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Sample records for pubmed medline cochrane

  1. Find Duplicates among the PubMed, EMBASE, and Cochrane Library Databases in Systematic Review

    PubMed Central

    Wang, Juan; Han, Guohong; Fan, Daiming

    2013-01-01

    Background Finding duplicates is an important phase of systematic review. However, no consensus regarding the methods to find duplicates has been provided. This study aims to describe a pragmatic strategy of combining auto- and hand-searching duplicates in systematic review and to evaluate the prevalence and characteristics of duplicates. Methods and Findings Literatures regarding portal vein thrombosis (PVT) and Budd-Chiari syndrome (BCS) were searched by the PubMed, EMBASE, and Cochrane library databases. Duplicates included one index paper and one or more redundant papers. They were divided into type-I (duplicates among different databases) and type-II (duplicate publications in different journals/issues) duplicates. For type-I duplicates, reference items were further compared between index and redundant papers. Of 10936 papers regarding PVT, 2399 and 1307 were identified as auto- and hand-searched duplicates, respectively. The prevalence of auto- and hand-searched redundant papers was 11.0% (1201/10936) and 6.1% (665/10936), respectively. They included 3431 type-I and 275 type-II duplicates. Of 11403 papers regarding BCS, 3275 and 2064 were identified as auto- and hand-searched duplicates, respectively. The prevalence of auto- and hand-searched redundant papers was 14.4% (1640/11403) and 9.1% (1039/11403), respectively. They included 5053 type-I and 286 type-II duplicates. Most of type-I duplicates were identified by auto-searching method (69.5%, 2385/3431 in PVT literatures; 64.6%, 3263/5053 in BCS literatures). Nearly all type-II duplicates were identified by hand-searching method (94.9%, 261/275 in PVT literatures; 95.8%, 274/286 in BCS literatures). Compared with those identified by auto-searching method, type-I duplicates identified by hand-searching method had a significantly higher prevalence of wrong items (47/2385 versus 498/1046, p<0.0001 in PVT literatures; 30/3263 versus 778/1790, p<0.0001 in BCS literatures). Most of wrong items originated from

  2. Technical development of PubMed Interact: an improved interface for MEDLINE/PubMed searches

    PubMed Central

    Muin, Michael; Fontelo, Paul

    2006-01-01

    Background The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results. Results PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience. Conclusion PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications. PMID:17083729

  3. Retrieval comparison of EndNote to search MEDLINE (Ovid and PubMed) versus searching them directly.

    PubMed

    Gall, Carole; Brahmi, Frances A

    2004-01-01

    Using EndNote version 7.0, the authors tested the search capabilities of the EndNote search engine for retrieving citations from MEDLINE for importation into EndNote, a citation management software package. Ovid MEDLINE and PubMed were selected for the comparison. Several searches were performed on Ovid MEDLINE and PubMed using EndNote as the search engine, and the same searches were run on both Ovid and PubMed directly. Findings indicate that it is preferable to search MEDLINE directly rather than using EndNote. The publishers of EndNote do warn its users about the limitations of their product as a search engine when searching external databases. In this article, the limitations of EndNote as a search engine for searching MEDLINE were explored as related to MeSH, non-MeSH, citation verification, and author searching. PMID:15364649

  4. PubMed Informer: Monitoring MEDLINE/PubMed through E-mail Alerts, SMS, PDA downloads and RSS feeds

    PubMed Central

    Muin, Michael; Fontelo, Paul; Ackerman, Michael

    2005-01-01

    Summary PubMed Informer is a Web-based monitoring tool for topics of interest from MEDLINE/PubMed primarily designed for healthcare professionals. Five tracking methods are available: Web access, e-mail, Short Message Service (SMS), PDA downloads and RSS feeds. PubMed Informer delivers focused search updates and specific information to users with varying information-seeking practices. PMID:16779344

  5. All Information Is Not Equal: Using the Literature Databases PubMed and The Cochrane Library for Identifying the Evidence on Granulocyte Transfusion Therapy

    PubMed Central

    Metzendorf, Maria-Inti; Schulz, Manuela; Braun, Volker

    2014-01-01

    Summary To be able to take well-informed decisions or carry out sound research, clinicians and researchers alike require specific information seeking skills matching their respective information needs. Biomedical information is traditionally available via different literature databases. This article gives an introduction to two diverging sources, PubMed (23 million references) and The Cochrane Library (800,000 references), both of which offer sophisticated instruments for searching an increasing amount of medical publications of varied quality and ambition. Whereas PubMed as an unfiltered source of primary literature comprises all different kinds of publication types occurring in academic journals, The Cochrane Library is a pre-filtered source which offers access to either synthesized publication types or critically appraised and carefully selected references. A search approach has to be carried out deliberately and requires a good knowledge on the scope and features of the databases as well as on the ability to build a search strategy in a structured way. We present a specific and a sensitive search approach, making use of both databases within two application case scenarios in order to identify the evidence on granulocyte transfusions for infections in adult patients with neutropenia. PMID:25538539

  6. PUBMED OR NLM GATEWAY

    EPA Science Inventory

    PubMed, a service of the National Library of Medicine, provides access to over 12 million MEDLINE citations back to the mid-1960's and additional life science journals. PubMed includes links to many sites providing full text articles and other related resources. PubMed was design...

  7. Metformin for endometrial hyperplasia: a Cochrane protocol

    PubMed Central

    Clement, Naomi S; Oliver, Thomas R W; Shiwani, Hunain; Saner, Juliane R F; Mulvaney, Caroline A; Atiomo, William

    2016-01-01

    Introduction Endometrial hyperplasia is a precancerous lesion of the endometrium, commonly presenting with uterine bleeding. If managed expectantly, it frequently progresses to endometrial carcinoma, rates of which are increasing dramatically worldwide. However, the established treatment for endometrial hyperplasia (progestogens) involves multiple side effects and leaves the risk of recurrence. Metformin is the most commonly used oral hypoglycaemic agent in type 2 diabetes mellitus. It has also been linked to the reversal of endometrial hyperplasia and may therefore contribute to decreasing the prevalence of endometrial carcinoma without the fertility and side effect consequences of current therapies. However, the efficacy and safety of metformin being used for this therapeutic target is unclear and, therefore, this systematic review will aim to determine this. Methods and analysis We will search the following trials and databases with no language restrictions: Cochrane Gynaecology and Fertility Specialised Register; Cochrane Central Register of Controlled Trials (CENTRAL); MEDLINE; EMBASE; EBSCO Cumulative Index to Nursing and Allied Health Literature; PubMed; Google Scholar; ClinicalTrials.gov; the WHO International Trials Registry Platform portal; OpenGrey and the Latin American and Caribbean Health Sciences Literature (LILACS). We will include randomised controlled trials (RCTs) of use of metformin compared with a placebo or no treatment, conventional medical treatment (eg, progestogens) or any other active intervention. Two review authors will independently assess the trial eligibility, risk of bias and extract appropriate data points. Trial authors will be contacted for additional data. The primary review outcome is the regression of endometrial hyperplasia histology towards normal histology. Secondary outcomes include hysterectomy rate; abnormal uterine bleeding; quality of life scores and adverse reactions to treatments. Ethics and dissemination

  8. The Cochrane tobacco addiction group.

    PubMed

    Mehta, Monaz

    2013-11-01

    The Cochrane Tobacco Addiction Group produces up-to-date systematic reviews of interventions for the cessation and prevention of tobacco use. Many of our Cochrane Reviews have also been published in scientific journals. Our review prioritization schedule is informed by our group's experience and expertise as well as identifying topics for reviews via regular searches of current scientific literature and from other news sources, such as the Action on Smoking and Health updates. The Cochrane Register of Studies allows identification of new trials, which might be eligible for review updates. Everyday challenges include timely publishing and updating of our reviews, and ensuring compliance to Cochrane methodological expectations of Cochrane intervention review standards. We are grateful for the contributions of our authors and peer reviewers, with whom we aim to have close working and productive relationships. We look forward to continuing our contribution toward a reliable evidence base on interventions to combat tobacco addiction. PMID:24325412

  9. FIRST BH COCHRANE SYMPOSIUM HELD

    PubMed Central

    Mahmic-Kaknjo, Mersiha; Novo, Ahmed; Krleza-Jeric, Karmela

    2016-01-01

    The first BH Cochrane Symposium was held on 12 October 2015 in Sarajevo, Bosnia and Herzegovina (BH), organized by the Agency for Quality and Accreditation in Healthcare in Federation of BH (AKAZ) and Medical Faculty University of Sarajevo. A group of ten national and international experts presented the Cochrane organization and systematic reviews, as well as the IMPACT Observatory, development of guidelines in BH, and the role of AKAZ. Examples of the development and use of Cochrane reviews in evidence informed decision making in health as well as research integrity were presented and discussed. Major BH decision makers and interested professionals from all over BH participated in a symposium and its lively discussion, especially from the perspective of Cochrane and its activities in BH, and the collaboration with the Croatian Cochrane. It can be expected that this symposium will inspire further growth of participation and use of Cochrane in BH and increase the awareness of various aspects of evidence informed medicine and research integrity. PMID:27047274

  10. A Study on Pubmed Search Tag Usage Pattern: Association Rule Mining of a Full-day Pubmed Query Log

    PubMed Central

    2013-01-01

    Background The practice of evidence-based medicine requires efficient biomedical literature search such as PubMed/MEDLINE. Retrieval performance relies highly on the efficient use of search field tags. The purpose of this study was to analyze PubMed log data in order to understand the usage pattern of search tags by the end user in PubMed/MEDLINE search. Methods A PubMed query log file was obtained from the National Library of Medicine containing anonymous user identification, timestamp, and query text. Inconsistent records were removed from the dataset and the search tags were extracted from the query texts. A total of 2,917,159 queries were selected for this study issued by a total of 613,061 users. The analysis of frequent co-occurrences and usage patterns of the search tags was conducted using an association mining algorithm. Results The percentage of search tag usage was low (11.38% of the total queries) and only 2.95% of queries contained two or more tags. Three out of four users used no search tag and about two-third of them issued less than four queries. Among the queries containing at least one tagged search term, the average number of search tags was almost half of the number of total search terms. Navigational search tags are more frequently used than informational search tags. While no strong association was observed between informational and navigational tags, six (out of 19) informational tags and six (out of 29) navigational tags showed strong associations in PubMed searches. Conclusions The low percentage of search tag usage implies that PubMed/MEDLINE users do not utilize the features of PubMed/MEDLINE widely or they are not aware of such features or solely depend on the high recall focused query translation by the PubMed’s Automatic Term Mapping. The users need further education and interactive search application for effective use of the search tags in order to fulfill their biomedical information needs from PubMed/MEDLINE. PMID:23302604

  11. Lida Cochran, Matriarch of Visual Literacy

    ERIC Educational Resources Information Center

    Davis, Harry

    2009-01-01

    In this article, the author describes the life and works of Lida Cochran, the matriarch of visual literacy. Lida was practicing "visual literacy" long before there was an association devoted to it. Lida has worked with the AECT, ECT Foundation (the Cochran Internship is named for her husband, Lee Cochran), and the International Visual Literacy…

  12. MEDLINE PLUS

    EPA Science Inventory

    MEDLINE plus is the National Library of Medicine's web site for consumer health information. MEDLINE plus has extensive information from the National Institutes of Health and other trusted sources on over 600 diseases and conditions. There are also lists of hospitals and physicia...

  13. Demystifying the Search Button: A Comprehensive PubMed Search Strategy for Performing an Exhaustive Literature Review.

    PubMed

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

    2015-08-01

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

  14. Teaching PubMed in cyberspace: the development of a self-learning package.

    PubMed

    King, Samuel; Kaplan, Richard; MacDonald, Kathleen

    2008-01-01

    This article discusses the development of a series of online modules for learning the PubMed version of MEDLINE. Funded by a National Library of Medicine grant and targeted initially to physician assistants practicing in New Hampshire, the project is approved for CE credit nationally by the American Association of Physician Assistants. The development of the project is described, the tutorial modules are reviewed, and issues encountered with technology and human factors are discussed and evaluated. PMID:19042708

  15. Dialogues with Marilyn Cochran-Smith

    ERIC Educational Resources Information Center

    Fiorentini, Dario; Crecci, Vanessa Moreira

    2015-01-01

    For more than 30 years, Dr. Marilyn Cochran-Smith has developed and directed research and contributed to publications about education and "practitioner research," especially about teachers' research and learning in inquiry communities. Her primary topics are inquiry communities, teacher research, teacher education for social…

  16. Cochran Q test with Turbo BASIC.

    PubMed

    Seuc, A H

    1995-01-01

    A microcomputer program written in Turbo BASIC for the sequential application of the Cochran Q test is given. A clinical application where the test is used in order to explore the structure of the agreement between observers is also presented. A program listing is available on request. PMID:7743778

  17. Acta Informatica Medica Is Indexed In Pubmed And Archived In Pubmed Central

    PubMed Central

    Masic, Izet

    2013-01-01

    Acta Informatica Medica journal has been accepted for archiving in PubMed Central from 2011 onward. The journal started in 1993 as the official journal of the Society for Medical Informatics of Bosnia and Herzegovina. During the last 3 years, Acta Informatica Medica has een included in almost all prestigious online databases, including PubMed, Scopus and EMBASE. The 20th volume of the journal is fully international, with papers from 18 countries. PMID:23572852

  18. SPELLING CORRECTION IN THE PUBMED SEARCH ENGINE.

    PubMed

    Wilbur, W John; Kim, Won; Xie, Natalie

    2006-11-01

    It is known that users of internet search engines often enter queries with misspellings in one or more search terms. Several web search engines make suggestions for correcting misspelled words, but the methods used are proprietary and unpublished to our knowledge. Here we describe the methodology we have developed to perform spelling correction for the PubMed search engine. Our approach is based on the noisy channel model for spelling correction and makes use of statistics harvested from user logs to estimate the probabilities of different types of edits that lead to misspellings. The unique problems encountered in correcting search engine queries are discussed and our solutions are outlined. PMID:18080004

  19. Criteria for evaluating alternative MEDLINE search engines.

    PubMed

    Jacobs, M; Edwards, A; Graves, R S; Johnson, E D

    1998-01-01

    With so many options available for searching MEDLINE on the World Wide Web or as a component of an online service, evaluation criteria are suggested as a means of assisting librarians in determining the positive and negative aspects of alternative MEDLINE sites. A set of searches was utilized to systematically compare MEDLINE sites. Sites evaluated included Avicenna, America Online, HealthGate, PubMed, Medscape, and Physicians' Online. Some features used to evaluate these sites were: default fields; operators (default); access to MeSH; subheadings; stop words protected in MeSH; truncation; and stemming. This article will describe the group process used to arrive at the evaluation criteria, as well as some general conclusions which will help librarians in directing their users to a particular MEDLINE site. PMID:10621384

  20. MedlinePlus: About MedlinePlus

    MedlinePlus

    ... Recognition Frequently Asked Questions (FAQs) MedlinePlus Connect for EHRs What's New Milestones MedlinePlus Use Use Statistics Visitor ... Accessibility Quality Guidelines Viewers & Players MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 ...

  1. A Cochrane systematic review finds tongue scrapers have short-term efficacy in controlling halitosis.

    PubMed

    Outhouse, Trent L; Fedorowicz, Zbigniew; Keenan, James V; Al-Alawi, Rashad

    2006-01-01

    The Cochrane systematic review promotes evidence-based outcome studies. This review was conducted to determine reliable evidence concerning the effectiveness of tongue scraping or cleaning, compared with other interventions for controlling halitosis. A competent search strategy was developed and used across several databases--including the Cochrane Oral Health Group Trials Register, the Cochrane Central Register of Controlled Trials, MEDLINE, EMBASE, and Google Scholar--to identify randomized controlled trials that compared different methods of tongue cleaning to reduce mouth odor in adults with halitosis. Methodological quality of studies was assessed based on criteria defined by the Cochrane Collaboration. Clinical outcome (expressed in terms of a reduction in mouth odor in adults with halitosis) was examined. The review included two trials involving a total of 40 participants. Based on the independent data from these two trials, the tongue cleaner or the tongue scraper demonstrated a statistically significant difference in reducing levels of volatile sulfur compounds (VSCs) when compared with the toothbrush. The findings indicate a small but statistically significant difference in reduction of VSC levels when tongue scrapers or cleaners, rather than toothbrushes, are used to reduce halitosis in adults. PMID:17004573

  2. MedlinePlus Connect

    MedlinePlus

    ... MedlinePlus Connect? MedlinePlus Connect links health IT systems, patient portals and electronic health record (EHR) systems to relevant, ... care providers when they need it via their patient portal or EHR. How does MedlinePlus Connect work? MedlinePlus ...

