63 TARs (37%) carried out a quantitative analysis of results. Of these, ten (43%) included trials that were available as abstracts/presentations in the review; however, only 60% (6/10) of these included data from abstracts/presentations in the data analysis of results. Thirteen TARs evaluated rapidly evolving technologies and only three of these identified and included trial data from conference abstracts/presentations and carried out a quantitative analysis where abstract/presentation data were used. These three TARs were used as case studies. In all three case studies the overall quality of reporting in abstracts/presentations was generally poor. In all case studies abstracts and presentations failed to describe the method of randomisation or allocation concealment. Overall, there was no mention of blinding in 66% (25/38) of the abstracts and in 26% (7/27) of the presentations included in case studies, and one presentation (4%) explicitly stated use of intention-to-treat analysis. Results from one case study demonstrated discrepancies in data made available in abstracts or online conference presentations. Not only were discrepancies evident between these sources, but also comparison of conference abstracts/presentations with subsequently published full-length articles demonstrates data discrepancies in reporting of results. Sensitivity analyses based on one case study indicated a change in significance of effect in two outcome measures when only full papers published to date were included. There are variations in policy and practice across TAR groups regarding searching for and inclusion of studies available as conference abstracts/presentations. There is also variation in the level of detail reported in TARs regarding the use of abstracts/presentations. Therefore, TAR teams should be encouraged to state explicitly their search strategies for identifying conference abstracts and presentations, their methods for assessing these for inclusion, and where appropriate how the data were used and their effect on the results. Comprehensive searching for trials available as conference abstracts/presentations is time consuming and may be of questionable value. However, there may be a case for searching for and including abstract/presentation data if, for example, other sources of data are limited. If conference abstracts/presentations are to be included, the TAR teams need to allocate additional time for searching and managing data from these sources. Incomplete reporting in conference abstracts and presentations limits the ability of reviewers to assess confidently the methodological quality of trials. Where conference abstracts and presentations are considered for inclusion in the review, the TAR teams should increase their efforts to obtain further study details by contacting trialists. Where abstract/presentation data are included, reviewers should discuss the effect of including data from these sources. Any data discrepancies identified across sources in TARs should be highlighted and their impact discussed in the review. In addition, there is a need to carry out, for example, a sensitivity analysis with and without abstract/presentation data in the analysis. There is a need for research into the development of search strategies specific to identification of studies available as conference abstracts and presentations in TARs. Such strategies may include guidance with regard to identification of relevant electronic databases and appropriate conference sites relevant to certain clinical areas. As there are limited case studies included in this report, analyses should be repeated as more TARs accrue, or include the work of other international HTA groups.

Applications of Technology to CAS Data-Base Production.

ERIC Educational Resources Information Center

Weisgerber, David W.

1984-01-01

Reviews the economic importance of applying computer technology to Chemical Abstracts Service database production from 1973 to 1983. Database building, technological applications for editorial processing (online editing, Author Index Manufacturing System), and benefits (increased staff productivity, reduced rate of increase of cost of services,…

Conversion of Plastic Surgery meeting abstract presentations to full manuscripts: a brazilian perspective.

PubMed

Denadai, Rafael; Pinho, André Silveira; Samartine, Hugo; Denadai, Rodrigo; Raposo-Amaral, Cassio Eduardo

2017-01-01

to assess the conversion rate of Plastic Surgery meeting abstract presentations to full manuscript publications and examine factors associated with this conversion. we assessed the abstracts presented at the 47th and 48th Brazilian Congresses of Plastic Surgery by cross-referencing with multiple databases. We analyzed the Abstracts' characteristics associated with full manuscript publications. of the 200 abstracts presented, 50 abstracts were subsequently published in full, giving the conference a conversion rate of 25%. The mean time to publish was 15.00±13.75 months. In total, there were 4.93±1.63 authors per abstract and 67.8±163 subjects per abstract; 43.5% of the abstracts were of retrospective studies; 69% comprised the plastic surgery topics head and neck, and chest and trunk, and 88.5% had no statistical analysis. Overall, 80% of the manuscripts were published in plastic surgery journals, 76% had no impact factor and 52% had no citations. Bivariate and multivariate analyses revealed the presence of statistical analysis to be the most significant (p<0.05) predictive factor of conversion of abstracts into full manuscripts. the conversion rate found from this bibliometric research appeared a bit lower than the conversion trend of international plastic surgery meetings, and statistical analysis was a determinant of conversion success. avaliar a taxa de conversão de resumos apresentados em congressos de Cirurgia Plástica em publicações de manuscritos completos e examinar fatores associados a essa conversão. resumos apresentados nos XLVII e XLVIII Congressos Brasileiros de Cirurgia Plástica foram avaliados por meio de referências cruzadas em diversos bancos de dados. Averiguaram-se as características dos resumos associadas às publicações de manuscritos completos. dos 200 resumos apresentados, 50 foram posteriormente publicados na íntegra, determinando uma taxa de publicação de 25%. O tempo médio para publicação foi 15,00±13,75 meses. No total, houve 4,93±1,63 autores/resumo e 67,8±163 pacientes/resumo; 43,5% dos resumos foram estudos retrospectivos; 69% pertenciam aos tópicos crânio, cabeça e pescoço, e tórax e tronco e 88,5% não apresentavam análise estatística. No geral, 80% dos manuscritos foram publicados em revistas de Cirurgia Plástica, 76% não exibiam fator de impacto e 52% não possuíam citações. As análises bivariada e multivariada revelaram que a presença de análise estatística foi o fator preditivo significativo (p<0,05) para a conversão de resumos em manuscritos completos. a taxa de conversão deste estudo bibliométrico foi inferior à tendência de conversão descrita em congressos internacionais de Cirurgia Plástica, e a presença de análise estatística foi um determinante para o sucesso de conversão.

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

PubMed Central

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

2017-01-01

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

[The impact of the annual scientific meetings of the Israel Society of Rheumatology as measured by publication rates of the abstracts in peer-reviewed journals].

PubMed

Perez, Shira; Hashkes, Philip J; Uziel, Yosef

2004-04-01

We aimed to examine the impact and quality of the research presented in the Israel Society of Rheumatology (ISR) annual scientific meetings by measuring publication rates of the abstracts in peer-reviewed journals and investigating the factors that influenced publication. We examined the outcome of all 79 abstracts submitted to the ISR for the 1998-2000 annual meetings. A MEDLINE search of all abstracts, by authors, topics and keywords was performed. Senior authors of abstracts not found to be published in this search were interviewed regarding publication and factors influencing submission. We described the effect of variable factors on the rate of publication. As of September 2002, 63 (80%) abstracts were published in peer-reviewed journals or are currently in-press. Most abstracts were published in prominent journals (with a high impact factor). The majority of the abstracts (61%) were published in rheumatologic journals, 65% of the studies originated from tertiary centers and 19% of the studies were multicenter. The most common diseases studied were antiphospholipid syndrome (20%), systemic lupus erythematosus (19%) and inflammatory arthritis (18%). Most of the studies were of disease pathogenesis (35%) and clinical manifestations (33%). The most common study designs were basic science (34%). An overall 57% of the studies reported "positive" results and 9% reported "negative" results. None of the factors studied were associated with publication or non-publication. The main cause cited by authors for not publishing their abstract was lack of time to prepare a full paper or a desire to further expand the study. Within this group of 16 authors of abstracts, 11 authors still plan to submit a paper. The ISR annual meetings have an important clinical scientific impact as measured by the high rate of abstracts published as full length articles in leading peer-reviewed journals.

STEM Education Related Dissertation Abstracts: A Bounded Qualitative Meta-Study

ERIC Educational Resources Information Center

Banning, James; Folkestad, James E.

2012-01-01

This article utilizes a bounded qualitative meta-study framework to examine the 101 dissertation abstracts found by searching the ProQuest Dissertation and Theses[TM] digital database for dissertations abstracts from 1990 through 2010 using the search terms education, science, technology, engineer, and STEM/SMET. Professional search librarians…

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases

PubMed Central

Foerster, Hartmut; Bombarely, Aureliano; Battey, James N D; Sierro, Nicolas; Ivanov, Nikolai V; Mueller, Lukas A

2018-01-01

Abstract SolCyc is the entry portal to pathway/genome databases (PGDBs) for major species of the Solanaceae family hosted at the Sol Genomics Network. Currently, SolCyc comprises six organism-specific PGDBs for tomato, potato, pepper, petunia, tobacco and one Rubiaceae, coffee. The metabolic networks of those PGDBs have been computationally predicted by the pathologic component of the pathway tools software using the manually curated multi-domain database MetaCyc (http://www.metacyc.org/) as reference. SolCyc has been recently extended by taxon-specific databases, i.e. the family-specific SolanaCyc database, containing only curated data pertinent to species of the nightshade family, and NicotianaCyc, a genus-specific database that stores all relevant metabolic data of the Nicotiana genus. Through manual curation of the published literature, new metabolic pathways have been created in those databases, which are complemented by the continuously updated, relevant species-specific pathways from MetaCyc. At present, SolanaCyc comprises 199 pathways and 29 superpathways and NicotianaCyc accounts for 72 pathways and 13 superpathways. Curator-maintained, taxon-specific databases such as SolanaCyc and NicotianaCyc are characterized by an enrichment of data specific to these taxa and free of falsely predicted pathways. Both databases have been used to update recently created Nicotiana-specific databases for Nicotiana tabacum, Nicotiana benthamiana, Nicotiana sylvestris and Nicotiana tomentosiformis by propagating verifiable data into those PGDBs. In addition, in-depth curation of the pathways in N.tabacum has been carried out which resulted in the elimination of 156 pathways from the 569 pathways predicted by pathway tools. Together, in-depth curation of the predicted pathway network and the supplementation with curated data from taxon-specific databases has substantially improved the curation status of the species–specific N.tabacum PGDB. The implementation of this strategy will significantly advance the curation status of all organism-specific databases in SolCyc resulting in the improvement on database accuracy, data analysis and visualization of biochemical networks in those species. Database URL https://solgenomics.net/tools/solcyc/ PMID:29762652

MimoSA: a system for minimotif annotation

PubMed Central

2010-01-01

Background Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many minimotifs in the primary literature, which have yet to be annotated, while entirely novel minimotifs continue to be published on a weekly basis. Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature. Results We have built the MimoSA application for minimotif annotation. The application supports management of the Minimotif Miner database, literature tracking, and annotation of new minimotifs. MimoSA enables the visualization, organization, selection and editing functions of minimotifs and their attributes in the MnM database. For the literature components, Mimosa provides paper status tracking and scoring of papers for annotation through a freely available machine learning approach, which is based on word correlation. The paper scoring algorithm is also available as a separate program, TextMine. Form-driven annotation of minimotif attributes enables entry of new minimotifs into the MnM database. Several supporting features increase the efficiency of annotation. The layered architecture of MimoSA allows for extensibility by separating the functions of paper scoring, minimotif visualization, and database management. MimoSA is readily adaptable to other annotation efforts that manually curate literature into a MySQL database. Conclusions MimoSA is an extensible application that facilitates minimotif annotation and integrates with the Minimotif Miner database. We have built MimoSA as an application that integrates dynamic abstract scoring with a high performance relational model of minimotif syntax. MimoSA's TextMine, an efficient paper-scoring algorithm, can be used to dynamically rank papers with respect to context. PMID:20565705

Population groups: indexing, coverage, and retrieval effectiveness of ethnically related health care issues in health sciences databases.

PubMed Central

Efthimiadis, E N; Afifi, M

1996-01-01

OBJECTIVES: This study examined methods of accessing (for indexing and retrieval purposes) medical research on population groups in the major abstracting and indexing services of the health sciences literature. DESIGN: The study of diseases in specific population groups is facilitated by the indexing of both diseases and populations in a database. The MEDLINE, PsycINFO, and Embase databases were selected for the study. The published thesauri for these databases were examined to establish the vocabulary in use. Indexing terms were identified and examined as to their representation in the current literature. Terms were clustered further into groups thought to reflect an end user's perspective and to facilitate subsequent analysis. The medical literature contained in the three online databases was searched with both controlled vocabulary and natural language terms. RESULTS: The three thesauri revealed shallow pre-coordinated hierarchical structures, rather difficult-to-use terms for post-coordination, and a blurring of cultural, genetic, and racial facets of populations. Post-coordination is difficult because of the system-oriented terminology, which is intended mostly for information professionals. The terminology unintentionally restricts access by the end users who lack the knowledge needed to use the thesauri effectively for information retrieval. CONCLUSIONS: Population groups are not represented adequately in the index languages of health sciences databases. Users of these databases need to be alerted to the difficulties that may be encountered in searching for information on population groups. Information and health professionals may not be able to access the literature if they are not familiar with the indexing policies on population groups. Consequently, the study points to a problem that needs to be addressed, through either the redesign of existing systems or the design of new ones to meet the goals of Healthy People 2000 and beyond. PMID:8883987

Enhancing navigation in biomedical databases by community voting and database-driven text classification

PubMed Central

Duchrow, Timo; Shtatland, Timur; Guettler, Daniel; Pivovarov, Misha; Kramer, Stefan; Weissleder, Ralph

2009-01-01

Background The breadth of biological databases and their information content continues to increase exponentially. Unfortunately, our ability to query such sources is still often suboptimal. Here, we introduce and apply community voting, database-driven text classification, and visual aids as a means to incorporate distributed expert knowledge, to automatically classify database entries and to efficiently retrieve them. Results Using a previously developed peptide database as an example, we compared several machine learning algorithms in their ability to classify abstracts of published literature results into categories relevant to peptide research, such as related or not related to cancer, angiogenesis, molecular imaging, etc. Ensembles of bagged decision trees met the requirements of our application best. No other algorithm consistently performed better in comparative testing. Moreover, we show that the algorithm produces meaningful class probability estimates, which can be used to visualize the confidence of automatic classification during the retrieval process. To allow viewing long lists of search results enriched by automatic classifications, we added a dynamic heat map to the web interface. We take advantage of community knowledge by enabling users to cast votes in Web 2.0 style in order to correct automated classification errors, which triggers reclassification of all entries. We used a novel framework in which the database "drives" the entire vote aggregation and reclassification process to increase speed while conserving computational resources and keeping the method scalable. In our experiments, we simulate community voting by adding various levels of noise to nearly perfectly labelled instances, and show that, under such conditions, classification can be improved significantly. Conclusion Using PepBank as a model database, we show how to build a classification-aided retrieval system that gathers training data from the community, is completely controlled by the database, scales well with concurrent change events, and can be adapted to add text classification capability to other biomedical databases. The system can be accessed at . PMID:19799796

Content Independence in Multimedia Databases.

ERIC Educational Resources Information Center

de Vries, Arjen P.

2001-01-01

Investigates the role of data management in multimedia digital libraries, and its implications for the design of database management systems. Introduces the notions of content abstraction and content independence. Proposes a blueprint of a new class of database technology, which supports the basic functionality for the management of both content…

The CIS Database: Occupational Health and Safety Information Online.

ERIC Educational Resources Information Center

Siegel, Herbert; Scurr, Erica

1985-01-01

Describes document acquisition, selection, indexing, and abstracting and discusses online searching of the CIS database, an online system produced by the International Occupational Safety and Health Information Centre. This database comprehensively covers information in the field of occupational health and safety. Sample searches and search…

The value of Institute of Human Virology meeting abstracts and beyond

PubMed Central

Jeang, Kuan-Teh

2005-01-01

This month Retrovirology publishes the meeting abstracts from the 10th annual Institute of Human Virology conference held August 29th to September 2nd, 2005 in Baltimore, Maryland, USA. In this editorial, the rationale for publishing meeting abstracts is discussed.

ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins

PubMed Central

Krassowski, Michal; Paczkowska, Marta; Cullion, Kim; Huang, Tina; Dzneladze, Irakli; Ouellette, B F Francis; Yamada, Joseph T; Fradet-Turcotte, Amelie

2018-01-01

Abstract Interpretation of genetic variation is needed for deciphering genotype-phenotype associations, mechanisms of inherited disease, and cancer driver mutations. Millions of single nucleotide variants (SNVs) in human genomes are known and thousands are associated with disease. An estimated 21% of disease-associated amino acid substitutions corresponding to missense SNVs are located in protein sites of post-translational modifications (PTMs), chemical modifications of amino acids that extend protein function. ActiveDriverDB is a comprehensive human proteo-genomics database that annotates disease mutations and population variants through the lens of PTMs. We integrated >385,000 published PTM sites with ∼3.6 million substitutions from The Cancer Genome Atlas (TCGA), the ClinVar database of disease genes, and human genome sequencing projects. The database includes site-specific interaction networks of proteins, upstream enzymes such as kinases, and drugs targeting these enzymes. We also predicted network-rewiring impact of mutations by analyzing gains and losses of kinase-bound sequence motifs. ActiveDriverDB provides detailed visualization, filtering, browsing and searching options for studying PTM-associated mutations. Users can upload mutation datasets interactively and use our application programming interface in pipelines. Integrative analysis of mutations and PTMs may help decipher molecular mechanisms of phenotypes and disease, as exemplified by case studies of TP53, BRCA2 and VHL. The open-source database is available at https://www.ActiveDriverDB.org. PMID:29126202

Abstracts of SIG Sessions.

ERIC Educational Resources Information Center

Proceedings of the ASIS Annual Meeting, 1997

1997-01-01

Presents abstracts of SIG Sessions. Highlights include digital collections; information retrieval methods; public interest/fair use; classification and indexing; electronic publication; funding; globalization; information technology projects; interface design; networking in developing countries; metadata; multilingual databases; networked…

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

PubMed

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

2018-05-01

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

A Database Evaluation Based on Information Needs of Academic Social Scientists.

ERIC Educational Resources Information Center

Buterbaugh, Nancy Toth

This study evaluates two databases, "Historical Abstracts" and REESWeb, to determine their effectiveness in supporting academic social science research. While many performance evaluations gather quantitative data from isolated query and response transactions, this study is a qualitative evaluation of the databases in the context of…

NCCDPHP PUBLICATION DATABASE

EPA Science Inventory

This database provides bibliographic citations and abstracts of publications produced by the CDC's National Center for Chronic Disease Prevention and Health Promotion (NCCDPHP) including journal articles, monographs, book chapters, reports, policy documents, and fact sheets. Full...

Publication Rates of Podium Versus Poster Presentations at the Arthroscopy Association of North America Meetings 2008-2012.

PubMed

Frank, Rachel M; Cvetanovich, Gregory L; Collins, Michael J; Arns, Thomas A; Black, Austin; Verma, Nikhil N; Cole, Brian J; Forsythe, Brian

2017-01-01

To analyze the publication rate of poster and podium presentations at Arthroscopy Association of North America (AANA) annual meetings from 2008 to 2012. An online search using PubMed and Google Scholar for all published manuscripts associated with abstracts presented from 2008 to 2012 AANA annual meetings was performed. Abstracts were classified by presentation type (poster vs podium), and the journal and publication date were recorded for all published abstracts. Descriptive statistics, logistic regression, and Fisher's exact tests were performed, with P < .05 considered significant. A total of 1,508 abstracts were submitted to AANA annual meetings from 2008 to 2012, with 976 abstracts accepted for presentation (65% overall acceptance rate). There were 328 podium (22% acceptance rate) and 648 poster (43% acceptance rate) presentations. Of the 976 accepted abstracts, 479 (49%) were published within 3 years in peer-reviewed journals. The overall publication rates for podium and poster presentations were 59% (n = 193) and 44% (n = 286), respectively. Podium presentations were significantly more likely to be published within 3 years compared with poster presentations (P < .0001; odds ratio 1.8095, confidence interval 1.3826-2.3682). There were no differences in time to publication between podium and poster presentations (1.3 ± 1.2 vs 1.1 ± 1.3 years, P = .0633). Over the 5-year study period, the overall abstract acceptance rate (P < .0001) and the rate of abstracts accepted for poster presentation (P < .0001) increased significantly over time, whereas there was no increase in the rate of abstracts accepted for podium presentation (P = .5638). The most common journals of publication were Arthroscopy (n = 157, 32.7%) followed by American Journal of Sports Medicine (n = 93, 19.4%). The overall publication rate of abstracts presented at AANA annual meetings is 49%, with podium presentations 1.8 times more likely to be published than poster presentations. The overall abstract acceptance rate and the rate of abstracts accepted for poster presentation increased significantly over time, whereas there was no significant increase in the rate of abstracts accepted for podium presentation. The publication rates of abstracts presented at the AANA annual meetings demonstrate the meetings' impact and importance to the advancement of the scientific literature. Copyright © 2016 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Check Sample Abstracts.

PubMed

Alter, David; Grenache, David G; Bosler, David S; Karcher, Raymond E; Nichols, James; Rajadhyaksha, Aparna; Camelo-Piragua, Sandra; Rauch, Carol; Huddleston, Brent J; Frank, Elizabeth L; Sluss, Patrick M; Lewandrowski, Kent; Eichhorn, John H; Hall, Janet E; Rahman, Saud S; McPherson, Richard A; Kiechle, Frederick L; Hammett-Stabler, Catherine; Pierce, Kristin A; Kloehn, Erica A; Thomas, Patricia A; Walts, Ann E; Madan, Rashna; Schlesinger, Kathie; Nawgiri, Ranjana; Bhutani, Manoop; Kanber, Yonca; Abati, Andrea; Atkins, Kristen A; Farrar, Robert; Gopez, Evelyn Valencerina; Jhala, Darshana; Griffin, Sonya; Jhala, Khushboo; Jhala, Nirag; Bentz, Joel S; Emerson, Lyska; Chadwick, Barbara E; Barroeta, Julieta E; Baloch, Zubair W; Collins, Brian T; Middleton, Owen L; Davis, Gregory G; Haden-Pinneri, Kathryn; Chu, Albert Y; Keylock, Joren B; Ramoso, Robert; Thoene, Cynthia A; Stewart, Donna; Pierce, Arand; Barry, Michelle; Aljinovic, Nika; Gardner, David L; Barry, Michelle; Shields, Lisa B E; Arnold, Jack; Stewart, Donna; Martin, Erica L; Rakow, Rex J; Paddock, Christopher; Zaki, Sherif R; Prahlow, Joseph A; Stewart, Donna; Shields, Lisa B E; Rolf, Cristin M; Falzon, Andrew L; Hudacki, Rachel; Mazzella, Fermina M; Bethel, Melissa; Zarrin-Khameh, Neda; Gresik, M Vicky; Gill, Ryan; Karlon, William; Etzell, Joan; Deftos, Michael; Karlon, William J; Etzell, Joan E; Wang, Endi; Lu, Chuanyi M; Manion, Elizabeth; Rosenthal, Nancy; Wang, Endi; Lu, Chuanyi M; Tang, Patrick; Petric, Martin; Schade, Andrew E; Hall, Geraldine S; Oethinger, Margret; Hall, Geraldine; Picton, Avis R; Hoang, Linda; Imperial, Miguel Ranoa; Kibsey, Pamela; Waites, Ken; Duffy, Lynn; Hall, Geraldine S; Salangsang, Jo-Anne M; Bravo, Lulette Tricia C; Oethinger, Margaret D; Veras, Emanuela; Silva, Elvia; Vicens, Jimena; Silva, Elvio; Keylock, Joren; Hempel, James; Rushing, Elizabeth; Posligua, Lorena E; Deavers, Michael T; Nash, Jason W; Basturk, Olca; Perle, Mary Ann; Greco, Alba; Lee, Peng; Maru, Dipen; Weydert, Jamie Allen; Stevens, Todd M; Brownlee, Noel A; Kemper, April E; Williams, H James; Oliverio, Brock J; Al-Agha, Osama M; Eskue, Kyle L; Newlands, Shawn D; Eltorky, Mahmoud A; Puri, Puja K; Royer, Michael C; Rush, Walter L; Tavora, Fabio; Galvin, Jeffrey R; Franks, Teri J; Carter, James Elliot; Kahn, Andrea Graciela; Lozada Muñoz, Luis R; Houghton, Dan; Land, Kevin J; Nester, Theresa; Gildea, Jacob; Lefkowitz, Jerry; Lacount, Rachel A; Thompson, Hannis W; Refaai, Majed A; Quillen, Karen; Lopez, Ana Ortega; Goldfinger, Dennis; Muram, Talia; Thompson, Hannis

2009-02-01

The following abstracts are compiled from Check Sample exercises published in 2008. These peer-reviewed case studies assist laboratory professionals with continuing medical education and are developed in the areas of clinical chemistry, cytopathology, forensic pathology, hematology, microbiology, surgical pathology, and transfusion medicine. Abstracts for all exercises published in the program will appear annually in AJCP.

Bone-Targeting Radiopharmaceuticals for the Treatment of Bone-Metastatic Castration-Resistant Prostate Cancer: Exploring the Implications of New Data

PubMed Central

Saylor, Philip J.; Everly, Jason J.; Sartor, Oliver

2014-01-01

Background. Clinical features of patients with castration-resistant prostate cancer (CRPC) are characterized by a high incidence of bone metastases, which are associated with impairment of quality of life, pain, skeletal-related events (SREs), and a negative impact on prognosis. Advances in the understanding of cancer cell-bone stroma interactions and molecular mechanisms have recently permitted the development of new agents. Purpose. We review the merits, applications, and limitations of emerging data sets on bone-metastatic CRPC with a focus on radium-223, an α-emitting radiopharmaceutical, and its use in therapy for this disease. Methods. References for this review were identified through searches of PubMed and Medline databases, and only papers published in English were considered. Related links in the databases were reviewed, along with relevant published guidelines, recently published abstracts from major medical meetings, and transcripts from a recent round table of clinical investigators. Results. Prior to radium-223, available bone-targeted therapies demonstrated the ability to delay SREs and palliate bone pain in patients with metastatic CRPC but without evidence of improvement in overall survival (OS). In a randomized controlled phase III trial, radium-223 demonstrated the ability to improve OS and delay SREs in docetaxel-pretreated or docetaxel-unfit men with symptomatic bone-metastatic CRPC and was not associated with significantly more grade 3 or 4 adverse events than placebo. Conclusion. Radium-223 has a targeted effect on bone metastases in CRPC and has an important role in docetaxel-pretreated or docetaxel-unfit men with symptomatic bone-metastatic CRPC. PMID:25232039

Glioblastoma research 2006-2010: pattern of citation and systematic review of highly cited articles.

PubMed

Nieder, Carsten; Astner, Sabrina T; Grosu, Anca L

2012-11-01

High and continuously increasing research activity related to different aspects of pathogenesis, epidemiology, diagnosis and treatment of glioblastoma has been performed between 2006 and 2010. Different measures of impact, visibility and quality of published research are available, each with its own pros and cons. For this review, article citation rate was chosen. Articles were identified through systematic search of the abstract database PubMed followed by analyses of total number of citations and proportion of highly cited articles, arbitrarily defined as those with ≥100, 50-99, and 25-49 citations, respectively (citation database Scopus). Overall 5831 scientific articles on the subject were published during this time period. 1.5% of all articles accumulated at least 100 citations, 3.2% were cited between 50 and 99 times, and 7.5% were cited between 25 and 49 times. Among the 10 most cited articles, 7 reported on genomic analyses, molecular subclasses of glioblastoma and/or stem cells. Overall, 18 randomized clinical trials were published between 2006 and 2010, including those with phase II design. Thirty-nine percent of them accumulated at least 50 citations and 72% were cited at least 25 times. In general, annual citation rate appeared to gradually increase during the first 2-3 years after publication before reaching high levels. A large variety of preclinical and clinical topics achieved at least 25 citations. However, areas such as quality of life, side effects, and end-of-life care were underrepresented. Efforts to increase their visibility might be warranted. Copyright © 2012 Elsevier B.V. All rights reserved.