  3. Studying PubMed usages in the field for complex problem solving: Implications for tool design.

    PubMed

    Mirel, Barbara; Song, Jean; Tonks, Jennifer Steiner; Meng, Fan; Xuan, Weijian; Ameziane, Rafiqa

    2013-05-01

    Many recent studies on MEDLINE-based information seeking have shed light on scientists' behaviors and associated tool innovations that may improve efficiency and effectiveness. Few if any studies, however, examine scientists' problem-solving uses of PubMed in actual contexts of work and corresponding needs for better tool support. Addressing this gap, we conducted a field study of novice scientists (14 upper level undergraduate majors in molecular biology) as they engaged in a problem solving activity with PubMed in a laboratory setting. Findings reveal many common stages and patterns of information seeking across users as well as variations, especially variations in cognitive search styles. Based on findings, we suggest tool improvements that both confirm and qualify many results found in other recent studies. Our findings highlight the need to use results from context-rich studies to inform decisions in tool design about when to offer improved features to users. PMID:24376375

  4. Studying PubMed usages in the field for complex problem solving: Implications for tool design

    PubMed Central

    Song, Jean; Tonks, Jennifer Steiner; Meng, Fan; Xuan, Weijian; Ameziane, Rafiqa

    2012-01-01

    Many recent studies on MEDLINE-based information seeking have shed light on scientists’ behaviors and associated tool innovations that may improve efficiency and effectiveness. Few if any studies, however, examine scientists’ problem-solving uses of PubMed in actual contexts of work and corresponding needs for better tool support. Addressing this gap, we conducted a field study of novice scientists (14 upper level undergraduate majors in molecular biology) as they engaged in a problem solving activity with PubMed in a laboratory setting. Findings reveal many common stages and patterns of information seeking across users as well as variations, especially variations in cognitive search styles. Based on findings, we suggest tool improvements that both confirm and qualify many results found in other recent studies. Our findings highlight the need to use results from context-rich studies to inform decisions in tool design about when to offer improved features to users. PMID:24376375

  5. Feasibility of a Knowledge Translation CME Program: "Courriels Cochrane"

    ERIC Educational Resources Information Center

    Pluye, Pierre; Grad, Roland; Granikov, Vera; Theriault, Guylene; Fremont, Pierre; Burnand, Bernard; Mercer, Jay; Marlow, Bernard; Arroll, Bruce; Luconi, Francesca; Legare, France; Labrecque, Michel; Ladouceur, Roger; Bouthillier, France; Sridhar, Soumya Bindiganavile; Moscovici, Jonathan

    2012-01-01

    Introduction: Systematic literature reviews provide best evidence, but are underused by clinicians. Thus, integrating Cochrane reviews into continuing medical education (CME) is challenging. We designed a pilot CME program where summaries of Cochrane reviews ("Courriels Cochrane") were disseminated by e-mail. Program participants automatically…

  6. The Cochrane Collaboration: international activity within Cochrane Review Groups in the first decade of the twenty-first century.

    PubMed

    Allen, Claire; Richmond, Kiley

    2011-02-01

    The Cochrane Collaboration (http://www.cochrane.org) is the world's largest organisation dedicated to preparing, maintaining and promoting the accessibility of systematic reviews of the effects of healthcare interventions. It is an international organisation with participants in more than 100 countries, principally focused around the Cochrane Review Groups that are responsible for the preparation and maintenance of Cochrane reviews. Since 2000, a periodic audit has been done to count the number of active members in the Cochrane Review Groups, subdivided by the countries in which these people are based. At the beginning of 2010, there were almost 28,000 people involved, an increase from about 5500 in 2000. The growth of activity has been dramatic, and especially large for authors of Cochrane reviews and protocols. In the year 2000, 2840 people were listed as authors by the Cochrane Review Groups. At the beginning of 2010, this had risen to over 21,000 people. PMID:21342476

  7. Effectiveness of psychosocial interventions in eating disorders: an overview of Cochrane systematic reviews

    PubMed Central

    Costa, Marcelle Barrueco; Melnik, Tamara

    2016-01-01

    ABSTRACT Eating disorders are psychiatric conditions originated from and perpetuated by individual, family and sociocultural factors. The psychosocial approach to treatment and prevention of relapse is crucial. To present an overview of the scientific evidence on effectiveness of psychosocial interventions in treatment of eating disorders. All systematic reviews published by the Cochrane Database of Systematic Reviews - Cochrane Library on the topic were included. Afterwards, as from the least recent date of these reviews (2001), an additional search was conducted at PubMed with sensitive search strategy and with the same keywords used. A total of 101 primary studies and 30 systematic reviews (5 Cochrane systematic reviews), meta-analysis, guidelines or narrative reviews of literature were included. The main outcomes were: symptomatic remission, body image, cognitive distortion, psychiatric comorbidity, psychosocial functioning and patient satisfaction. The cognitive behavioral approach was the most effective treatment, especially for bulimia nervosa, binge eating disorder and the night eating syndrome. For anorexia nervosa, the family approach showed greater effectiveness. Other effective approaches were interpersonal psychotherapy, dialectic behavioral therapy, support therapy and self-help manuals. Moreover, there was an increasing number of preventive and promotional approaches that addressed individual, family and social risk factors, being promising for the development of positive self-image and self-efficacy. Further studies are required to evaluate the impact of multidisciplinary approaches on all eating disorders, as well as the cost-effectiveness of some effective modalities, such as the cognitive behavioral therapy. PMID:27462898

  8. Bibliometric and content analysis of the Cochrane Complementary Medicine Field specialized register of controlled trials

    PubMed Central

    2013-01-01

    Background The identification of eligible controlled trials for systematic reviews of complementary and alternative medicine (CAM) interventions can be difficult. To increase access to these difficult to locate trials, the Cochrane Collaboration Complementary Medicine Field (CAM Field) has established a specialized register of citations of CAM controlled trials. The objective of this study is to describe the sources and characteristics of citations included in the CAM Field specialized register. Methods Between 2006 and 2011, regular searches for citations of CAM trials in MEDLINE and the Cochrane Central Register of Controlled Trials (CENTRAL) were supplemented with contributions of controlled trial citations from international collaborators. The specialized register was ‘frozen’ for analysis in 2011, and frequencies were calculated for publication date, language, journal, presence in MEDLINE, type of intervention, and type of medical condition. Results The CAM Field specialized register increased in size from under 5,000 controlled trial citations in 2006 to 44,840 citations in 2011. Most citations (60%) were from 2000 or later, and the majority (71%) were reported in English; the next most common language was Chinese (23%). The journals with the greatest number of citations were CAM journals published in Chinese and non-CAM nutrition journals published in English. More than one-third of register citations (36%) were not indexed in MEDLINE. The most common CAM intervention type in the register was non-vitamin, non-mineral dietary supplements (e.g., glucosamine, fish oil) (34%), followed by Chinese herbal medicines (e.g., Astragalus membranaceus, Schisandra chinensis) (27%). Conclusions The availability of the CAM Field specialized register presents both opportunities and challenges for CAM systematic reviewers. While the register provides access to thousands of difficult to locate trial citations, many of these trials are of low quality and may overestimate

  9. Bosnian and Herzegovinian medical scientists in PubMed database.

    PubMed

    Masic, Izet

    2013-01-01

    In this paper it is shortly presented PubMed as one of the most important on-line databases of the scientific biomedical literature. Also, the author has analyzed the most cited authors, professors of the medical faculties in Bosnia and Herzegovina, from the published papers in the biomedical journals abstracted and indexed in PubMed. PMID:24341067

  10. Interventions to improve the appropriate use of polypharmacy in older people: a Cochrane systematic review

    PubMed Central

    Cooper, Janine A; Cadogan, Cathal A; Patterson, Susan M; Bradley, Marie C; Ryan, Cristín; Hughes, Carmel M

    2015-01-01

    Objective To summarise the findings of an updated Cochrane review of interventions aimed at improving the appropriate use of polypharmacy in older people. Design Cochrane systematic review. Multiple electronic databases were searched including MEDLINE, EMBASE and the Cochrane Central Register of Controlled Trials (from inception to November 2013). Hand searching of references was also performed. Randomised controlled trials (RCTs), controlled clinical trials, controlled before-and-after studies and interrupted time series analyses reporting on interventions targeting appropriate polypharmacy in older people in any healthcare setting were included if they used a validated measure of prescribing appropriateness. Evidence quality was assessed using the Cochrane risk of bias tool and GRADE (Grades of Recommendation, Assessment, Development and Evaluation). Setting All healthcare settings. Participants Older people (≥65 years) with ≥1 long-term condition who were receiving polypharmacy (≥4 regular medicines). Primary and secondary outcome measures Primary outcomes were the change in prevalence of appropriate polypharmacy and hospital admissions. Medication-related problems (eg, adverse drug reactions), medication adherence and quality of life were included as secondary outcomes. Results 12 studies were included: 8 RCTs, 2 cluster RCTs and 2 controlled before-and-after studies. 1 study involved computerised decision support and 11 comprised pharmaceutical care approaches across various settings. Appropriateness was measured using validated tools, including the Medication Appropriateness Index, Beers’ criteria and Screening Tool of Older Person's Prescriptions (STOPP)/ Screening Tool to Alert doctors to Right Treatment (START). The interventions demonstrated a reduction in inappropriate prescribing. Evidence of effect on hospital admissions and medication-related problems was conflicting. No differences in health-related quality of life were reported

  11. The Cochrane collaboration in neurology: acquisitions, research, and new initiatives.

    PubMed

    Tonini, C; Beghi, E; Telaro, E; Candelise, L

    2001-05-01

    The Cochrane Collaboration (CC) is an international organization involving 16 national centers around the world, set up in response to the need for collecting all randomized controlled trials on health care interventions, with the aim of facilitating and coordinating the preparation, maintenance and dissemination of periodic systematic reviews of these trials. These are prepared by Collaborative Review Groups (CRGs) working together in an area of common interest under the guidance of an editorial team, supported by national Cochrane centers. Nine CRGs are involved in each neurological field, with more than 300 reviewers and members of editorial teams. For a review to be called a 'Cochrane review', it must be structured in the format outlined in the Cochrane Handbook. It is then published and disseminated through the Cochrane Database of Systematic Reviews (CDSR) in the Cochrane Library (CL). Each Cochrane review is prepared using the Review Manager software distributed to CRGs by CC. The editorial team is responsible for assembling an edited module of reviews prepared by CRGs for incorporation and dissemination using electronic media through the CDSR located in the CL. The CL contains information about the CC and 4 other databases: the Database of Abstracts of Reviews of Effectiveness, the Cochrane Controlled Trials Register, the Cochrane Review Methodology Database and the NHS Economic Evaluation Database. The authors use an example of Cochrane reviews about cerebrovascular disorders to illustrate that the CL is a powerful source of evidence for answering clinical questions and providing information as a basis for therapeutic decisions, for the improvement of neurological practice. A new initiative, the Cochrane Neurological Network, has recently been set up with the aim of improving communication among neurological CRGs, and between them and health care professionals interested in neurological diseases so as to update neurologists on the activity of the CC. PMID

  12. MEDLINE SDI services: how do they compare?*

    PubMed Central

    Shultz, Mary; De Groote, Sandra L.

    2003-01-01

    Introduction: Selective dissemination of information (SDI) services regularly alert users to new information on their chosen topics. This type of service can increase a user's ability to keep current and may have a positive impact on efficiency and productivity. Currently, there are many venues available where users can establish, store, and automatically run MEDLINE searches. Purpose: To describe, evaluate, and compare SDI services for MEDLINE. Resources: The following SDI services were selected for this study: PubMed Cubby, BioMail, JADE, PubCrawler, OVID, and ScienceDirect. Methodology: Identical searches were established in four of the six selected SDI services and were run on a weekly basis over a period of two months. Eight search strategies were used in each system to test performance under various search conditions. The PubMed Cubby system was used as the baseline against which the other systems were compared. Other aspects were evaluated in all six services and include ease of use, frequency of results, ability to use MeSH, ability to access and edit existing search strategies, and ability to download to a bibliographic management program. Results: Not all MEDLINE SDI services retrieve identical results, even when identical search strategies are used. This study also showed that the services vary in terms of features and functions offered. PMID:14566377

  13. Systematic Differences between Cochrane and Non-Cochrane Meta-Analyses on the Same Topic: A Matched Pair Analysis

    PubMed Central

    Useem, Johanna; Brennan, Alana; LaValley, Michael; Vickery, Michelle; Ameli, Omid; Reinen, Nichole; Gill, Christopher J.

    2015-01-01

    Background Meta-analyses conducted via the Cochrane Collaboration adhere to strict methodological and reporting standards aiming to minimize bias, maximize transparency/reproducibility, and improve the accuracy of summarized data. Whether this results in differences in the results reported by meta-analyses on the same topic conducted outside the Cochrane Collaboration is an open question. Methods We conducted a matched-pair analysis with individual meta-analyses as the unit of analysis, comparing Cochrane and non-Cochrane reviews. Using meta-analyses from the cardiovascular literature, we identified pairs that matched on intervention and outcome. The pairs were contrasted in terms of how frequently results disagreed between the Cochrane and non-Cochrane reviews, whether effect sizes and statistical precision differed systematically, and how these differences related to the frequency of secondary citations of those reviews. Results Our search yielded 40 matched pairs of reviews. The two sets were similar in terms of which was first to publication, how many studies were included, and average sample sizes. The paired reviews included a total of 344 individual clinical trials: 111 (32.3%) studies were included only in a Cochrane review, 104 (30.2%) only in a non-Cochrane review, and 129 (37.5%) in both. Stated another way, 62.5% of studies were only included in one or the other meta-analytic literature. Overall, 37.5% of pairs had discrepant results. The most common involved shifts in the width of 95% confidence intervals that would yield a different statistical interpretation of the significance of results (7 pairs). Additionally, 20% differed in the direction of the summary effect size (5 pairs) or reported greater than a 2-fold difference in its magnitude (3 pairs). Non-Cochrane reviews reported significantly higher effect sizes (P< 0.001) and lower precision (P<0.001) than matched Cochrane reviews. Reviews reporting an effect size at least 2-fold greater than their

  14. Review of Cochrane Reviews on Acupuncture: How Chinese Resources Contribute to Cochrane Reviews

    PubMed Central

    Jiao, Shuang; Tsutani, Kiichiro

    2013-01-01

    Abstract Background Cochrane Systematic Reviews (CSRs) are frequently referenced by acupuncture efficacy studies currently. In this study, the CSRs on acupuncture are reviewed, and the disease fields they covered and the conclusions they reached are analyzed. In order to explore the potential contribution to CSRs by Chinese resources, the authors analyzed whether the participation of Chinese reviewers, the utilization of Chinese databases, and the inclusion of Chinese clinical trials would affect the positive conclusion ratios of the CSRs. Methods Acupuncture-related CSRs in the Cochrane Library were searched and classified based on the International Classification of Diseases-10 (ICD-10). The CSRs were further designated as positive or negative according to the conclusion statements. CSRs with the participation of Chinese reviewers, the utilization of Chinese databases, or the inclusion of Chinese clinical trials were extracted, and the positive ratios of conclusions were compared separately with corresponding CSRs without those three Chinese resources. Results Thirty-two (32) CSRs were identified, 9 (28.1%) of which reached positive conclusions. The CSRs with positive conclusions were mainly about multifarious pains, nausea and vomiting, and functional disorders. Seventeen (17; 53.1%) included the participation of Chinese reviewers, 18 (56.3%) involved the utilization of Chinese databases, and 20 (62.5%) included Chinese clinical trials. No differences on the positive conclusion ratios were observed between CSRs with reviewers from Chinese institutions and those that did not (odds ratio [OR]: 0.32, 95% confidence interval [CI]: 0.06, 1.62), the utilization of Chinese databases and those that did not (OR: 0.51, 95% CI: 0.11, 2.44), or the inclusion of Chinese clinical trials and those that did not (OR: 1.29, 95% CI: 0.26, 6.49). Conclusions Most CSRs on acupuncture are inconclusive. No significant differences regarding the positive conclusion ratios were found