Determinants of seat belt use behaviour: a protocol for a systematic review

PubMed Central

Ghaffari, Mohtasham; Armoon, Bahram; Rakhshanderou, Sakineh; Mehrabi, Yadollah; Soori, Hamid; Simsekoghlu, Ozelem; Harooni, Javad

2018-01-01

Introduction The use of seat belts could prevent severe collision damage to people in vehicle accidents and keep passengers safe from sustaining serious injuries; for instance, it could prevent passengers from being thrown out of a vehicle after the collision. The current systematic review will identify and analyse the determinants of seat belt use behaviour. Methods and analysis We will include qualitative, quantitative and mixed methods studies reporting the acquired data from passengers aged more than 12 years and drivers, from both commercial and personal vehicles. Online databases including MEDLINE/PubMed, Scopus, Web of Science, Embase, Cochrane Database of Systematic Reviews and PsycINFO will be investigated in the current study. Published and available articles will be evaluated according to their titles and abstracts. Published papers conforming to the inclusion criteria will be organised for a complete review. Next, the full text of the remaining articles will be studied independently for eligibility by two authors. The quality of the selected studies will be assessed with appropriate tools. Based on the information obtained from the data extraction, the type of determinants of seat belt use will be classified. Ethics and dissemination Ethics approval is not required, because this is a protocol for a systematic review and no primary data will be collected. The authors will ensure to maintain the rights of the used and included articles in the present systematic review. The findings of this review will be published in a relevant peer-reviewed journal. PROSPERO registration number CRD42017067511. PMID:29724739

Development of Conceptual Framework to Understand Factors Associated with Return to Work among Cancer Survivors: A Systematic Review

PubMed Central

CHOW, Sze Loon; TING, Anselm Su; SU, Tin Tin

2014-01-01

Abstract This systematic review was conducted to develop a conceptual framework that addresses various factors associated with return to work among cancer survivors. Databases Medline, EMBASE, ProQuest, PubMed and ScienceDirect were systematically searched using medical subject headings [MeSH] for studies published in English from 1990 to 2013. Studies that described adult cancer patients’ self-reported data or patients’ point of view on factors associated with return to work or employment status following cancer diagnosis were included. Articles selection was conducted in three steps: selection based on title and abstract, retrieval of full text and additions of articles from reference lists and recommendations from experts. Disagreement in data extraction was solved by consultation of third reviewer. Out of twenty seven articles, breast cancer was the most studied type of cancer (30%) while colorectal cancer was studied independently in two articles (7.4%). Conceptual framework on return to work identifies factors under environmental, personal, work demand, work ability, health status and financial factors. Extensive search of scientific databases over last 24 years and the development of the conceptual frame-work are the strength of this review. Conceptual framework reveals the various factors including non-medical factors associated with return to work upon cancer diagnosis. It serves as a reminder to the policy makers to focus on modifiable factors as potential areas for intervention to assist cancer survivors return to work, especially those with little financial assistance and health insurance. PMID:28435811

Substance Abuse Intensive Outpatient Programs: Assessing the Evidence

PubMed Central

McCarty, Dennis; Braude, Lisa; Dougherty, Richard H.; Daniels, Allen S.; Ghose, Sushmita Shoma; Delphin-Rittmon, Miriam E.

2014-01-01

Objective Substance abuse intensive outpatient programs (IOPs) are direct services for people with substance use disorders or co-occurring mental and substance use disorders who do not require medical detoxification or 24-hour supervision. IOPs are alternatives to inpatient and residential treatment. They are designed to establish psychosocial supports and facilitate relapse management and coping strategies. This article assesses their evidence base. Methods Authors searched major databases: PubMed, PsycINFO, Applied Social Sciences Index and Abstracts, Sociological Abstracts, Social Services Abstracts, Published International Literature on Traumatic Stress, the Educational Resources Information Center, and the Cumulative Index to Nursing and Allied Health Literature. They identified 12 individual studies and one review published between 1995 and 2012. They chose from three levels of research evidence (high, moderate, and low) based on benchmarks for the number of studies and quality of their methodology. They also described the evidence of service effectiveness. Results Based on the quality of trials, diversity of settings, and consistency of outcomes, the level of evidence for IOP research was considered high. Multiple randomized trials and naturalistic analyses compared IOPs with inpatient or residential care; these types of services had comparable outcomes. All studies reported substantial reductions in alcohol and drug use between baseline and follow-up. However, substantial variability in the operationalization of IOPs and outcome measures was apparent. Conclusions IOPs are an important part of the continuum of care for alcohol and drug use disorders. They are as effective as inpatient treatment for most individuals seeking care. Public and commercial health plans should consider IOP treatment as a covered health benefit. Standardization of the elements included in IOPs may improve their quality and effectiveness. PMID:24445620

Machine Learning-Based Classification of 38 Years of Spine-Related Literature Into 100 Research Topics.

PubMed

Sing, David C; Metz, Lionel N; Dudli, Stefan

2017-06-01

Retrospective review. To identify the top 100 spine research topics. Recent advances in "machine learning," or computers learning without explicit instructions, have yielded broad technological advances. Topic modeling algorithms can be applied to large volumes of text to discover quantifiable themes and trends. Abstracts were extracted from the National Library of Medicine PubMed database from five prominent peer-reviewed spine journals (European Spine Journal [ESJ], The Spine Journal [SpineJ], Spine, Journal of Spinal Disorders and Techniques [JSDT], Journal of Neurosurgery: Spine [JNS]). Each abstract was entered into a latent Dirichlet allocation model specified to discover 100 topics, resulting in each abstract being assigned a probability of belonging in a topic. Topics were named using the five most frequently appearing terms within that topic. Significance of increasing ("hot") or decreasing ("cold") topic popularity over time was evaluated with simple linear regression. From 1978 to 2015, 25,805 spine-related research articles were extracted and classified into 100 topics. Top two most published topics included "clinical, surgeons, guidelines, information, care" (n = 496 articles) and "pain, back, low, treatment, chronic" (424). Top two hot trends included "disc, cervical, replacement, level, arthroplasty" (+0.05%/yr, P < 0.001), and "minimally, invasive, approach, technique" (+0.05%/yr, P < 0.001). By journal, the most published topics were ESJ-"operative, surgery, postoperative, underwent, preoperative"; SpineJ-"clinical, surgeons, guidelines, information, care"; Spine-"pain, back, low, treatment, chronic"; JNS- "tumor, lesions, rare, present, diagnosis"; JSDT-"cervical, anterior, plate, fusion, ACDF." Topics discovered through latent Dirichlet allocation modeling represent unbiased meaningful themes relevant to spine care. Topic dynamics can provide historical context and direction for future research for aspiring investigators and trainees interested in spine careers. Please explore https://singdc.shinyapps.io/spinetopics. N A.

Oral health of children with type 1 diabetes mellitus: A systematic review.

PubMed

Ismail, Ahmad Faisal; McGrath, Colman Patrick; Yiu, Cynthia K Y

2015-06-01

This systematic review investigated the oral health status of children with type 1 diabetes. A systematic search was conducted using PubMed/Medline, Web of Knowledge, SCOPUS and EMBASE. The search included all studies published from inception of database to January 2014. A total of 1179 abstracts were analyzed for selection in 2 phases. The first phase selection was based on the title and abstracts alone. The selected abstracts were then included for second phase, where full articles were obtained. The selection was carried out by 2 independent reviewers (Kappa value=0.809). Only 37 articles were included for final analysis in this review. There is conflicting evidence in the caries experience between children with type 1 diabetes and healthy children. For periodontal health, most studies reported significantly greater plaque accumulation and higher gingival index in children with type 1 diabetes. Cohort studies reported no significant differences in perioodontal parameters over time. There is conflicting evidence regarding the caries experience of children with type 1 diabetes, but they exhibit poorer periodontal health status with greater plaque accumulation compared to healthy children. Further studies are warranted to assess the oral health status of children with type 1 diabetes. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Geophysical abstracts 167, October-December 1956

USGS Publications Warehouse

Rabbitt, Mary C.; Vitaliano, Dorothy B.; Vesselowsky, S.T.; ,

1956-01-01

Geophysical Abstracts includes abstracts of technical papers and books on the physics of the solid earth, the application of physical methods and techniques to geologic problems, and geophysical exploration. The table of contents, which is alphabetically arranged, shows the material covered.Abstracts are prepared only of material that is believed to be generally available. Ordinarily abstracts are not published of material with limited circulation (such as dissertations, open-file reports, or memoranda) or of other papers presented orally at meetings unless summaries of substantial length are published. Abstracts of papers in Japanese and Chinese are based on abstracts or summaries in a western language accompanying the paper.

Geophysical abstracts 164, January-March 1956

USGS Publications Warehouse

Rabbitt, Mary C.; Vitaliano, Dorothy B.; Vesselowsky, S.T.; ,

1956-01-01

Geophysical Abstracts includes abstracts of technical papers and books on the physics of the solid earth, the application of physical methods and techniques to geologic problems, and geophysical exploration. A new table of contents, alphabetically arranged, has been adapted to show more clearly the material covered.Abstracts are prepared only of material that is believed to be generally available. Ordinarily abstracts are not published of material with limited circulation (such as dissertations, open-file reports, or memoranda) or of papers presented orally at meetings unless summaries of substantial length are published. Abstracts of papers in Japanese and Chinese are based on abstracts or summaries in a western language accompanying the paper.

Geophysical abstracts 166, July-September 1956

USGS Publications Warehouse

Rabbitt, Mary C.; Vitaliano, Dorothy B.; Vesselowsky, S.T.; ,

1956-01-01

Geophysical Abstracts includes abstracts of technical papers and books on the physics of the solid earth, the application of physical methods and techniques to geologic problems, and geophysical exploration. The table of contents, which is alphabetically arranged, shows the material covered.Abstracts are prepared only of material that is believed to be generally available. Ordinarily abstracts are not published of material with limited circulation (such as dissertations, open-file reports, or memoranda) or of other papers presented orally at meetings unless summaries of substantial length are published. Abstracts of papers in Japanese and Chinese are based on abstracts or summaries in a western language accompanying the paper.

Geophysical abstracts 165, April-June 1956

USGS Publications Warehouse

Rabbitt, Mary C.; Vitaliano, Dorothy B.; Vesselowsky, S.T.; ,

1956-01-01

Geophysical Abstracts includes abstracts of technical papers and books on the physics of the solid earth, the application of physical methods and techniques to geologic problems, and geophysical exploration. The table of contents, which is alphabetically arranged, shows the material covered.Abstracts are prepared only of material that is believed to be generally available. Ordinarily abstracts are not published of material with limited circulation (such as dissertations, open-file reports, or memoranda) or of other papers presented orally at meetings unless summaries of substantial length are published. Abstracts of papers in Japanese and Chinese are based on abstracts or summaries in a western language accompanying the paper.

Twenty years of meta-analyses in orthopaedic surgery: has quality kept up with quantity?

PubMed

Dijkman, Bernadette G; Abouali, Jihad A K; Kooistra, Bauke W; Conter, Henry J; Poolman, Rudolf W; Kulkarni, Abhaya V; Tornetta, Paul; Bhandari, Mohit

2010-01-01

As the number of studies in the literature is increasing, orthopaedic surgeons highly depend on meta-analyses as their primary source of scientific evidence. The objectives of this review were to assess the scientific quality and number of published meta-analyses on orthopaedics-related topics over time. We conducted, in duplicate and independently, a systematic review of published meta-analyses in orthopaedics in the years 2005 and 2008 and compared them with a previous systematic review of meta-analyses from 1969 to 1999. A search of electronic databases (MEDLINE, EMBASE, and the Cochrane Database of Systematic Reviews) was performed to identify meta-analyses published in 2005 and 2008. We searched bibliographies and contacted content experts to identify additional relevant studies. Two investigators independently assessed the quality of the studies, using the Oxman and Guyatt index, and abstracted relevant data. We included forty-five and forty-four meta-analyses from 2005 and 2008, respectively. While the number of meta-analyses increased fivefold from 1999 to 2008, the mean quality score did not change significantly over time (p = 0.067). In the later years, a significantly lower proportion of meta-analyses had methodological flaws (56% in 2005 and 68% in 2008) compared with meta-analyses published prior to 2000 (88%) (p = 0.006). In 2005 and 2008, respectively, 18% and 30% of the meta-analyses had major to extensive flaws in their methodology. Studies from 2008 with positive conclusions used and described appropriate criteria for the validity assessment less often than did those with negative results. The use of random-effects and fixed-effects models as pooling methods became more popular toward 2008. Although the methodological quality of orthopaedic meta-analyses has increased in the past twenty years, a substantial proportion continues to show major to extensive flaws. As the number of published meta-analyses is increasing, a routine checklist for scientific quality should be used in the peer-review process to ensure methodological standards for publication.

The Wannabee Culture: Why No-One Does What They Used To.

ERIC Educational Resources Information Center

Dixon, Anne

1998-01-01

Electronic publishing has been an agent for change in not just how one publishes but in what one publishes. Describes HyperCite, a joint project with the Institution of Electrical Engineers (IEE) to create INSPEC database. Highlights include the database; the research phase (cross database searching and new interface); and what and how much was…

Speech-Language Pathology production regarding voice in popular singing.

PubMed

Drumond, Lorena Badaró; Vieira, Naymme Barbosa; Oliveira, Domingos Sávio Ferreira de

2011-12-01

To present a literature review about the Brazilian scientific production in Speech-Language Pathology and Audiology regarding voice in popular singing in the last decade, as for number of publications, musical styles studied, focus of the researches, and instruments used for data collection. Cross-sectional descriptive study carried out in two stages: search in databases and publications encompassing the last decade of researches in this area in Brazil, and reading of the material obtained for posterior categorization. The databases LILACS and SciELO, the Databasis of Dissertations and Theses organized by CAPES, the online version of Acta ORL, and the online version of OPUS were searched, using the following uniterms: voice, professional voice, singing voice, dysphonia, voice disorders, voice training, music, dysodia. Articles published between the years 2000 and 2010 were selected. The researches found were classified and categorized after reading their abstracts and, when necessary, the whole study. Twenty researches within the proposed theme were selected, all of which were descriptive, involving several musical styles. Twelve studies focused on the evaluation of the popular singer's voice, and the most frequently used data collection instrument was the auditory-perceptual evaluation. The results of the publications found corroborate the objectives proposed by the authors and the different methodologies. The number of studies published is still restricted when compared to the diversity of musical genres and the uniqueness of popular singer.

Scientific publications in gastroenterology and hepatology in Taiwan: An analysis of Web of Science from 1993 to 2013.

PubMed

Chang, Hsiao-Ting; Lin, Ming-Hwai; Hwang, I-Hsuan; Chen, Tzeng-Ji; Lin, Han-Chieh; Hou, Ming-Chih; Hwang, Shinn-Jang

2017-02-01

Scientific publications are important for evaluating the achievements of a medical specialty or discipline. Gastroenterology and Hepatology is a medical specialty in great demand in Taiwan, therefore, this study aimed to analyze the Gastroenterology and Hepatology publications from 1993 to 2013 in Taiwan, using the Web of Science (WoS) database. Scientific publications from departments/institutes of gastroenterology and hepatology were retrieved and analyzed from the WoS database, which included articles published in the Science Citation Index Expanded and Social Science Citation Index journals from 1993 to 2013. Among 229,030 articles published from departments/institutes of gastroenterology and hepatology worldwide during 1993-2013, 5061 (2.21%) were published in Taiwan, ranking the country 13 th in the world. In total, 4759 articles from Taiwan were selected for further analysis, excluding meeting abstracts and corrections. During these two decades, the number of gastroenterology and hepatology publications increased rapidly. There were 440 articles published during 1993-1997, 646 articles during 1998-2002, 1211 articles during 2003-2007, and up to 2462 articles during 2008-2013. However, the mean number of articles cited decreased from 25.35 to 27.25 to 20.64 to 7.28, and the mean impact factor of publishing journals decreased from 5.0 to 4.20 to 4.13 to 4.03 during 1993-1997, 1998-2002, 2003-2007, and 2008-2013, respectively. Most of those publications belong to the subject category gastroenterology and hepatology (2346 articles, 49.30%), followed by surgery (677 articles, 14.23%), medicine, general and internal (358 articles, 7.52%), oncology (316 articles, 6.64%), and pharmacology pharmacy (286 articles, 6.01%). The Journal of Gastroenterology and Hepatology published the most papers (326 articles, 6.9%), followed by World Journal of Gastroenterology (201 articles, 4.2%), Hepato-Gastroenterology (165 articles, 3.5%), Gastrointestinal Endoscopy (159 articles, 3.3%), and Hepatology (146 articles, 3.1%). Scientific publications from departments/institutes of gastroenterology and hepatology in Taiwan increased rapidly from 1993 to 2013. However, there were decreasing trends in the number of articles cited and journal impact factors. Copyright © 2016. Published by Elsevier Taiwan LLC.

Presentation to publication: proportion of abstracts published for ESPR, SPR and IPR.

PubMed

Shelmerdine, Susan C; Lynch, Jeremy O; Langan, Dean; Arthurs, Owen J

2016-09-01

Advancement of knowledge requires presentation and publication of high-quality scientific research. Studies submitted for presentation undergo initial peer review before acceptance and the rate of subsequent publication may be taken as an indicator of access to publication for pediatric radiology studies. Evaluate the proportion of abstracts also published in journals for pediatric radiology conferences and identify factors associated with publication success. All Medline articles that originated from oral presentations at the European Society for Paediatric Radiology (ESPR), the Society for Pediatric Radiology (SPR) or the International Pediatric Radiology (IPR) conferences between 2010 - 2012 were evaluated. Descriptive statistics to evaluate published and unpublished groups were calculated overall and split by characteristics of the abstracts such as number of authors. Overall number of abstracts published was 300/715 (41.9%), with most articles published in radiology specific journals (181/300; 60.3%), with median impact factor 2.31 (interquartile range [IQR]: 1.65-3.14, range: 0-18.03). Those published after the conference (262/300, 87.6%) had a median time to publication of 18 months and for those published before, the median time was -11 months. Median sample size in published articles was 52 (IQR: 33-105, range: 1-6,351). Of pediatric radiology oral abstracts, 41.9% achieve publication after a period of at least 3 years from presentation. Studies originating from certain countries and on certain subspecialty topics were more likely to get published.

Microsatellite markers: what they mean and why they are so useful

PubMed Central

Vieira, Maria Lucia Carneiro; Santini, Luciane; Diniz, Augusto Lima; Munhoz, Carla de Freitas

2016-01-01

Abstract Microsatellites or Single Sequence Repeats (SSRs) are extensively employed in plant genetics studies, using both low and high throughput genotyping approaches. Motivated by the importance of these sequences over the last decades this review aims to address some theoretical aspects of SSRs, including definition, characterization and biological function. The methodologies for the development of SSR loci, genotyping and their applications as molecular markers are also reviewed. Finally, two data surveys are presented. The first was conducted using the main database of Web of Science, prospecting for articles published over the period from 2010 to 2015, resulting in approximately 930 records. The second survey was focused on papers that aimed at SSR marker development, published in the American Journal of Botany's Primer Notes and Protocols in Plant Sciences (over 2013 up to 2015), resulting in a total of 87 publications. This scenario confirms the current relevance of SSRs and indicates their continuous utilization in plant science. PMID:27561112

ALL RUSSIAN INSTITUTE FOR SCIENTIFIC AND TECHNICAL INFORMATION (VINITI) OF THE RUSSIAN ACADEMY OF SCIENCES

PubMed Central

Markusova, Valentina

2012-01-01

The aim of the paper is to overview the leading information processing domain in Russia and Eastern Europe, namely All Russian Institute for Scientific and Technical Information (VINITI ) of the Russian Academy of Sciences. Russian science structure is different from that in the Western Europe and the US. The main aim of VINITI is to collect, process and disseminate scientific information on various fields of science and technology, published in 70 countries in 40 languages, selected from books, journals, conference proceedings, and patents. A special attention is given to the journal selection and depositing manuscripts (a kind of grey literature), an important source for Russian research. VINITI has created the largest database containing about 30 million records dating back to 1980. About 80,000-100,000 new records are added monthly. VINITI publishes the Journal Abstract (JA) on 19 fields of science, including medicine, containing about a million publications annually. Two thirds of these records are foreign and 36.7% – Russian sources. PMID:23322964

All Russian institute for scientific and technical information (viniti) of the Russian academy of sciences.

PubMed

Markusova, Valentina

2012-06-01

The aim of the paper is to overview the leading information processing domain in Russia and Eastern Europe, namely All Russian Institute for Scientific and Technical Information (VINITI ) of the Russian Academy of Sciences. Russian science structure is different from that in the Western Europe and the US. The main aim of VINITI is to collect, process and disseminate scientific information on various fields of science and technology, published in 70 countries in 40 languages, selected from books, journals, conference proceedings, and patents. A special attention is given to the journal selection and depositing manuscripts (a kind of grey literature), an important source for Russian research. VINITI has created the largest database containing about 30 million records dating back to 1980. About 80,000-100,000 new records are added monthly. VINITI publishes the Journal Abstract (JA) on 19 fields of science, including medicine, containing about a million publications annually. Two thirds of these records are foreign and 36.7% - Russian sources.

Sensory-Cognitive Interactions in Older Adults

PubMed Central

Humes, Larry E.; Young, Levi A.

2016-01-01

Objectives To review evidence regarding sensory and cognitive interactions in older adults published since 2009, the approximate date of the most recent reviews on this topic. Design Following an electronic database search of articles published in English since 2009 on measures of hearing and cognition or vision and cognition in older adults, a total of 437 articles were identified. Screening by title and abstract for appropriateness of topic and for articles presenting original research in peer-reviewed journals reduced the final number of articles reviewed to 34. These articles were qualitatively evaluated and synthesized with the existing knowledge base. Results Additional evidence has been obtained since 2009 associating declines in vision, hearing, or both with declines in cognition among older adults. The observed sensory-cognitive associations are generally stronger when more than one sensory domain is measured and when the sensory measures involve more than simple threshold sensitivity. Conclusions Evidence continues to accumulate supporting a link between decline in sensory function and cognitive decline in older adults. PMID:27355770

A corpus and a concordancer of academic journal articles.

PubMed

Kwary, Deny A

2018-02-01

This data article presents a corpus (i.e. a selection of a big number of words in an electronic form) and a concordancer (i.e. a tool to show the word in its context of use) of academic journal articles. As the title suggests, the data were collected from research articles published in academic journals. The corpus contains 5,686,428 words selected from 895 journal articles published by Elsevier in 2011-2015. The corpus is classified into four subject areas: Health sciences, Life sciences, Physical Sciences, and Social Sciences, following the classifications of Scopus, which is the largest abstract and citation database of peer-reviewed scientific journals, books and conference proceedings. To ease the access and utilization of the corpus, a program to produce the key word in context (KWIC) and word frequency was created and placed on the website: corpus.kwary.net. The corpus is a valuable resource for researchers, teachers, and translators working on academic English.

Child labour and health: a systematic review.

PubMed

Batomen Kuimi, Brice Lionel; Oppong-Nkrumah, Oduro; Kaufman, Jay; Nazif-Munoz, Jose Ignacio; Nandi, Arijit

2018-06-01

This study aimed to synthesise the available knowledge, identify unexplored areas and discuss general limits of the published evidence. We focused on outcomes commonly hypothesised to be affected by child labour: nutritional status, harmful exposures and injuries. Four electronic databases (EMBASE, MEDLINE, Scopus, ISI Web of Science) were searched in November 2017. All articles published since 1996, without restrictions on language, were considered for inclusion. Out of the 1090 abstracts initially identified by the search, 78 articles were selected for inclusion and reviewed. Most of the studies were conducted in Asia and South America, and only a third of them compared working children to a control group of non-working children. Child labour appears to be associated with poor nutritional status, diseases due to harmful exposures, and a higher prevalence of injuries. Despite evidence for a negative relation between child work and health, the cross-sectional design of most studies limits the causal interpretation of existing findings. More rigorous observational studies are needed to confirm and better quantify these associations.

Sensory-Cognitive Interactions in Older Adults.

PubMed

Humes, Larry E; Young, Levi A

2016-01-01

The objective of this study was regarding sensory and cognitive interactions in older adults published since 2009, the approximate date of the most recent reviews on this topic. After an electronic database search of articles published in English since 2009 on measures of hearing and cognition or vision and cognition in older adults, a total of 437 articles were identified. Screening by title and abstract for appropriateness of topic and for articles presenting original research in peer-reviewed journals reduced the final number of articles reviewed to 34. These articles were qualitatively evaluated and synthesized with the existing knowledge base. Additional evidence has been obtained since 2009 associating declines in vision, hearing, or both with declines in cognition among older adults. The observed sensory-cognitive associations are generally stronger when more than one sensory domain is measured and when the sensory measures involve more than simple threshold sensitivity. Evidence continues to accumulate supporting a link between decline in sensory function and cognitive decline in older adults.

Prevalence and Diagnosis of Molar-Incisor- Hypomineralisation (MIH): A systematic review.

PubMed

Jälevik, B

2010-04-01

This was to review the literature published, to point out shortcomings and to suggest areas in need of improvement concerning the diagnosis and prevalence of MIH. A broad search of the PubMed database was conducted. Relevant papers published in English were identified after a review of their titles, abstracts or full reading of the papers. Papers were selected if the number of children with at least one first permanent molar affected by demarcated opacities could be deciphered. Targeted publications were critically assessed by the author concerning examination criteria, selection and character of the study groups, examiners' calibration and result presentation. The initial search revealed 414 papers of which 24 met the inclusion criteria. A wide variation in defect prevalence (2.4 - 40.2 %) was reported. Cross comparison of the results of the various studies were difficult because of use of different indices and criteria, examination variability, methods of recording and different age groups. Further standardization of study design and methods is needed to make the results comparable.

Almost 40 years investigating near-death experiences: an overview of mainstream scientific journals.

PubMed

Sleutjes, Adriana; Moreira-Almeida, Alexander; Greyson, Bruce

2014-11-01

This article reviews mainstream scientific publications on near-death experiences (NDEs). We searched near-death experience in titles, key words, and abstracts at the Web of Knowledge database published between 1945 and 2013. We identified 266 relevant documents, the oldest from 1977. There was a strong predominance of opinion articles (book reviews, commentaries, and editorials), review articles, phenomenological description articles, and articles that originated in the United States. Since 2000, the number of longitudinal and cross-sectional studies has increased; there has been a diversification in the countries that have published on the subject and more articles that discuss the implications of NDEs for the mind-brain relationship. The results indicate that most scholarly publications on NDEs are recent, usually have no original empirical data, and are concentrated in North America and Western Europe. Future studies should focus on increasing the cultural diversity in the field and on testing explanatory hypotheses based on high-quality empirical data.

Impact of cancer anorexia-cachexia syndrome on health-related quality of life and resource utilisation: A systematic review.

PubMed

Tarricone, Rosanna; Ricca, Giada; Nyanzi-Wakholi, Barbara; Medina-Lara, Antonieta

2016-03-01

Cancer anorexia-cachexia syndrome (CACS) negatively impacts patients' quality of life (QoL) and increases the burden on healthcare resources. To review published CACS data regarding health-related QOL (HRQoL) and its economic impact on the healthcare system. Searches were conducted in MEDLINE, EMBASE, DARE, and NHS EED databases. A total of 458 HRQoL and 189 healthcare resources utilisation abstracts were screened, and 42 and 2 full-text articles were included, respectively. The EORTC QLQ-C30 and FAACT instruments were most favoured for assessing HRQOL but none of the current tools cover all domains affected by CACS. Economic estimates for managing CACS are scarce, with studies lacking a breakdown of healthcare resource utilisation items. HRQoL instruments that can better assess and incorporate all the domains affected by CACS are required. Rigorous assessment of costs and benefits of treatment are needed to understand the magnitude of the impact of CACS. Copyright © 2016. Published by Elsevier Ireland Ltd.

Revista de Saúde Pública: 50 years disseminating the knowledge in nutrition

PubMed Central

Sichieri, Rosely; Pereira, Rosangela A

2016-01-01

ABSTRACT This work describes and comments on articles in the area of Public Health Nutrition published in Revista de Saúde Pública (RSP – Public Health Journal) from 1967 to 2016. We searched in the PubMed database restricted to the periodical “Revista de Saúde Pública” and using terms related to key topics in the area of Public Health Nutrition. We retrieved 742 articles and, after exclusion of duplicates and articles unrelated to the subject, we analyzed 441 articles, grouped according to subject: dental caries, anemia, hypovitaminosis A, macro/micronutrients, malnutrition, nutritional assessment, overweight/obesity, food consumption, low birthweight, and breastfeeding. We observed significant increase in the number of articles published and diversification of subjects addressed over the 50 years, representing the consistent development of the scientific field of Nutrition in Brazil. Since its inception, RSP has played an important role in the dissemination of knowledge about the main nutritional issues in Brazil. PMID:28099649

MANAGEMENT OF PANCREATICOPLEURAL FISTULAS SECONDARY TO CHRONIC PANCREATITIS

PubMed Central

CAZZO, Everton; APODACA-RUEDA, Márcio; GESTIC, Martinho Antonio; CHAIM, Fábio Henrique Mendonça; de SAITO, Helena Paes de Almeida; UTRINI, Murillo Pimentel; CALLEJAS-NETO, Francisco; CHAIM, Elinton Adami

2017-01-01

ABSTRACT Introduction: Pancreaticopleural fistula is a rare complication of chronic pancreatitis. Objective: To describe pancreaticopleural fistula due to chronic pancreatitis and perform an extensive review of literature on this topic. Methods: Comprehensive narrative review through online research on the databases Medline and Lilacs for articles published over the last 20 years. There were 22 case reports and four case series selected. Results: The main indication for surgical treatment is the failure of clinical and/or endoscopic treatments. Surgery is based on internal pancreatic drainage, especially by means of pancreaticojejunostomy, and/or pancreatic resections. Conclusion: Pancreaticopleural fistula is a rare complication of chronic pancreatitis and the Frey procedure may be an appropriate therapeutic option in selected cases when clinical and endoscopic treatments are unsuccessful. PMID:29019567

Haloperidol for the treatment of nausea and vomiting in palliative care patients.

PubMed

Murray-Brown, Fay; Dorman, Saskie

2015-11-02

Nausea and vomiting are common symptoms in patients with terminal, incurable illnesses. Both nausea and vomiting can be distressing. Haloperidol is commonly prescribed to relieve these symptoms. This is an updated version of the original Cochrane review published in Issue 2, 2009, of Haloperidol for the treatment of nausea and vomiting in palliative care patients. To evaluate the efficacy and adverse events associated with the use of haloperidol for the treatment of nausea and vomiting in palliative care patients. For this updated review, we performed updated searches of CENTRAL, EMBASE and MEDLINE in November 2013 and in November 2014. We searched controlled trials registers in March 2015 to identify any ongoing or unpublished trials. We imposed no language restrictions. For the original review, we performed database searching in August 2007, including CENTRAL, MEDLINE, EMBASE, CINAHL and AMED, using relevant search terms and synonyms. Handsearching complemented the electronic searches (using reference lists of included studies, relevant chapters and review articles) for the original review. We considered randomised controlled trials (RCTs) of haloperidol for the treatment of nausea or vomiting, or both, in any setting, for inclusion. The studies had to be conducted with adults receiving palliative care or suffering from an incurable progressive medical condition. We excluded studies where nausea or vomiting, or both, were thought to be secondary to pregnancy or surgery. We imported records from each of the electronic databases into a bibliographic package and merged them into a core database where we inspected titles, keywords and abstracts for relevance. If it was not possible to accept or reject an abstract with certainty, we obtained the full text of the article for further evaluation. The two review authors independently assessed studies in accordance with the inclusion criteria. There were no differences in opinion between the authors with regard to the assessment of studies. We considered 27 studies from the 2007 search. In this update we considered a further 38 studies from the 2013 search, and two in the 2014 search. We identified one RCT of moderate quality with low risk of bias overall which met the inclusion criteria for this update, comparing ABH (Ativan®, Benadryl®, Haldol®) gel, applied to the wrist, with placebo for the relief of nausea in 22 participants. ABH gel includes haloperidol as well as diphenhydramine and lorazepam. The gel was not significantly better than placebo in this small study; however haloperidol is reported not to be absorbed significantly when applied topically, therefore the trial does not address the issue of whether haloperidol is effective or well-tolerated when administered by other routes (e.g. by mouth, subcutaneously or intravenously). We identified one ongoing trial of haloperidol for the management of nausea and vomiting in patients with cancer, with initial results published in a conference abstract suggesting that haloperidol is effective for 65% of patients. The trial had not been fully published at the time of our review. A further trial has opened, comparing oral haloperidol with oral methotrimeprazine (levomepromazine) for patients with cancer and nausea unrelated to their treatment, which we aim to include in the next review update. Since the last version of this review, we found one new study for inclusion but the conclusion remains unchanged. There is incomplete evidence from published RCTs to determine the effectiveness of haloperidol for nausea and vomiting in palliative care. Other than the trial of ABH gel vs placebo, we did not identify any fully published RCTs exploring the effectiveness of haloperidol for nausea and vomiting in palliative care patients for this update, but two trials are underway.

Non-normal Distributions Commonly Used in Health, Education, and Social Sciences: A Systematic Review

PubMed Central

Bono, Roser; Blanca, María J.; Arnau, Jaume; Gómez-Benito, Juana

2017-01-01

Statistical analysis is crucial for research and the choice of analytical technique should take into account the specific distribution of data. Although the data obtained from health, educational, and social sciences research are often not normally distributed, there are very few studies detailing which distributions are most likely to represent data in these disciplines. The aim of this systematic review was to determine the frequency of appearance of the most common non-normal distributions in the health, educational, and social sciences. The search was carried out in the Web of Science database, from which we retrieved the abstracts of papers published between 2010 and 2015. The selection was made on the basis of the title and the abstract, and was performed independently by two reviewers. The inter-rater reliability for article selection was high (Cohen’s kappa = 0.84), and agreement regarding the type of distribution reached 96.5%. A total of 262 abstracts were included in the final review. The distribution of the response variable was reported in 231 of these abstracts, while in the remaining 31 it was merely stated that the distribution was non-normal. In terms of their frequency of appearance, the most-common non-normal distributions can be ranked in descending order as follows: gamma, negative binomial, multinomial, binomial, lognormal, and exponential. In addition to identifying the distributions most commonly used in empirical studies these results will help researchers to decide which distributions should be included in simulation studies examining statistical procedures. PMID:28959227

Improving taxonomic accuracy for fungi in public sequence databases: applying ‘one name one species’ in well-defined genera with Trichoderma/Hypocrea as a test case

PubMed Central

Strope, Pooja K; Chaverri, Priscila; Gazis, Romina; Ciufo, Stacy; Domrachev, Michael; Schoch, Conrad L

2017-01-01

Abstract The ITS (nuclear ribosomal internal transcribed spacer) RefSeq database at the National Center for Biotechnology Information (NCBI) is dedicated to the clear association between name, specimen and sequence data. This database is focused on sequences obtained from type material stored in public collections. While the initial ITS sequence curation effort together with numerous fungal taxonomy experts attempted to cover as many orders as possible, we extended our latest focus to the family and genus ranks. We focused on Trichoderma for several reasons, mainly because the asexual and sexual synonyms were well documented, and a list of proposed names and type material were recently proposed and published. In this case study the recent taxonomic information was applied to do a complete taxonomic audit for the genus Trichoderma in the NCBI Taxonomy database. A name status report is available here: https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi. As a result, the ITS RefSeq Targeted Loci database at NCBI has been augmented with more sequences from type and verified material from Trichoderma species. Additionally, to aid in the cross referencing of data from single loci and genomes we have collected a list of quality records of the RPB2 gene obtained from type material in GenBank that could help validate future submissions. During the process of curation misidentified genomes were discovered, and sequence records from type material were found hidden under previous classifications. Source metadata curation, although more cumbersome, proved to be useful as confirmation of the type material designation. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353 PMID:29220466

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.

UKPMC: a full text article resource for the life sciences.

PubMed

McEntyre, Johanna R; Ananiadou, Sophia; Andrews, Stephen; Black, William J; Boulderstone, Richard; Buttery, Paula; Chaplin, David; Chevuru, Sandeepreddy; Cobley, Norman; Coleman, Lee-Ann; Davey, Paul; Gupta, Bharti; Haji-Gholam, Lesley; Hawkins, Craig; Horne, Alan; Hubbard, Simon J; Kim, Jee-Hyub; Lewin, Ian; Lyte, Vic; MacIntyre, Ross; Mansoor, Sami; Mason, Linda; McNaught, John; Newbold, Elizabeth; Nobata, Chikashi; Ong, Ernest; Pillai, Sharmila; Rebholz-Schuhmann, Dietrich; Rosie, Heather; Rowbotham, Rob; Rupp, C J; Stoehr, Peter; Vaughan, Philip

2011-01-01

UK PubMed Central (UKPMC) is a full-text article database that extends the functionality of the original PubMed Central (PMC) repository. The UKPMC project was launched as the first 'mirror' site to PMC, which in analogy to the International Nucleotide Sequence Database Collaboration, aims to provide international preservation of the open and free-access biomedical literature. UKPMC (http://ukpmc.ac.uk) has undergone considerable development since its inception in 2007 and now includes both a UKPMC and PubMed search, as well as access to other records such as Agricola, Patents and recent biomedical theses. UKPMC also differs from PubMed/PMC in that the full text and abstract information can be searched in an integrated manner from one input box. Furthermore, UKPMC contains 'Cited By' information as an alternative way to navigate the literature and has incorporated text-mining approaches to semantically enrich content and integrate it with related database resources. Finally, UKPMC also offers added-value services (UKPMC+) that enable grantees to deposit manuscripts, link papers to grants, publish online portfolios and view citation information on their papers. Here we describe UKPMC and clarify the relationship between PMC and UKPMC, providing historical context and future directions, 10 years on from when PMC was first launched.

Institutional Review Board approval and innovation in urology: current practice and safety issues.

PubMed

Sundaram, Varun; Vemana, Goutham; Bhayani, Sam B

2014-02-01

To retrospectively review recent publications describing novel procedures/techniques, and describe the Institutional Review Board (IRB)/ethics approval process and potential ethical dilemmas in their reporting. We searched PubMed for papers about innovative or novel procedures/techniques between 2011 and August 2012. A query of titles/abstracts in the Journal of Urology, Journal of Endourology, European Urology, BJU International, and Urology identified relevant papers. These results were reviewed for human studies that described an innovative technique, procedure, approach, initial series, and/or used new technology. In all, 91 papers met criteria for inclusion; 25 from the Journal of Endourology, 14 from the Journal of Urology, nine from European Urology, 15 from the BJU International and 28 from Urology. IRB/ethics approval was given for an experimental procedure or database in 24% and 22%, respectively. IRB/ethics approval was not mentioned in 52.7% of studies. Published IRB/ethics approvals for innovative techniques are heterogeneous including database, retrospective, and prospective approvals. Given the concept that innovations are likely not in the legal or ethical standard of care, strong consideration should be given to obtaining IRB/ethics approval before the actual procedure, instead of approval to merely report database outcomes. © 2013 The Authors. BJU International © 2013 BJU International.

SCPortalen: human and mouse single-cell centric database

PubMed Central

Noguchi, Shuhei; Böttcher, Michael; Hasegawa, Akira; Kouno, Tsukasa; Kato, Sachi; Tada, Yuhki; Ura, Hiroki; Abe, Kuniya; Shin, Jay W; Plessy, Charles; Carninci, Piero

2018-01-01

Abstract Published single-cell datasets are rich resources for investigators who want to address questions not originally asked by the creators of the datasets. The single-cell datasets might be obtained by different protocols and diverse analysis strategies. The main challenge in utilizing such single-cell data is how we can make the various large-scale datasets to be comparable and reusable in a different context. To challenge this issue, we developed the single-cell centric database ‘SCPortalen’ (http://single-cell.clst.riken.jp/). The current version of the database covers human and mouse single-cell transcriptomics datasets that are publicly available from the INSDC sites. The original metadata was manually curated and single-cell samples were annotated with standard ontology terms. Following that, common quality assessment procedures were conducted to check the quality of the raw sequence. Furthermore, primary data processing of the raw data followed by advanced analyses and interpretation have been performed from scratch using our pipeline. In addition to the transcriptomics data, SCPortalen provides access to single-cell image files whenever available. The target users of SCPortalen are all researchers interested in specific cell types or population heterogeneity. Through the web interface of SCPortalen users are easily able to search, explore and download the single-cell datasets of their interests. PMID:29045713

UKPMC: a full text article resource for the life sciences

PubMed Central

McEntyre, Johanna R.; Ananiadou, Sophia; Andrews, Stephen; Black, William J.; Boulderstone, Richard; Buttery, Paula; Chaplin, David; Chevuru, Sandeepreddy; Cobley, Norman; Coleman, Lee-Ann; Davey, Paul; Gupta, Bharti; Haji-Gholam, Lesley; Hawkins, Craig; Horne, Alan; Hubbard, Simon J.; Kim, Jee-Hyub; Lewin, Ian; Lyte, Vic; MacIntyre, Ross; Mansoor, Sami; Mason, Linda; McNaught, John; Newbold, Elizabeth; Nobata, Chikashi; Ong, Ernest; Pillai, Sharmila; Rebholz-Schuhmann, Dietrich; Rosie, Heather; Rowbotham, Rob; Rupp, C. J.; Stoehr, Peter; Vaughan, Philip

2011-01-01

UK PubMed Central (UKPMC) is a full-text article database that extends the functionality of the original PubMed Central (PMC) repository. The UKPMC project was launched as the first ‘mirror’ site to PMC, which in analogy to the International Nucleotide Sequence Database Collaboration, aims to provide international preservation of the open and free-access biomedical literature. UKPMC (http://ukpmc.ac.uk) has undergone considerable development since its inception in 2007 and now includes both a UKPMC and PubMed search, as well as access to other records such as Agricola, Patents and recent biomedical theses. UKPMC also differs from PubMed/PMC in that the full text and abstract information can be searched in an integrated manner from one input box. Furthermore, UKPMC contains ‘Cited By’ information as an alternative way to navigate the literature and has incorporated text-mining approaches to semantically enrich content and integrate it with related database resources. Finally, UKPMC also offers added-value services (UKPMC+) that enable grantees to deposit manuscripts, link papers to grants, publish online portfolios and view citation information on their papers. Here we describe UKPMC and clarify the relationship between PMC and UKPMC, providing historical context and future directions, 10 years on from when PMC was first launched. PMID:21062818

An automatic method to generate domain-specific investigator networks using PubMed abstracts.

PubMed

Yu, Wei; Yesupriya, Ajay; Wulf, Anja; Qu, Junfeng; Gwinn, Marta; Khoury, Muin J

2007-06-20

Collaboration among investigators has become critical to scientific research. This includes ad hoc collaboration established through personal contacts as well as formal consortia established by funding agencies. Continued growth in online resources for scientific research and communication has promoted the development of highly networked research communities. Extending these networks globally requires identifying additional investigators in a given domain, profiling their research interests, and collecting current contact information. We present a novel strategy for building investigator networks dynamically and producing detailed investigator profiles using data available in PubMed abstracts. We developed a novel strategy to obtain detailed investigator information by automatically parsing the affiliation string in PubMed records. We illustrated the results by using a published literature database in human genome epidemiology (HuGE Pub Lit) as a test case. Our parsing strategy extracted country information from 92.1% of the affiliation strings in a random sample of PubMed records and in 97.0% of HuGE records, with accuracies of 94.0% and 91.0%, respectively. Institution information was parsed from 91.3% of the general PubMed records (accuracy 86.8%) and from 94.2% of HuGE PubMed records (accuracy 87.0). We demonstrated the application of our approach to dynamic creation of investigator networks by creating a prototype information system containing a large database of PubMed abstracts relevant to human genome epidemiology (HuGE Pub Lit), indexed using PubMed medical subject headings converted to Unified Medical Language System concepts. Our method was able to identify 70-90% of the investigators/collaborators in three different human genetics fields; it also successfully identified 9 of 10 genetics investigators within the PREBIC network, an existing preterm birth research network. We successfully created a web-based prototype capable of creating domain-specific investigator networks based on an application that accurately generates detailed investigator profiles from PubMed abstracts combined with robust standard vocabularies. This approach could be used for other biomedical fields to efficiently establish domain-specific investigator networks.

An automatic method to generate domain-specific investigator networks using PubMed abstracts

PubMed Central

Yu, Wei; Yesupriya, Ajay; Wulf, Anja; Qu, Junfeng; Gwinn, Marta; Khoury, Muin J

2007-01-01

Background Collaboration among investigators has become critical to scientific research. This includes ad hoc collaboration established through personal contacts as well as formal consortia established by funding agencies. Continued growth in online resources for scientific research and communication has promoted the development of highly networked research communities. Extending these networks globally requires identifying additional investigators in a given domain, profiling their research interests, and collecting current contact information. We present a novel strategy for building investigator networks dynamically and producing detailed investigator profiles using data available in PubMed abstracts. Results We developed a novel strategy to obtain detailed investigator information by automatically parsing the affiliation string in PubMed records. We illustrated the results by using a published literature database in human genome epidemiology (HuGE Pub Lit) as a test case. Our parsing strategy extracted country information from 92.1% of the affiliation strings in a random sample of PubMed records and in 97.0% of HuGE records, with accuracies of 94.0% and 91.0%, respectively. Institution information was parsed from 91.3% of the general PubMed records (accuracy 86.8%) and from 94.2% of HuGE PubMed records (accuracy 87.0). We demonstrated the application of our approach to dynamic creation of investigator networks by creating a prototype information system containing a large database of PubMed abstracts relevant to human genome epidemiology (HuGE Pub Lit), indexed using PubMed medical subject headings converted to Unified Medical Language System concepts. Our method was able to identify 70–90% of the investigators/collaborators in three different human genetics fields; it also successfully identified 9 of 10 genetics investigators within the PREBIC network, an existing preterm birth research network. Conclusion We successfully created a web-based prototype capable of creating domain-specific investigator networks based on an application that accurately generates detailed investigator profiles from PubMed abstracts combined with robust standard vocabularies. This approach could be used for other biomedical fields to efficiently establish domain-specific investigator networks. PMID:17584920

dSED: A database tool for modeling sediment early diagenesis

NASA Astrophysics Data System (ADS)

Katsev, S.; Rancourt, D. G.; L'Heureux, I.

2003-04-01

Sediment early diagenesis reaction transport models (RTMs) are becoming powerful tools in providing kinetic descriptions of the metal and nutrient diagenetic cycling in marine, lacustrine, estuarine, and other aquatic sediments, as well as of exchanges with the water column. Whereas there exist several good database/program combinations for thermodynamic equilibrium calculations in aqueous systems, at present there exist no database tools for classification and analysis of the kinetic data essential to RTM development. We present a database tool that is intended to serve as an online resource for information about chemical reactions, solid phase and solute reactants, sorption reactions, transport mechanisms, and kinetic and equilibrium parameters that are relevant to sediment diagenesis processes. The list of reactive substances includes but is not limited to organic matter, Fe and Mn oxides and oxyhydroxides, sulfides and sulfates, calcium, iron, and manganese carbonates, phosphorus-bearing minerals, and silicates. Aqueous phases include dissolved carbon dioxide, oxygen, methane, hydrogen sulfide, sulfate, nitrate, phosphate, some organic compounds, and dissolved metal species. A number of filters allow extracting information according to user-specified criteria, e.g., about a class of substances contributing to the cycling of iron. The database also includes bibliographic information about published diagenetic models and the reactions and processes that they consider. At the time of preparing this abstract, dSED contained 128 reactions and 12 pre-defined filters. dSED is maintained by the Lake Sediment Structure and Evolution (LSSE) group at the University of Ottawa (www.science.uottawa.ca/LSSE/dSED) and we invite input from the geochemical community.

Identifying complications of interventional procedures from UK routine healthcare databases: a systematic search for methods using clinical codes.

PubMed

Keltie, Kim; Cole, Helen; Arber, Mick; Patrick, Hannah; Powell, John; Campbell, Bruce; Sims, Andrew

2014-11-28

Several authors have developed and applied methods to routine data sets to identify the nature and rate of complications following interventional procedures. But, to date, there has been no systematic search for such methods. The objective of this article was to find, classify and appraise published methods, based on analysis of clinical codes, which used routine healthcare databases in a United Kingdom setting to identify complications resulting from interventional procedures. A literature search strategy was developed to identify published studies that referred, in the title or abstract, to the name or acronym of a known routine healthcare database and to complications from procedures or devices. The following data sources were searched in February and March 2013: Cochrane Methods Register, Conference Proceedings Citation Index - Science, Econlit, EMBASE, Health Management Information Consortium, Health Technology Assessment database, MathSciNet, MEDLINE, MEDLINE in-process, OAIster, OpenGrey, Science Citation Index Expanded and ScienceDirect. Of the eligible papers, those which reported methods using clinical coding were classified and summarised in tabular form using the following headings: routine healthcare database; medical speciality; method for identifying complications; length of follow-up; method of recording comorbidity. The benefits and limitations of each approach were assessed. From 3688 papers identified from the literature search, 44 reported the use of clinical codes to identify complications, from which four distinct methods were identified: 1) searching the index admission for specified clinical codes, 2) searching a sequence of admissions for specified clinical codes, 3) searching for specified clinical codes for complications from procedures and devices within the International Classification of Diseases 10th revision (ICD-10) coding scheme which is the methodology recommended by NHS Classification Service, and 4) conducting manual clinical review of diagnostic and procedure codes. The four distinct methods identifying complication from codified data offer great potential in generating new evidence on the quality and safety of new procedures using routine data. However the most robust method, using the methodology recommended by the NHS Classification Service, was the least frequently used, highlighting that much valuable observational data is being ignored.

Second Annual Conference on Astronomical Data Analysis Software and Systems. Abstracts

NASA Technical Reports Server (NTRS)

1992-01-01

Abstracts from the conference are presented. The topics covered include the following: next generation software systems and languages; databases, catalogs, and archives; user interfaces/visualization; real-time data acquisition/scheduling; and IRAF/STSDAS/PROS status reports.

Rule-Based Statistical Calculations on a Database Abstract.

DTIC Science & Technology

1983-06-01

quadruples 17 L.6.6. Our methds ~ in distributed systems 17 L.6.7. Easy extensions 17 17. The datibms abstract as a database 17 17.1.w S orae mu is 1.7.2...the largest item in the intersection of two sets cannot be any larger that the minima of the maxima of the two sets for some numeric attribute. On the...from "range analysis" of arbitrary numeric attributes. Suppose the length range of tankers is from 300 to 1000 feet and that of American ships 50 to

Publication rates of abstracts presented at the Association of Chiropractic Colleges Educational Conference/Research Agenda Conference from 2002 to 2008

PubMed Central

Bakkum, Barclay W.; Chapman, Cynthia; Johnson, Claire

2014-01-01

Objective The purposes of this study were to investigate the overall publication rates of presentations at the Association of Chiropractic Colleges Educational Conference/Research Agenda Conference (ACC/RAC) meetings (2002–2008), differences in the publication rates of platform vs poster presentations, and the consistency of the meeting abstract compared to the full-length journal article. Methods Abstracts were obtained from proceedings published in the Journal of Chiropractic Education. Literature searches using PubMed and the Index to the Chiropractic Literature (ICL) were performed to locate peer-reviewed journal articles based upon those abstracts. Whether the article was based upon a poster or platform presentation, and the congruence of the information in the abstract and article were recorded. Results We identified 776 proceeding abstracts, 249 of which eventually were published between 2002 and 2012. The overall publication rate was 32.2%. A total of 42.7% of platform presentations eventually were published vs 20.3% of posters. Congruency showed that 43.2% had the same title as the meeting abstract, 59.7% had the same authorship, and 88.8% had the same methods. Conclusion Publication rates of abstracts from spine and orthopedic surgery national meetings range from 34% to 59%. The ACC/RAC meetings have similar publication rates. More platform than poster presentations reach full publication. The congruency of ACC/RAC abstracts to published articles is higher than national meetings in other fields. PMID:24295363

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

Distributed Episodic Exploratory Planning (DEEP)

DTIC Science & Technology

2008-12-01

API). For DEEP, Hibernate offered the following advantages: • Abstracts SQL by utilizing HQL so any database with a Java Database Connectivity... Hibernate SQL ICCRTS International Command and Control Research and Technology Symposium JDB Java Distributed Blackboard JDBC Java Database Connectivity...selected because of its opportunistic reasoning capabilities and implemented in Java for platform independence. Java was chosen for ease of

Common Database Interface for Heterogeneous Software Engineering Tools.

DTIC Science & Technology

1987-12-01

SUB-GROUP Database Management Systems ;Programming(Comuters); 1e 05 Computer Files;Information Transfer;Interfaces; 19. ABSTRACT (Continue on reverse...Air Force Institute of Technology Air University In Partial Fulfillment of the Requirements for the Degree of Master of Science in Information Systems ...Literature ..... 8 System 690 Configuration ......... 8 Database Functionis ............ 14 Software Engineering Environments ... 14 Data Manager

Abstracts of Remediation Case Studies, Volume 9

EPA Pesticide Factsheets

This report, published by the Federal Remediation Technologies Roundtable (FRTR), is a collection of recently published abstracts summarizing 13 cost and performance case studies on the use of remediation technologies at contaminated sites.