  15. Automated Determination of Publications Related to Adverse Drug Reactions in PubMed

    PubMed Central

    Adams, Hayden; Friedman, Carol; Finkelstein, Joseph

    2015-01-01

    Timely dissemination of up-to-date information concerning adverse drug reactions (ADRs) at the point of care can significantly improve medication safety and prevent ADRs. Automated methods for finding relevant articles in MEDLINE which discuss ADRs for specific medications can facilitate decision making at the point of care. Previous work has focused on other types of clinical queries and on retrieval for specific ADRs or drug-ADR pairs, but little work has been published on finding ADR articles for a specific medication. We have developed a method to generate a PubMED query based on MESH, supplementary concepts, and textual terms for a particular medication. Evaluation was performed on a limited sample, resulting in a sensitivity of 90% and precision of 93%. Results demonstrated that this method is highly effective. Future work will integrate this method within an interface aimed at facilitating access to ADR information for specified drugs at the point of care. PMID:26306227

  16. Finding related sentence pairs in MEDLINE

    PubMed Central

    Wilbur, W. John

    2010-01-01

    We explore the feasibility of automatically identifying sentences in different MEDLINE abstracts that are related in meaning. We compared traditional vector space models with machine learning methods for detecting relatedness, and found that machine learning was superior. The Huber method, a variant of Support Vector Machines which minimizes the modified Huber loss function, achieves 73% precision when the score cutoff is set high enough to identify about one related sentence per abstract on average. We illustrate how an abstract viewed in PubMed might be modified to present the related sentences found in other abstracts by this automatic procedure. PMID:21170415

  17. PubMed searches: overview and strategies for clinicians.

    PubMed

    Lindsey, Wesley T; Olin, Bernie R

    2013-04-01

    PubMed is a biomedical and life sciences database maintained by a division of the National Library of Medicine known as the National Center for Biotechnology Information (NCBI). It is a large resource with more than 5600 journals indexed and greater than 22 million total citations. Searches conducted in PubMed provide references that are more specific for the intended topic compared with other popular search engines. Effective PubMed searches allow the clinician to remain current on the latest clinical trials, systematic reviews, and practice guidelines. PubMed continues to evolve by allowing users to create a customized experience through the My NCBI portal, new arrangements and options in search filters, and supporting scholarly projects through exportation of citations to reference managing software. Prepackaged search options available in the Clinical Queries feature also allow users to efficiently search for clinical literature. PubMed also provides information regarding the source journals themselves through the Journals in NCBI Databases link. This article provides an overview of the PubMed database's structure and features as well as strategies for conducting an effective search. PMID:23442731

  18. A MEDLINE feasibility study.

    PubMed Central

    McGee, J L

    1980-01-01

    A MEDLINE feasibility study was conducted with the Northeastern Consortium for Health Information (NECHI) and sponsored by the New England Regional Medical Library Service. It is based on the theory that most potential users and supporters of MEDLINE within hospitals are unaware of its usefulness and applications, and that there exists a need for expanding MEDLINE services to more hospital libraries. The purpose of the study was to provide NECHI with an evaluation of MEDLINE as a feasible service by ascertaining the need and by evaluating the usefulness, satisfaction, and costs of the system. The study demonstrated sufficient use of MEDLINE to justify implementation within NECHI and it provided useful data to determine the future of MEDLINE in each institution. It documented that utilization improved rapidly with publicity and the presence of the system within an institution, that MEDLINE can be an effective and economical complement to the traditional reference services used to support information needs in hospitals, and that more hospital libraries should be able to implement MEDLINE to their advantage once potential users and supporters have been exposed to the system. PMID:6998531

  19. MedlinePlus Tour

    MedlinePlus

    ... videos on health topics, watch surgical procedures, explore health check tools and play games. Still looking for more? You can always search MedlinePlus using the search box. Or from the homepage, you'll find ... also find the latest health news, browse the MedlinePlus Magazine, or sign up ...

  20. Videos & Tools: MedlinePlus

    MedlinePlus Videos and Cool Tools

    Skip navigation U.S. National Library of Medicine Menu Health Topics Drugs & Supplements Videos & Tools About MedlinePlus Search Search MedlinePlus GO GO About MedlinePlus Site Map FAQs Contact Us Health ...

  1. Email Updates: MedlinePlus

    MedlinePlus

    ... MedlinePlus emails from being marked as "spam" or "junk" To ensure that MedlinePlus email updates are delivered ... our emails from being marked as "spam" or "junk." About MedlinePlus Site Map FAQs Contact Us Get ...

  2. Linking to MedlinePlus

    MedlinePlus

    ... to use the MedlinePlus RSS feeds on your web site or information services. For more information on copyrighted materials on MedlinePlus, please ... Guidelines Viewers & Players MedlinePlus Connect for EHRs For Developers U.S. ...

  3. Cochrane review on screening for breast cancer with mammography.

    PubMed

    Olsen, O; Gøtzsche, P C

    2001-10-20

    In 2000, we reported that there is no reliable evidence that screening for breast cancer reduces mortality. As we discuss here, a Cochrane review has now confirmed and strengthened our previous findings. The review also shows that breast-cancer mortality is a misleading outcome measure. Finally, we use data supplemental to those in the Cochrane review to show that screening leads to more aggressive treatment. PMID:11684218

  4. GeneView: a comprehensive semantic search engine for PubMed.

    PubMed

    Thomas, Philippe; Starlinger, Johannes; Vowinkel, Alexander; Arzt, Sebastian; Leser, Ulf

    2012-07-01

    Research results are primarily published in scientific literature and curation efforts cannot keep up with the rapid growth of published literature. The plethora of knowledge remains hidden in large text repositories like MEDLINE. Consequently, life scientists have to spend a great amount of time searching for specific information. The enormous ambiguity among most names of biomedical objects such as genes, chemicals and diseases often produces too large and unspecific search results. We present GeneView, a semantic search engine for biomedical knowledge. GeneView is built upon a comprehensively annotated version of PubMed abstracts and openly available PubMed Central full texts. This semi-structured representation of biomedical texts enables a number of features extending classical search engines. For instance, users may search for entities using unique database identifiers or they may rank documents by the number of specific mentions they contain. Annotation is performed by a multitude of state-of-the-art text-mining tools for recognizing mentions from 10 entity classes and for identifying protein-protein interactions. GeneView currently contains annotations for >194 million entities from 10 classes for ∼21 million citations with 271,000 full text bodies. GeneView can be searched at http://bc3.informatik.hu-berlin.de/. PMID:22693219

  5. Gaps in affiliation indexing in Scopus and PubMed

    PubMed Central

    Schmidt, Cynthia M.; Cox, Roxanne; Fial, Alissa V.; Hartman, Teresa L.; Magee, Martha L.

    2016-01-01

    Objective The authors sought to determine whether unexpected gaps existed in Scopus's author affiliation indexing of publications written by the University of Nebraska Medical Center or Nebraska Medicine (UNMC/NM) authors during 2014. Methods First, we compared Scopus affiliation identifier search results to PubMed affiliation keyword search results. Then, we searched Scopus using affiliation keywords (UNMC, etc.) and compared the results to PubMed affiliation keyword and Scopus affiliation identifier searches. Results We found that Scopus's records for approximately 7% of UNMC/NM authors' publications lacked appropriate UNMC/NM author affiliation identifiers, and many journals' publishers were supplying incomplete author affiliation information to PubMed. Conclusions Institutions relying on Scopus to track their impact should determine whether Scopus's affiliation identifiers will, in fact, identify all articles published by their authors and investigators. PMID:27076801

  6. pubmed.mineR: an R package with text-mining algorithms to analyse PubMed abstracts.

    PubMed

    Rani, Jyoti; Shah, A B Rauf; Ramachandran, Srinivasan

    2015-10-01

    The PubMed literature database is a valuable source of information for scientific research. It is rich in biomedical literature with more than 24 million citations. Data-mining of voluminous literature is a challenging task. Although several text-mining algorithms have been developed in recent years with focus on data visualization, they have limitations such as speed, are rigid and are not available in the open source. We have developed an R package, pubmed.mineR, wherein we have combined the advantages of existing algorithms, overcome their limitations, and offer user flexibility and link with other packages in Bioconductor and the Comprehensive R Network (CRAN) in order to expand the user capabilities for executing multifaceted approaches. Three case studies are presented, namely, 'Evolving role of diabetes educators', 'Cancer risk assessment' and 'Dynamic concepts on disease and comorbidity' to illustrate the use of pubmed.mineR. The package generally runs fast with small elapsed times in regular workstations even on large corpus sizes and with compute intensive functions. The pubmed.mineR is available at http://cran.rproject. org/web/packages/pubmed.mineR. PMID:26564970

  7. MedlinePlus: Croup

    MedlinePlus

    ... GO National Institutes of Health The primary NIH organization for research on Croup is the National Institute of Child Health and Human Development Disclaimers MedlinePlus links to health information from the ...

  8. MEDLINE (MEDLARS ONLINE)

    EPA Science Inventory

    MEDLINE (MEDlars onLINE) is the National Library of Medicines (NLM) premier bibliographic database covering the fields of medicine, nursing, dentistry, veterinary medicine, the health care system, and the preclinical sciences. It contains bibliographic citations (e.g., authors, ...

  9. PubMed Central Canada: Beyond an Open Access Repository?

    ERIC Educational Resources Information Center

    Nariani, Rajiv

    2013-01-01

    PubMed Central Canada (PMC Canada) represents a partnership between the Canadian Institutes of Health Research (CIHR), the National Research Council's Canada Institute for Scientific and Technical Information (NRC-CISTI), and the National Library of Medicine of the US. The present study was done to gauge faculty awareness about the CIHR Policy on…

  10. How Complementary and Alternative Medicine Practitioners Use PubMed

    PubMed Central

    Quint-Rapoport, Mia

    2007-01-01

    Background PubMed is the largest bibliographic index in the life sciences. It is freely available online and is used by professionals and the public to learn more about medical research. While primarily intended to serve researchers, PubMed provides an array of tools and services that can help a wider readership in the location, comprehension, evaluation, and utilization of medical research. Objective This study sought to establish the potential contributions made by a range of PubMed tools and services to the use of the database by complementary and alternative medicine practitioners. Methods In this study, 10 chiropractors, 7 registered massage therapists, and a homeopath (N = 18), 11 with prior research training and 7 without, were taken through a 2-hour introductory session with PubMed. The 10 PubMed tools and services considered in this study can be divided into three functions: (1) information retrieval (Boolean Search, Limits, Related Articles, Author Links, MeSH), (2) information access (Publisher Link, LinkOut, Bookshelf ), and (3) information management (History, Send To, Email Alert). Participants were introduced to between six and 10 of these tools and services. The participants were asked to provide feedback on the value of each tool or service in terms of their information needs, which was ranked as positive, positive with emphasis, negative, or indifferent. Results The participants in this study expressed an interest in the three types of PubMed tools and services (information retrieval, access, and management), with less well-regarded tools including MeSH Database and Bookshelf. In terms of their comprehension of the research, the tools and services led the participants to reflect on their understanding as well as their critical reading and use of the research. There was universal support among the participants for greater access to complete articles, beyond the approximately 15% that are currently open access. The abstracts provided by PubMed were

  11. MedlinePlus FAQ: What's the difference between MedlinePlus and MedlinePlus Connect?

    MedlinePlus

    ... a free service that allows electronic health record (EHR) systems to easily link users to MedlinePlus, an ... a replacement to MedlinePlus. It helps users of EHRs find health information from MedlinePlus. MedlinePlus Connect accepts ...

  12. Effectiveness of psychosocial interventions in eating disorders: an overview of Cochrane systematic reviews.

    PubMed

    Costa, Marcelle Barrueco; Melnik, Tamara

    2016-01-01

    Eating disorders are psychiatric conditions originated from and perpetuated by individual, family and sociocultural factors. The psychosocial approach to treatment and prevention of relapse is crucial. To present an overview of the scientific evidence on effectiveness of psychosocial interventions in treatment of eating disorders. All systematic reviews published by the Cochrane Database of Systematic Reviews - Cochrane Library on the topic were included. Afterwards, as from the least recent date of these reviews (2001), an additional search was conducted at PubMed with sensitive search strategy and with the same keywords used. A total of 101 primary studies and 30 systematic reviews (5 Cochrane systematic reviews), meta-analysis, guidelines or narrative reviews of literature were included. The main outcomes were: symptomatic remission, body image, cognitive distortion, psychiatric comorbidity, psychosocial functioning and patient satisfaction. The cognitive behavioral approach was the most effective treatment, especially for bulimia nervosa, binge eating disorder and the night eating syndrome. For anorexia nervosa, the family approach showed greater effectiveness. Other effective approaches were interpersonal psychotherapy, dialectic behavioral therapy, support therapy and self-help manuals. Moreover, there was an increasing number of preventive and promotional approaches that addressed individual, family and social risk factors, being promising for the development of positive self-image and self-efficacy. Further studies are required to evaluate the impact of multidisciplinary approaches on all eating disorders, as well as the cost-effectiveness of some effective modalities, such as the cognitive behavioral therapy. RESUMO Transtornos alimentares são doenças psiquiátricas originadas de e perpetuadas por fatores individuais, familiares e socioculturais. A abordagem psicossocial é essencial para o tratamento e a prevenção de recaídas. Apresentar uma vis

  13. Best Available Evidence in Cochrane Reviews on Herbal Medicine?

    PubMed Central

    Davidson, Elyad; Vlachojannis, Julia; Cameron, Melainie; Chrubasik, Sigrun

    2013-01-01

    Cochrane reviews are considered by many to be the “gold standard” or the final word in medical conversation on a topic. We explored the eleven most relevant Cochrane reviews on herbal medicine and identified that frequently herbal medicines in the included studies had not been sufficiently well characterised. If data on the effects of the plant parts are unavailable, effects of co-active ingredients need to be considered and the plausibility of the study medications for the specific indications discussed. Effect sizes calculated from exploratory studies would be best used to determine the sample sizes required for future confirmatory studies, rather than as definitive reports of intervention effects. Reviews should be comprehensive, including discussion of putative adverse events and possible drug interactions. We suggest that the guidelines for preparing Cochrane reviews be revised and offer assistance in this task. PMID:23840246

  14. Risk of bias reporting in Cochrane systematic reviews.

    PubMed

    Hopp, Lisa

    2015-10-01

    Risk of bias is an inherent quality of primary research and therefore of systematic reviews. This column addresses the Cochrane Collaboration's approach to assessing, risks of bias, the meaning of each, indicators of low, high and uncertain, and ways that risk of bias can be represented in a Cochrane systematic review report. The sources of risk of bias that reviewers evaluate include selection, performance, detection, attrition and reporting bias. Each poses threat to the internal validity of the primary studies and requires the reviewer to judge the level of risk as high, low or unclear. Reviewers need to address how studies of higher risk of bias might impact the pooled effect. PMID:24621329