Update in Outpatient General Internal Medicine: Practice-Changing Evidence Published in 2015.

PubMed

Szostek, Jason H; Wieland, Mark L; Post, Jason A; Sundsted, Karna K; Mauck, Karen F

2016-08-01

Identifying new practice-changing articles is challenging. To determine the 2015 practice-changing articles most relevant to outpatient general internal medicine, 3 internists independently reviewed the titles and abstracts of original articles, synopses of single studies and syntheses, and databases of syntheses. For original articles, internal medicine journals with the 7 highest impact factors were reviewed: New England Journal of Medicine, Lancet, Journal of the American Medical Association (JAMA), British Medical Journal, Public Library of Science Medicine, Annals of Internal Medicine, and JAMA Internal Medicine. For synopses of single studies and syntheses, collections in American College of Physicians Journal Club, Journal Watch, and Evidence-Based Medicine were reviewed. For databases of synthesis, Evidence Updates and the Cochrane Library were reviewed. More than 100 articles were identified. Criteria for inclusion were as follows: clinical relevance, potential for practice change, and strength of evidence. Clusters of important articles around one topic were considered as a single-candidate series. The 5 authors used a modified Delphi method to reach consensus on inclusion of 7 topics for in-depth appraisal. Copyright © 2016 Elsevier Inc. All rights reserved.

Orthodontic Research Output from Iran in International and National Journals

PubMed Central

Badri, Samareh; Akhoundi, Mohammad Sadegh Ahmad; Fard, Mohammad JavadKharrazi; Momeni, Nafiseh; Hedayati, Zohreh; Vakili, Vajihe

2014-01-01

Objective: The number of scientific papers is a conventional metric to measure a country’s research performance in a particular area. The aim of this survey was to demonstrate statistical information about orthodontic research published in international and national journals. Materials and Methods: Pubmed as an international and IranMedex and SID as national databases were searched between1997 and 2012. The keyword searching method was used in English and Persian. Abstracts were reviewed and unrelated articles were omitted. Data were obtained and transferred to Microsoft Excel to survey the scintometric indicators. Results: According to the defined criteria, a total of 733 papers were found showing a considerable increase. Five hundred papers (68.2%) were published in domestic journals, and 233 (31.8%) were published in PubMed indexed journals. Most of the orthodontic articles originated from Shahid Beheshti University of Medical Sciences (22.9%). The Journal of Dental School, Shahid Beheshti University of Medical Sciences published most of the national papers (27.8%) and the Australian Orthodontic Journal published the majority of international papers (9.9%) In terms of study design, 52.5% of the articles were observational and 39.4% were interventional. Conclusion: Orthodontic research production in Iran has made significant strides in the recent years and researchers should focus on the quality of the study in this field in order to apply research production in evidence base dentistry. PMID:24910678

Fate of abstracts presented at a National Turkish Orthopedics and Traumatology Congress: publication rates and consistency of abstracts compared with their subsequent full-text publications.

PubMed

Yalçınkaya, Merter; Bagatur, Erdem

2013-01-01

The aim of this study was to evaluate the publication rates of full-text articles after presentation of abstracts at a Turkish National Orthopaedics and Traumatology Congress, determine the time lag from the congress date to publication of full-text articles and assess the consistency between abstracts and the subsequent publications. All abstracts from the scientific program of the 20th Turkish National Orthopaedics and Traumatology Congress (2007) were identified and computerized PubMed searches were conducted to determine whether an abstract had been followed by publication of a full-text article and key features were compared to evaluate their consistency. The time lag to publication and the impact factors of the journals where the articles were published were noted. Of the 770 abstracts (264 oral, 506 poster presentations), 227 (29.5%) were followed by a full-text and 116 (44%) of the 264 oral and 111 (22%) of the 506 poster presentations were published. The mean time to publication was 14.9±16.075 (range: 33 to 55) months. Thirty-three (14.5%) were published prior to the presentation at the congress. The likelihood of publication decreased after the third year (26 of 227, 11.5%). A total of 182 (80.2%) articles showed inconsistencies with the abstract; 74 (32.6%) minor, 14 (6.2%) major, and 94 (41.4%) minor and major inconsistencies. The mean impact factor of the journals was 1.152±0.858. The vast majority of abstracts presented at this congress were not followed by publication of a full-text article. Additionally, frequent inconsistencies between the final published article and the original abstract indicated the inadequacy of quality of reporting in abstracts.

Syphilis Trends among Men Who Have Sex with Men in the United States and Western Europe: A Systematic Review of Trend Studies Published between 2004 and 2015.

PubMed

Abara, Winston E; Hess, Kristen L; Neblett Fanfair, Robyn; Bernstein, Kyle T; Paz-Bailey, Gabriela

2016-01-01

Globally, men who have sex with men (MSM) are disproportionately burdened with syphilis. This review describes the published literature on trends in syphilis infections among MSM in the US and Western Europe from 1998, the period with the fewest syphilis infections in both geographical areas, onwards. We also describe disparities in syphilis trends among various sub-populations of MSM. We searched electronic databases (Medline, Embase, Global Health, PsychInfo, CAB Abstracts, CINAHL, Sociological Abstracts, Web of Science, Cochrane Library, and LILACS) for peer-reviewed journal articles that were published between January 2004 and June 2015 and reported on syphilis cases among MSM at multiple time points from 1998 onwards. Ten articles (12 syphilis trend studies/reports) from the US and eight articles (12 syphilis trend studies/reports) from Western Europe were identified and included in this review. Taken together, our findings indicate an increase in the numbers and rates (per 100,000) of syphilis infections among MSM in the US and Western Europe since 1998. Disparities in the syphilis trends among MSM were also noted, with greater increases observed among HIV-positive MSM than HIV-negative MSM in both the US and Western Europe. In the US, racial minority MSM and MSM between 20 and 29 years accounted for the greatest increases in syphilis infections over time whereas White MSM accounted for most syphilis infections over time in Western Europe. Multiple strategies, including strengthening and targeting current syphilis screening and testing programs, and the prompt treatment of syphilis cases are warranted to address the increase in syphilis infections among all MSM in the US and Western Europe, but particularly among HIV-infected MSM, racial minority MSM, and young MSM in the US.

Syphilis Trends among Men Who Have Sex with Men in the United States and Western Europe: A Systematic Review of Trend Studies Published between 2004 and 2015

PubMed Central

Abara, Winston E.; Hess, Kristen L.; Neblett Fanfair, Robyn; Bernstein, Kyle T.; Paz-Bailey, Gabriela

2016-01-01

Globally, men who have sex with men (MSM) are disproportionately burdened with syphilis. This review describes the published literature on trends in syphilis infections among MSM in the US and Western Europe from 1998, the period with the fewest syphilis infections in both geographical areas, onwards. We also describe disparities in syphilis trends among various sub-populations of MSM. We searched electronic databases (Medline, Embase, Global Health, PsychInfo, CAB Abstracts, CINAHL, Sociological Abstracts, Web of Science, Cochrane Library, and LILACS) for peer-reviewed journal articles that were published between January 2004 and June 2015 and reported on syphilis cases among MSM at multiple time points from 1998 onwards. Ten articles (12 syphilis trend studies/reports) from the US and eight articles (12 syphilis trend studies/reports) from Western Europe were identified and included in this review. Taken together, our findings indicate an increase in the numbers and rates (per 100,000) of syphilis infections among MSM in the US and Western Europe since 1998. Disparities in the syphilis trends among MSM were also noted, with greater increases observed among HIV-positive MSM than HIV-negative MSM in both the US and Western Europe. In the US, racial minority MSM and MSM between 20 and 29 years accounted for the greatest increases in syphilis infections over time whereas White MSM accounted for most syphilis infections over time in Western Europe. Multiple strategies, including strengthening and targeting current syphilis screening and testing programs, and the prompt treatment of syphilis cases are warranted to address the increase in syphilis infections among all MSM in the US and Western Europe, but particularly among HIV-infected MSM, racial minority MSM, and young MSM in the US. PMID:27447943

CBD: a biomarker database for colorectal cancer

PubMed Central

Zhang, Xueli; Sun, Xiao-Feng; Ye, Benchen; Peng, Qiliang; Liu, Xingyun; Shen, Bairong; Zhang, Hong

2018-01-01

Abstract Colorectal cancer (CRC) biomarker database (CBD) was established based on 870 identified CRC biomarkers and their relevant information from 1115 original articles in PubMed published from 1986 to 2017. In this version of the CBD, CRC biomarker data were collected, sorted, displayed and analysed. The CBD with the credible contents as a powerful and time-saving tool provide more comprehensive and accurate information for further CRC biomarker research. The CBD was constructed under MySQL server. HTML, PHP and JavaScript languages have been used to implement the web interface. The Apache was selected as HTTP server. All of these web operations were implemented under the Windows system. The CBD could provide to users the multiple individual biomarker information and categorized into the biological category, source and application of biomarkers; the experiment methods, results, authors and publication resources; the research region, the average age of cohort, gender, race, the number of tumours, tumour location and stage. We only collect data from the articles with clear and credible results to prove the biomarkers are useful in the diagnosis, treatment or prognosis of CRC. The CBD can also provide a professional platform to researchers who are interested in CRC research to communicate, exchange their research ideas and further design high-quality research in CRC. They can submit their new findings to our database via the submission page and communicate with us in the CBD. Database URL: http://sysbio.suda.edu.cn/CBD/ PMID:29846545

Update in outpatient general internal medicine: practice-changing evidence published in 2014.

PubMed

Sundsted, Karna K; Wieland, Mark L; Szostek, Jason H; Post, Jason A; Mauck, Karen F

2015-10-01

The practice of outpatient general internal medicine requires a diverse and evolving knowledge base. General internists must identify practice-changing shifts in the literature and reflect on their impact. Accordingly, we conducted a review of practice-changing articles published in outpatient general internal medicine in 2014. To identify high-quality, clinically relevant publications, we reviewed all titles and abstracts published in the following primary data sources in 2014: New England Journal of Medicine, Journal of the American Medical Association (JAMA), Annals of Internal Medicine, JAMA Internal Medicine, and the Cochrane Database of Systematic Reviews. All 2014 primary data summaries from Journal Watch-General Internal Medicine and ACP JournalWise also were reviewed. The authors used a modified Delphi method to reach consensus on inclusion of 8 articles using the following criteria: clinical relevance to outpatient internal medicine, potential for practice change, and strength of evidence. Clusters of important articles around one clinical question were considered as a single-candidate series. The article merits were debated until consensus was reached on the final 8, spanning a variety of topics commonly encountered in outpatient general internal medicine. Copyright © 2015 Elsevier Inc. All rights reserved.

Research progress in muscle-derived stem cells: Literature retrieval results based on international database.

PubMed

Zhang, Li; Wang, Wei

2012-04-05

To identify global research trends of muscle-derived stem cells (MDSCs) using a bibliometric analysis of the Web of Science, Research Portfolio Online Reporting Tools of the National Institutes of Health (NIH), and the Clinical Trials registry database (ClinicalTrials.gov). We performed a bibliometric analysis of data retrievals for MDSCs from 2002 to 2011 using the Web of Science, NIH, and ClinicalTrials.gov. (1) Web of Science: (a) peer-reviewed articles on MDSCs that were published and indexed in the Web of Science. (b) Type of articles: original research articles, reviews, meeting abstracts, proceedings papers, book chapters, editorial material and news items. (c) Year of publication: 2002-2011. (d) Citation databases: Science Citation Index-Expanded (SCI-E), 1899-present; Conference Proceedings Citation Index-Science (CPCI-S), 1991-present; Book Citation Index-Science (BKCI-S), 2005-present. (2) NIH: (a) Projects on MDSCs supported by the NIH. (b) Fiscal year: 1988-present. (3) ClinicalTrials.gov: All clinical trials relating to MDSCs were searched in this database. (1) Web of Science: (a) Articles that required manual searching or telephone access. (b) We excluded documents that were not published in the public domain. (c) We excluded a number of corrected papers from the total number of articles. (d) We excluded articles from the following databases: Social Sciences Citation Index (SSCI), 1898-present; Arts & Humanities Citation Index (A&HCI), 1975-present; Conference Proceedings Citation Index - Social Science & Humanities (CPCI-SSH), 1991-present; Book Citation Index - Social Sciences & Humanities (BKCI-SSH), 2005-present; Current Chemical Reactions (CCR-EXPANDED), 1985-present; Index Chemicus (IC), 1993-present. (2) NIH: (a) We excluded publications related to MDSCs that were supported by the NIH. (b) We limited the keyword search to studies that included MDSCs within the title or abstract. (3) ClinicalTrials.gov: (a) We excluded clinical trials that were not in the ClinicalTrials.gov database. (b) We excluded clinical trials that dealt with stem cells other than MDSCs in the ClinicalTrials.gov database. (1) Type of literature; (2) annual publication output; (3) distribution according to journals; (4) distribution according to country; (5) distribution according to institution; (6) top cited authors over the last 10 years; (7) projects financially supported by the NIH; and (8) clinical trials registered. (1) In all, 802 studies on MDSCs appeared in the Web of Science from 2002 to 2011, almost half of which derived from American authors and institutes. The number of studies on MDSCs has gradually increased over the past 10 years. Most papers on MDSCs appeared in journals with a particular focus on cell biology research, such as Experimental Cell Research, Journal of Cell Science, and PLoS One. (2) Eight MDSC research projects have received over US$6 billion in funding from the NIH. The current project led by Dr. Johnny Huard of the University of Pittsburgh-"Muscle-Based Tissue Engineering to Improve Bone Healing"-is supported by the NIH. Dr. Huard has been the most productive and top-cited author in the field of gene therapy and adult stem cell research in the Web of Science over last 10 years. (3) On ClinicalTrials.gov, "Muscle Derived Cell Therapy for Bladder Exstrophy Epispadias Induced Incontinence" Phase 1 is registered and sponsored by Johns Hopkins University and has been led by Dr. John P. Gearhart since November 2009. From our analysis of the literature and research trends, we found that MDSCs may offer further benefits in regenerative medicine.

GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique

PubMed Central

Yu, Wei; Clyne, Melinda; Dolan, Siobhan M; Yesupriya, Ajay; Wulf, Anja; Liu, Tiebin; Khoury, Muin J; Gwinn, Marta

2008-01-01

Background Synthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into health applications. Although genetic association studies account for a substantial proportion of the abstracts in PubMed, identifying them with standard queries is not always accurate or efficient. Further automating the literature-screening process can reduce the burden of a labor-intensive and time-consuming traditional literature search. The Support Vector Machine (SVM), a well-established machine learning technique, has been successful in classifying text, including biomedical literature. The GAPscreener, a free SVM-based software tool, can be used to assist in screening PubMed abstracts for human genetic association studies. Results The data source for this research was the HuGE Navigator, formerly known as the HuGE Pub Lit database. Weighted SVM feature selection based on a keyword list obtained by the two-way z score method demonstrated the best screening performance, achieving 97.5% recall, 98.3% specificity and 31.9% precision in performance testing. Compared with the traditional screening process based on a complex PubMed query, the SVM tool reduced by about 90% the number of abstracts requiring individual review by the database curator. The tool also ascertained 47 articles that were missed by the traditional literature screening process during the 4-week test period. We examined the literature on genetic associations with preterm birth as an example. Compared with the traditional, manual process, the GAPscreener both reduced effort and improved accuracy. Conclusion GAPscreener is the first free SVM-based application available for screening the human genetic association literature in PubMed with high recall and specificity. The user-friendly graphical user interface makes this a practical, stand-alone application. The software can be downloaded at no charge. PMID:18430222

The clinical effectiveness and cost-effectiveness of testing for cytochrome P450 polymorphisms in patients with schizophrenia treated with antipsychotics: a systematic review and economic evaluation.

PubMed

Fleeman, N; McLeod, C; Bagust, A; Beale, S; Boland, A; Dundar, Y; Jorgensen, A; Payne, K; Pirmohamed, M; Pushpakom, S; Walley, T; de Warren-Penny, P; Dickson, R

2010-01-01

To determine whether testing for cytochrome P450 (CYP) polymorphisms in adults entering antipsychotic treatment for schizophrenia leads to improvement in outcomes, is useful in medical, personal or public health decision-making, and is a cost-effective use of health-care resources. The following electronic databases were searched for relevant published literature: Cochrane Controlled Trials Register, Cochrane Database of Systematic Reviews, Database of Abstracts of Reviews of Effectiveness, EMBASE, Health Technology Assessment database, ISI Web of Knowledge, MEDLINE, PsycINFO, NHS Economic Evaluation Database, Health Economic Evaluation Database, Cost-effectiveness Analysis (CEA) Registry and the Centre for Health Economics website. In addition, publicly available information on various genotyping tests was sought from the internet and advisory panel members. A systematic review of analytical validity, clinical validity and clinical utility of CYP testing was undertaken. Data were extracted into structured tables and narratively discussed, and meta-analysis was undertaken when possible. A review of economic evaluations of CYP testing in psychiatry and a review of economic models related to schizophrenia were also carried out. For analytical validity, 46 studies of a range of different genotyping tests for 11 different CYP polymorphisms (most commonly CYP2D6) were included. Sensitivity and specificity were high (99-100%). For clinical validity, 51 studies were found. In patients tested for CYP2D6, an association between genotype and tardive dyskinesia (including Abnormal Involuntary Movement Scale scores) was found. The only other significant finding linked the CYP2D6 genotype to parkinsonism. One small unpublished study met the inclusion criteria for clinical utility. One economic evaluation assessing the costs and benefits of CYP testing for prescribing antidepressants and 28 economic models of schizophrenia were identified; none was suitable for developing a model to examine the cost-effectiveness of CYP testing. Tests for determining genotypes appear to be accurate although not all aspects of analytical validity were reported. Given the absence of convincing evidence from clinical validity studies, the lack of clinical utility and economic studies, and the unsuitability of published schizophrenia models, no model was developed; instead key features and data requirements for economic modelling are presented. Recommendations for future research cover both aspects of research quality and data that will be required to inform the development of future economic models.

Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature.

PubMed

Ravikumar, Komandur Elayavilli; Wagholikar, Kavishwar B; Li, Dingcheng; Kocher, Jean-Pierre; Liu, Hongfang

2015-06-06

Advances in the next generation sequencing technology has accelerated the pace of individualized medicine (IM), which aims to incorporate genetic/genomic information into medicine. One immediate need in interpreting sequencing data is the assembly of information about genetic variants and their corresponding associations with other entities (e.g., diseases or medications). Even with dedicated effort to capture such information in biological databases, much of this information remains 'locked' in the unstructured text of biomedical publications. There is a substantial lag between the publication and the subsequent abstraction of such information into databases. Multiple text mining systems have been developed, but most of them focus on the sentence level association extraction with performance evaluation based on gold standard text annotations specifically prepared for text mining systems. We developed and evaluated a text mining system, MutD, which extracts protein mutation-disease associations from MEDLINE abstracts by incorporating discourse level analysis, using a benchmark data set extracted from curated database records. MutD achieves an F-measure of 64.3% for reconstructing protein mutation disease associations in curated database records. Discourse level analysis component of MutD contributed to a gain of more than 10% in F-measure when compared against the sentence level association extraction. Our error analysis indicates that 23 of the 64 precision errors are true associations that were not captured by database curators and 68 of the 113 recall errors are caused by the absence of associated disease entities in the abstract. After adjusting for the defects in the curated database, the revised F-measure of MutD in association detection reaches 81.5%. Our quantitative analysis reveals that MutD can effectively extract protein mutation disease associations when benchmarking based on curated database records. The analysis also demonstrates that incorporating discourse level analysis significantly improved the performance of extracting the protein-mutation-disease association. Future work includes the extension of MutD for full text articles.

Outcome of abstracts presented at the British Association of Paediatric Surgeons congresses (1999-2008).

PubMed

Macdonald, Alexander L; Parsons, Christopher; Davenport, Mark

2012-02-01

Abstracts presented at the British Association of Paediatric Surgeons annual congress have the potential to influence practice. However, it is not known what percentage of accepted abstracts actually go on to withstand peer review and be published in the literature. Abstract books were reviewed for the period 1999 to 2008. A MEDLINE search using keywords from title and authors' names was used to identify subsequent publication. Categorical analysis for variation and trend with P < .05 was accepted as significant. Data were expressed as median (interquartile range). During the 10-year period, 862 abstracts were presented orally and were derived from 36 countries, with a median of 18 (17-19) countries represented each year. Of these, 375 (43%) abstracts originated from 25 United Kingdom (UK) institutions with most (45%) from London and specifically the Institute of Child Health/Great Ormond Street Hospital (n = 118, 14%). The annual median number of presentations was 81 (74-97). This fell during the first half of the decade but is now rising with a significant increase in the UK proportion (P = .001). Thirty (27-35) abstracts per year (overall, n = 302) were subsequently published with the proportion (36% [33%-39%]) remaining remarkably consistent over the period. Abstracts were published in a range of 26 journals, but most (69%) were published in the Journal of Pediatric Surgery. The publication rate of the British Association of Paediatric Surgeons congress and hence entry into the "evidence base" as published material is consistent at just over one third of submissions. Whether this represents a waste of scientific endeavor or further refinement of quality is a moot point. Copyright © 2012 Elsevier Inc. All rights reserved.

A re-appraisal of publication rates of scientific papers presented at the Otorhinolaryngology Research Society meetings.

PubMed

Lau, A S; Krishnan, M; Williams, S P; Mamais, C; Sweed, A; Bhat, J; Somashekar, S; Leong, S C

2016-12-01

To review the rate of publication of papers in peer-reviewed journals after oral presentations at the Otorhinolaryngology Research Society meetings between 1996 and 2013 and to compare trends with the previous review (1979-1995). Literature review. Merseyside ENT Research Collaborative. The abstracts of presentations at Otorhinolaryngology Research Society meetings are published in Clinical Otolaryngology. A structured search of PubMed was undertaken to identify published Otorhinolaryngology Research Society presentations. Publication rates. A total of 460 abstracts were identified. The interobserver reliability among reviewers was 98%. Of the total, 259 (56.3%) abstracts were published in peer-reviewed journals. The average time from Otorhinolaryngology Research Society presentation to publication was 27.7 months (median 23), which was not significantly different from the previous review. Publication by subspeciality was as follows: head and neck (45.6%), otology (30.5%), rhinology (22%) and others (1.9%). Most published Otorhinolaryngology Research Society presentations were published in Clinical Otolaryngology (22.4%), followed by the Journal of Laryngology and Otology (8.1%) and the Laryngoscope (7.3%). Clinical research was the most common category of abstracts being presented at Otorhinolaryngology Research Society meetings, followed by laboratory-based research. Over half (56.5%) of laboratory research presented were head and neck themed, while otology and rhinology predominated clinical research presentations. Over half (52.1%) of Otorhinolaryngology Research Society abstracts originated from units in the North of England. Bristol presented the most abstracts (30.1%), followed by Newcastle (25.1%). The publication rate of Otorhinolaryngology Research Society presentations remains high and many are subsequently published in high-impact factor otolaryngology journals. More Otorhinolaryngology Research Society presentations are now published in American and European journals. © 2015 John Wiley & Sons Ltd.

Cancer studies based on secondary data analysis of the Taiwan's National Health Insurance Research Database: A computational text analysis and visualization study.

PubMed

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

2017-04-01

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

Does varenicline worsen psychiatric symptoms in patients with schizophrenia or schizoaffective disorder? A review of published studies.

PubMed

Cerimele, Joseph M; Durango, Alejandra

2012-08-01

To review published cases and prospective studies describing the use of varenicline in patients with schizophrenia and schizoaffective disorder. PubMed, PsychINFO, and the Cochrane Database were searched in July 2011 using the key words schizophrenia, schizoaffective disorder, psychosis, positive symptoms, negative symptoms, aggression, hostility, suicidal ideation AND varenicline to identify reports published between January 2006 and July 2011 in English. Five case reports, 1 case series, 1 retrospective study, 10 prospective studies (17 publications), and 1 meeting abstract describing the use of varenicline in patients with schizophrenia or schizoaffective disorder were identified. Review articles and articles describing findings other than the use of varenicline in patients with schizophrenia or schizoaffective disorder were excluded. Thirteen reports were included in the final analysis. Information on each study's patient population, age, diagnosis, medication treatment, tobacco use history, adverse effects, and outcome was collected from the published reports. Of the 260 patients with schizophrenia or schizoaffective disorder who received varenicline in these published reports, 13 patients (5%) experienced the onset or worsening of any psychiatric symptom, although 3 of the 13 patients experienced a very brief negative effect after 1 dose. No patients experienced suicidal ideation or suicidal behaviors. Published reports suggest that, in most stable, closely monitored patients with schizophrenia or schizoaffective disorder, varenicline treatment is not associated with worsening of psychiatric symptoms. Current, prospective studies are assessing effectiveness and further assessing safety in this population. © Copyright 2012 Physicians Postgraduate Press, Inc.

Determinants of seat belt use behaviour: a protocol for a systematic review.

PubMed

Ghaffari, Mohtasham; Armoon, Bahram; Rakhshanderou, Sakineh; Mehrabi, Yadollah; Soori, Hamid; Simsekoghlu, Ozelem; Harooni, Javad

2018-05-03

The use of seat belts could prevent severe collision damage to people in vehicle accidents and keep passengers safe from sustaining serious injuries; for instance, it could prevent passengers from being thrown out of a vehicle after the collision. The current systematic review will identify and analyse the determinants of seat belt use behaviour. We will include qualitative, quantitative and mixed methods studies reporting the acquired data from passengers aged more than 12 years and drivers, from both commercial and personal vehicles. Online databases including MEDLINE/PubMed, Scopus, Web of Science, Embase, Cochrane Database of Systematic Reviews and PsycINFO will be investigated in the current study. Published and available articles will be evaluated according to their titles and abstracts. Published papers conforming to the inclusion criteria will be organised for a complete review. Next, the full text of the remaining articles will be studied independently for eligibility by two authors. The quality of the selected studies will be assessed with appropriate tools. Based on the information obtained from the data extraction, the type of determinants of seat belt use will be classified. Ethics approval is not required, because this is a protocol for a systematic review and no primary data will be collected. The authors will ensure to maintain the rights of the used and included articles in the present systematic review. The findings of this review will be published in a relevant peer-reviewed journal. CRD42017067511. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Database System Design and Implementation for Marine Air-Traffic-Controller Training

DTIC Science & Technology

2017-06-01

NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS Approved for public release. Distribution is unlimited. DATABASE SYSTEM DESIGN AND...thesis 4. TITLE AND SUBTITLE DATABASE SYSTEM DESIGN AND IMPLEMENTATION FOR MARINE AIR-TRAFFIC-CONTROLLER TRAINING 5. FUNDING NUMBERS 6. AUTHOR(S...12b. DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) This project focused on the design , development, and implementation of a centralized

Quality of reviews on sugar-sweetened beverages and health outcomes: a systematic review123

PubMed Central

Weed, Douglas L; Mink, Pamela J

2011-01-01

Background: Medical and public health decisions are informed by reviews, which makes the quality of reviews an important scientific concern. Objective: We systematically assessed the quality of published reviews on sugar-sweetened beverages (SSBs) and health, which is a controversial topic that is important to public health. Design: We performed a search of PubMed and Cochrane databases and a hand search of reference lists. Studies that were selected were published reviews and meta-analyses (June 2001 to June 2011) of epidemiologic studies of the relation between SSBs and obesity, type 2 diabetes, metabolic syndrome, and coronary heart disease. A standardized data-abstraction form was used. Review quality was assessed by using the validated instrument AMSTAR (assessment of multiple systematic reviews), which is a one-page tool with 11 questions. Results: Seventeen reviews met our inclusion and exclusion criteria: obesity or weight (16 reviews), diabetes (3 reviews), metabolic syndrome (3 reviews), and coronary heart disease (2 reviews). Authors frequently used a strictly narrative review (7 of 17 reviews). Only 6 of 17 reviews reported quantitative data in a table format. Overall, reviews of SSBs and health outcomes received moderately low–quality scores by the AMSTAR [mean: 4.4 points; median: 4 points; range: 1–8.5 points (out of a possible score of 11 points)]. AMSTAR scores were not related to the conclusions of authors (8 reviews reported an association with a mean AMSTAR score of 4.1 points; 9 reviews with equivocal conclusions scored 4.7 points; P value = 0.84). Less than one-third of published reviews reported a comprehensive literature search, listed included and excluded studies, or used duplicate study selection and data abstraction. Conclusion: The comprehensive reporting of epidemiologic evidence and use of systematic methodologies to interpret evidence were underused in published reviews on SSBs and health. PMID:21918218

Systematic Review: FDA-Approved Prescription Medications for Adults With Constipation

PubMed Central

Lacy, Brian E.