  15. Exploring MEDLINE Space with Random Indexing and Pathfinder Networks

    PubMed Central

    Cohen, Trevor

    2008-01-01

    The integration of disparate research domains is a prerequisite for the success of the translational science initiative. MEDLINE abstracts contain content from a broad range of disciplines, presenting an opportunity for the development of methods able to integrate the knowledge they contain. Latent Semantic Analysis (LSA) and related methods learn human-like associations between terms from unannotated text. However, their computational and memory demands limits their ability to address a corpus of this size. Furthermore, visualization methods previously used in conjunction with LSA have limited ability to define the local structure of the associative networks LSA learns. This paper explores these issues by (1) processing the entire MEDLINE corpus using Random Indexing, a variant of LSA, and (2) exploring learned associations using Pathfinder Networks. Meaningful associations are inferred from MEDLINE, including a drug-disease association undetected by PUBMED search. PMID:18999236

  16. Complex event extraction at PubMed scale

    PubMed Central

    Björne, Jari; Ginter, Filip; Pyysalo, Sampo; Tsujii, Jun'ichi; Salakoski, Tapio

    2010-01-01

    Motivation: There has recently been a notable shift in biomedical information extraction (IE) from relation models toward the more expressive event model, facilitated by the maturation of basic tools for biomedical text analysis and the availability of manually annotated resources. The event model allows detailed representation of complex natural language statements and can support a number of advanced text mining applications ranging from semantic search to pathway extraction. A recent collaborative evaluation demonstrated the potential of event extraction systems, yet there have so far been no studies of the generalization ability of the systems nor the feasibility of large-scale extraction. Results: This study considers event-based IE at PubMed scale. We introduce a system combining publicly available, state-of-the-art methods for domain parsing, named entity recognition and event extraction, and test the system on a representative 1% sample of all PubMed citations. We present the first evaluation of the generalization performance of event extraction systems to this scale and show that despite its computational complexity, event extraction from the entire PubMed is feasible. We further illustrate the value of the extraction approach through a number of analyses of the extracted information. Availability: The event detection system and extracted data are open source licensed and available at http://bionlp.utu.fi/. Contact: jari.bjorne@utu.fi PMID:20529932

  17. Avoidable Ignorance and the Role of Cochrane and Campbell Reviews

    ERIC Educational Resources Information Center

    Gambrill, Eileen

    2015-01-01

    The Campbell and Cochrane Collaborations were created to reveal the evidentiary status of claims focusing especially on the effectiveness of specific interventions. Such reviews are constrained by the population of studies available and biases that may influence this availability such as preferred framing of problems. This highlights the…

  18. Parenting Training for Intellectually Disabled Parents: A Cochrane Systematic Review

    ERIC Educational Resources Information Center

    Coren, Esther; Thomae, Manuela; Hutchfield, Jemeela

    2011-01-01

    Objectives: This article presents a Cochrane/Campbell systematic review of the evidence on the effect of parent training to support the parenting of parents with intellectual disabilities. Method: Randomized controlled trials (RCTs) comparing parent training interventions for parents with intellectual disability with usual care or with a control…

  19. MedlinePlus FAQ: Linking to MedlinePlus

    MedlinePlus

    ... need permission to link to MedlinePlus from your Web site. Please see our guidelines and instructions on linking to ... Guidelines Viewers & Players MedlinePlus Connect for EHRs For Developers U.S. ...

  20. Evidence from the Cochrane Collaboration for Traditional Chinese Medicine Therapies

    PubMed Central

    Wieland, Susan; Kimbrough, Elizabeth; Cheng, Ker; Berman, Brian M.

    2009-01-01

    Abstract Background The Cochrane Collaboration, an international not-for-profit organization that prepares and maintains systematic reviews of randomized trials of health care therapies, has produced reviews summarizing much of the evidence on Traditional Chinese Medicine (TCM). Our objective was to review the evidence base according to Cochrane systematic reviews. Methods In order to detect reviews focusing on TCM, we searched the titles and abstracts of all reviews in Issue 4, 2008 of the Cochrane Database of Systematic Reviews. For each review, we extracted data on the number of trials included and the total number of participants. We provided an indication of the strength of the review findings by assessing the reviewers' abstract conclusions statement. We supplemented our assessment of the abstract conclusions statements with a listing of the comparisons and outcomes showing statistically significant meta-analyses results. Results We identified 70 Cochrane systematic reviews of TCM, primarily acupuncture (n = 26) and Chinese herbal medicine (n = 42), and 1 each of moxibustion and t'ai chi. Nineteen (19) of 26 acupuncture reviews and 22/42 herbal medicine reviews concluded that there was not enough good quality trial evidence to make any conclusion about the efficacy of the evaluated treatment, while the remaining 7 acupuncture and 20 herbal medicine reviews and each of the moxibustion and t'ai chi reviews indicated a suggestion of benefit, which was qualified by a caveat about the poor quality and quantity of studies. Most reviews included many distinct interventions, controls, outcomes, and populations, and a large number of different comparisons were made, each with a distinct forest plot. Conclusions Most Cochrane systematic reviews of TCM are inconclusive, due specifically to the poor methodology and heterogeneity of the studies reviewed. Some systematic reviews provide preliminary evidence of Chinese medicine's benefits to certain patient populations

  1. MedlinePlus FAQ: Statistics about MedlinePlus

    MedlinePlus

    ... faq/stats.html Can you give me some statistics about MedlinePlus? To use the sharing features on ... For page requests and unique visitors, see MedlinePlus statistics . Return to the list of MedlinePlus FAQs About ...

  2. Interventions for hirsutism excluding laser and photoepilation therapy alone: abridged Cochrane systematic review including GRADE assessments.

    PubMed

    van Zuuren, E J; Fedorowicz, Z

    2016-07-01

    Hirsutism is a common disorder with a major impact on quality of life. The most frequent cause is polycystic ovary syndrome. Effects of interventions (except laser and light-based therapies) were evaluated, including Grading of Recommendations Assessment, Development and Evaluation assessments. Searches included Cochrane Skin Group Specialised Register, CENTRAL in The Cochrane Library, Medline, Embase and five trials registers to June 2014. We included 157 randomized controlled trials (RCTs) with 10 550 participants. The majority were assessed as having a 'high risk' of bias (123 of 157). The quality of evidence was rated moderate to very low for most outcomes. Pooled data for an oral contraceptive (OCP) (ethinyl oestradiol and cyproterone acetate) compared with another OCP (ethinyl oestradiol and desogestrel) demonstrated that both treatments were effective in reducing Ferriman-Gallwey scores, but the mean difference (MD) was not statistically significant [-1·84, 95% confidence interval (CI): -3·86-0·18]. Flutamide was more effective than placebo in two studies (MD -7·60, 95% CI: -10·53 to -4·67 and MD -7·20, 95% CI: -10·15 to -4·25), as was spironolactone (MD -7·69, 95% CI: -10·12 to -5·26). Spironolactone appeared to be as effective as flutamide (two studies) and finasteride (two studies). However, finasteride and the gonadotropin-releasing analogues showed discrepant results in several RCTs. Metformin was ineffective. Cyproterone acetate combined with OCPs demonstrated greater reductions in Ferriman-Gallwey scores. Lifestyle interventions reduced body mass index but did not show improvement in hirsutism, and although cosmetic measures are frequently used, no RCTs investigating cosmetic treatments were identified. RCTs investigating OCPs in combination with antiandrogens or finasteride vs. OCP alone, or the different antiandrogens and 5α-reductase inhibitors are warranted. PMID:26892495

  3. XML Files: MedlinePlus

    MedlinePlus

    ... page: https://medlineplus.gov/xml.html MedlinePlus XML Files To use the sharing features on this page, ... information on all English and Spanish topic groups. Files generated on September 15, 2016 MedlinePlus Health Topic ...

  4. MedlinePlus: Wilms' Tumor

    MedlinePlus

    ... Articles References and abstracts from MEDLINE/PubMed (National Library of Medicine) Article: Multilocular Cystic Nephroma: A Systematic ... MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, Bethesda, MD 20894 ...

  5. MedlinePlus Connect

    MedlinePlus

    ... Web application provide responses in different formats. The Web application returns a link to a formatted MedlinePlus Connect response page. This page will include links to information relevant to the problem/diagnosis, medication, or lab test. For a diagnosis/problem code, the response page ...

  6. MedlinePlus: Accessibility

    MedlinePlus

    ... Tools Español You Are Here: Home → MedlinePlus Accessibility URL of this page: https://medlineplus.gov/accessibility.html ... or (301) 594-5983 and provide the address (URL) of the page on which you need assistance, ...

  7. MedlinePlus: Urinalysis

    MedlinePlus

    ... Spanish Urine pH test Also in Spanish Urine specific gravity test Also in Spanish Topic Image MedlinePlus Email ... Urine - bloody Urine odor Urine pH test Urine specific gravity test Show More Show Less National Institutes of ...

  8. Assessing and presenting summaries of evidence in Cochrane Reviews

    PubMed Central

    2013-01-01

    Cochrane Reviews are intended to help providers, practitioners and patients make informed decisions about health care. The goal of the Cochrane Applicability and Recommendation Methods Group (ARMG) is to develop approaches, strategies and guidance that facilitate the uptake of information from Cochrane Reviews and their use by a wide audience with specific focus on developers of recommendations and on healthcare decision makers. This paper is part of a series highlighting developments in systematic review methodology in the 20 years since the establishment of The Cochrane Collaboration, and its aim is to present current work and highlight future developments in assessing and presenting summaries of evidence, with special focus on Summary of Findings (SoF) tables and Plain Language Summaries. A SoF table provides a concise and transparent summary of the key findings of a review in a tabular format. Several studies have shown that SoF tables improve accessibility and understanding of Cochrane Reviews. The ARMG and GRADE Working Group are working on further development of the SoF tables, for example by evaluating the degree of acceptable flexibility beyond standard presentation of SoF tables, developing SoF tables for diagnostic test accuracy reviews and interactive SoF tables (iSoF). The plain language summary (PLS) is the other main building block for dissemination of review results to end-users. The PLS aims to summarize the results of a review in such a way that health care consumers can readily understand them. Current efforts include the development of a standardized language to describe statistical results, based on effect size and quality of supporting evidence. Producing high quality PLS and SoF tables and making them compatible and linked would make it easier to produce dissemination products targeting different audiences (for example, providers, health policy makers, guideline developers). Current issues of debate include optimal presentation formats of So

  9. Assessing and presenting summaries of evidence in Cochrane Reviews.

    PubMed

    Langendam, Miranda W; Akl, Elie A; Dahm, Philipp; Glasziou, Paul; Guyatt, Gordon; Schünemann, Holger J

    2013-01-01

    Cochrane Reviews are intended to help providers, practitioners and patients make informed decisions about health care. The goal of the Cochrane Applicability and Recommendation Methods Group (ARMG) is to develop approaches, strategies and guidance that facilitate the uptake of information from Cochrane Reviews and their use by a wide audience with specific focus on developers of recommendations and on healthcare decision makers. This paper is part of a series highlighting developments in systematic review methodology in the 20 years since the establishment of The Cochrane Collaboration, and its aim is to present current work and highlight future developments in assessing and presenting summaries of evidence, with special focus on Summary of Findings (SoF) tables and Plain Language Summaries.A SoF table provides a concise and transparent summary of the key findings of a review in a tabular format. Several studies have shown that SoF tables improve accessibility and understanding of Cochrane Reviews.The ARMG and GRADE Working Group are working on further development of the SoF tables, for example by evaluating the degree of acceptable flexibility beyond standard presentation of SoF tables, developing SoF tables for diagnostic test accuracy reviews and interactive SoF tables (iSoF).The plain language summary (PLS) is the other main building block for dissemination of review results to end-users. The PLS aims to summarize the results of a review in such a way that health care consumers can readily understand them. Current efforts include the development of a standardized language to describe statistical results, based on effect size and quality of supporting evidence.Producing high quality PLS and SoF tables and making them compatible and linked would make it easier to produce dissemination products targeting different audiences (for example, providers, health policy makers, guideline developers).Current issues of debate include optimal presentation formats of So

  10. An Experiment in Teaching Medline.

    ERIC Educational Resources Information Center

    Rees, Alan M.; And Others

    Case Western Reserve University added training in MEDLINE analysis to its health sciences librarianship program in 1974, with help and some funding from the National Library of Medicine and with the cooperation of the Cleveland Health Sciences Library. MEDLINE was introduced at a 2-1/2 day intersession in January, and a MEDLINE module was included…

  11. Web Service: MedlinePlus

    MedlinePlus

    ... this page: https://medlineplus.gov/webservices.html MedlinePlus Web Service To use the sharing features on this ... please enable JavaScript. MedlinePlus offers a search-based Web service that provides access to MedlinePlus health topic ...

  12. Medical Questions? Medline has Answers.

    ERIC Educational Resources Information Center

    Modlin, Melanie

    1998-01-01

    Developed by the National Library of Medicine (NLM), the electronic version of "Index Medicus," Medline is the world's largest collection of published medical knowledge. Discussion includes accessing Medline (cost-free) with a Web browser, librarians as links between patients and physicians; and examples of Medline searches. (AEF)

  13. MedlinePlus FAQ: MedlinePlus and MEDLINE/PubMed

    MedlinePlus

    ... links to preformulated searches of the MEDLINE/PubMed database, allowing you to find references to latest health ... articles on your topic. MEDLINE/PubMed: Is a database of professional biomedical literature Is a Web-based, ...

  14. PubMed related articles: a probabilistic topic-based model for content similarity

    PubMed Central

    Lin, Jimmy; Wilbur, W John

    2007-01-01

    Background We present a probabilistic topic-based model for content similarity called pmra that underlies the related article search feature in PubMed. Whether or not a document is about a particular topic is computed from term frequencies, modeled as Poisson distributions. Unlike previous probabilistic retrieval models, we do not attempt to estimate relevance–but rather our focus is "relatedness", the probability that a user would want to examine a particular document given known interest in another. We also describe a novel technique for estimating parameters that does not require human relevance judgments; instead, the process is based on the existence of MeSH ® in MEDLINE ®. Results The pmra retrieval model was compared against bm25, a competitive probabilistic model that shares theoretical similarities. Experiments using the test collection from the TREC 2005 genomics track shows a small but statistically significant improvement of pmra over bm25 in terms of precision. Conclusion Our experiments suggest that the pmra model provides an effective ranking algorithm for related article search. PMID:17971238

  15. Prevention of bacterial meningitis: an overview of Cochrane systematic reviews.

    PubMed

    Prasad, Kameshwar; Karlupia, Neha

    2007-10-01

    Acute bacterial meningitis (ABM) is an acute inflammation of leptomeninges caused by bacteria, and has a case fatality rate of 10-30%. Prevention strategies, such as vaccination and prophylactic antibiotics, can prevent ABM and have substantial public health impact by reducing the disease burden associated with it. The aim of this paper is to summarize the main findings from Cochrane systematic reviews that have considered the evidence for measures to prevent ABM. We assessed the evidence available in the Cochrane Library. We found five Cochrane reviews focused on the prevention of ABM; three with use of vaccination and two with prophylactic antibiotics. Polysaccharide serogroup A vaccine is strongly protective for the first year, against serogroup A meningococcal meningitis in adults and children over 5 years of age. Meningococcal serogroup C conjugate (MCC) vaccine is safe and effective in infants. Haemophilus influenzae type b (Hib) vaccine is safe and effective against Hib-invasive disease at all ages. Ceftriaxone, rifampicin and ciprofloxacin are the most effective prophylactic antibiotics against Neisseria meningitidis. There is sufficient evidence to use polysaccharide serogroup A vaccine to prevent serogroup A meningococcal meningitis, MCC conjugate vaccines to prevent meningococcal C meningitis and Hib conjugate vaccine to prevent Hib infections. More studies are needed to evaluate the effects of Hib conjugate vaccine on mortality. Further, studies are required to compare the relative effectiveness of ceftriaxone, ciprofloxacin and rifampicin in chemoprophylaxis against meningococcal infection. PMID:17706408