2006-01-01

Constipation is a common, often chronic, gastrointestinal disorder that can negatively impact the lives of those it affects and can be difficult to treat satisfactorily. The objective of this systematic review is to identify and analyze the available published literature on US Food and Drug Administration–approved prescription therapies for adults with constipation (episodic and chronic) and to assess their place in therapy, based on the methodologic strength and results of identified clinical trials. Ovid MEDLINE, PubMed, and EMBASE databases were used to search the published literature. Studies were included if they were randomized and prospective, conducted in adults (age ≥18), published as full-length manuscripts in English, and compared the test agent with placebo or a comparator(s). Studies were excluded if they involved patients with constipation attributed to secondary causes. Because fully published manuscripts from phase III efficacy trials involving the recently approved medication lubiprostone were not available, a manual search was performed of abstracts from the two annual major gastroenterology meetings (American College of Gastroenterology and Digestive Disease Week) from the past 4 years. Data on study design; number, age, and sex of patients; duration of treatment period; primary efficacy variable; secondary efficacy variables; adverse events; and discontinuations because of adverse events were abstracted from eligible articles. Eligible studies were assessed using well-established recommendations and a preformatted standardized form. A scoring system, with scores ranging from 1 to 15, was used to individually and separately assess the methodologic quality of the studies. Results of this analysis indicate a general lack of methodologically high-quality clinical trials supporting the use of lactulose and PEG 3350 to treat patients with chronic constipation, but data support their use in acute, episodic constipation. Conversely, high-quality evidence for tegaserod and lubiprostone in patients with chronic constipation does exist, though conclusions regarding the role in therapy for lubiprostone are still in development. PMID:28325992

A systematic review of ethical issues in vaccine studies involving pregnant women

PubMed Central

Beeler, Jennifer A.; Lambach, Philipp; Fulton, T. Roice; Narayanan, Divya; Ortiz, Justin R.; Omer, Saad B.

2016-01-01

ABSTRACT Background: Immunization during pregnancy can provide protection for mother and child. However, there have been only a limited number of studies documenting the efficacy and safety of this strategy. Aims: To determine the extent and nature of subject matter related to ethics in maternal immunization by systematically documenting the spectrum of ethical issues in vaccine studies involving pregnant women. Method: We conducted a systematic literature review of published works pertaining to vaccine and therapeutic studies involving pregnant women through searches of PubMed, EMBASE, Web of Science, the Cochrane Database, and ClinicalTrials.gov. We selected literature meeting the inclusion criteria published between 1988 and June 2014. We systematically abstracted subject matter pertaining to ethical issues in immunization studies during pregnancy. Immunization-specific ethical issues were matched and grouped into major categories and subcategories. Results: Seventy-seven published articles met the inclusion criteria. Published articles reported findings on data that had been collected in 26 countries, the majority of which were classified as high-income or upper-middle-income nations according to World Bank criteria. Review of these publications produced 60 immunization-specific ethical issues, grouped into six major categories. Notably, many studies demonstrated limited acknowledgment of key ethical issues including the rights and welfare of participants. Additionally, there was no discussion pertaining to the ethics of program implementation, including integration of maternal immunization programs into existing routine immunization programs. Conclusion: This review of ethical issues in immunization studies of pregnant women can be used to help inform future vaccine trials in this important population. Consistent documentation of these ethical issues by investigators will facilitate a broader and more nuanced discussion of ethics in immunization of pregnant women – offering new and valuable insights for programs developed to prevent disease in newborn children in low- and middle-income countries. PMID:27246403

Development and operations of the astrophysics data system

NASA Technical Reports Server (NTRS)

Murray, Stephen S.; Oliversen, Ronald (Technical Monitor)

2005-01-01

Abstract service - Continued regular updates of abstracts in the databases, both at SA0 and at all mirror sites. - Modified loading scripts to accommodate changes in data format (PhyS) - Discussed data deliveries with providers to clear up problems with format or other errors (EGU) - Continued inclusion of large numbers of historical literature volumes and physics conference volumes xeroxed from the library. - Performed systematic fixes on some data sets in the database to account for changes in article numbering (AGU journals) - Implemented linking of ADS bibliographic records with multimedia files - Debugged and fixed obscure connection problems with the ADS Korean mirror site which were preventing successful updates of the data holdings. - Wrote procedure to parse citation data and characterize an ADS record based on its citation ratios within each database.

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

PubMed

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

2011-11-01

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

Systematic review of ureteral access sheaths: facts and myths.

PubMed

De Coninck, Vincent; Keller, Etienne Xavier; Rodríguez-Monsalve, María; Audouin, Marie; Doizi, Steeve; Traxer, Olivier

2018-05-11

The aim of the present paper was to review the literature on all available ureteral access sheaths (UASs) with their indications, limitations, risks, advantages and disadvantages in current modern endourological practice. Two authors searched Medline, Scopus, Embase and Web of Science databases to identify studies on UASs published in English. No time period restriction was applied. All original articles reporting outcomes or innovations were included. Additional articles identified through references lists were also included. Case reports, editorials, letters, review articles and meeting abstracts were excluded. A total of 754 abstracts were screened, 176 original articles were assessed for eligibility and 83 articles were included in the review. Based on a low level of evidence, UASs increase irrigation flow during flexible ureteroscopy and decrease intrapelvic pressure and probably infectious complications. Data were controversial and sparse on the impact of UASs on multiple reinsertions and withdrawals of a ureteroscope, stone-free rates, ureteroscope protection or damage, postoperative pain, risk of ureteral strictures, and also on its cost-effectiveness. Studies on the benefit of UASs in paediatrics and in patients with a coagulopathy were inconclusive. In the absence of good randomized data, the true impact of UASs on surgery outcome remains unclear. The present review may contribute to the evidence-based decision-making process at the individual patient level regarding whether or not a UAS should be used. © 2018 The Authors BJU International © 2018 BJU International Published by John Wiley & Sons Ltd.

Factors related to the association of social anxiety disorder and alcohol use among adolescents: a systematic review.

PubMed

Cruz, Elisabeth Lima Dias da; Martins, Priscila Diniz de Carvalho; Diniz, Paula Rejane Beserra

To identify the risk factors related to the association between social anxiety disorder and alcohol use in adolescents. The PICO research strategy was used to perform a systematic review in Medline, LILACS, Pubmed, IBECS and Cochrane Library databases. DeCS/MeSH: Phobic Disorders, Adolescent, Behavior, Ethanol, Risk Factors, and the Boolean operator "AND" were used. Inclusion criteria were: cross-sectional, prospective/retrospective cohort, and case-control studies, carried out in adolescents (10-19 years), original articles on social anxiety disorder and alcohol use published between 2010 and 2015. Studies that did not report the terms "anxiety disorder" and "alcohol use" in the title and abstract were excluded. 409 articles were retrieved; after the exclusion of 277 repeated articles, the following were eligible: 94 in MEDLINE, 68 in Pubmed, 12 in IBCS, and three in LILACS. Titles and abstracts were independently read by two examiners, which resulted in the selection of eight articles for the analysis. Risk factors associated to the two disorders were female gender, age, peer approval and affective problems for alcohol use, confrontation situations and/or compliance reasons, frequency of alcohol use, and secondary comorbidities, such as depression and generalized anxiety. It is necessary to assess the period of social anxiety disorders first symptom onset, as well as the risks for alcohol use in order to establish corrective intervention guidelines, especially for socially anxious students. Copyright © 2017. Published by Elsevier Editora Ltda.

Urological research in sub-Saharan Africa: a retrospective cohort study of abstracts presented at the Nigerian Association of Urological Surgeons conferences.

PubMed

Bello, Jibril Oyekunle

2013-11-14

Nigeria is one of the top three countries in Africa in terms of science research output and Nigerian urologists' biomedical research output contributes to this. Each year, urologists in Nigeria gather to present their recent research at the conference of the Nigerian Association of Urological Surgeons (NAUS). These abstracts are not thoroughly vetted as are full length manuscripts published in peer reviewed journals but the information they disseminate may affect clinical practice of attendees. This study aims to describe the characteristics of abstracts presented at the annual conferences of NAUS, the quality of the abstracts as determined by the subsequent publication of full length manuscripts in peer-review indexed journals and the factors that influence such successful publication. Abstracts presented at the 2007 to 2010 NAUS conferences were identified through conference abstracts books. Using a strict search protocol, publication in peer-reviewed journals was determined. The abstracts characteristics were analyzed and their quality judged by subsequent successful publishing of full length manuscripts. Statistical analysis was performed using SPSS 16.0 software to determine factors predictive of successful publication. Only 75 abstracts were presented at the NAUS 2007 to 2010 conferences; a quarter (24%) of the presented abstracts was subsequently published as full length manuscripts. Median time to publication was 15 months (range 2-40 months). Manuscripts whose result data were analyzed with 'beyond basic' statistics of frequencies and averages were more likely to be published than those with basic or no statistics. Quality of the abstracts and thus subsequent publication success is influenced by the use of 'beyond basic' statistics in analysis of the result data presented. There is a need for improvement in the quality of urological research from Nigeria.

Protocol for a scoping review study to identify and classify patient-centred quality indicators.

PubMed

Jolley, Rachel J; Lorenzetti, Diane L; Manalili, Kimberly; Lu, Mingshan; Quan, Hude; Santana, Maria J

2017-01-05

The concept of patient-centred care (PCC) is changing the way healthcare is understood, accepted and delivered. The Institute of Medicine has defined PCC as 1 of its 6 aims to improve healthcare quality. However, in Canada, there are currently no nationwide standards in place for measuring and evaluating healthcare from a patient-centred approach. In this paper, we outline our scoping review protocol to systematically review published and unpublished literature specific to patient-centred quality indicators that have been implemented and evaluated across various care settings. Arksey and O'Malley's scoping review methodology framework will guide the conduct of this scoping review. We will search electronic databases (MEDLINE, EMBASE, the Cochrane Library, Cumulative Index to Nursing and Allied Health Literature (CINAHL), PsycINFO, Social Work Abstracts, Social Services Abstracts), grey literature sources and the reference lists of key studies to identify studies appropriate for inclusion. 2 reviewers will independently screen all abstracts and full-text studies for inclusion. We will include any study which focuses on quality indicators in the context of PCC. All bibliographic data, study characteristics and indicators will be collected and analysed using a tool developed through an iterative process by the research team. Indicators will be classified according to a predefined conceptual framework and categorised and described using qualitative content analysis. The scoping review will synthesise patient-centred quality indicators and their characteristics as described in the literature. This review will be the first step to formally identify what quality indicators have been used to evaluate PCC across the healthcare continuum, and will be used to inform a stakeholder consensus process exploring the development of a generic set of patient-centred quality indicators applicable to multiple care settings. The results will be disseminated through a peer-reviewed publication, conference presentations and a one-day stakeholder meeting. 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/.

Brazilian medicinal plants to treat upper respiratory tract and bronchial illness: systematic review and meta-analyses-study protocol.

PubMed

Lopes, Luciane C; Silva, Maria Carolina O; Motta, Cristiane Bergamashi; Macho Quirós, Antonio; Biavatti, Maique Weber; de Oliveira, Jardel Corrêa; Guyatt, Gordon

2014-07-23

Respiratory illness, often associated with cough and sputum, is frequent. In Brazil, herbal medicines are often recommended as a first-line treatment for respiratory illness. There exists uncertainty regarding the effectiveness of these treatments. No systematic review has evaluated Brazilian medicinal plants (BMP) to treat upper respiratory tract and bronchial illness (URTI). We will conduct a systematic review and, if appropriate, a series of meta-analyses evaluating the safety and effectiveness of BMP for URTI. Eligible randomised controlled trials and observational studies will enrol adult or paediatric patients presenting with URTI treated by BMP approved by the Brazilian Health Surveillance Agency compared with placebo, no treatment or an alternative therapy. Our search will include the Cochrane Central Register of Controlled Trials (CENTRAL), which contains the Cochrane Acute Respiratory Illness Group's Specialized Register; MEDLINE; EMBASE; CINAHL (Cumulative Index to Nursing and Allied Health Literature); Web of Science; AMED; LILACS; CAB abstracts; clinical trial.gov; the WHO Trial Register and the Brazilian thesis database (CAPES) without any language restrictions. Outcomes of interest are time to resolution of clinical symptoms and/or signs (cough, sputum production or activity limitations), severity of symptoms prior to resolution and major/minor adverse events. Teams of reviewers will, independently and in duplicate, screen titles and abstracts and the complete full text to determine eligibility. For eligible studies, reviewers will perform data abstraction and assess risk of bias of eligible trials. When appropriate, we will conduct meta-analyses. We will also assess the quality of body of evidence (confidence in estimates of effect) for each of the outcomes using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach. The systematic review will be published in a peer-reviewed journal. Brief reports of review findings will be disseminated directly to appropriate audiences via email and other modes of communication. The review will guide healthcare practice and policy in Brazil. Prospero CRD42014007057. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Bibliographic Databases Outside of the United States.

ERIC Educational Resources Information Center

McGinn, Thomas P.; And Others

1988-01-01

Eight articles describe the development, content, and structure of databases outside of the United States. Features discussed include library involvement, authority control, shared cataloging services, union catalogs, thesauri, abstracts, and distribution methods. Countries and areas represented are Latin America, Australia, the United Kingdom,…

Digital Equipment Corporation's CRDOM Software and Database Publications.

ERIC Educational Resources Information Center

Adams, Michael Q.

1986-01-01

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

RREL TREATABILITY DATABASE - VERSION 5.0

EPA Science Inventory

There is no abstract available for this product. If further information is requested, please refer to the bibliographic citation and contact the person listed under Contact field. This database can be obtained by contacting Tom Holdsworth, U.S. EPA, 26 West Martin Luther King D...

SERS internship: Spring 1994 abstracts and research papers

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

Goldman, B.

1994-05-06

This document contains abstracts from the science and engineering research semester from the Lawrence Livermore National Laboratory. Projects cover many areas in the fields of contaminant removal from the environment, physics, and genetics research. Individual projects were processed separately for the Department of Energy databases.

Coding the Eggen Cards (Poster abstract)

NASA Astrophysics Data System (ADS)

Silvis, G.

2014-06-01

(Abstract only) A look at the Eggen Portal for accessing the Eggen cards. And a call for volunteers to help code the cards: 100,000 cards must be looked at and their star references identified and coded into the database for this to be a valuable resource.

A CONCEPTUAL FRAMEWORK FOR INCORPORATING COGNITIVE PRINCIPLES INTO GEOGRAPHICAL DATABASE REPRESENTATION. (R825195)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Effects of maternal nicotine on breastfeeding infants

PubMed Central

Primo, Cândida Caniçali; Ruela, Priscilla Bôa F.; Brotto, Léia Damasceno de A.; Garcia, Telma Ribeiro; Lima, Eliane de Fátima

2013-01-01

OBJECTIVE To assess scientific evidence about the effects of maternal nicotine on infant by an integrative review. DATA SOURCES Studies published in Portuguese, English and Spanish, from 1990 to 2009, with abstracts available in the Latin American Health Sciences Literature (Lilacs) and Medical Literature Analysis and Retrieval System On-Line (Medline) databases. The descriptors were: "breastfeeding", "lactation" and "smoking". DATA SYNTHESIS The main identified effects of nicotine on infants were: changes in sleep and wakefulness patterns; reduction of iodine supply; hystopathological damage on liver and lung; intracellular oxidative damage; reduction of pancreatic ß cells; and decreased glucose tolerance. CONCLUSIONS It is recommended to inform mothers about harmful chemicals contained in cigarettes that can be secreted into breast milk. They should be strongly encouraged to stop smoking during lactation. PMID:24142324

Applications of Quantum Theory of Atomic and Molecular Scattering to Problems in Hypersonic Flow

NASA Technical Reports Server (NTRS)

Malik, F. Bary

1995-01-01

The general status of a grant to investigate the applications of quantum theory in atomic and molecular scattering problems in hypersonic flow is summarized. Abstracts of five articles and eleven full-length articles published or submitted for publication are included as attachments. The following topics are addressed in these articles: fragmentation of heavy ions (HZE particles); parameterization of absorption cross sections; light ion transport; emission of light fragments as an indicator of equilibrated populations; quantum mechanical, optical model methods for calculating cross sections for particle fragmentation by hydrogen; evaluation of NUCFRG2, the semi-empirical nuclear fragmentation database; investigation of the single- and double-ionization of He by proton and anti-proton collisions; Bose-Einstein condensation of nuclei; and a liquid drop model in HZE particle fragmentation by hydrogen.

Publication Rates of Abstracts Presented at the 2006 Meeting of the American Academy of Optometry.

PubMed

Bakkum, Barclay W; Trachimowicz, Ruth

2015-11-01

The purposes of this study were to investigate the publication rates of presentations at the 2006 meeting of the American Academy of Optometry (AAO), differences in the publication rates of platform versus poster presentations, consistency of the meeting abstract compared with the full-length journal article, whether abstracts were clinical or basic science, and when and in which journals articles appeared. Abstracts were obtained directly from the AAO. Literature searches using PubMed and VisionCite were performed to locate peer-reviewed journal articles based on those abstracts. Whether the article was based on a poster or platform presentation, congruence of the information in the abstract and the article (i.e., authorship, title, methods, and conclusions), type of study (clinical or basic science), subject category, and journal and year in which the article appeared were recorded. We identified 518 proceeding abstracts, 108 of which ultimately were published between 2006 and 2013, giving an overall publication rate of 21%. Thirty-three percent of platform presentations eventually were published versus 18% of posters. Congruency showed that 17% of articles had the same title as the meeting abstract, 36% had the same authorship, and 53% had the same methods. Eighty-one percent of articles were clinical in nature, whereas 19% of them were basic science. Thirty-seven percent of articles dealt with the subjects of cornea and contact lenses. Articles were found in 39 different journals, with 34% of them appearing in Optometry and Vision Science. Eighty-eight percent of articles were published within 4 years after the meeting. The publication rate from the 2006 AAO meeting was 21%. Platform presentations were more likely to be published than posters. Congruency rates of abstracts to articles are lower than national meetings in other fields. The vast majority of articles were published within 4 years after the meeting.

16 CFR 1102.28 - Publication of reports of harm.

Code of Federal Regulations, 2012 CFR

2012-01-01

... REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102.28... publish reports of harm that meet the requirements for publication in the Database. The Commission will... Commission may publish a report of harm that meets the requirements of § 1102.10(d) in the Database beyond...

16 CFR 1102.28 - Publication of reports of harm.

Code of Federal Regulations, 2014 CFR

2014-01-01

... REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102.28... publish reports of harm that meet the requirements for publication in the Database. The Commission will... Commission may publish a report of harm that meets the requirements of § 1102.10(d) in the Database beyond...

Academic Journal Embargoes and Full Text Databases.

ERIC Educational Resources Information Center

Brooks, Sam

2003-01-01

Documents the reasons for embargoes of academic journals in full text databases (i.e., publisher-imposed delays on the availability of full text content) and provides insight regarding common misconceptions. Tables present data on selected journals covering a cross-section of subjects and publishers and comparing two full text business databases.…

An Analysis of the Abstracts Presented at the Annual Meetings of the Society for Neuroscience from 2001 to 2006

PubMed Central

Lin, John M.; Bohland, Jason W.; Andrews, Peter; Burns, Gully A. P. C.; Allen, Cara B.; Mitra, Partha P.

2008-01-01

Annual meeting abstracts published by scientific societies often contain rich arrays of information that can be computationally mined and distilled to elucidate the state and dynamics of the subject field. We extracted and processed abstract data from the Society for Neuroscience (SFN) annual meeting abstracts during the period 2001–2006 in order to gain an objective view of contemporary neuroscience. An important first step in the process was the application of data cleaning and disambiguation methods to construct a unified database, since the data were too noisy to be of full utility in the raw form initially available. Using natural language processing, text mining, and other data analysis techniques, we then examined the demographics and structure of the scientific collaboration network, the dynamics of the field over time, major research trends, and the structure of the sources of research funding. Some interesting findings include a high geographical concentration of neuroscience research in the north eastern United States, a surprisingly large transient population (66% of the authors appear in only one out of the six studied years), the central role played by the study of neurodegenerative disorders in the neuroscience community, and an apparent growth of behavioral/systems neuroscience with a corresponding shrinkage of cellular/molecular neuroscience over the six year period. The results from this work will prove useful for scientists, policy makers, and funding agencies seeking to gain a complete and unbiased picture of the community structure and body of knowledge encapsulated by a specific scientific domain. PMID:18446237

City-based action to reduce harmful alcohol use: review of reviews.

PubMed

Anderson, Peter; Jané-Llopis, Eva; Hasan, Omer Syed Muhammad; Rehm, Jürgen

2018-01-01

Background: The World Health Organization global strategy on alcohol called for municipal policies to reduce the harmful use of alcohol. Yet, there is limited evidence that documents the impact of city-level alcohol policies. Methods: Review of reviews for all years to July 2017. Searches on OVID Medline, Healthstar, Embase, PsycINFO, AMED, Social Work Abstracts, CAB Abstracts, Mental Measurements Yearbook, Health and Psychosocial Instruments, International Pharmaceutical Abstracts, International Political Science Abstracts, NASW Clinical Register, and Epub Ahead of Print databases. All reviews that address adults, without language or date restrictions resulting from combining the terms ("review" or "literature review" or "review literature" or "data pooling" or "comparative study" or "systematic review" or "meta-analysis" or "pooled analysis"), and "alcohol", and "intervention" and ("municipal" or "city" or "community"). Results: Five relevant reviews were identified. Studies in the reviews were all from high income countries and focussed on the acute consequences of drinking, usually with one target intervention, commonly bars, media, or drink-driving. No studies in the reviews reported the impact of comprehensive city-based action. One community cluster randomized controlled trial in Australia, published after the reviews, failed to find convincing evidence of an impact of community-based interventions in reducing adult harmful use of alcohol.     Conclusions: To date, with one exception, the impact of adult-oriented comprehensive community and municipal action to reduce the harmful use of alcohol has not been studied. The one exception failed to find a convincing effect. We conclude with recommendations for closing this evidence gap.

Multiple overlapping systematic reviews facilitate the origin of disputes: the case of thrombolytic therapy for pulmonary embolism.

PubMed

Riva, Nicoletta; Puljak, Livia; Moja, Lorenzo; Ageno, Walter; Schünemann, Holger; Magrini, Nicola; Squizzato, Alessandro

2018-05-01

To explore disagreements in multiple systematic reviews (SRs) assessing the benefit-to-harm ratio of thrombolytic therapy in patients with intermediate-risk pulmonary embolism (PE). MEDLINE, EMBASE, Cochrane Database of Systematic Reviews, and Database of Abstracts and Reviews of Effectiveness were searched up to April 14, 2016. We included SRs and guidelines that evaluated thrombolytic therapy, compared with anticoagulation alone, in intermediate-risk PE. We calculated pooled risk ratio (RR) and absolute risk difference (RD), with interquartile range (IQR), for all-cause mortality, recurrent PE, and major bleeding. We marked the Pulmonary Embolism Thrombolysis trial, the largest trial, as a research milestone. Since its release in 2014, 12 SRs (2-15 included trials) and two major guidelines were published. Studies were concordant in reporting that thrombolysis reduced all-cause mortality (median RD -1.55%, IQR -1.60% to -1.40%; median RR 0.55, IQR 0.48-0.61). Discordant results were found for major bleeding (median RD 4.70%, IQR 0.90%-5.70%), with SRs reporting results in opposite directions. Relevant magnitude of effects and precision for benefits and harms were never prespecified. Fourteen evidence syntheses were published within 25 months. Conclusions suggested mortality reduction associated with thrombolytics. Therapy harm was more dispersed and alternatively considered. Interpretation of the benefit-to-harm ratio was elusive, and modest incremental advantages might or not be important, facilitating the origin of disputes. Copyright © 2017 Elsevier Inc. All rights reserved.

A bibliometric analysis of two decades of aromatherapy research.

PubMed

Koo, Malcolm

2017-01-18

Quantitative data are lacking on the profile of published research in aromatherapy. The objective of the study was to investigate the profile of original and review articles under the topic aromatherapy using bibliometric analysis. Articles on aromatherapy, published between 1995 and 2014, were retrieved from the Science Citation Index-Expanded database from the Web of Science. The records extracted were analyzed for citation characteristics, including the distribution of publication years, languages, countries or regions, journals, articles, and authors using HistCite 12.03.17. VOSviewer v.1.61 was used to construct bibliometric diagrams. A total of 549 original and review articles, published in 287 different peer-reviewed journals by 1888 authors, were identified. There was a steady increase in the number of published articles from 1995 to 2014. The majority of the articles was written in English (95.8%) and the United States was the leading country in the total number of published articles (n = 107, 19.5%) Journal of Alternative and Complementary Medicine published the greatest number of articles on the topic (n = 31, 5.6%). The article that received the greatest number of citations was published in Complementary Therapies in Medicine. Visualization analysis based on co-occurrences of words in the title and abstract revealed three clusters of research topics, including essential oil, intervention, and complementary medicine. This study provided a systematic overview of productivity and visibility of research work in aromatherapy and the findings could be used for organizing and prioritizing future research efforts in aromatherapy research.

Database Changes (Post-Publication). ERIC Processing Manual, Section X.

ERIC Educational Resources Information Center

Brandhorst, Ted, Ed.

The purpose of this section is to specify the procedure for making changes to the ERIC database after the data involved have been announced in the abstract journals RIE or CIJE. As a matter of general ERIC policy, a document or journal article is not re-announced or re-entered into the database as a new accession for the purpose of accomplishing a…

Written Language and Writing Abilities: Abstracts of Doctoral Dissertations Published in "Dissertation Abstracts International," January through June 1985 (Vol. 45 Nos. 7 through 12).

ERIC Educational Resources Information Center

ERIC Clearinghouse on Reading and Communication Skills, Urbana, IL.

This collection of abstracts is part of a continuing series providing information on recent doctoral dissertations. The 16 titles deal with a variety of topics, including the following: (1) a study of the meanings of experience of ten published feminist women writers; (2) the composing activities of computer literate writers; (3) the informational…

Assessment of reporting quality of conference abstracts in sports injury prevention according to CONSORT and STROBE criteria and their subsequent publication rate as full papers.

PubMed

Yoon, Uzung; Knobloch, Karsten

2012-04-11

The preliminary results of a study are usually presented as an abstract in conference meetings. The reporting quality of those abstracts and the relationship between their study designs and full paper publication rate is unknown. We hypothesized that randomized controlled trials are more likely to be published as full papers than observational studies. 154 oral abstracts presented at the World Congress of Sports Injury Prevention 2005 Oslo and the corresponding full paper publication were identified and analysed. The main outcome measures were frequency of publication, time to publication, impact factor, CONSORT (for Consolidated Standards of Reporting Trials) score, STROBE (for Strengthening the Reporting of Observational Studies in Epidemiology) score, and minor and major inconsistencies between the abstract and the full paper publication. Overall, 76 of the 154 (49%) presented abstracts were published as full papers in a peer-reviewed journal with an impact factor of 1.946 ± 0.812. No significant difference existed between the impact factor for randomized controlled trials (2.122 ± 1.015) and observational studies (1.913 ± 0.765, p = 0.469). The full papers for the randomized controlled trials were published after an average (SD) of 17 months (± 13 months); for observational studies, the average (SD) was 12 months (± 14 months) (p = 0.323). A trend was observed in this study that a higher percentage of randomized controlled trial abstracts were published as full papers (71% vs. 47%, p = 0.078) than observational trials. The reporting quality of abstracts, published as full papers, significantly increased compared to conference abstracts both in randomized control studies ( 5.7 ± 0.7 to 7.2 ± 1.3; p = 0.018, CI -2.7 to -0.32) and in observational studies (STROBE: 8.2 ± 1.3 to 8.6 ± 1.4; p = 0.007, CI -0.63 to -0.10). All of the published abstracts had at least one minor inconsistency (title, authors, research center, outcome presentation, conclusion), while 65% had at least major inconsistencies (study objective, hypothesis, study design, primary outcome measures, sample size, statistical analysis, results, SD/CI). Comparing the results of conference and full paper; results changed in 90% vs. 68% (randomized, controlled studies versus observational studies); data were added (full paper reported more result data) in 60% vs. 30%, and deleted (full paper reported fewer result data) in 40% vs. 30%. No significant differences with respect to type of study (randomized controlled versus observational), impact factor, and time to publication existed for the likelihood that a World Congress of Sports Injury conference abstract could be published as a full paper.

Safety and Efficacy of Lacrimal Drainage System Plugs for Dry Eye Syndrome: A Report by the American Academy of Ophthalmology.

PubMed

Marcet, Marcus M; Shtein, Roni M; Bradley, Elizabeth A; Deng, Sophie X; Meyer, Dale R; Bilyk, Jurij R; Yen, Michael T; Lee, W Barry; Mawn, Louise A

2015-08-01

To review the published literature assessing the efficacy and safety of lacrimal drainage system plug insertion for dry eye in adults. Literature searches of the PubMed and Cochrane Library databases were last conducted on March 9, 2015, without date restrictions and were limited to English language abstracts. The searches retrieved 309 unique citations. The primary authors reviewed the titles and abstracts. Inclusion criteria specified reports that provided original data on plugs for the treatment of dry eyes in at least 25 patients. Fifty-three studies of potential relevance were assigned to full-text review. The 27 studies that met the inclusion criteria underwent data abstraction by the panels. Abstracted data included study characteristics, patient characteristics, plug type, insertion technique, treatment response, and safety information. All studies were observational and rated by a methodologist as level II or III evidence. The plugs included punctal, intracanalicular, and dissolving types. Fifteen studies reported metrics of improvement in dry eye symptoms, ocular-surface status, artificial tear use, contact lens comfort, and tear break-up time. Twenty-five studies included safety data. Plug placement resulted in ≥50% improvement of symptoms, improvement in ocular-surface health, reduction in artificial tear use, and improved contact lens comfort in patients with dry eye. Serious complications from plugs were infrequent. Plug loss was the most commonly reported problem with punctal plugs, occurring on average in 40% of patients. Overall, among all plug types, approximately 9% of patients experienced epiphora and 10% required removal because of irritation from the plugs. Canaliculitis was the most commonly reported problem for intracanalicular plugs and occurred in approximately 8% of patients. Other complications were reported in less than 4% of patients on average and included tearing, discomfort, pyogenic granuloma, and dacryocystitis. On the basis of level II and III evidence in these studies, plugs improve the signs and symptoms of moderate dry eye that are not improved with topical lubrication, and they are well tolerated. There are no level I studies that describe the efficacy or safety of lacrimal drainage system plugs. Copyright © 2015 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Extraction of Pharmacokinetic Evidence of Drug–Drug Interactions from the Literature

PubMed Central

Kolchinsky, Artemy; Lourenço, Anália; Wu, Heng-Yi; Li, Lang; Rocha, Luis M.

2015-01-01

Drug-drug interaction (DDI) is a major cause of morbidity and mortality and a subject of intense scientific interest. Biomedical literature mining can aid DDI research by extracting evidence for large numbers of potential interactions from published literature and clinical databases. Though DDI is investigated in domains ranging in scale from intracellular biochemistry to human populations, literature mining has not been used to extract specific types of experimental evidence, which are reported differently for distinct experimental goals. We focus on pharmacokinetic evidence for DDI, essential for identifying causal mechanisms of putative interactions and as input for further pharmacological and pharmacoepidemiology investigations. We used manually curated corpora of PubMed abstracts and annotated sentences to evaluate the efficacy of literature mining on two tasks: first, identifying PubMed abstracts containing pharmacokinetic evidence of DDIs; second, extracting sentences containing such evidence from abstracts. We implemented a text mining pipeline and evaluated it using several linear classifiers and a variety of feature transforms. The most important textual features in the abstract and sentence classification tasks were analyzed. We also investigated the performance benefits of using features derived from PubMed metadata fields, various publicly available named entity recognizers, and pharmacokinetic dictionaries. Several classifiers performed very well in distinguishing relevant and irrelevant abstracts (reaching F1≈0.93, MCC≈0.74, iAUC≈0.99) and sentences (F1≈0.76, MCC≈0.65, iAUC≈0.83). We found that word bigram features were important for achieving optimal classifier performance and that features derived from Medical Subject Headings (MeSH) terms significantly improved abstract classification. We also found that some drug-related named entity recognition tools and dictionaries led to slight but significant improvements, especially in classification of evidence sentences. Based on our thorough analysis of classifiers and feature transforms and the high classification performance achieved, we demonstrate that literature mining can aid DDI discovery by supporting automatic extraction of specific types of experimental evidence. PMID:25961290

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.

16 CFR § 1102.28 - Publication of reports of harm.

Code of Federal Regulations, 2013 CFR

2013-01-01

... REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102.28... publish reports of harm that meet the requirements for publication in the Database. The Commission will... Commission may publish a report of harm that meets the requirements of § 1102.10(d) in the Database beyond...

What is an evidence map? A systematic review of published evidence maps and their definitions, methods, and products.

PubMed

Miake-Lye, Isomi M; Hempel, Susanne; Shanman, Roberta; Shekelle, Paul G

2016-02-10

The need for systematic methods for reviewing evidence is continuously increasing. Evidence mapping is one emerging method. There are no authoritative recommendations for what constitutes an evidence map or what methods should be used, and anecdotal evidence suggests heterogeneity in both. Our objectives are to identify published evidence maps and to compare and contrast the presented definitions of evidence mapping, the domains used to classify data in evidence maps, and the form the evidence map takes. We conducted a systematic review of publications that presented results with a process termed "evidence mapping" or included a figure called an "evidence map." We identified publications from searches of ten databases through 8/21/2015, reference mining, and consulting topic experts. We abstracted the research question, the unit of analysis, the search methods and search period covered, and the country of origin. Data were narratively synthesized. Thirty-nine publications met inclusion criteria. Published evidence maps varied in their definition and the form of the evidence map. Of the 31 definitions provided, 67 % described the purpose as identification of gaps and 58 % referenced a stakeholder engagement process or user-friendly product. All evidence maps explicitly used a systematic approach to evidence synthesis. Twenty-six publications referred to a figure or table explicitly called an "evidence map," eight referred to an online database as the evidence map, and five stated they used a mapping methodology but did not present a visual depiction of the evidence. The principal conclusion of our evaluation of studies that call themselves "evidence maps" is that the implied definition of what constitutes an evidence map is a systematic search of a broad field to identify gaps in knowledge and/or future research needs that presents results in a user-friendly format, often a visual figure or graph, or a searchable database. Foundational work is needed to better standardize the methods and products of an evidence map so that researchers and policymakers will know what to expect of this new type of evidence review. Although an a priori protocol was developed, no registration was completed; this review did not fit the PROSPERO format.

Publication patterns of oral and poster presentations at the annual meetings of the Congress of Neurological Surgeons and the American Association of Neurological Surgeons.

PubMed

Patel, Akash J; Cherian, Jacob; Fox, Benjamin D; Whitehead, William E; Curry, Daniel J; Luerssen, Thomas G; Jea, Andrew

2011-12-01

National and international meetings, such as the Congress of Neurological Surgeons (CNS) and the American Association of Neurological Surgeons (AANS) meetings, provide a central location for the gathering and dissemination of research. The purpose of this study was to determine the publication rates of both oral and poster presentations at CNS and AANS meetings in peer-reviewed journals. The authors reviewed all accepted abstracts, presented as either oral or poster presentations, at the CNS and AANS meetings from 2003 to 2005. This information was then used to search PubMed to determine the rate of publication of the abstracts presented at the meetings. Abstracts were considered published if the data presented at the meeting was identical to that in the publication. The overall publication rate was 32.48% (1243 of 3827 abstracts). On average, 41.28% of oral presentations and 29.03% of poster presentations were eventually published. Of those studies eventually published, 98.71% were published within 5 years of presentation at the meeting. Published abstracts were published most frequently in the Journal of Neurosurgery and Neurosurgery. Approximately one-third of all presentations at the annual CNS and AANS meetings will be published in peer-reviewed, MEDLINE-indexed journals. These meetings are excellent forums for neurosurgical practitioners to be exposed to current research. Oral presentations have a significantly higher rate of eventual publication compared with poster presentations, reflecting their higher quality. The Journal of Neurosurgery and Neurosurgery have been the main outlets of neurosurgical research from these meetings.

TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data

PubMed Central

Liu, Wanting; Xiang, Lunping; Zheng, Tingkai; Jin, Jingjie

2018-01-01

Abstract Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translatomedb.net/) which provides collection and integrated analysis of published and user-generated translatome sequencing data. The current version includes 2453 Ribo-seq, 10 RNC-seq and their 1394 corresponding mRNA-seq datasets in 13 species. The database emphasizes the analysis functions in addition to the dataset collections. Differential gene expression (DGE) analysis can be performed between any two datasets of same species and type, both on transcriptome and translatome levels. The translation indices translation ratios, elongation velocity index and translational efficiency can be calculated to quantitatively evaluate translational initiation efficiency and elongation velocity, respectively. All datasets were analyzed using a unified, robust, accurate and experimentally-verifiable pipeline based on the FANSe3 mapping algorithm and edgeR for DGE analyzes. TranslatomeDB also allows users to upload their own datasets and utilize the identical unified pipeline to analyze their data. We believe that our TranslatomeDB is a comprehensive platform and knowledgebase on translatome and proteome research, releasing the biologists from complex searching, analyzing and comparing huge sequencing data without needing local computational power. PMID:29106630

DDMGD: the database of text-mined associations between genes methylated in diseases from different species.

PubMed

Bin Raies, Arwa; Mansour, Hicham; Incitti, Roberto; Bajic, Vladimir B

2015-01-01

Gathering information about associations between methylated genes and diseases is important for diseases diagnosis and treatment decisions. Recent advancements in epigenetics research allow for large-scale discoveries of associations of genes methylated in diseases in different species. Searching manually for such information is not easy, as it is scattered across a large number of electronic publications and repositories. Therefore, we developed DDMGD database (http://www.cbrc.kaust.edu.sa/ddmgd/) to provide a comprehensive repository of information related to genes methylated in diseases that can be found through text mining. DDMGD's scope is not limited to a particular group of genes, diseases or species. Using the text mining system DEMGD we developed earlier and additional post-processing, we extracted associations of genes methylated in different diseases from PubMed Central articles and PubMed abstracts. The accuracy of extracted associations is 82% as estimated on 2500 hand-curated entries. DDMGD provides a user-friendly interface facilitating retrieval of these associations ranked according to confidence scores. Submission of new associations to DDMGD is provided. A comparison analysis of DDMGD with several other databases focused on genes methylated in diseases shows that DDMGD is comprehensive and includes most of the recent information on genes methylated in diseases. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology

PubMed Central

Yue, Zongliang; Zheng, Qi; Neylon, Michael T; Yoo, Minjae; Shin, Jimin; Zhao, Zhiying; Tan, Aik Choon

2018-01-01

Abstract Integrative Gene-set, Network and Pathway Analysis (GNPA) is a powerful data analysis approach developed to help interpret high-throughput omics data. In PAGER 1.0, we demonstrated that researchers can gain unbiased and reproducible biological insights with the introduction of PAGs (Pathways, Annotated-lists and Gene-signatures) as the basic data representation elements. In PAGER 2.0, we improve the utility of integrative GNPA by significantly expanding the coverage of PAGs and PAG-to-PAG relationships in the database, defining a new metric to quantify PAG data qualities, and developing new software features to simplify online integrative GNPA. Specifically, we included 84 282 PAGs spanning 24 different data sources that cover human diseases, published gene-expression signatures, drug–gene, miRNA–gene interactions, pathways and tissue-specific gene expressions. We introduced a new normalized Cohesion Coefficient (nCoCo) score to assess the biological relevance of genes inside a PAG, and RP-score to rank genes and assign gene-specific weights inside a PAG. The companion web interface contains numerous features to help users query and navigate the database content. The database content can be freely downloaded and is compatible with third-party Gene Set Enrichment Analysis tools. We expect PAGER 2.0 to become a major resource in integrative GNPA. PAGER 2.0 is available at http://discovery.informatics.uab.edu/PAGER/. PMID:29126216

Patient safety and systematic reviews: finding papers indexed in MEDLINE, EMBASE and CINAHL.

PubMed

Tanon, A A; Champagne, F; Contandriopoulos, A-P; Pomey, M-P; Vadeboncoeur, A; Nguyen, H

2010-10-01

To develop search strategies for identifying papers on patient safety in MEDLINE, EMBASE and CINAHL. Six journals were electronically searched for papers on patient safety published between 2000 and 2006. Identified papers were divided into two gold standards: one to build and the other to validate the search strategies. Candidate terms for strategy construction were identified using a word frequency analysis of titles, abstracts and keywords used to index the papers in the databases. Searches were run for each one of the selected terms independently in every database. Sensitivity, precision and specificity were calculated for each candidate term. Terms with sensitivity greater than 10% were combined to form the final strategies. The search strategies developed were run against the validation gold standard to assess their performance. A final step in the validation process was to compare the performance of each strategy to those of other strategies found in the literature. We developed strategies for all three databases that were highly sensitive (range 95%-100%), precise (range 40%-60%) and balanced (the product of sensitivity and precision being in the range of 30%-40%). The strategies were very specific and outperformed those found in the literature. The strategies we developed can meet the needs of users aiming to maximise either sensitivity or precision, or seeking a reasonable compromise between sensitivity and precision, when searching for papers on patient safety in MEDLINE, EMBASE or CINAHL.

Criteria for use of composite end points for competing risks-a systematic survey of the literature with recommendations.

PubMed

Manja, Veena; AlBashir, Siwar; Guyatt, Gordon

2017-02-01

Composite end points are frequently used in reports of clinical trials. One rationale for the use of composite end points is to account for competing risks. In the presence of competing risks, the event rate of a specific event depends on the rates of other competing events. One proposed solution is to include all important competing events in one composite end point. Clinical trialists require guidance regarding when this approach is appropriate. To identify publications describing criteria for use of composite end points for competing risk and to offer guidance regarding when a composite end point is appropriate on the basis of competing risks. We searched MEDLINE, CINAHL, EMBASE, The Cochrane's Central & Systematic Review databases including the Health Technology Assessment database, and the Cochrane's Methodology register from inception to April 2015, and candidate textbooks, to identify all articles providing guidance on this issue. Eligible publications explicitly addressed the issue of a composite outcome to address competing risks. Two reviewers independently screened the titles and abstracts for full-text review; independently reviewed full-text publications; and abstracted specific criteria authors offered for use of composite end points to address competing risks. Of 63,645 titles and abstracts, 166 proved potentially relevant of which 43 publications were included in the final review. Most publications note competing risks as a reason for using composite end points without further elaboration. None of the articles or textbook chapters provide specific criteria for use of composite end points for competing risk. Some advocate using composite end points to avoid bias due to competing risks and others suggest that composite end points seldom or never be used for this purpose. We recommend using composite end points for competing risks only if the competing risk is plausible and if it occurs with sufficiently high frequency to influence the interpretation of the effect of intervention on the end point of interest. These criteria will seldom be met. Review of heart failure trials published in the New England Journal of Medicine revealed that many of them use the composite end point of death or hospitalization; none of the trials, however, satisfied our criteria. The existing literature fails to provide clear guidance regarding use of composite end point for competing risks. We recommend using composite end points for competing risks only if the competing risk is plausible and if it occurs sufficiently often. Published by Elsevier Inc.

The Hidden Dimensions of Databases.

ERIC Educational Resources Information Center

Jacso, Peter

1994-01-01

Discusses methods of evaluating commercial online databases and provides examples that illustrate their hidden dimensions. Topics addressed include size, including the number of records or the number of titles; the number of years covered; and the frequency of updates. Comparisons of Readers' Guide Abstracts and Magazine Article Summaries are…

Body of Knowledge: Tomorrow's Research Agenda.

ERIC Educational Resources Information Center

VanLeuven, James K.

1990-01-01

Reviews the history of the Public Relations Body of Knowledge Abstracts, a database of public relations research and literature. Describes the uses of the abstracts for research purposes, and reports assessments of new research directions as set forth by members of the Public Relations Society of America's permanent Body of Knowledge Board. (MM)

CONSTRUCTING KNOWLEDGE FROM MULTIVARIATE SPATIOTEMPORAL DATA: INTEGRATING GEOGRAPHIC VISUALIZATION WITH KNOWLEDGE DISCOVERY IN DATABASE METHODS. (R825195)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases.

PubMed

Costa, Marta; Manton, James D; Ostrovsky, Aaron D; Prohaska, Steffen; Jefferis, Gregory S X E

2016-07-20

Neural circuit mapping is generating datasets of tens of thousands of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches. We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1,052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types, including searching neurons against transgene expression patterns. Finally, we show that NBLAST is effective with data from other invertebrates and zebrafish. VIDEO ABSTRACT. Copyright © 2016 MRC Laboratory of Molecular Biology. Published by Elsevier Inc. All rights reserved.

Update in Outpatient General Internal Medicine: Practice-Changing Evidence Published in 2017.

PubMed

Wieland, Mark L; Szostek, Jason H; Wingo, Majken T; Post, Jason A; Mauck, Karen F

2018-02-26

Clinicians are challenged to identify new practice-changing articles in the medical literature. To identify the practice-changing articles published in 2017 most relevant to outpatient general internal medicine, 5 internists reviewed the following sources: 1) titles and abstracts from internal medicine journals with the 7 highest impact factors, including New England Journal of Medicine, Lancet, Journal of the American Medical Association, British Medical Journal, Public Library of Science Medicine, Annals of Internal Medicine, and JAMA Internal Medicine; 2) synopses and syntheses of individual studies, including collections in the American College of Physicians Journal Club, Journal Watch, and Evidence-Based Medicine; 3) databases of synthesis, including Evidence Updates and the Cochrane Library. Inclusion criteria were perceived clinical relevance to outpatient general medicine, potential for practice change, and strength of evidence. This process yielded 140 articles. Clusters of important articles around one topic were considered as a single-candidate series. A modified Delphi method was utilized by the 5 authors to reach consensus on 7 topics to highlight and appraise from the 2017 literature. Copyright © 2018 Elsevier Inc. All rights reserved.

Febuxostat for the treatment of gout.

PubMed

Bridgeman, Mary Barna; Chavez, Benjamin

2015-02-01

Gout is a rheumatologic condition associated with elevated serum uric acid levels and deposition of monosodium urate crystals in joints and soft tissues. The xanthine oxidase inhibitor, allopurinol, has historically been the principle agent utilized for reducing elevated uric acid levels and treating underlying cause of gout symptoms; the availability of febuxostat, a newer non-purine selective xanthine oxidase inhibitor, represents an alternative therapy for those patients with contraindications or intolerance to allopurinol. This article reviews the published literature on the pharmacologic characteristics and clinical safety and efficacy data on the use of febuxostat in the treatment of gout. A literature search of MEDLINE and MEDLINE In-Process & Other Non-Indexed Citations Databases (1996-November 2014) was conducted utilizing the key words 'febuxostat', 'allopurinol', and 'gout'. All published articles regarding febuxostat were evaluated. References of selected articles, data from poster presentations, and abstract publications were additionally reviewed. Febuxostat has shown benefit with respect to symptomatic relief and uric acid level reduction. The safety profile of this agent makes it an ideal alternative in those patients with contraindications to or who are intolerant of allopurinol.

A systematic review of microfinance and women's health literature: Directions for future research.

PubMed

O'Malley, T L; Burke, J G

2017-11-01

While growing evidence suggests that microfinance is an effective approach for improved women's health, a significant gap remains in our understanding. The objective of this review is to synthesise the findings from published literature focused on microfinance and health issues particularly affecting women, including HIV/AIDS, reproductive health, mental health, and violence. Forty-one articles that examine the impact of microfinance participation on women's health were identified through a systematic search of electronic databases, coded using a structured abstraction form, and synthesised. Review results indicate that the impact of microfinance on women's health is an area in great need of research and publication attention. Varied quality and reporting in the identified articles restricted the ability to draw concrete conclusions regarding the relationship between microfinance participation and women's health, but led to the identification of current gaps in existing published research. Future research should work to address the recommendations provided in order to offer additional evidence to better understand the use of microfinance programming as a structural intervention to improve women's health.

Novel citation-based search method for scientific literature: application to meta-analyses.

PubMed

Janssens, A Cecile J W; Gwinn, M

2015-10-13

Finding eligible studies for meta-analysis and systematic reviews relies on keyword-based searching as the gold standard, despite its inefficiency. Searching based on direct citations is not sufficiently comprehensive. We propose a novel strategy that ranks articles on their degree of co-citation with one or more "known" articles before reviewing their eligibility. In two independent studies, we aimed to reproduce the results of literature searches for sets of published meta-analyses (n = 10 and n = 42). For each meta-analysis, we extracted co-citations for the randomly selected 'known' articles from the Web of Science database, counted their frequencies and screened all articles with a score above a selection threshold. In the second study, we extended the method by retrieving direct citations for all selected articles. In the first study, we retrieved 82% of the studies included in the meta-analyses while screening only 11% as many articles as were screened for the original publications. Articles that we missed were published in non-English languages, published before 1975, published very recently, or available only as conference abstracts. In the second study, we retrieved 79% of included studies while screening half the original number of articles. Citation searching appears to be an efficient and reasonably accurate method for finding articles similar to one or more articles of interest for meta-analysis and reviews.

Web of Science use in published research and review papers 1997-2017: a selective, dynamic, cross-domain, content-based analysis.

PubMed

Li, Kai; Rollins, Jason; Yan, Erjia

2018-01-01

Clarivate Analytics's Web of Science (WoS) is the world's leading scientific citation search and analytical information platform. It is used as both a research tool supporting a broad array of scientific tasks across diverse knowledge domains as well as a dataset for large-scale data-intensive studies. WoS has been used in thousands of published academic studies over the past 20 years. It is also the most enduring commercial legacy of Eugene Garfield. Despite the central position WoS holds in contemporary research, the quantitative impact of WoS has not been previously examined by rigorous scientific studies. To better understand how this key piece of Eugene Garfield's heritage has contributed to science, we investigated the ways in which WoS (and associated products and features) is mentioned in a sample of 19,478 English-language research and review papers published between 1997 and 2017, as indexed in WoS databases. We offered descriptive analyses of the distribution of the papers across countries, institutions and knowledge domains. We also used natural language processingtechniques to identify the verbs and nouns in the abstracts of these papers that are grammatically connected to WoS-related phrases. This is the first study to empirically investigate the documentation of the use of the WoS platform in published academic papers in both scientometric and linguistic terms.

Gene annotation from scientific literature using mappings between keyword systems.

PubMed

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

2004-09-01

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

StemTextSearch: Stem cell gene database with evidence from abstracts.

PubMed

Chen, Chou-Cheng; Ho, Chung-Liang

2017-05-01

Previous studies have used many methods to find biomarkers in stem cells, including text mining, experimental data and image storage. However, no text-mining methods have yet been developed which can identify whether a gene plays a positive or negative role in stem cells. StemTextSearch identifies the role of a gene in stem cells by using a text-mining method to find combinations of gene regulation, stem-cell regulation and cell processes in the same sentences of biomedical abstracts. The dataset includes 5797 genes, with 1534 genes having positive roles in stem cells, 1335 genes having negative roles, 1654 genes with both positive and negative roles, and 1274 with an uncertain role. The precision of gene role in StemTextSearch is 0.66, and the recall is 0.78. StemTextSearch is a web-based engine with queries that specify (i) gene, (ii) category of stem cell, (iii) gene role, (iv) gene regulation, (v) cell process, (vi) stem-cell regulation, and (vii) species. StemTextSearch is available through http://bio.yungyun.com.tw/StemTextSearch.aspx. Copyright © 2017. Published by Elsevier Inc.

Designing for sustainability: ergonomics--carpe diem.

PubMed

Martin, K; Legg, S; Brown, C

2013-01-01

Sustainability is a global issue that has worldwide attention but the role of ergonomics in designing for sustainability is poorly understood and seldom considered. An analysis of the literature on ergonomics, design and sustainability was conducted via a search of electronic databases: Scopus, Business Source Complete, Google Scholar, Emerald Publishing, Academic Search Premiere, Web of Science, Discover and Ergonomics Abstracts, for the years 1995-2012. A total of 1934 articles fulfilled the search criteria, but content analysis of the abstracts indicated that only 14 refereed articles addressed the main search criteria. Of those seven were in ergonomics journals and seven were in other journals (and were not written by ergonomists). It is concluded that the contribution of ergonomics to sustainability and sustainable design has been limited, even though the goals of sustainability and ergonomics are congruent. Ergonomists have not been at the forefront of research contributing to sustainability - and it is time for them to 'seize the day' - 'carpe diem'. This literature review shows that ergonomics contribution to sustainability is limited but since there is congruence between the disciplines it calls for ergonomists to become more involved and to seize the day - carpe diem.