  16. Medline/PubMed revisited: new, semantic tools to explore the biomedical literature.

    PubMed

    Giglia, E

    2009-06-01

    The aim of this contribution was to present some new search engines developed upon the logic of the semantic Web to explore the worldwide known Medline database in a way alternative to the common PubMed interface, clustering the results and allowing a different search. PMID:19532114

  17. MEDLINE in the UK: pioneering the past, present and future.

    PubMed

    Pritchard, Steve J; Weightman, Alison L

    2005-09-01

    This article provides a brief history of the development of the MEDLINE database and its huge impact within the UK, from its inception to the present time. The origins of MEDLINE can be traced back to a collection of books in the US Surgeon General's Office during the American Civil War and John Shaw Billings' decision, during 1867, to make this Library as complete as possible. From these beginnings, Index Medicus was developed in the early years of the 20th century, and electronic versions of the database began with the computerized on-demand search service MEDLARS in 1964 and then via CD-ROM and Internet Grateful Med to the web-based and free-to-all service, PubMed, in 1997. The response to PubMed was immediate and startling with usage increasing from 7 million searches per annum in 1996 to 400 million searches per annum in 2001 and the service continues to improve. MEDLINE providers are now offering mapping of natural language queries to the sophisticated indexing vocabulary (Medical Subject Headings, MeSH) and the provision of specific filters for different types of publication to improve searching efficiency, as well as links to full-text versions of the papers where available. The next steps are likely to involve an increased blurring of database and full-text boundaries, incorporating seamless access to the best available evidence within MEDLINE and a wide range of other information resources within a single search and to an increasing amount of full-text via various open-archive initiatives. As ever, the US National Library of Medicine is in the vanguard of research and further applications of its MEDLINE database for users within the UK will be awaited with great interest. PMID:16109026

  18. How to improve your PubMed/MEDLINE searches: 1. background and basic searching.

    PubMed

    Fatehi, Farhad; Gray, Leonard C; Wootton, Richard

    2013-12-01

    PubMed provides free access via the Internet to more than 23 million records, of which over 19 million are from the MEDLINE database of journal articles. PubMed also provides access to other databases, such as the NCBI Bookshelf. To perform a basic search, you can simply enter the search terms or the concept that you are looking for in the search box. However, taking care to clarify your key concepts may save much time later on, because a non-specific search is likely to produce an overwhelming number of result hits. One way to make your search more specific is to specify which field you want to search using field tags. By default, the results of a search are sorted by the date added to PubMed and displayed in summary format with 20 result hits (records) on each page. In summary format, the title of the article, list of authors, source of information (e.g., journal name followed by date of publication, volume, issue, pages) and the unique PubMed record number called the PubMed identifier (PMID) are shown. Although information is stored about the articles, PubMed/MEDLINE does not store the full text of the papers themselves. However, PubMedCentral (PMC) stores more than 2.8 million articles (roughly 10% of the articles in PubMed) and provides access to them for free to the users. PMID:24197398

  19. Mobile app versus Web app: a comparison using 2008-2012 "PubMed for Handhelds" server data.

    PubMed

    Fontelo, Paul; Liu, Fang

    2013-01-01

    Recent surveys show that mobile apps are more popular than Web apps. Apple's iTunes Store, now has about 800,000 apps and reported to have about 40 billion downloads. Android apps, although fewer, is available to the most number of smartphones today. About 40,000 apps are medical or health related. We developed a PubMed4Hh mobile app for iPhone/iPad users to search MEDLINE/PubMed with same features as our Web-based search tools, in use since 2002. Five-year (2008-2012) server data for PubMed4Hh and Web app were analyzed. Searches using the mobile app significantly increased compared to the same five-year time period. Month-by-month comparison showed a 3 to 5-fold increase in queries. The six-month total accesses comparison increased 280% from the previous four-year average. A review of 500 randomly selected queries revealed that the majority of queries were clinical questions ((97.8%) and 61% of these queries are searches related to therapy. PMID:24551349

  20. MedlinePlus Survey Results 2015

    MedlinePlus

    ... Index survey used to gather MedlinePlus survey data. Customer Satisfaction Score During 2015, users reported the following overall ... MedlinePlus users 2% MedlinePlus en español users 3% Consumer MedlinePlus users 49% MedlinePlus en español users 31% ...

  1. 4. ALABAMA, PICKENS CO., COCHRANE COLLAPSED RAILROAD BRIDGE 1.5 miles ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    4. ALABAMA, PICKENS CO., COCHRANE COLLAPSED RAILROAD BRIDGE 1.5 miles N. from Cochrane on Ala. route 17. Western half of collapsed Alabama, Tenn. & Northern RR. Bridge Jack Donnell, Columbus, Ms., photographer, 1973. Copy by Sarcone Photography, Columbs, Ms Sep 1978. - Bridges of the Upper Tombigbee River Valley, Cochrane, Pickens County, AL

  2. 5. ALABAMA, PICKENS CO., COCHRANE COLLAPSED RAILROAD BRIDGE 1.5 miles ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. ALABAMA, PICKENS CO., COCHRANE COLLAPSED RAILROAD BRIDGE 1.5 miles N. from Cochrane on Ala. route 17. Copy of photo by Jack Donnell, Columbus, Ms., after bridge collapsed in 1973. Shows broken turn span and overturned center pier. Sarcone Photography, Columbus, Ms. Sep 1978. - Bridges of the Upper Tombigbee River Valley, Cochrane, Pickens County, AL

  3. 6. ALABAMA, PICKENS CO., COCHRANE RAILROAD BRIDGE 1.5 miles N. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    6. ALABAMA, PICKENS CO., COCHRANE RAILROAD BRIDGE 1.5 miles N. from Cochrane on Ala. route 17 Copy of photo by Jack Donnell, Columbus, Ms., 192. Shows center turn span and part of one fixed span. Sarcone Photography, Columbus, Ms. Sep 1978. - Bridges of the Upper Tombigbee River Valley, Cochrane, Pickens County, AL

  4. 3. ALABAMA, PICKENS CO., COCHRANE RAILROAD BRIDGE AND FERRY 1.5 ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. ALABAMA, PICKENS CO., COCHRANE RAILROAD BRIDGE AND FERRY 1.5 miles N. from Cochrane on Ala. route 17. Copy of photo by Jack Donnell, Columbus, Ms., 1927. West ferry landing ferry barge, andcar in foreground. Alabama, Tennessee & Northern (later Frisco) RR bridge in background. Sarcone Photography, Columbus, Ms. Sep 1978. - Bridges of the Upper Tombigbee River Valley, Cochrane, Pickens County, AL

  5. 2. ALABAMA, PICKENS, CO., COCHRANE HIGHWAY BRIDGE 1.5 miles N. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. ALABAMA, PICKENS, CO., COCHRANE HIGHWAY BRIDGE 1.5 miles N. from Cochrane on Ala. route 17. Aerial view of Milner bridge, from SE. David J. Kaminsky, Architecturl Photography, Atlanta Ga. Aug 1978. - Bridges of the Upper Tombigbee River Valley, Cochrane, Pickens County, AL

  6. 1. ALABAMA, PICKENS CO., COCHRANE HIGHWAY BRIDGE 1.5 miles N. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. ALABAMA, PICKENS CO., COCHRANE HIGHWAY BRIDGE 1.5 miles N. from Cochrane on Ala. route 17 Aerial view of Milner bridge, from SW. David J. Kaminsky, Architectural Photography, Atlanta Ga. Aug 1978. - Bridges of the Upper Tombigbee River Valley, Cochrane, Pickens County, AL

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

    PubMed Central

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

    2016-01-01

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

  8. MedlineRanker: flexible ranking of biomedical literature.

    PubMed

    Fontaine, Jean-Fred; Barbosa-Silva, Adriano; Schaefer, Martin; Huska, Matthew R; Muro, Enrique M; Andrade-Navarro, Miguel A

    2009-07-01

    The biomedical literature is represented by millions of abstracts available in the Medline database. These abstracts can be queried with the PubMed interface, which provides a keyword-based Boolean search engine. This approach shows limitations in the retrieval of abstracts related to very specific topics, as it is difficult for a non-expert user to find all of the most relevant keywords related to a biomedical topic. Additionally, when searching for more general topics, the same approach may return hundreds of unranked references. To address these issues, text mining tools have been developed to help scientists focus on relevant abstracts. We have implemented the MedlineRanker webserver, which allows a flexible ranking of Medline for a topic of interest without expert knowledge. Given some abstracts related to a topic, the program deduces automatically the most discriminative words in comparison to a random selection. These words are used to score other abstracts, including those from not yet annotated recent publications, which can be then ranked by relevance. We show that our tool can be highly accurate and that it is able to process millions of abstracts in a practical amount of time. MedlineRanker is free for use and is available at http://cbdm.mdc-berlin.de/tools/medlineranker. PMID:19429696

  9. MedlineRanker: flexible ranking of biomedical literature

    PubMed Central

    Fontaine, Jean-Fred; Barbosa-Silva, Adriano; Schaefer, Martin; Huska, Matthew R.; Muro, Enrique M.; Andrade-Navarro, Miguel A.

    2009-01-01

    The biomedical literature is represented by millions of abstracts available in the Medline database. These abstracts can be queried with the PubMed interface, which provides a keyword-based Boolean search engine. This approach shows limitations in the retrieval of abstracts related to very specific topics, as it is difficult for a non-expert user to find all of the most relevant keywords related to a biomedical topic. Additionally, when searching for more general topics, the same approach may return hundreds of unranked references. To address these issues, text mining tools have been developed to help scientists focus on relevant abstracts. We have implemented the MedlineRanker webserver, which allows a flexible ranking of Medline for a topic of interest without expert knowledge. Given some abstracts related to a topic, the program deduces automatically the most discriminative words in comparison to a random selection. These words are used to score other abstracts, including those from not yet annotated recent publications, which can be then ranked by relevance. We show that our tool can be highly accurate and that it is able to process millions of abstracts in a practical amount of time. MedlineRanker is free for use and is available at http://cbdm.mdc-berlin.de/tools/medlineranker. PMID:19429696

  10. Connecting the Dots between PubMed Abstracts

    PubMed Central

    Hossain, M. Shahriar; Gresock, Joseph; Edmonds, Yvette; Helm, Richard; Potts, Malcolm; Ramakrishnan, Naren

    2012-01-01

    Background There are now a multitude of articles published in a diversity of journals providing information about genes, proteins, pathways, and diseases. Each article investigates subsets of a biological process, but to gain insight into the functioning of a system as a whole, we must integrate information from multiple publications. Particularly, unraveling relationships between extra-cellular inputs and downstream molecular response mechanisms requires integrating conclusions from diverse publications. Methodology We present an automated approach to biological knowledge discovery from PubMed abstracts, suitable for “connecting the dots” across the literature. We describe a storytelling algorithm that, given a start and end publication, typically with little or no overlap in content, identifies a chain of intermediate publications from one to the other, such that neighboring publications have significant content similarity. The quality of discovered stories is measured using local criteria such as the size of supporting neighborhoods for each link and the strength of individual links connecting publications, as well as global metrics of dispersion. To ensure that the story stays coherent as it meanders from one publication to another, we demonstrate the design of novel coherence and overlap filters for use as post-processing steps. Conclusions We demonstrate the application of our storytelling algorithm to three case studies: i) a many-one study exploring relationships between multiple cellular inputs and a molecule responsible for cell-fate decisions, ii) a many-many study exploring the relationships between multiple cytokines and multiple downstream transcription factors, and iii) a one-to-one study to showcase the ability to recover a cancer related association, viz. the Warburg effect, from past literature. The storytelling pipeline helps narrow down a scientist's focus from several hundreds of thousands of relevant documents to only around a hundred

  11. Videos & Tools: MedlinePlus

    MedlinePlus Videos and Cool Tools

    Skip navigation U.S. National Library of Medicine Menu Health Topics Drugs & Supplements Videos & Tools About MedlinePlus Search ... GO About MedlinePlus Site Map FAQs Contact Us Health Topics Drugs & Supplements Videos & Tools Español You Are ...

  12. MedlinePlus: For Developers

    MedlinePlus

    ... health IT providers to link patient portals and electronic health record (EHR) systems to content from MedlinePlus.gov. MedlinePlus Connect accepts code-based requests for information on diagnoses (problem codes), medications, and lab tests, and returns related ...

  13. MedlinePlus: Cardiac Arrest

    MedlinePlus

    ... Journal Articles References and abstracts from MEDLINE/PubMed (National Library of Medicine) Article: A Prospective Study of Sudden Cardiac Death ... Players MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, Bethesda, MD 20894 U.S. Department ...

  14. MedlinePlus: Birth Weight

    MedlinePlus

    ... Journal Articles References and abstracts from MEDLINE/PubMed (National Library of Medicine) Article: Infant BMI is 'good predictor' of obesity. ... Players MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, Bethesda, MD 20894 U.S. Department ...

  15. MedlinePlus: Erectile Dysfunction

    MedlinePlus

    ... Journal Articles References and abstracts from MEDLINE/PubMed (National Library of Medicine) Article: A Nationwide Population-Based Cohort Study of ... Players MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, Bethesda, MD 20894 U.S. Department ...

  16. MedlinePlus: Heart Surgery

    MedlinePlus

    ... Journal Articles References and abstracts from MEDLINE/PubMed (National Library of Medicine) Article: Effect of a Cerebral Protection Device on ... Players MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, Bethesda, MD 20894 U.S. Department ...

  17. MedlinePlus FAQ: Search Cloud

    MedlinePlus

    ... widget code and display the widget on your Web site. Return to the list of MedlinePlus FAQs About MedlinePlus Site ... Guidelines Viewers & Players MedlinePlus Connect for EHRs For Developers U.S. ...

  18. MedlinePlus: Awards and Recognition

    MedlinePlus

    ... reliable drug and supplement content. MedlinePlus #1 in User Satisfaction MedlinePlus and MedlinePlus en español tied for first place for user satisfaction in the Federal News and Information Website category ...