The Fate of Abstracts Presented at the 2013 and 2014 Annual Meetings of the Romanian Society of Gastroenterology and Hepatology.

PubMed

Trifan, Anca; Chihaia, Catalin-Alexandru; Tanase, Oana; Lungu, Cristina-Maria; Stanciu, Carol

2016-12-01

Oral and poster presentations at annual national meetings of the Romanian Society of Gastroenterology and Hepatology (RSGH) provide a forum for education, communication and discussion of new research. However, for the wide-spread dissemination of the new research work, each presentation should be subsequently published as a full-text article in peer-reviewed, indexed journals. to evaluate the publication rate of full-text articles in peer-reviewed journals after being first presented as abstracts at two consecutive RSGH annual meetings. A retrospective review of all abstracts presented at the annual meetings in 2013 and 2014 was performed. PubMed and Google Scholar were searched using abstract titles, first author's name and affiliation, and key words from the title to identify whether an abstract resulted in a peer-reviewed publication. Abstracts published in full-text were subsequently assessed for study type, study center, topics, publication year, journals and their impact factors (IFs). We chose the 2013 and 2014 meetings to ensure a minimum two-year follow-up period since the last meeting for the publication as full-length articles. A total of 562 abstracts were presented (275 in 2013, 287 in 2014). There were 150 oral presentations (93 in 2013, 57 in 2014) and 412 poster presentations (182 in 2013, 230 in 2014). Fifty seven of them (10.1%) were published as full-text articles, among them 26 (17.3%) after oral presentations and 31 (7.5%) after poster presentations (P=0.001). University affiliation and original research work were most likely to be published. The average IFs of the journals which published the articles were 2.42 in 2013 and 1.87 in 2014. The publication rate for the annual RSGH meetings abstracts as full-text articles in peer-reviewed journals is very low compared to the analyses performed in gastroenterology or other medical specialities from other countries. It is not clear yet what are the factors responsible for the failure of publication.

Development of a General Conceptual-numerical Model to Simulate the Fate and Subsurface Transport of Explosives, and the Moisture and Temperature Signatures Around Land Mines

DTIC Science & Technology

2008-12-01

Šimůnek, J. W. Hopmans, and A. Tuli , Numerical evaluation of the heat pulse probe for simultaneous estimation of water fluxes and soil hydraulic and...America annual meeting, Agronomy Abstracts, published on a CD-ROM as abstract 132-2, ASA, Madison, 2006. Saito, H., J. Šimunek, A. Tuli and J. W...Abstracts, published on a CD-ROM as abstract 183-8, ASA, Madison, 2007. Tuli , A., T. Kamai, H. Saito, J. Hopmans, and J. Šimunek, Experimental and

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…

Biological Databases for Behavioral Neurobiology

PubMed Central

Baker, Erich J.

2014-01-01

Databases are, at their core, abstractions of data and their intentionally derived relationships. They serve as a central organizing metaphor and repository, supporting or augmenting nearly all bioinformatics. Behavioral domains provide a unique stage for contemporary databases, as research in this area spans diverse data types, locations, and data relationships. This chapter provides foundational information on the diversity and prevalence of databases, how data structures support the various needs of behavioral neuroscience analysis and interpretation. The focus is on the classes of databases, data curation, and advanced applications in bioinformatics using examples largely drawn from research efforts in behavioral neuroscience. PMID:23195119

Improving publication rates in a collaborative clinical trials research network.

PubMed

Archer, Stephanie Wilson; Carlo, Waldemar A; Truog, William E; Stevenson, David K; Van Meurs, Krisa P; Sánchez, Pablo J; Das, Abhik; Devaskar, Uday; Nelin, Leif D; Petrie Huitema, Carolyn M; Crawford, Margaret M; Higgins, Rosemary D

2016-10-01

Unpublished results can bias biomedical literature, favoring positive over negative findings, primary over secondary analyses, and can lead to duplicate studies that unnecessarily endanger subjects and waste resources. The Neonatal Research Network's (NRN) publication policies for approving, reviewing, and tracking abstracts and papers work to combat these problems. In 2003, the NRN restricted investigators with unfinished manuscripts from proposing new ones and in 2010, urged authors to complete long-outstanding manuscripts. Data from 1991 to 2015 were analyzed to determine effectiveness of these policy changes. The NRN has achieved an overall publication rate of 78% for abstracts. For 1990-2002, of 137 abstracts presented, 43 (31%) were published within 2 years; for 2003-2009, after the manuscript completion policy was instituted, of 140 abstracts presented, 68 (49%) were published within 2 years. Following the effort in 2010, the rate increased to 64%. The NRN surpassed reported rates by developing a comprehensive process, holding investigators accountable and tracking abstracts from presentation to publication. Copyright © 2016. Published by Elsevier Inc.

Epidemiology and clinical characteristics of traumatic brain injury in Lebanon

PubMed Central

Abou-Abbass, Hussein; Bahmad, Hisham; Ghandour, Hiba; Fares, Jawad; Wazzi-Mkahal, Rayyan; Yacoub, Basel; Darwish, Hala; Mondello, Stefania; Harati, Hayat; El Sayed, Mazen J.; Tamim, Hani; Kobeissy, Firas

2016-01-01

Abstract Background: Traumatic brain injury (TBI) is a debilitating medical and emerging public health problem that is affecting people worldwide due to a multitude of factors including both domestic and war-related acts. The objective of this paper is to systematically review the status of TBI in Lebanon – a Middle Eastern country with a weak health system that was chartered by several wars and intermittent outbursts of violence - in order to identify the present gaps in knowledge, direct future research initiatives and to assist policy makers in planning progressive and rehabilitative policies. Methods: OVID/Medline, PubMed, Scopus databases and Google Scholar were lastly searched on April 15th, 2016 to identify all published research studies on TBI in Lebanon. Studies published in English, Arabic or French that assessed Lebanese patients afflicted by TBI in Lebanon were warranting inclusion in this review. Case reports, reviews, biographies and abstracts were excluded. Throughout the whole review process, reviewers worked independently and in duplicate during study selection, data abstraction and methodological assessment using the Downs and Black Checklist. Results: In total, 11 studies were recognized eligible as they assessed Lebanese patients afflicted by TBI on Lebanese soils. Considerable methodological variation was found among the identified studies. All studies, except for two that evaluated domestic causes such as falls, reported TBI due to war-related injuries. Age distribution of TBI victims revealed two peaks, young adults between 18 and 40 years, and older adults aged 60 years and above, where males constituted the majority. Only three studies reported rates of mild TBI. Mortality, rehabilitation and systemic injury rates were rarely reported and so were the complications involved; infections were an exception. Conclusion: Apparently, status of TBI in Lebanon suffers from several gaps which need to be bridged through implementing more basic, epidemiological, clinical and translational research in this field in the future. PMID:27893670

Advanced light source: Compendium of user abstracts and technical reports,1993-1996

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

None, None

1997-04-01

This compendium contains abstracts written by users summarizing research completed or in progress from 1993-1996, ALS technical reports describing ongoing efforts related to improvement in machine operations and research and development projects, and information on ALS beamlines planned through 1998. Two tables of contents organize the user abstracts by beamline and by area of research, and an author index makes abstracts accessible by author and by principal investigator. Technical details for each beamline including whom to contact for additional information can be found in the beamline information section. Separate abstracts have been indexed into the database for contributions to thismore » compendium.« less

Assignment of adverse event indexing terms in randomized clinical trials involving spinal manipulative therapy: an audit of records in MEDLINE and EMBASE databases.

PubMed

Gorrell, Lindsay M; Engel, Roger M; Lystad, Reidar P; Brown, Benjamin T

2017-03-14

Reporting of adverse events in randomized clinical trials (RCTs) is encouraged by the authors of The Consolidated Standards of Reporting Trials (CONSORT) statement. With robust methodological design and adequate reporting, RCTs have the potential to provide useful evidence on the incidence of adverse events associated with spinal manipulative therapy (SMT). During a previous investigation, it became apparent that comprehensive search strategies combining text words with indexing terms was not sufficiently sensitive for retrieving records that were known to contain reports on adverse events. The aim of this analysis was to compare the proportion of articles containing data on adverse events associated with SMT that were indexed in MEDLINE and/or EMBASE and the proportion of those that included adverse event-related words in their title or abstract. A sample of 140 RCT articles previously identified as containing data on adverse events associated with SMT was used. Articles were checked to determine if: (1) they had been indexed with relevant terms describing adverse events in the MEDLINE and EMBASE databases; and (2) they mentioned adverse events (or any related terms) in the title or abstract. Of the 140 papers, 91% were MEDLINE records, 85% were EMBASE records, 81% were found in both MEDLINE and EMBASE records, and 4% were not in either database. Only 19% mentioned adverse event-related text words in the title or abstract. There was no significant difference between MEDLINE and EMBASE records in the proportion of available papers (p = 0.078). Of the 113 papers that were found in both MEDLINE and EMBASE records, only 3% had adverse event-related indexing terms assigned to them in both databases, while 81% were not assigned an adverse event-related indexing term in either database. While there was effective indexing of RCTs involving SMT in the MEDLINE and EMBASE databases, there was a failure of allocation of adverse event indexing terms in both databases. We recommend the development of standardized definitions and reporting tools for adverse events associated with SMT. Adequate reporting of adverse events associated with SMT will facilitate accurate indexing of these types of manuscripts in the databases.

Structuring osteosarcoma knowledge: an osteosarcoma-gene association database based on literature mining and manual annotation.

PubMed

Poos, Kathrin; Smida, Jan; Nathrath, Michaela; Maugg, Doris; Baumhoer, Daniel; Neumann, Anna; Korsching, Eberhard

2014-01-01

Osteosarcoma (OS) is the most common primary bone cancer exhibiting high genomic instability. This genomic instability affects multiple genes and microRNAs to a varying extent depending on patient and tumor subtype. Massive research is ongoing to identify genes including their gene products and microRNAs that correlate with disease progression and might be used as biomarkers for OS. However, the genomic complexity hampers the identification of reliable biomarkers. Up to now, clinico-pathological factors are the key determinants to guide prognosis and therapeutic treatments. Each day, new studies about OS are published and complicate the acquisition of information to support biomarker discovery and therapeutic improvements. Thus, it is necessary to provide a structured and annotated view on the current OS knowledge that is quick and easily accessible to researchers of the field. Therefore, we developed a publicly available database and Web interface that serves as resource for OS-associated genes and microRNAs. Genes and microRNAs were collected using an automated dictionary-based gene recognition procedure followed by manual review and annotation by experts of the field. In total, 911 genes and 81 microRNAs related to 1331 PubMed abstracts were collected (last update: 29 October 2013). Users can evaluate genes and microRNAs according to their potential prognostic and therapeutic impact, the experimental procedures, the sample types, the biological contexts and microRNA target gene interactions. Additionally, a pathway enrichment analysis of the collected genes highlights different aspects of OS progression. OS requires pathways commonly deregulated in cancer but also features OS-specific alterations like deregulated osteoclast differentiation. To our knowledge, this is the first effort of an OS database containing manual reviewed and annotated up-to-date OS knowledge. It might be a useful resource especially for the bone tumor research community, as specific information about genes or microRNAs is quick and easily accessible. Hence, this platform can support the ongoing OS research and biomarker discovery. Database URL: http://osteosarcoma-db.uni-muenster.de. © The Author(s) 2014. Published by Oxford University Press.

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

USGS Publications Warehouse

Granato, Gregory E.; Tessler, Steven

2001-01-01

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

A Bibliometric Analysis of U.S.-Based Research on the Behavioral Risk Factor Surveillance System

PubMed Central

Khalil, George M.; Gotway Crawford, Carol A.

2017-01-01

Background Since Alan Pritchard defined bibliometrics as “the application of statistical methods to media of communication” in 1969, bibliometric analyses have become widespread. To date, however, bibliometrics has not been used to analyze publications related to the U.S. Behavioral Risk Factor Surveillance System (BRFSS). Purpose To determine the most frequently cited BRFSS-related topical areas, institutions, and journals. Methods A search of the Web of Knowledge database in 2013 identified U.S.-published studies related to BRFSS, from its start in 1984 through 2012. Search terms were BRFSS, Behavioral Risk Factor Surveillance System, or Behavioral Risk Survey. The resulting 1,387 articles were analyzed descriptively and produced data for VOSviewer, a computer program that plotted a relevance distance–based map and clustered keywords from text in titles and abstracts. Results Topics, journals, and publishing institutions ranged widely. Most research was clustered by content area, such as cancer screening, access to care, heart health, and quality of life. The American Journal of Preventive Medicine and American Journal of Public Health published the most BRFSS-related papers (95 and 70, respectively). Conclusions Bibliometrics can help identify the most frequently published BRFSS-related topics, publishing journals, and publishing institutions. BRFSS data are widely used, particularly by CDC and academic institutions such as the University of Washington and other universities hosting top-ranked schools of public health. Bibliometric analysis and mapping provides an innovative way of quantifying and visualizing the plethora of research conducted using BRFSS data and summarizing the contribution of this surveillance system to public health. PMID:25442231

The Evaluation of Published Indexes, and Abstract Journals:, Criteria and Possible Procedures

PubMed Central

Lancaster, F. W.

1971-01-01

This paper describes possible criteria by which the effectiveness of a published index may be evaluated and suggest procedures that might be used to conduct an evaluation of a published index. The procedures were developed for the National Library of Medicine and relate specifically to the recurring bibliographies produced by MEDLARS in various specialized areas of biomedicine. The methods described should, however, be applicable to other printed indexes and abstract journals. Factors affecting the performance of a published index are also discussed and some research projects relevant to the evaluation of published indexes are reviewed. PMID:5146770

Outcome of Pediatric Critical Care Medicine Abstracts Presented at North American Academic National Meetings.

PubMed

Basu, Sonali; Pollack, Murray M

2017-05-05

Pediatric critical care medicine abstracts presented at North American national academic meetings have not been followed up to determine their publication outcomes. Our objective was to determine the following: 1) the proportion of these presentations that are published in peer-reviewed journals within 5 years; 2) the impact of trainee status on time to and success of publication; and 3) the quality of the research as reflected in the publishing journal's impact factor. Four years of abstracts (2007-2011) were reviewed from the American Academy of Pediatrics, Pediatric Academic Societies, and Society of Critical Care Medicine national meetings. Pediatric critical care medicine abstracts were delineated by the meeting or identified by keyword search. Data included mode of presentation, trainee status of first author, publication status within 5 years based on a PubMed search, trainee position in the journal of publication authorship list, and the impact factor of journal of publication. We evaluated 267 pediatric critical care medicine abstracts, 85-94 from each meeting. Overall, 41% were published, with the highest rate in Pediatric Academic Societies abstracts (54% Pediatric Academic Societies, 38% Society of Critical Care Medicine, and 33% American Academy of Pediatrics; p = 0.011). Mean time to publication was 22 (± 3) months and did not differ by conference or presentation mode. Journal first authorship was retained in 84%. Journal impact factor was highest in Society of Critical Care Medicine abstracts (3.38 Society of Critical Care Medicine, 2.64 Pediatric Academic Societies, and 1.92 American Academy of Pediatrics; p = 0.006). First author trainee status was not associated with publication rate, time to publication, and impact factor. A total of 100% of trainees but only 79% of nontrainees who published retained first authorship. Less than half of pediatric critical care medicine research abstracts presented at North American national academic meetings culminate in articles. Pediatric Academic Societies had the highest publication success rate, and Society of Critical Care Medicine abstracts were published in journals with the highest impact factors. All trainees who were first authors retained that status in the journal publications.

Warmed, humidified CO2 insufflation benefits intraoperative core temperature during laparoscopic surgery: A meta‐analysis

PubMed Central

Dean, Meara; Ramsay, Robert; Heriot, Alexander; Mackay, John; Hiscock, Richard

2016-01-01

Abstract Background Intraoperative hypothermia is linked to postoperative adverse events. The use of warmed, humidified CO2 to establish pneumoperitoneum during laparoscopy has been associated with reduced incidence of intraoperative hypothermia. However, the small number and variable quality of published studies have caused uncertainty about the potential benefit of this therapy. This meta‐analysis was conducted to specifically evaluate the effects of warmed, humidified CO2 during laparoscopy. Methods An electronic database search identified randomized controlled trials performed on adults who underwent laparoscopic abdominal surgery under general anesthesia with either warmed, humidified CO2 or cold, dry CO2. The main outcome measure of interest was change in intraoperative core body temperature. Results The database search identified 320 studies as potentially relevant, and of these, 13 met the inclusion criteria and were included in the analysis. During laparoscopic surgery, use of warmed, humidified CO2 is associated with a significant increase in intraoperative core temperature (mean temperature change, 0.3°C), when compared with cold, dry CO2 insufflation. Conclusion Warmed, humidified CO2 insufflation during laparoscopic abdominal surgery has been demonstrated to improve intraoperative maintenance of normothermia when compared with cold, dry CO2. PMID:27976517

Learning concepts of cinenurducation: an integrative review.

PubMed

Oh, Jina; Kang, Jeongae; De Gagne, Jennie C

2012-11-01

Cinenurducation is the use of films in both didactic and clinical nursing education. Although films are already used as instructional aids in nursing education, few studies have been made that demonstrate the learning concepts that can be attributed to this particular teaching strategy. The purpose of this paper is to describe the learning concepts of cinenurducation and its conceptual metaphor based on a review of literature. The databases CINAHL, MEDLINE, PsychINFO, ERIC, EBSCO, ProQuest Library Journal, and Scopus databases were searched for articles. Fifteen peer-reviewed articles were selected through title and abstract screening from "films in nursing" related articles found in internationally published articles in English from the past 20 years. Four common concepts emerged that relate to cinenurducation: (a) student-centered, (b) experiential, (c) reflective, and (d) problem-solving learning. Current literature corroborates cinenurducation as an effective teaching strategy with its learning activities in nursing education. Future studies may include instructional guides of sample films that could be practically used in various domains to teach nursing competencies, as well as in the development of evaluation criteria and standards to assess students' learning outcomes. Copyright © 2012 Elsevier Ltd. All rights reserved.

CRYSTMET—The NRCC Metals Crystallographic Data File

PubMed Central

Wood, Gordon H.; Rodgers, John R.; Gough, S. Roger; Villars, Pierre

1996-01-01

CRYSTMET is a computer-readable database of critically evaluated crystallographic data for metals (including alloys, intermetallics and minerals) accompanied by pertinent chemical, physical and bibliographic information. It currently contains about 60 000 entries and covers the literature exhaustively from 1913. Scientific editing of the abstracted entries, consisting of numerous automated and manual checks, is done to ensure consistency with related, previously published studies, to assign structure types where necessary and to help guarantee the accuracy of the data and related information. Analyses of the entries and their distribution across key journals as a function of time show interesting trends in the complexity of the compounds studied as well as in the elements they contain. Two applications of CRYSTMET are the identification of unknowns and the prediction of properties of materials. CRYSTMET is available either online or via license of a private copy from the Canadian Scientific Numeric Database Service (CAN/SND). The indexed online search and analysis system is easy and economical to use yet fast and powerful. Development of a new system is under way combining the capabilities of ORACLE with the flexibility of a modern interface based on the Netscape browsing tool. PMID:27805157

SAO/NASA ADS at SAO: ADS Abstract Service

Science.gov Websites

Service provides a gateway to the online Astronomy and Physics literature. You can navigate this content filtering options as well as visualizations. Astronomy and Astrophysics Classic Search, an legacy interface which searches the 2,311,600 records currently in the Astronomy database, including 198,834 abstracts

The Distribution of Information: The Role for Online Public Access Catalogs.

ERIC Educational Resources Information Center

Matthews, Joseph R.

1994-01-01

Describes the Online Public Access Catalog (OPAC) and the inclusion of abstracting and indexing industry databases in OPACs. Topics addressed include the implications of including abstracting and indexing tape and CD-ROM products in OPACs; the need for standards allowing library systems to communicate with dissimilar CD-ROM products; and computer,…

MetPetDB: A database for metamorphic geochemistry

NASA Astrophysics Data System (ADS)

Spear, Frank S.; Hallett, Benjamin; Pyle, Joseph M.; Adalı, Sibel; Szymanski, Boleslaw K.; Waters, Anthony; Linder, Zak; Pearce, Shawn O.; Fyffe, Matthew; Goldfarb, Dennis; Glickenhouse, Nickolas; Buletti, Heather

2009-12-01

We present a data model for the initial implementation of MetPetDB, a geochemical database specific to metamorphic rock samples. The database is designed around the concept of preservation of spatial relationships, at all scales, of chemical analyses and their textural setting. Objects in the database (samples) represent physical rock samples; each sample may contain one or more subsamples with associated geochemical and image data. Samples, subsamples, geochemical data, and images are described with attributes (some required, some optional); these attributes also serve as search delimiters. All data in the database are classified as published (i.e., archived or published data), public or private. Public and published data may be freely searched and downloaded. All private data is owned; permission to view, edit, download and otherwise manipulate private data may be granted only by the data owner; all such editing operations are recorded by the database to create a data version log. The sharing of data permissions among a group of collaborators researching a common sample is done by the sample owner through the project manager. User interaction with MetPetDB is hosted by a web-based platform based upon the Java servlet application programming interface, with the PostgreSQL relational database. The database web portal includes modules that allow the user to interact with the database: registered users may save and download public and published data, upload private data, create projects, and assign permission levels to project collaborators. An Image Viewer module provides for spatial integration of image and geochemical data. A toolkit consisting of plotting and geochemical calculation software for data analysis and a mobile application for viewing the public and published data is being developed. Future issues to address include population of the database, integration with other geochemical databases, development of the analysis toolkit, creation of data models for derivative data, and building a community-wide user base. It is believed that this and other geochemical databases will enable more productive collaborations, generate more efficient research efforts, and foster new developments in basic research in the field of solid earth geochemistry.

Is there publication bias towards brazilian articles on cancer?

PubMed Central

Loureiro, Luiz Victor Maia; Callegaro, Donato; Rocha, Altieres de Arruda; Prado, Bernard Lobato; Mutão, Taciana Sousa; Donnarumma, Carlos del Cistia; del Giglio, Auro

2013-01-01

ABSTRACT Objective: To investigate whether Brazilian articles on cancer are published in journals with an impact factor and/or repercussion (measured by the number of citations) inferior to those that come from foreign organizations. Methods: A search was carried out in PubMed for the MeSH term “neoplasm” with the limits clinical trial, affiliation of the Brazilian author(s), and interval from July 1st, 2009 to June 30, 2010. Selected for matching were non-Brazilian related articles published from three months prior to three months after the date of publication of the Brazilian study. The numbers of citations were obtained from two databases, as well as the impact factor for the journals in which the articles were published. Results: Fortythree national and 876 related international articles were identified. The Brazilian publications had a mean impact factor of 3.000 versus 3.430 of the international ones (p=0.041). There was no statistically significant difference as to the number of citations between the two groups. The affiliation of the first author with a Brazilian or foreign organization did not significantly influence the number of citations or the impact factor. Conclusion: Brazilian articles are significantly less accepted in journals with higher impact factors, although it does not compromise its repercussion on the scientific community. PMID:23579739

Epidemiology characteristics, reporting characteristics, and methodological quality of systematic reviews and meta-analyses on traditional Chinese medicine nursing interventions published in Chinese journals.

PubMed

Yang, Min; Jiang, Li; Wang, Aihong; Xu, Guihua

2017-02-01

To evaluate the epidemiological characteristics, reporting characteristics, and methodological quality of systematic reviews in the traditional Chinese medicine nursing field published in Chinese journals. The number of systematic reviews in the traditional Chinese medicine nursing field has increased, but their epidemiology, quality, and reporting characteristics have not been assessed completely. We generated an overview of reviews using a narrative approach. Four Chinese databases were searched for systematic reviews from inception to December 2015. The Preferred Reporting Items of Systematic Reviews and Meta-analyses and the Assessment of Multiple Systematic Reviews checklists were adopted to evaluate reporting and methodological quality, respectively. A total of 73 eligible systematic reviews, published from 2005 to 2015, were included. The deficiencies in reporting characteristics mainly lay in the lack of structured abstract or protocol, incomplete reporting of search strategies, study selection, and risk of bias. The deficiencies in methodological quality were reflected in the lack of a priori design and conflict of interest, incomplete literature searches, and assessment of publication bias. The quality of the evaluated reviews was unsatisfactory; attention should be paid to the improvement of reporting and methodological quality in the conduct of systematic reviews. © 2016 John Wiley & Sons Australia, Ltd.

The cost of drug development: a systematic review.

PubMed

Morgan, Steve; Grootendorst, Paul; Lexchin, Joel; Cunningham, Colleen; Greyson, Devon

2011-04-01

We aimed to systematically review and assess published estimates of the cost of developing new drugs. We sought English language research articles containing original estimates of the cost of drug development that were published from 1980 to 2009, inclusive. We searched seven databases and used citation tracing and expert referral to identify studies. We abstracted qualifying studies for information about methods, data sources, study samples, and key results. Thirteen articles were found to meet our inclusion criteria. Estimates of the cost of drug development ranged more than 9-fold, from USD$92 million cash (USD$161 million capitalized) to USD$883.6 million cash (USD$1.8 billion capitalized). Differences in methods, data sources, and time periods explain some of the variation in estimates. Lack of transparency limits many studies. Confidential information provided by unnamed companies about unspecified products forms all or part of the data underlying 10 of the 13 studies. Despite three decades of research in this area, no published estimate of the cost of developing a drug can be considered a gold standard. Studies on this topic should be subjected to reasonable audit and disclosure of - at the very least - the drugs which authors purport to provide development cost estimates for. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

2008 Niday Perinatal Database quality audit: report of a quality assurance project.

PubMed

Dunn, S; Bottomley, J; Ali, A; Walker, M

2011-12-01

This quality assurance project was designed to determine the reliability, completeness and comprehensiveness of the data entered into Niday Perinatal Database. Quality of the data was measured by comparing data re-abstracted from the patient record to the original data entered into the Niday Perinatal Database. A representative sample of hospitals in Ontario was selected and a random sample of 100 linked mother and newborn charts were audited for each site. A subset of 33 variables (representing 96 data fields) from the Niday dataset was chosen for re-abstraction. Of the data fields for which Cohen's kappa statistic or intraclass correlation coefficient (ICC) was calculated, 44% showed substantial or almost perfect agreement (beyond chance). However, about 17% showed less than 95% agreement and a kappa or ICC value of less than 60% indicating only slight, fair or moderate agreement (beyond chance). Recommendations to improve the quality of these data fields are presented.