  19. MICROTASK CROWDSOURCING FOR DISEASE MENTION ANNOTATION IN PUBMED ABSTRACTS

    PubMed Central

    Good, Benjamin M; Nanis, Max; Wu, Chunlei; Su, Andrew I

    2014-01-01

    Identifying concepts and relationships in biomedical text enables knowledge to be applied in computational analyses. Many biological natural language processing (BioNLP) projects attempt to address this challenge, but the state of the art still leaves much room for improvement. Progress in BioNLP research depends on large, annotated corpora for evaluating information extraction systems and training machine learning models. Traditionally, such corpora are created by small numbers of expert annotators often working over extended periods of time. Recent studies have shown that workers on microtask crowdsourcing platforms such as Amazon’s Mechanical Turk (AMT) can, in aggregate, generate high-quality annotations of biomedical text. Here, we investigated the use of the AMT in capturing disease mentions in PubMed abstracts. We used the NCBI Disease corpus as a gold standard for refining and benchmarking our crowdsourcing protocol. After several iterations, we arrived at a protocol that reproduced the annotations of the 593 documents in the ‘training set’ of this gold standard with an overall F measure of 0.872 (precision 0.862, recall 0.883). The output can also be tuned to optimize for precision (max = 0.984 when recall = 0.269) or recall (max = 0.980 when precision = 0.436). Each document was completed by 15 workers, and their annotations were merged based on a simple voting method. In total 145 workers combined to complete all 593 documents in the span of 9 days at a cost of $.066 per abstract per worker. The quality of the annotations, as judged with the F measure, increases with the number of workers assigned to each task; however minimal performance gains were observed beyond 8 workers per task. These results add further evidence that microtask crowdsourcing can be a valuable tool for generating well-annotated corpora in BioNLP. Data produced for this analysis are available at http

  20. Development of biomedical publications on ametropia research in PubMed from 1845 to 2010: a bibliometric analysis

    PubMed Central

    Xu, Chang-Tai; Li, Shan-Qu; Lü, Yong-Gang; Pan, Bo-Rong

    2011-01-01

    AIM We have carried out a bibliometric analysis on the development of ametropia literature to determine its growth rule and tendency, and to provide the basis for the problems related to ametropia research. METHODS Literatures that contained the descriptors of ametropia in title or paper published before Nov. 10, 2010 in PubMed databases (www.ncbi.nlm.nih.gov/Pubmed) were selected. As bibliometric indicators of ametropia, biomedical journals referring to ophthalmology by ISSN were calculated. The principal bibliometric indicators: Price's and Bradford's laws were applied on the increase or dispersion of scientific literature, the participation index of languages and the journals. By means of manual coding, literatures were classified according to documents study and statistical analysis. RESULTS The literatures cited in ametropia, astigmatism, myopia and hypermetropia had accumulated to 26475, which consists of Review (n=1560), Randomized Controlled Trial (n=776), Practice Guideline (n=10), Meta-Analysis (n=23), Letter (n=1222), Editorial (n=328), Clinical Trial (n=1726) and Others (n=20830), and Humans (n=23073), Animals(n=1434) and others (n=1968). 1136 literatures were included in PubMed Central, 22384 in MEDLINE and 2955 in others. The ametropia literatures rose every 5 years which of the ametropia-year cumulated amount of the literatures had three periods: before 1900, slowly increasing from 1901 to 1950, rapidly rising from 1951 to 2010 (increased approximate exponentiation exponent). Sixty kinds of languages listed in PubMed databases, of which English is dominant for aborting to ametropia research documents before 2010 (77.32%, 20471/26475). The document languages of top eight account for 95.58% (English, German, French, Japanese, Russian, Italian, Spanish, Chinese), and others for 4.42% (1171/26475). The SCI database includes 48 ophthalmologic journals and the impact factor of 39 journals is ≥1 on Thomson-Reuters in 2010. Of 48 ophthalmologic journals

  1. Mobile MedlinePlus | NIH MedlinePlus the Magazine

    MedlinePlus

    ... Table of Contents Trusted medical information on your mobile phone http://m.medlineplus.gov Wondering what the side ... of disease and wellness topics The latest health news An illustrated medical encyclopedia Mobile MedlinePlus: http://m. ...

  2. MedlinePlus FAQ: What is MedlinePlus?

    MedlinePlus

    ... also find preformulated searches of the MEDLINE/PubMed database, which allow you to find references to latest ... AHFS ® Consumer Medication Information, and Natural Medicines Comprehensive Database Consumer Version. AHFS ® Consumer Medication Information provides extensive ...

  3. Mobile MedlinePlus | NIH MedlinePlus Magazine

    MedlinePlus

    ... Table of Contents Trusted medical information on your mobile phone http://m.medlineplus.gov Wondering what the side effects are for your new prescription? Go to Mobile MedlinePlus while you're waiting for the pharmacist ...

  4. Mobile MedlinePlus | NIH MedlinePlus the Magazine

    MedlinePlus

    ... Table of Contents Trusted medical information on your mobile phone http://m.medlineplus.gov Wondering what the side effects are for your new prescription? Go to Mobile MedlinePlus ( http://m.medlineplus.gov ) while you're ...

  5. Death, dying and informatics: misrepresenting religion on MedLine

    PubMed Central

    Rodríguez del Pozo, Pablo; Fins, Joseph J

    2005-01-01

    Background The globalization of medical science carries for doctors worldwide a correlative duty to deepen their understanding of patients' cultural contexts and religious backgrounds, in order to satisfy each as a unique individual. To become better informed, practitioners may turn to MedLine, but it is unclear whether the information found there is an accurate representation of culture and religion. To test MedLine's representation of this field, we chose the topic of death and dying in the three major monotheistic religions. Methods We searched MedLine using PubMed in order to retrieve and thematically analyze full-length scholarly journal papers or case reports dealing with religious traditions and end-of-life care. Our search consisted of a string of words that included the most common denominations of the three religions, the standard heading terms used by the National Reference Center for Bioethics Literature (NRCBL), and the Medical Subject Headings (MeSH) used by the National Library of Medicine. Eligible articles were limited to English-language papers with an abstract. Results We found that while a bibliographic search in MedLine on this topic produced instant results and some valuable literature, the aggregate reflected a selection bias. American writers were over-represented given the global prevalence of these religious traditions. Denominationally affiliated authors predominated in representing the Christian traditions. The Islamic tradition was under-represented. Conclusion MedLine's capability to identify the most current, reliable and accurate information about purely scientific topics should not be assumed to be the same case when considering the interface of religion, culture and end-of-life care. PMID:15992401

  6. BabelMeSH2 and PICO Linguist2: combined language search for MEDLINE/PubMed.

    PubMed

    Liu, Fang; Fontelo, Paul; Ackerman, Michael

    2007-01-01

    BabelMeSH2 is a transparent interface for searching MEDLINE/PubMed in one or a combination of nine currently supported languages. The search algorithm automatically detects mix language entries, finds the English equivalent, and retrieves the relevant PubMed citations. We believe this is the first search application that allows mixed language entries. PMID:18694134

  7. Cochrane reviews on the benefits/risks of fluoride toothpastes.

    PubMed

    Wong, M C M; Clarkson, J; Glenny, A-M; Lo, E C M; Marinho, V C C; Tsang, B W K; Walsh, T; Worthington, H V

    2011-05-01

    This concise review presents two Cochrane Reviews undertaken to determine: (1) the relative effectiveness of fluoride toothpastes of different concentrations in preventing dental caries in children and adolescents; and (2) the relationship between the use of topical fluorides in young children and their risk of developing dental fluorosis. To determine the relative effectiveness of fluoride toothpastes of different concentrations, we undertook a network meta-analysis utilizing both direct and indirect comparisons from randomized controlled trials (RCTs). The review examining fluorosis included evidence from experimental and observational studies. The findings of the reviews confirm the benefits of using fluoride toothpaste, when compared with placebo, in preventing caries in children and adolescents, but only significantly for fluoride concentrations of 1000 ppm and above. The relative caries-preventive effects of fluoride toothpastes of different concentrations increase with higher fluoride concentration. However, there is weak, unreliable evidence that starting the use of fluoride toothpaste in children under 12 months of age may be associated with an increased risk of fluorosis. The decision of what fluoride levels to use for children under 6 years should be balanced between the risk of developing dental caries and that of mild fluorosis. PMID:21248357

  8. The MEDLINE Button.

    PubMed Central

    Cimino, J. J.; Johnson, S. B.; Aguirre, A.; Roderer, N.; Clayton, P. D.

    1992-01-01

    We have developed a computerized method for performing bibliographic searches directly from patient data involving five steps: 1) identifying specific patient data which raises a question in the mind of the user, 2) selection (from a list of generic questions) of a small number of questions which fit the selected patient data, 3) automated translation of the patient data into appropriate terms used for bibliographic indexing, 4) conversion of the question selected by the user into a search strategy, and 5) transfer of the search strategy to a search engine for a bibliographic database. We have modified the Columbia-Presbyterian Clinical Information System to experiment with this method. The first implementation converts patient diagnoses and procedures coded in ICD9-CM into Medical Subject Headings (MeSH) and searches Medline using BRS/Onsite. Challenges include development of a useful set of generic questions and translation from ICD9-CM to MeSH using the Unified Medical Language System (UMLS). PMID:1482993

  9. MedlinePlus: Assistive Devices

    MedlinePlus

    ... Rehabilitation National Institutes of Health The primary NIH organization for research on Assistive Devices is the National Institute on Deafness and Other Communication Disorders NIH MedlinePlus Magazine Robots for Better Health ...

  10. MedlinePlus: Alzheimer's Caregivers

    MedlinePlus

    ... Aging) - PDF Sleep Issues and Sundowning (Alzheimer's Association) Wandering (National Institute on Aging) - PDF Genetics Genetics Home ... Aging) - PDF Traveling Overnight (National Institute on Aging) Wandering (National Institute on Aging) - PDF Topic Image MedlinePlus ...

  11. Search Tips: MedlinePlus

    MedlinePlus

    ... of this page: https://medlineplus.gov/searchtips.html Search Tips To use the sharing features on this page, please enable JavaScript. How do I search MedlinePlus? The search box appears at the top ...

  12. MedlinePlus: Healthy Aging

    MedlinePlus

    ... in America (Centers for Disease Control and Prevention) Journal Articles References and abstracts from MEDLINE/PubMed (National Library of Medicine) Article: The benefits of social prescribing. Article: Healthy ...

  13. MedlinePlus FAQ: MedlinePlus and MEDLINE/PubMed

    MedlinePlus

    ... topic. MEDLINE/PubMed: Is a database of professional biomedical literature Is a Web-based, searchable database of ... million article references published in more than 5600 biomedical journals. Can be searched for free Includes links ...

  14. Visit the MedlinePlus Search Cloud | NIH MedlinePlus the Magazine

    MedlinePlus

    ... please turn Javascript on. Visit the MedlinePlus Search Cloud Past Issues / Winter 2011 Table of Contents Free, ... Visit the new MedlinePlus Visit the MedlinePlus search cloud, featuring the top 100 search terms of the ...

  15. MedlinePlus FAQ: What's New on Medline Plus Page and Email Updates

    MedlinePlus

    ... the What's New on MedlinePlus page and RSS feed different from the email updates? To use the ... The What's New on MedlinePlus page and RSS feed include alerts about new MedlinePlus features, useful resources, ...

  16. [Analysis of the Cochrane Review: Antihistamines for the Common Cold. Cochrane Database Syst Rev. 2015;11:CD009345].

    PubMed

    Sterrantino, Carmel; Duarte, Gonçalo; Costa, João; Vaz-Carneiro, António

    2016-03-01

    The common cold is an acute, self-limiting inflammation of the mucosa of the upper airways, which may involve one or all the sinuses, nasopharynx, oropharynx and larynx. It is common to have at least one episode per year. Common cold symptoms, which may include sore throat, sneezing, nasal congestion, runny nose, headache, malaise and mild fever usually disappear within a few days without treatment. The causative agent of most colds is rhinovirus. Although not associated with mortality, common cold is associated with significant morbidity. There is no vaccine or cure for common cold and, therefore, their treatment is centered on relieving the symptoms. This Cochrane review aimed to synthesize the existing evidence about the clinical benefit of antihistamines, used as monotherapy, compared with placebo or no treatment in children and adult patients with common cold. A total of 18 randomized clinical trials with 4342 participants were included. Main results were: 1) Antihistamines have a small (days one and two) beneficial effect in the short term on the severity of overall symptoms in adult patients, although this effect is not present in the medium to long term; 2) antihistamines were not associated with a clinically significant beneficial effect on the individual symptoms (nasal congestion, rhinorrhea, and sneezing); 3) Antihistamines are not associated with an increased risk of adverse effects; 4) No conclusion can be made about the effectiveness of antihistamines in pediatric populations. Our interpretation of the results is that the available evidence is insufficient to support the prescription or buying OTC antihistamines to relieve the symptoms of common cold without allergic component. PMID:27285091

  17. Awareness and Use of Evidence-based Medicine Databases and Cochrane Library Among Physicians in Croatia

    PubMed Central

    Novak, Katarina; Mirić, Dino; Jurin, Ana; Vukojević, Katarina; Aljinović, Jure; Čarić, Ana; Marinović Guić, Maja; Poljičanin, Ana; Košta, Vana; Rako, Dalibora; Marušić, Ana; Marušić, Matko; Puljak, Livia

    2010-01-01

    Aim To assess awareness and use of evidence-based medicine (EBM) databases and The Cochrane Library among physicians in Croatia. Methods A cross-sectional study with a telephone survey was performed among 573 physicians (88.6% response rate from 647 contacted physicians) from family practice and 4 major university hospital centers in Croatia. The main outcome measures were physicians' awareness of The Cochrane Collaboration, awareness and use of The Cochrane Library, access to EBM databases, and access to internet at work. Results Overall, 54% of respondents said they had access to EBM databases, but when asked which databases they used, they named mostly non-EBM databases. The question on the highest level of evidence in EBM was correctly answered by 53% respondents, 30% heard of The Cochrane Collaboration, and 34% heard about The Cochrane Library. They obtained information about The Cochrane Library mostly from colleagues and research articles, whereas the information about EBM was gained mainly during continuous medical education. There were more respondents who thought The Cochrane Library could help them in practice (58%) than those who heard about The Cochrane Library (30%). Only 20% of the respondents heard about the initiative for the establishment of the Croatian branch of The Cochrane Collaboration. Family physicians had significantly lower level of awareness, knowledge, and use of EBM and The Cochrane Library than physicians from university hospitals. Conclusion There is low awareness about EBM and The Cochrane Library among physicians in Croatia, which creates a need for educational interventions about EBM for the benefit of health care in Croatia. PMID:20401959

  18. Home based versus centre based cardiac rehabilitation: Cochrane systematic review and meta-analysis

    PubMed Central

    Zawada, Anna; Jolly, Kate; Moxham, Tiffany; Taylor, Rod S

    2010-01-01

    Objective To compare the effect of home based and supervised centre based cardiac rehabilitation on mortality and morbidity, health related quality of life, and modifiable cardiac risk factors in patients with coronary heart disease. Design Systematic review. Data sources Cochrane Central Register of Controlled Trials (CENTRAL) in the Cochrane Library, Medline, Embase, CINAHL, and PsycINFO, without language restriction, searched from 2001 to January 2008. Review methods Reference lists checked and advice sought from authors. Included randomised controlled trials that compared centre based cardiac rehabilitation with home based programmes in adults with acute myocardial infarction, angina, or heart failure or who had undergone coronary revascularisation. Two reviewers independently assessed the eligibility of the identified trials and extracted data independently. Authors were contacted when possible to obtain missing information. Results 12 studies (1938 participants) were included. Most studies recruited patients with a low risk of further events after myocardial infarction or revascularisation. No difference was seen between home based and centre based cardiac rehabilitation in terms of mortality (relative risk 1.31, 95% confidence interval 0.65 to 2.66), cardiac events, exercise capacity (standardised mean difference −0.11, −0.35 to 0.13), modifiable risk factors (weighted mean difference systolic blood pressure (0.58 mm Hg, −3.29 mm Hg to 4.44 mm Hg), total cholesterol (−0.13 mmol/l, −0.31 mmol/l to 0.05 mmol/l), low density lipoprotein cholesterol (−0.15 mmol/l, −0.31 mmol/l to 0.01 mmol/l), or relative risk for proportion of smokers at follow-up (0.98, 0.73 to 1.31)), or health related quality of life, with the exception of high density lipoprotein cholesterol (−0.06, −0.11 to −0.02) mmol/l). In the home based participants, there was evidence of superior adherence. No consistent difference was seen in the healthcare costs of the two forms

  19. The inclusion of an online journal in PubMed central - a difficult path.

    PubMed

    Grech, Victor

    2016-01-01

    The indexing of a journal in a prominent database (such as PubMed) is an important imprimatur. Journals accepted for inclusion in PubMed Central (PMC) are automatically indexed in PubMed but must provide the entire contents of their publications as XML-tagged (Extensible Markup Language) data files compliant with PubMed's document type definition (DTD). This paper describes the various attempts that the journal Images in Paediatric Cardiology made in its efforts to convert the journal contents (including all of the extant backlog) to PMC-compliant XML for archiving and indexing in PubMed after the journal was accepted for inclusion by the database. PMID:27244254

  20. Development and classification of an operational definition of complementary and alternative medicine for the Cochrane Collaboration

    PubMed Central

    Wieland, L. Susan; Manheimer, Eric; Berman, Brian M.