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

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

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

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

Letter to the editor regarding “The role of age-sex interaction in the development of post-herpetic neuralgia”

PubMed Central

López-Lacort, Mónica; Orrico-Sánchez, Alejandro; Díez-Domingo, Javier

2018-01-01

ABSTRACT The objective of the study was to evaluate the role of age and sex and their combined effect in the development of post-herpetic neuralgia (PHN) in a large population-based study, in order to confirm the results published previously by Amicizia et al. Data were extracted from population and healthcare databases from the Valencia Region (2009–2014). Logistic regressions were implemented to estimate the effect of increasing age on the probability of developing PHN stratified by sex. From a cohort of 2,289,485 subjects ≥ 50 years, 87,086 cases of HZ were registered and 13,658 (15.7%) of them developed PHN. In our population, PHN cases were more common in women and rose with increasing age independently of the sex. PMID:29244612

HIV Structural Database using Chem BLAST for all classes of AIDS inhibitors

National Institute of Standards and Technology Data Gateway

SRD 155 HIV Structural Database using Chem BLAST for all classes of AIDS inhibitors (Web, free access)   The HIV structural database (HIVSDB) is a comprehensive collection of the structures of HIV protease, both of unliganded enzyme and of its inhibitor complexes. It contains abstracts and crystallographic data such as inhibitor and protein coordinates for 248 data sets, of which only 141 are from the Protein Data Bank (PDB).

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

NASA Technical Reports Server (NTRS)

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

2017-01-01

Introduction: For small communities in diverse fields such as astrobiology, publishing and sharing data can be a difficult challenge. While large, homogenous fields often have repositories and existing data standards, small groups of independent researchers have few options for publishing standards and data that can be utilized within their community. In conjunction with teams at NASA Ames and the University of Arizona, the Open Data Repository's (ODR) Data Publisher has been conducting ongoing pilots to assess the needs of diverse research groups and to develop software to allow them to publish and share their data collaboratively. Objectives: The ODR's Data Publisher aims to provide an easy-to-use and implement software tool that will allow researchers to create and publish database templates and related data. The end product will facilitate both human-readable interfaces (web-based with embedded images, files, and charts) and machine-readable interfaces utilizing semantic standards. Characteristics: The Data Publisher software runs on the standard LAMP (Linux, Apache, MySQL, PHP) stack to provide the widest server base available. The software is based on Symfony (www.symfony.com) which provides a robust framework for creating extensible, object-oriented software in PHP. The software interface consists of a template designer where individual or master database templates can be created. A master database template can be shared by many researchers to provide a common metadata standard that will set a compatibility standard for all derivative databases. Individual researchers can then extend their instance of the template with custom fields, file storage, or visualizations that may be unique to their studies. This allows groups to create compatible databases for data discovery and sharing purposes while still providing the flexibility needed to meet the needs of scientists in rapidly evolving areas of research. Research: As part of this effort, a number of ongoing pilot and test projects are currently in progress. The Astrobiology Habitable Environments Database Working Group is developing a shared database standard using the ODR's Data Publisher and has a number of example databases where astrobiology data are shared. Soon these databases will be integrated via the template-based standard. Work with this group helps determine what data researchers in these diverse fields need to share and archive. Additionally, this pilot helps determine what standards are viable for sharing these types of data from internally developed standards to existing open standards such as the Dublin Core (http://dublincore.org) and Darwin Core (http://rs.twdg.org) metadata standards. Further studies are ongoing with the University of Arizona Department of Geosciences where a number of mineralogy databases are being constructed within the ODR Data Publisher system. Conclusions: Through the ongoing pilots and discussions with individual researchers and small research teams, a definition of the tools desired by these groups is coming into focus. As the software development moves forward, the goal is to meet the publication and collaboration needs of these scientists in an unobtrusive and functional way.

A Review of Equation of State Models, Chemical Equilibrium Calculations and CERV Code Requirements for SHS Detonation Modelling

DTIC Science & Technology

2009-10-01

parameters for a large number of species. These authors provide many sample calculations with the JCZS database incorporated in CHEETAH 2.0, including...FORM (highest classification of Title, Abstract, Keywords) DOCUMENT CONTROL DATA (Security classification of title, body of abstract and...CLASSIFICATION OF FORM 13. ABSTRACT (a brief and factual summary of the document. It may also appear elsewhere in the body of the document itself

Alternative treatment technology information center computer database system

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

Sullivan, D.

1995-10-01

The Alternative Treatment Technology Information Center (ATTIC) computer database system was developed pursuant to the 1986 Superfund law amendments. It provides up-to-date information on innovative treatment technologies to clean up hazardous waste sites. ATTIC v2.0 provides access to several independent databases as well as a mechanism for retrieving full-text documents of key literature. It can be accessed with a personal computer and modem 24 hours a day, and there are no user fees. ATTIC provides {open_quotes}one-stop shopping{close_quotes} for information on alternative treatment options by accessing several databases: (1) treatment technology database; this contains abstracts from the literature on all typesmore » of treatment technologies, including biological, chemical, physical, and thermal methods. The best literature as viewed by experts is highlighted. (2) treatability study database; this provides performance information on technologies to remove contaminants from wastewaters and soils. It is derived from treatability studies. This database is available through ATTIC or separately as a disk that can be mailed to you. (3) underground storage tank database; this presents information on underground storage tank corrective actions, surface spills, emergency response, and remedial actions. (4) oil/chemical spill database; this provides abstracts on treatment and disposal of spilled oil and chemicals. In addition to these separate databases, ATTIC allows immediate access to other disk-based systems such as the Vendor Information System for Innovative Treatment Technologies (VISITT) and the Bioremediation in the Field Search System (BFSS). The user may download these programs to their own PC via a high-speed modem. Also via modem, users are able to download entire documents through the ATTIC system. Currently, about fifty publications are available, including Superfund Innovative Technology Evaluation (SITE) program documents.« less

Oncology trial abstracts showed suboptimal improvement in reporting: a comparative before-and-after evaluation using CONSORT for Abstract guidelines.

PubMed

Ghimire, Saurav; Kyung, Eunjung; Lee, Heeyoung; Kim, Eunyoung

2014-06-01

The aims of this study were to evaluate the quality of randomized controlled trial (RCT) abstracts published in the field of oncology and identify characteristics associated with better reporting quality. All phase III trials published during 2005-2007 [before Consolidated Standards of Reporting Trials (CONSORT)] and 2010-2012 (after CONSORT) were searched electronically in MEDLINE/PubMed and retrieved for review using an 18-point overall quality score (OQS) for reporting based on the CONSORT for Abstract guidelines. Descriptive statistics followed by multivariate linear regression were used to identify features associated with improved reporting quality. The mean OQS was 8.2 (range: 5-13; 95% confidence interval (CI): 8.0, 8.3) and 9.9 (range: 5-18; 95% CI: 9.7, 10.2) in the pre- and post-CONSORT periods, respectively. The method for random sequence generation, allocation concealment, blinding details, and funding sources were missing in pre-CONSORT abstracts and insufficiently reported (<20%) in post-CONSORT abstracts. A high impact factor (P < 0.001) and the journal of publication (P < 0.001) were independent factors that were significantly associated with higher reporting quality on multivariate analysis. The reporting quality of RCT abstracts in oncology showed suboptimal improvement over time. Thus, stricter adherence to the CONSORT for Abstract guidelines is needed to improve the reporting quality of RCT abstracts published in oncology. Copyright © 2014 Elsevier Inc. All rights reserved.

Publication rates of full-text journal articles converted from abstracts presented during the 22nd Turkish National Urology Congress

PubMed Central

Kocaaslan, Ramazan; Kayalı, Yunus; Tok, Adem; Tepeler, Abdulkadir

2016-01-01

Objective To analyze the publication rates of full-text journal articles converted from the abstracts presented in the 22nd Turkish National Urology Congress in 2012. Material and Methods A total of 576 abstracts accepted for presentation at the 22nd Turkish National Urology Association Meeting were identified from the published abstract book. The abstracts were categorized into subsections such as endourology and pediatric urology. The subsequent publication rate for the studies was evaluated by scanning PubMed Medline. Abstracts published before the proceedings were excluded from the study. Results The abstracts were categorized as being presented orally (n=155), by poster (n=421), or by video (n=78). Of the 28 (18.3%) of 155 oral and 34 (8.15%) of 421 poster presentations, were subsequently published in several journals until March 2015. The publication rates of the abstracts based on urology subsections were as follows: neurology (25%), andrology (18.6%), endourology (17.2%), urolithiasis (15.3%), general urology (12.5%), infectious diseases (7.14%), pediatric urology (6.25%), uro-gynecology (6.06%), reconstructive urology (5.8%), and urooncology (3.8%). The average time to publication was 11.77 (0–33) months. Conclusion This is the first study assessing the publication rates of abstracts presented at a Turkish National Urology Congress. It reveals that more qualified randomized studies need to be done to improve the rate of publication. PMID:27011876

Epidemiology of brucellosis in Iran: A comprehensive systematic review and meta-analysis study.

PubMed

Mirnejad, Reza; Jazi, Faramarz Masjedian; Mostafaei, Shayan; Sedighi, Mansour

2017-08-01

Brucellosis is still one of the most challenging issues for health and the economy in many developing countries such as Iran. Considering the high prevalence of brucellosis, the aim of the current study was to systematically review published data about the annual incidence rate of this infection from different parts of Iran and provide an overall relative frequency (RF) for Iran using meta-analysis. We searched several databases including PubMed, ISI Web of Science, Scopus, google scholar, IranMedex and Iranian Scientific Information Database (SID) by using the following keywords: "Brucella", "Brucellosis", "Malta fever", "Mediterranean fever", "undulant fever", "zoonosis" and "Iran" in Title/Abstract/Keywords fields. Articles/Abstracts, which used clinical specimens and reported the incidence of brucellosis, were included in this review. Quality of studies was assessed by STROB and PRISMA forms. All statistical analyses were performed using STATA 11.0 (STATA Corp, College Station, TX) and P-values under 0.05 were considered statistically significant. Out of the 8326 results, we found 34 articles suitable, according to inclusion and exlusion criteria, for inclusion in this systematic review and meta-analysis. The pooled incidence of brucellosis was estimated 0.001% (95% confidence interval (CI) = 0.0005-0.0015%) annually. Relative frequency of brucellosis in different studies varied from 7.0/100000 to 276.41/100000 in Qom and Kermanshah provinces, respectively. This systematic-review and meta-analysis study showed that the highest incidences of brucellosis are occurred in west and northwest regions of Iran. Totally, the incidence of the disease in Iran is in the high range. Copyright © 2017 Elsevier Ltd. All rights reserved.

Lost in translation: Review of identification bias, translation bias and research waste in dentistry.

PubMed

Layton, Danielle M; Clarke, Michael

2016-01-01

To review how articles are retrieved from bibliographic databases, what article identification and translation problems have affected research, and how these problems can contribute to research waste and affect clinical practice. This literature review sought and appraised articles regarding identification- and translation-bias in the medical and dental literature, which limit the ability of users to find research articles and to use these in practice. Articles can be retrieved from bibliographic databases by performing a word or index-term (for example, MeSH for MEDLINE) search. Identification of articles is challenging when it is not clear which words are most relevant, and which terms have been allocated to indexing fields. Poor reporting quality of abstracts and articles has been reported across the medical literature at large. Specifically in dentistry, research regarding time-to-event survival analyses found the allocation of MeSH terms to be inconsistent and inaccurate, important words were omitted from abstracts by authors, and the quality of reporting in the body of articles was generally poor. These shortcomings mean that articles will be difficult to identify, and difficult to understand if found. Use of specialized electronic search strategies can decrease identification bias, and use of tailored reporting guidelines can decrease translation bias. Research that cannot be found, or cannot be used results in research waste, and undermines clinical practice. Identification- and translation-bias have been shown to affect time-to-event dental articles, are likely affect other fields of research, and are largely unrecognized by authors and evidence seekers alike. By understanding that the problems exist, solutions can be sought to improve identification and translation of our research. Copyright © 2015 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Serum Uric Acid and the Risk of Incident and Recurrent Gout: A Systematic Review.

PubMed

Shiozawa, Aki; Szabo, Shelagh M; Bolzani, Anna; Cheung, Antoinette; Choi, Hyon K

2017-03-01

Lowering serum uric acid (SUA) levels can essentially cure gout; however, this is not widely practiced. To summarize epidemiologic evidence related to this causal link, we conducted a systematic review of the published literature reporting the association between SUA level and incident and recurrent gout (i.e., gout flares). We systematically searched Medline, EMBASE, and the Cochrane Database of Systematic Reviews using separate search strategies for incident gout and recurrent gout. We screened 646 abstracts to identify 8 eligible articles reporting gout incidence and 913 abstracts to identify 18 articles reporting recurrent gout. For both gout incidence and recurrence, a graded trend was observed where the risk was increased with higher SUA levels. Gout incidence rates per 1000 person-years from population-based studies ranged from 0.8 (SUA ≤ 6 mg/dl) to 70.2 cases (SUA ≥ 10 mg/dl). Recurrent gout risk in clinical cohorts ranged from 12% (SUA ≤ 6 mg/dl) to 61% (SUA ≥ 9 mg/dl) among those receiving urate-lowering therapy (ULT), and 3.7% (SUA 6-7 mg/dl) to 61% (SUA > 9.3 mg/dl) after successful ULT. Retrospective database studies also showed a graded relationship, although the strength of the association was weaker. Studies reporting mean flares or time-to-flare according to SUA showed similar findings. This systematic review confirms that higher SUA levels are associated with increased risk of incident and recurrent gout in a graded manner. Although few prospective cohorts have evaluated incident and recurrent gout according to SUA, the existing evidence underscores the need to treat to SUA targets, as recommended by the American College of Rheumatology and the European League Against Rheumatism.

Pediatric hydrocephalus: systematic literature review and evidence-based guidelines. Part 3: Endoscopic computer-assisted electromagnetic navigation and ultrasonography as technical adjuvants for shunt placement.

PubMed

Flannery, Ann Marie; Duhaime, Ann-Christine; Tamber, Mandeep S; Kemp, Joanna

2014-11-01

This systematic review was undertaken to answer the following question: Do technical adjuvants such as ventricular endoscopic placement, computer-assisted electromagnetic guidance, or ultrasound guidance improve ventricular shunt function and survival? The US National Library of Medicine PubMed/MEDLINE database and the Cochrane Database of Systematic Reviews were queried using MeSH headings and key words specifically chosen to identify published articles detailing the use of cerebrospinal fluid shunts for the treatment of pediatric hydrocephalus. Articles meeting specific criteria that had been delineated a priori were then examined, and data were abstracted and compiled in evidentiary tables. These data were then analyzed by the Pediatric Hydrocephalus Systematic Review and Evidence-Based Guidelines Task Force to consider evidence-based treatment recommendations. The search yielded 163 abstracts, which were screened for potential relevance to the application of technical adjuvants in shunt placement. Fourteen articles were selected for full-text review. One additional article was selected during a review of literature citations. Eight of these articles were included in the final recommendations concerning the use of endoscopy, ultrasonography, and electromagnetic image guidance during shunt placement, whereas the remaining articles were excluded due to poor evidence or lack of relevance. The evidence included 1 Class I, 1 Class II, and 6 Class III papers. An evidentiary table of relevant articles was created. CONCLUSIONS/RECOMMENDATION: There is insufficient evidence to recommend the use of endoscopic guidance for routine ventricular catheter placement. Level I, high degree of clinical certainty. The routine use of ultrasound-assisted catheter placement is an option. Level III, unclear clinical certainty. The routine use of computer-assisted electromagnetic (EM) navigation is an option. Level III, unclear clinical certainty.

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.

Deep Question Answering for protein annotation.

PubMed

Gobeill, Julien; Gaudinat, Arnaud; Pasche, Emilie; Vishnyakova, Dina; Gaudet, Pascale; Bairoch, Amos; Ruch, Patrick

2015-01-01

Biomedical professionals have access to a huge amount of literature, but when they use a search engine, they often have to deal with too many documents to efficiently find the appropriate information in a reasonable time. In this perspective, question-answering (QA) engines are designed to display answers, which were automatically extracted from the retrieved documents. Standard QA engines in literature process a user question, then retrieve relevant documents and finally extract some possible answers out of these documents using various named-entity recognition processes. In our study, we try to answer complex genomics questions, which can be adequately answered only using Gene Ontology (GO) concepts. Such complex answers cannot be found using state-of-the-art dictionary- and redundancy-based QA engines. We compare the effectiveness of two dictionary-based classifiers for extracting correct GO answers from a large set of 100 retrieved abstracts per question. In the same way, we also investigate the power of GOCat, a GO supervised classifier. GOCat exploits the GOA database to propose GO concepts that were annotated by curators for similar abstracts. This approach is called deep QA, as it adds an original classification step, and exploits curated biological data to infer answers, which are not explicitly mentioned in the retrieved documents. We show that for complex answers such as protein functional descriptions, the redundancy phenomenon has a limited effect. Similarly usual dictionary-based approaches are relatively ineffective. In contrast, we demonstrate how existing curated data, beyond information extraction, can be exploited by a supervised classifier, such as GOCat, to massively improve both the quantity and the quality of the answers with a +100% improvement for both recall and precision. Database URL: http://eagl.unige.ch/DeepQA4PA/. © The Author(s) 2015. Published by Oxford University Press.

Protocol for developing a Database of Zoonotic disease Research in India (DoZooRI).

PubMed

Chatterjee, Pranab; Bhaumik, Soumyadeep; Chauhan, Abhimanyu Singh; Kakkar, Manish

2017-12-10

Zoonotic and emerging infectious diseases (EIDs) represent a public health threat that has been acknowledged only recently although they have been on the rise for the past several decades. On an average, every year since the Second World War, one pathogen has emerged or re-emerged on a global scale. Low/middle-income countries such as India bear a significant burden of zoonotic and EIDs. We propose that the creation of a database of published, peer-reviewed research will open up avenues for evidence-based policymaking for targeted prevention and control of zoonoses. A large-scale systematic mapping of the published peer-reviewed research conducted in India will be undertaken. All published research will be included in the database, without any prejudice for quality screening, to broaden the scope of included studies. Structured search strategies will be developed for priority zoonotic diseases (leptospirosis, rabies, anthrax, brucellosis, cysticercosis, salmonellosis, bovine tuberculosis, Japanese encephalitis and rickettsial infections), and multiple databases will be searched for studies conducted in India. The database will be managed and hosted on a cloud-based platform called Rayyan. Individual studies will be tagged based on key preidentified parameters (disease, study design, study type, location, randomisation status and interventions, host involvement and others, as applicable). The database will incorporate already published studies, obviating the need for additional ethical clearances. The database will be made available online, and in collaboration with multisectoral teams, domains of enquiries will be identified and subsequent research questions will be raised. The database will be queried for these and resulting evidence will be analysed and published in peer-reviewed journals. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Association between race/skin color and premature birth: a systematic review with meta-analysis

PubMed Central

de Oliveira, Kelly Albuquerque; de Araújo, Edna Maria; de Oliveira, Keyte Albuquerque; Casotti, Cesar Augusto; da Silva, Carlos Alberto Lima; dos Santos, Djanilson Barbosa

2018-01-01

ABSTRACT OBJECTIVE To analyze the association between race/skin color and the occurrence of prematurity. METHODS Meta-analysis with observational studies, selected by a systematic review in the bibliographic databases Medline and Biblioteca Virtual da Saúde with the descriptors: “Race or ethnic group” and “ethnicity and health” associated with the words “infant premature” and “obstetric labor premature”. Articles published in the period from 2010 to 2014, of the observational epidemiological type, in Portuguese, English and Spanish, were included. Articles that did not have abstracts or that were review articles, theses, dissertations, and editorials were excluded. We adopted the relative risk and their respective confidence intervals (95%CI) as measures of effect, obtained through the random effect model and represented by the forest plot type graph. The Egger test and the Newcastle-Ottawa scale, respectively, were used to analyze possible publication biases and the quality of the studies. RESULTS Of the 926 articles identified, 17 were eligible for the study. Of the 17 full texts published, seven were retrospective cohort studies, nine were cross-sectional studies, and one was a case-control study. Except for one study, the others reported a positive association between race/color of skin and prematurity. Compared with full-term newborns, the relative risk of the combined effect in those born preterm was 1.51 (95%CI 1.39-1.69). The funnel chart suggested publication bias. CONCLUSIONS The present meta-analysis indicated a positive association for the risk of prematurity according to race/skin color. PMID:29641651

Electronic nicotine delivery system (electronic cigarette) awareness, use, reactions and beliefs: a systematic review

PubMed Central

Pepper, Jessica K; Brewer, Noel T

2015-01-01

Objective We sought to systematically review the literature on electronic nicotine delivery systems (ENDS, also called electronic cigarettes) awareness, use, reactions and beliefs. Data sources We searched five databases for articles published between 2006 and 1 July 2013 that contained variations of the phrases ‘electronic cigarette’, ‘e-cigarette’ and ‘electronic nicotine delivery’. Study selection Of the 244 abstracts identified, we excluded articles not published in English, articles unrelated to ENDS, dissertation abstracts and articles without original data on prespecified outcomes. Data extraction Two reviewers coded each article for ENDS awareness, use, reactions and beliefs. Data synthesis 49 studies met inclusion criteria. ENDS awareness increased from 16% to 58% from 2009 to 2011, and use increased from 1% to 6%. The majority of users were current or former smokers. Many users found ENDS satisfying, and some engaged in dual use of ENDS and other tobacco. No longitudinal studies examined whether ENDS serve as ‘gateways’ to future tobacco use. Common reasons for using ENDS were quitting smoking and using a product that is healthier than cigarettes. Self-reported survey data and prospective trials suggest that ENDS might help cigarette smokers quit, but no randomised controlled trials with probability samples compared ENDS with other cessation tools. Some individuals used ENDS to avoid smoking restrictions. Conclusions ENDS use is expanding rapidly despite experts’ concerns about safety, dual use and possible ‘gateway’ effects. More research is needed on effective public health messages, perceived health risks, validity of self-reports of smoking cessation and the use of different kinds of ENDS. PMID:24259045

The effect of Tai Chi on four chronic conditions-cancer, osteoarthritis, heart failure and chronic obstructive pulmonary disease: a systematic review and meta-analyses.

PubMed

Chen, Yi-Wen; Hunt, Michael A; Campbell, Kristin L; Peill, Kortni; Reid, W Darlene

2016-04-01

Many middle-aged and older persons have more than one chronic condition. Thus, it is important to synthesise the effectiveness of interventions across several comorbidities. The aim of this systematic review was to summarise current evidence regarding the effectiveness of Tai Chi in individuals with four common chronic conditions-cancer, osteoarthritis (OA), heart failure (HF) and chronic obstructive pulmonary disease (COPD). 4 databases (MEDLINE, EMBASE, CINAHL and SPORTDiscus) were searched for original articles. Two reviewers independently screened the titles and abstracts and then conducted full-text reviews, quality assessment and finally data abstraction. 33 studies met the inclusion criteria. Meta-analyses were performed on disease-specific symptoms, physiological outcomes and physical performance of each chronic condition. Subgroup analyses on disease-specific symptoms were conducted by categorising studies into subsets based on the type of comparison groups. Meta-analyses showed that Tai Chi improved or showed a tendency to improve physical performance outcomes, including 6-min walking distance (6MWD) and knee extensor strength, in most or all four chronic conditions. Tai Chi also improved disease-specific symptoms of pain and stiffness in OA. The results demonstrated a favourable effect or tendency of Tai Chi to improve physical performance and showed that this type of exercise could be performed by individuals with different chronic conditions, including COPD, HF and OA. 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/

Liver-related safety assessment of green tea extracts in humans: a systematic review of randomized controlled trials

PubMed Central

Isomura, T; Suzuki, S; Origasa, H; Hosono, A; Suzuki, M; Sawada, T; Terao, S; Muto, Y; Koga, T

2016-01-01

There remain liver-related safety concerns, regarding potential hepatotoxicity in humans, induced by green tea intake, despite being supposedly beneficial. Although many randomized controlled trials (RCTs) of green tea extracts have been reported in the literature, the systematic reviews published to date were only based on subjective assessment of case reports. To more objectively examine the liver-related safety of green tea intake, we conducted a systematic review of published RCTs. A systematic literature search was conducted using three databases (PubMed, EMBASE and Cochrane Central Register of Controlled Trials) in December 2013 to identify RCTs of green tea extracts. Data on liver-related adverse events, including laboratory test abnormalities, were abstracted from the identified articles. Methodological quality of RCTs was assessed. After excluding duplicates, 561 titles and abstracts and 119 full-text articles were screened, and finally 34 trials were identified. Of these, liver-related adverse events were reported in four trials; these adverse events involved seven subjects (eight events) in the green tea intervention group and one subject (one event) in the control group. The summary odds ratio, estimated using a meta-analysis method for sparse event data, for intervention compared with placebo was 2.1 (95% confidence interval: 0.5–9.8). The few events reported in both groups were elevations of liver enzymes. Most were mild, and no serious liver-related adverse events were reported. Results of this review, although not conclusive, suggest that liver-related adverse events after intake of green tea extracts are expected to be rare. PMID:27188915

Managing Heterogeneous Information Systems through Discovery and Retrieval of Generic Concepts.

ERIC Educational Resources Information Center

Srinivasan, Uma; Ngu, Anne H. H.; Gedeon, Tom

2000-01-01

Introduces a conceptual integration approach to heterogeneous databases or information systems that exploits the similarity in metalevel information and performs metadata mining on database objects to discover a set of concepts that serve as a domain abstraction and provide a conceptual layer above existing legacy systems. Presents results of…

Students' Attitudes toward ABI/INFORM on CD-ROM: A Factor Analysis.

ERIC Educational Resources Information Center

Wang, Vicky; Lau, Shuk-fong

Two years after the introduction of CD-ROM bibliographic database searching in the Memphis State University libraries (Tennessee), a survey was conducted to examine students' attitudes toward the business database, ABI/INFORM. ABI/INFORM contains indexes and abstracts of articles from over 800 journals on management, accounting, banking, human…

Annual patents review, January-December 2004

Treesearch

Roland Gleisner; Karen Scallon; Michael Fleischmann; Julie Blankenburg; Marguerite Sykes

2005-01-01

This review summarizes patents related to paper recycling that first appeared in patent databases during the 2004. Two on-line databases, Claims/U.S. Patents Abstracts and Derwent World Patents Index, were searched for this review. This feature is intended to inform readers about recent developments in equipment design, chemicals, and process technologies for recycling...

New Directions in Library and Information Science Education. Final Report. Volume 2.5: Database Producer Professional Competencies.

ERIC Educational Resources Information Center

Griffiths, Jose-Marie; And Others

This document contains validated activities and competencies needed by librarians working in a database producer organization. The activities and competencies are organized according to the functions which these librarians perform: acquisitions; thesaurus development and control; indexing/abstracting; and publications and product management.…

Database of Sources of Environmental Releases of Dioxin-Like Compounds in the United States

EPA Science Inventory

The Database of Sources of Environmental Releases of Dioxin-like Compounds in the United States (US)ARTI refrigerant database