    2011-01-01

    Over the past decade the Cochrane Collaboration has been an increasingly important source of information on complementary and alternative medicine (CAM) therapies. From 2007 to 2008 the Cochrane CAM Field developed a topics list that allowed us to categorize all 396 Cochrane reviews related to CAM (as of The Cochrane Library, Issue 4, 2009). This topics list is an advance in making Cochrane reviews on CAM topics accessible to the public. In this paper, we discuss challenges in developing the topics list, including developing an operational definition of CAM, deciding which reviews should be included within the CAM Field’s scope, developing the structured list of CAM Field-specific topics, and determining where in the topics list the reviews should be placed. Although aspects of our operational definition of CAM are open to revision, a standardized definition provides us with an objective, reproducible and systematic method for defining and classifying CAM therapies. PMID:21717826

  1. Research synthesis and dissemination as a bridge to knowledge management: the Cochrane Collaboration.

    PubMed Central

    Volmink, Jimmy; Siegfried, Nandi; Robertson, Katharine; Gülmezoglu, A. Metin

    2004-01-01

    In the current information age, research synthesis is a particularly useful tool for keeping track of scientific research and making sense of the large volumes of frequently conflicting data derived from primary studies. The Cochrane Collaboration is a global initiative "to help people make well-informed decisions about health care by preparing, maintaining and promoting the accessibility of systematic reviews of the effects of healthcare interventions". In this paper we set the work of the Cochrane Collaboration in historical perspective, explain what a Cochrane review is, and describe initiatives for promoting worldwide dissemination of synthesized information. We also consider emerging evidence of the Cochrane Collaboration's impact on health-care practice, policy, research and education. Finally, we highlight the need for increased investment in the preparation and maintenance of Cochrane reviews, particularly those that address health issues that are relevant to people living in low- and middle-income countries. PMID:15643800

  2. Retrieving Clinical Evidence: A Comparison of PubMed and Google Scholar for Quick Clinical Searches

    PubMed Central

    Bejaimal, Shayna AD; Sontrop, Jessica M; Iansavichus, Arthur V; Haynes, R Brian; Weir, Matthew A; Garg, Amit X

    2013-01-01

    Background Physicians frequently search PubMed for information to guide patient care. More recently, Google Scholar has gained popularity as another freely accessible bibliographic database. Objective To compare the performance of searches in PubMed and Google Scholar. Methods We surveyed nephrologists (kidney specialists) and provided each with a unique clinical question derived from 100 renal therapy systematic reviews. Each physician provided the search terms they would type into a bibliographic database to locate evidence to answer the clinical question. We executed each of these searches in PubMed and Google Scholar and compared results for the first 40 records retrieved (equivalent to 2 default search pages in PubMed). We evaluated the recall (proportion of relevant articles found) and precision (ratio of relevant to nonrelevant articles) of the searches performed in PubMed and Google Scholar. Primary studies included in the systematic reviews served as the reference standard for relevant articles. We further documented whether relevant articles were available as free full-texts. Results Compared with PubMed, the average search in Google Scholar retrieved twice as many relevant articles (PubMed: 11%; Google Scholar: 22%; P<.001). Precision was similar in both databases (PubMed: 6%; Google Scholar: 8%; P=.07). Google Scholar provided significantly greater access to free full-text publications (PubMed: 5%; Google Scholar: 14%; P<.001). Conclusions For quick clinical searches, Google Scholar returns twice as many relevant articles as PubMed and provides greater access to free full-text articles. PMID:23948488

  3. MedlinePlus.gov Turns 10!

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    ... page please turn Javascript on. Photo courtesy of Michael Spencer, NIH NIH MedlinePlus Advisory Group celebrates 10 years of success. Photo courtesy of Michael Spencer, NIH NIH's MedlinePlus.gov , the popular, consumer- ...

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  9. MedlinePlus Milestones: 1998-present

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  13. Poor Reliability between Cochrane Reviewers and Blinded External Reviewers When Applying the Cochrane Risk of Bias Tool in Physical Therapy Trials

    PubMed Central

    Armijo-Olivo, Susan; Ospina, Maria; da Costa, Bruno R.; Egger, Matthias; Saltaji, Humam; Fuentes, Jorge; Ha, Christine; Cummings, Greta G.

    2014-01-01

    Objectives To test the inter-rater reliability of the RoB tool applied to Physical Therapy (PT) trials by comparing ratings from Cochrane review authors with those of blinded external reviewers. Methods Randomized controlled trials (RCTs) in PT were identified by searching the Cochrane Database of Systematic Reviews for meta-analysis of PT interventions. RoB assessments were conducted independently by 2 reviewers blinded to the RoB ratings reported in the Cochrane reviews. Data on RoB assessments from Cochrane reviews and other characteristics of reviews and trials were extracted. Consensus assessments between the two reviewers were then compared with the RoB ratings from the Cochrane reviews. Agreement between Cochrane and blinded external reviewers was assessed using weighted kappa (κ). Results In total, 109 trials included in 17 Cochrane reviews were assessed. Inter-rater reliability on the overall RoB assessment between Cochrane review authors and blinded external reviewers was poor (κ  =  0.02, 95%CI: −0.06, 0.06]). Inter-rater reliability on individual domains of the RoB tool was poor (median κ  = 0.19), ranging from κ  =  −0.04 (“Other bias”) to κ  =  0.62 (“Sequence generation”). There was also no agreement (κ  =  −0.29, 95%CI: −0.81, 0.35]) in the overall RoB assessment at the meta-analysis level. Conclusions Risk of bias assessments of RCTs using the RoB tool are not consistent across different research groups. Poor agreement was not only demonstrated at the trial level but also at the meta-analysis level. Results have implications for decision making since different recommendations can be reached depending on the group analyzing the evidence. Improved guidelines to consistently apply the RoB tool and revisions to the tool for different health areas are needed. PMID:24824199

  14. MedlinePlus XML Data Sources

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  15. MedlinePlus XML Data Sources

    MedlinePlus

    MedlinePlus XML Data Sources MedlinePlus Web Service The MedlinePlus Web service accepts keyword searches as requests and returns relevant health topics ... about the health topic, as well as associated data, such as all of the links that appear ...

  16. MEDLINE on the Internet: "Healthier" than Before?

    ERIC Educational Resources Information Center

    Buntrock, Robert E.

    1997-01-01

    Examines some of the many Internet/World Wide Web versions of MEDLINE and reports whether the file is "healthier" now than it was before. Describes two search examples and two non-National Library of Medicine Web MEDLINE sites. Notes that for MEDLINE searching, the user should pick a couple of sites and perform a personal comparisons and…

  17. [Use of PubMed to improve evidence-based medicine in routine urological practice].

    PubMed

    Rink, M; Kluth, L A; Shariat, S F; Chun, F K; Fisch, M; Dahm, P

    2013-03-01

    Applying evidence-based medicine in daily clinical practice is the basis of patient-centered medicine and knowledge of accurate literature acquisition skills is necessary for informed clinical decision-making. PubMed is an easy accessible, free bibliographic database comprising over 21 million citations from the medical field, life-science journals and online books. The article summarizes the effective use of PubMed in routine urological clinical practice based on a common case scenario. This article explains the simple use of PubMed to obtain the best search results with the highest evidence. Accurate knowledge about the use of PubMed in routine clinical practice can improve evidence-based medicine and also patient treatment. PMID:23503794

  18. Impact of Including Korean Randomized Controlled Trials in Cochrane Reviews of Acupuncture

    PubMed Central

    Kim, Kun Hyung; Kong, Jae Cheol; Choi, Jun-Yong; Choi, Tae-Young; Shin, Byung-Cheul; McDonald, Steve; Lee, Myeong Soo

    2012-01-01

    Objective Acupuncture is commonly practiced in Korea and is regularly evaluated in clinical trials. Although many Cochrane reviews of acupuncture include searches of both English and Chinese databases, there is no information on the value of searching Korean databases. This study aimed to investigate the impact of searching Korean databasesand journals for trials eligible for inclusion in existing Cochrane acupuncture reviews. Methods We searched 12 Korean databases and seven Korean journals to identify randomised trials meeting the inclusion criteria for acupuncture reviews in the Cochrane Database of Systematic Reviews. We compared risk of bias assessments of the Korean trials with the trials included in the Cochrane acupuncture reviews. Where possible, we added data from the Korean trials to the existing meta-analyses in the relevant Cochrane review and conducted sensitivity analyses to test the robustness of the results. Results Sixteen Korean trials (742 participants) met the inclusion criteria for eight Cochrane acupuncture reviews (125 trials; 13,041 participants). Inclusion of the Korean trials provided data for 20% of existing meta-analyses (24 out of 120). Inclusion of the Korean trials did not change the direction of effect in any of the existing meta-analyses. The effect size and heterogeneity remained mostly unchanged. In only one meta-analysis did the significance change. Compared to the studies included in the Cochrane acupuncture reviews, the risk of bias in the Korean trials was higher in terms of outcome assessor blinding and allocation concealment. Conclusions Many Korean studies contributed additional data to the existing meta-analyses in Cochrane acupuncture reviews. Although inclusion of these studies did not alter the results of the meta-analyses, comprehensive searches of the literature are important to avoid potential language bias. The identification and inclusion of eligible Korean trials should be considered for reviews of acupuncture

  19. The Next Wave of Biological Agents for the Treatment of IBD: Evidence from Cochrane Reviews.

    PubMed

    Khanna, Reena; Chande, Nilesh; Vermeire, Séverine; Sandborn, William J; Parker, Claire E; Feagan, Brian G

    2016-07-01

    Multiple new biological treatments for Crohn's disease and ulcerative colitis are becoming available. Specifically, vedolizumab and ustekinumab are monoclonal antibodies that target molecular pathways relevant to disease pathogenesis. What can Cochrane reviews tell us about the efficacy, safety, and immunogenicity of these new agents? A Cochrane inflammatory bowel disease group symposium held at the 2015 Digestive Diseases Week annual meeting addressed these questions. This article reviews the data presented at that session. PMID:27306074

  20. Considerations from the risk of bias perspective for updating Cochrane reviews.

    PubMed

    Mayhew, Alain D; Kabir, Monisha; Ansari, Mohammed T

    2015-01-01

    Authors of Cochrane reviews are expected to update their reviews every 2 years. The updating process helps to ensure that reviews are current and include recent evidence. However, the updating process is time-consuming for authors, particularly when Cochrane methods evolve and authors are required to revisit some of the originally included studies.The Cochrane Collaboration's 'Risk of bias' tool is a mandatory component of Cochrane reviews, providing an assessment of the potential biases of included studies. The tool has been modified most recently in 2011, and the expectation is that new versions will continue to be produced and utilised in all Cochrane reviews. In this commentary we discuss, in the context of updating scenarios that are likely to be encountered, the potential options systematic review authors may have recourse to when the Cochrane Collaboration's 'Risk of bias' tool has been modified between the original review and its update. We recommend that authors who are updating reviews should revise their original assessments of included studies using the most recent version of the risk of bias tool. Despite the increased workload, use of the most recent version of the tool facilitates consistency of methods and reporting both across and within reviews, and ensures currency to the methodological rigour. PMID:26445323

  1. Author Name Disambiguation in MEDLINE

    PubMed Central

    TORVIK, VETLE I.; SMALHEISER, NEIL R.

    2009-01-01

    Background We recently described “Author-ity,” a model for estimating the probability that two articles in MEDLINE, sharing the same author name, were written by the same individual. Features include shared title words, journal name, coauthors, medical subject headings, language, affiliations, and author name features (middle initial, suffix, and prevalence in MEDLINE). Here we test the hypothesis that the Author-ity model will suffice to disambiguate author names for the vast majority of articles in MEDLINE. Methods Enhancements include: (a) incorporating first names and their variants, email addresses, and correlations between specific last names and affiliation words; (b) new methods of generating large unbiased training sets; (c) new methods for estimating the prior probability; (d) a weighted least squares algorithm for correcting transitivity violations; and (e) a maximum likelihood based agglomerative algorithm for computing clusters of articles that represent inferred author-individuals. Results Pairwise comparisons were computed for all author names on all 15.3 million articles in MEDLINE (2006 baseline), that share last name and first initial, to create Author-ity 2006, a database that has each name on each article assigned to one of 6.7 million inferred author-individual clusters. Recall is estimated at ~98.8%. Lumping (putting two different individuals into the same cluster) affects ~0.5% of clusters, whereas splitting (assigning articles written by the same individual to >1 cluster) affects ~2% of articles. Impact The Author-ity model can be applied generally to other bibliographic databases. Author name disambiguation allows information retrieval and data integration to become person-centered, not just document-centered, setting the stage for new data mining and social network tools that will facilitate the analysis of scholarly publishing and collaboration behavior. Availability The Author-ity 2006 database is available for nonprofit academic

  2. MET network in PubMed: a text-mined network visualization and curation system

    PubMed Central

    Dai, Hong-Jie; Su, Chu-Hsien; Lai, Po-Ting; Huang, Ming-Siang; Jonnagaddala, Jitendra; Rose Jue, Toni; Rao, Shruti; Chou, Hui-Jou; Milacic, Marija; Singh, Onkar; Syed-Abdul, Shabbir; Hsu, Wen-Lian

    2016-01-01

    Metastasis is the dissemination of a cancer/tumor from one organ to another, and it is the most dangerous stage during cancer progression, causing more than 90% of cancer deaths. Improving the understanding of the complicated cellular mechanisms underlying metastasis requires investigations of the signaling pathways. To this end, we developed a METastasis (MET) network visualization and curation tool to assist metastasis researchers retrieve network information of interest while browsing through the large volume of studies in PubMed. MET can recognize relations among genes, cancers, tissues and organs of metastasis mentioned in the literature through text-mining techniques, and then produce a visualization of all mined relations in a metastasis network. To facilitate the curation process, MET is developed as a browser extension that allows curators to review and edit concepts and relations related to metastasis directly in PubMed. PubMed users can also view the metastatic networks integrated from the large collection of research papers directly through MET. For the BioCreative 2015 interactive track (IAT), a curation task was proposed to curate metastatic networks among PubMed abstracts. Six curators participated in the proposed task and a post-IAT task, curating 963 unique metastatic relations from 174 PubMed abstracts using MET. Database URL: http://btm.tmu.edu.tw/metastasisway PMID:27242035

  3. Measuring Medical Student Preference: A Comparison of Classroom Versus Online Instruction for Teaching Pubmed*EC

    PubMed Central

    Schimming, Laura M.

    2008-01-01

    Objective: The research analyzed evaluation data to assess medical student satisfaction with the learning experience when required PubMed training is offered entirely online. Methods: A retrospective study analyzed skills assessment scores and student feedback forms from 455 first-year medical students who completed PubMed training either through classroom sessions or an online tutorial. The class of 2006 (n = 99) attended traditional librarian-led sessions in a computer classroom. The classes of 2007 (n = 120), 2008 (n = 121), and 2009 (n = 115) completed the training entirely online through a self-paced tutorial. PubMed skills assessment scores and student feedback about the training were compared for all groups. Results: As evidenced by open-ended comments about the training, students who took the online tutorial were equally or more satisfied with the learning experience than students who attended classroom sessions, with the classes of 2008 and 2009 reporting greater satisfaction (P<0.001) than the other 2 groups. The mean score on the PubMed skills assessment (91%) was the same for all groups of students. Conclusions: Student satisfaction improved and PubMed assessment scores did not change when instruction was offered online to first-year medical students. Comments from the students who received online training suggest that the increased control and individual engagement with the web-based content led to their satisfaction with the online tutorial. PMID:18654658

  4. MET network in PubMed: a text-mined network visualization and curation system.

    PubMed

    Dai, Hong-Jie; Su, Chu-Hsien; Lai, Po-Ting; Huang, Ming-Siang; Jonnagaddala, Jitendra; Rose Jue, Toni; Rao, Shruti; Chou, Hui-Jou; Milacic, Marija; Singh, Onkar; Syed-Abdul, Shabbir; Hsu, Wen-Lian

    2016-01-01

    Metastasis is the dissemination of a cancer/tumor from one organ to another, and it is the most dangerous stage during cancer progression, causing more than 90% of cancer deaths. Improving the understanding of the complicated cellular mechanisms underlying metastasis requires investigations of the signaling pathways. To this end, we developed a METastasis (MET) network visualization and curation tool to assist metastasis researchers retrieve network information of interest while browsing through the large volume of studies in PubMed. MET can recognize relations among genes, cancers, tissues and organs of metastasis mentioned in the literature through text-mining techniques, and then produce a visualization of all mined relations in a metastasis network. To facilitate the curation process, MET is developed as a browser extension that allows curators to review and edit concepts and relations related to metastasis directly in PubMed. PubMed users can also view the metastatic networks integrated from the large collection of research papers directly through MET. For the BioCreative 2015 interactive track (IAT), a curation task was proposed to curate metastatic networks among PubMed abstracts. Six curators participated in the proposed task and a post-IAT task, curating 963 unique metastatic relations from 174 PubMed abstracts using MET.Database URL: http://btm.tmu.edu.tw/metastasisway. PMID:27242035

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

    PubMed Central

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

    2006-01-01

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

  6. Cochrane Summary of Findings: Horse Chestnut Seed Extract for Chronic Venous Insufficiency

    PubMed Central

    Underland, Vigdis; Sæterdal, Ingvil

    2012-01-01

    As part of its efforts to disseminate the results of Cochrane reviews to a wider audience, the Cochrane Complementary and Alternative Medicine (CAM) Field develops Summary of Findings (SoF) tables and then uses these tables as a basis for its Plain Language Summaries. In each SoF table, the most important outcomes of the review, the effect of the intervention on each outcome, and the quality of the evidence for each outcome are presented. The process of developing the SoF table involves deciding which outcomes to present for which time points and evaluating the strength and quality of the evidence for the outcomes. The Cochrane CAM Field contacted the authors of this review to request clarification on any points that are not understood in the Cochrane review and also to request their review of the SoF. In this article, review authors in the Cochrane Collaboration reviewed the effects of horse chestnut seed extract for chronic venous insufficiency. PMID:24278808

  7. NIH Quickfinder and NIH Medline Plus Advisory Group | NIH MedlinePlus the Magazine

    MedlinePlus

    ... on. NIH Quickfinder and NIH Medline Plus Advisory Group Past Issues / Summer 2015 Table of Contents For ... nih.gov (301) 402-1770 NIH MedlinePlus Advisory Group Marin P. Allen, Ph.D., Office of Communications ...

  8. Visit the new MedlinePlus | NIH MedlinePlus the Magazine

    MedlinePlus

    ... of this page please turn Javascript on. Visit the new MedlinePlus Past Issues / Fall 2010 Table of ... Free, trusted, up-to-date medical information Visit the new MedlinePlus From the top medical experts at ...

  9. Visit the new MedlinePlus | NIH MedlinePlus the Magazine

    MedlinePlus

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  10. The impact of Cochrane Systematic Reviews: a mixed method evaluation of outputs from Cochrane Review Groups supported by the UK National Institute for Health Research

    PubMed Central

    2014-01-01

    Background There has been a growing emphasis on evidence-informed decision-making in health care. Systematic reviews, such as those produced by the Cochrane Collaboration, have been a key component of this movement. The UK National Institute for Health Research (NIHR) Systematic Review Programme currently supports 20 Cochrane Review Groups (CRGs). The aim of this study was to identify the impacts of Cochrane reviews published by NIHR-funded CRGs during the years 2007–2011. Methods We sent questionnaires to CRGs and review authors, interviewed guideline developers and used bibliometrics and documentary review to get an overview of CRG impact and to evaluate the impact of a sample of 60 Cochrane reviews. We used a framework with four categories (knowledge production, research targeting, informing policy development and impact on practice/services). Results A total of 1,502 new and updated reviews were produced by the 20 NIHR-funded CRGs between 2007 and 2011. The clearest impacts were on policy with a total of 483 systematic reviews cited in 247 sets of guidance: 62 were international, 175 national (87 from the UK) and 10 local. Review authors and CRGs provided some examples of impact on practice or services, for example, safer use of medication, the identification of new effective drugs or treatments and potential economic benefits through the reduction in the use of unproven or unnecessary procedures. However, such impacts are difficult to objectively document, and the majority of reviewers were unsure if their review had produced specific impacts. Qualitative data suggested that Cochrane reviews often play an instrumental role in informing guidance, although a poor fit with guideline scope or methods, reviews being out of date and a lack of communication between CRGs and guideline developers were barriers to their use. Conclusions Health and economic impacts of research are generally difficult to measure. We found that to be the case with this evaluation

  11. Systematic Reviews Published in the October 2015 Issue of the Cochrane Library.

    PubMed

    Wiffen, Philip J

    2016-01-01

    The Cochrane Library of Systematic Reviews is published quarterly as a DVD and monthly online (http://www.thecochranelibrary.com). The October 2015 issue (fourth DVD for 2015) contains 6622 complete reviews, 2429 protocols for reviews in production, and 36,600 short summaries of systematic reviews published in the general medical literature (this short summary database is no longer being updated). In addition, there are citations of 848,000 randomized controlled trials, and 15,700 cited papers in the Cochrane Methodology Register. The Health Technology Assessment database contains some 15,000 citations. One hundred and nine new reviews have been published in the previous 3 months, of which six have potential relevance for practitioners in pain and palliative medicine. The impact factor of the Cochrane Library stands at 5.939. Readers are encouraged to access the full report for any articles of interest as only a brief commentary is provided. PMID:27007584

  12. An enhanced version of Cochran-Armitage trend test for genome-wide association studies.

    PubMed

    Ghodsi, Mansi; Amiri, Saeid; Hassani, Hossein; Ghodsi, Zara

    2016-09-01

    Genome-wide association studies the evaluation of association between candidate gene and disease status is widely carried out using Cochran-Armitage trend test. However, only a small number of research papers have evaluated the distribution of p-values for the Cochran-Armitage trend test. In this paper, an enhanced version of Cochran-Armitage trend test based on bootstrap approach is introduced. The achieved results confirm that the distribution of p-values of the proposed approach fits better to the uniform distribution, and it is thus concluded that the proposed method, which needs less assumptions in comparison with the conventional method, can be successfully used to test the genetic association. PMID:27617223

  13. Information for Librarians and Trainers: MedlinePlus

    MedlinePlus

    ... with your classes and health fairs. Resources for Teaching MedlinePlus MedlinePlus Tour MedlinePlus Tour in English and ... MedlinePlus Quality Guidelines MedlinePlus Search Tips Resources for Teaching How to Find Health Information Online General Evaluating ...

  14. Visit the MedlinePlus Search Cloud | NIH MedlinePlus the Magazine

    MedlinePlus

    ... of this page please turn Javascript on. Visit the MedlinePlus Search Cloud Past Issues / Winter 2011 Table ... Free, trusted, up-to-date medical information Visit the new MedlinePlus Visit the MedlinePlus search cloud, featuring ...

  15. Risk Factors for Bladder Cancer: Challenges of Conducting a Literature Search Using PubMed

    PubMed Central

    Joshi, Ashish; Preslan, Elicia

    2011-01-01

    The objective of this study was to assess the risk factors for bladder cancer using PubMed articles from January 2000 to December 2009. The study also aimed to describe the challenges encountered in the methodology of a literature search for bladder cancer risk factors using PubMed. Twenty-six categories of risk factors for bladder cancer were identified using the National Cancer Institute Web site and the Medical Subject Headings (MeSH) Web site. A total of 1,338 PubMed searches were run using the term “urinary bladder cancer” and a risk factor term (e.g., “cigarette smoking”) and were screened to identify 260 articles for final analysis. The search strategy had an overall precision of 3.42 percent, relative recall of 12.64 percent, and an F -measure of 5.39 percent. Although search terms derived from MeSH had the highest overall precision and recall, the differences did not reach significance, which indicates that for generalized, free-text searches of the PubMed database, the searchers' own terms are generally as effective as MeSH terms. PMID:21464862

  16. Multi-lingual search engine to access PubMed monolingual subsets: a feasibility study.

    PubMed

    Darmoni, Stéfan J; Soualmia, Lina F; Griffon, Nicolas; Grosjean, Julien; Kerdelhué, Gaétan; Kergourlay, Ivan; Dahamna, Badisse

    2013-01-01

    PubMed contains many articles in languages other than English but it is difficult to find them using the English version of the Medical Subject Headings (MeSH) Thesaurus. The aim of this work is to propose a tool allowing access to a PubMed subset in one language, and to evaluate its performance. Translations of MeSH were enriched and gathered in the information system. PubMed subsets in main European languages were also added in our database, using a dedicated parser. The CISMeF generic semantic search engine was evaluated on the response time for simple queries. MeSH descriptors are currently available in 11 languages in the information system. All the 654,000 PubMed citations in French were integrated into CISMeF database. None of the response times exceed the threshold defined for usability (2 seconds). It is now possible to freely access biomedical literature in French using a tool in French; health professionals and lay people with a low English language may find it useful. It will be expended to several European languages: German, Spanish, Norwegian and Portuguese. PMID:23920740

  17. MedlinePlus Connect: Technical Information

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  1. MedlinePlus FAQ: News Coverage

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  11. The updated Cochrane review 2014 on GnRH agonist trigger: repeating the same errors.

    PubMed

    Kol, Shahar; Humaidan, Peter; Alsbjerg, Birgit; Engmann, Lawrence; Benadiva, Claudio; García-Velasco, Juan A; Fatemi, Human; Andersen, Claus Yding

    2015-06-01

    Cochrane reviews are powerful tools, internationally recognized as the highest standard in evidence-based health care. A Cochrane analysis makes use of precise, reproducible criteria in the selection of studies for review. In the context of a previous Cochrane review (2010) on the subject of gonadotrophin-releasing hormone agonist (GnRHa) trigger, we questioned whether a review should be conducted during the research phase when new concepts are being developed. Recently, an updated Cochrane review was published, reaching the same general conclusion as the first one, i.e., GnRHa triggers lower the chance of pregnancy in fresh autologous IVF and intracytoplasmic injection treatment cycles. We argue that the new review repeats previous errors by compiling data from studies that were not comparable as different luteal phase protocols were used. From the clinical point of view, the luteal support used is the variable which affects the pregnancy rate and not the use of the GnRHa trigger for final oocyte maturation. Therefore, a meaningful comparison between GnRHa and HCG trigger must be confined to outcome measures that are not affected by the luteal support used. We conclude that the updated review falls short of addressing meaningful clinical and fundamental questions in the context of GnRHa trigger. PMID:25892499

  12. 78 FR 62678 - Morris W. Cochran, M.D.; Decision and Order

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-22

    ... action.'' R.D. at 11 (citing Kamal Tiwari, 76 FR 76 FR 71604, 71605 (2011)). This is an... finding that the practitioner's federal registration had been suspended. See 76 FR at 71606 (discussing... Morris W. Cochran, 77 FR 17505 (2012). Following the hearing, which lasted three days, the ALJ issued...

  13. Assessing Diagnostic Expertise of Counselors Using the Cochran-Weiss-Shanteau (CWS) Index

    ERIC Educational Resources Information Center

    Witteman, Cilia L. M.; Weiss, David J.; Metzmacher, Martin

    2012-01-01

    Counseling studies have shown that increasing experience is not always associated with better judgments. However, in such studies performance is assessed against external criteria, which may lack validity. The authors applied the Cochran-Weiss-Shanteau (CWS) index, which assesses the ability to consistently discriminate. Results showed that novice…

  14. A Cochran-Armitage-type and a score-free global test for multivariate ordinal data.

    PubMed

    Jelizarow, Monika; Mansmann, Ulrich; Goeman, Jelle J

    2016-07-20

    We propose a Cochran-Armitage-type and a score-free global test that can be used to assess the presence of an association between a set of ordinally scaled covariates and an outcome variable within the range of generalized linear models. Both tests are developed within the framework of the well-established 'global test' methodology and as such are feasible in high-dimensional data situations under any correlation and enable adjustment for covariates. The Cochran-Armitage-type test, for which an intimate connection with the traditional score-based Cochran-Armitage test is shown, rests upon explicit assumptions on the distances between the covariates' ordered categories. The score-free test, in contrast, parametrizes these distances and thus keeps them flexible, rendering it ideally suited for covariates measured on an ordinal scale. As confirmed by means of simulations, the Cochran-Armitage-type test focuses its power on set-outcome relationships where the distances between the covariates' categories are equal or close to those assumed, whereas the score-free test spreads its power over a wide range of possible set-outcome relationships, putting more emphasis on monotonic than on non-monotonic ones. Based on the tests' power properties, it is discussed when to favour one or the other, and the practical merits of both of them are illustrated by an application in the field of rehabilitation medicine. Our proposed tests are implemented in the R package globaltest. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26924287

  15. Ideology and Reform in Teacher Education in England: Some Reflections on Cochran-Smith and Fries.

    ERIC Educational Resources Information Center

    Furlong, John

    2002-01-01

    Presents an international perspective on Cochran-Smith and Fries' recent analysis of the ways that two competing ideologies (deregulation and professionalization) are being employed in the United States to support teacher education reform, noting important differences between the United States and England in how these ideologies have been advanced…

  16. Issues in the incorporation of economic perspectives and evidence into Cochrane reviews

    PubMed Central

    2013-01-01

    Background Methods for systematic reviews of the effects of health interventions have focused mainly on addressing the question of 'What works?’ or 'Is this intervention effective in achieving one or more specific outcomes?’ Addressing the question 'Is it worth it given the resources available?’ has received less attention. This latter question can be addressed by applying an economic lens to the systematic review process. This paper reflects on the value and desire for the consideration by end users for coverage of an economic perspective in a Cochrane review and outlines two potential approaches and future directions. Methods Two frameworks to guide review authors who are seeking to include an economic perspective are outlined. The first involves conducting a full systematic review of economic evaluations that is integrated into a review of intervention effects. The second involves developing a brief economic commentary. The two approaches share a set of common stages but allow the tailoring of the economic component of the Cochrane review to the skills and resources available to the review team. Results The number of studies using the methods outlined in the paper is limited, and further examples are needed both to explore the value of these approaches and to further develop them. The rate of progress will hinge on the organisational leadership, capacity and resources available to the CCEMG, author teams and other Cochrane entities. Particular methodological challenges to overcome relate to understanding the key economic trade-offs and casual relationships for a given decision problem and informing the development of evaluations designed to support local decision-makers. Conclusions Methods for incorporating economic perspectives and evidence into Cochrane intervention reviews are established. Their role is not to provide a precise estimate of 'cost-effectiveness’ but rather to help end-users of Cochrane reviews to determine the implications of the

  17. An analysis of gene/protein associations at PubMed scale

    PubMed Central

    2011-01-01

    Background Event extraction following the GENIA Event corpus and BioNLP shared task models has been a considerable focus of recent work in biomedical information extraction. This work includes efforts applying event extraction methods to the entire PubMed literature database, far beyond the narrow subdomains of biomedicine for which annotated resources for extraction method development are available. Results In the present study, our aim is to estimate the coverage of all statements of gene/protein associations in PubMed that existing resources for event extraction can provide. We base our analysis on a recently released corpus automatically annotated for gene/protein entities and syntactic analyses covering the entire PubMed, and use named entity co-occurrence, shortest dependency paths and an unlexicalized classifier to identify likely statements of gene/protein associations. A set of high-frequency/high-likelihood association statements are then manually analyzed with reference to the GENIA ontology. Conclusions We present a first estimate of the overall coverage of gene/protein associations provided by existing resources for event extraction. Our results suggest that for event-type associations this coverage may be over 90%. We also identify several biologically significant associations of genes and proteins that are not addressed by these resources, suggesting directions for further extension of extraction coverage. PMID:22166173

  18. Classification of Clinically Useful Sentences in MEDLINE

    PubMed Central

    Morid, Mohammad Amin; Jonnalagadda, Siddhartha; Fiszman, Marcelo; Raja, Kalpana; Fiol, Guilherme Del

    2015-01-01

    Objective In a previous study, we investigated a sentence classification model that uses semantic features to extract clinically useful sentences from UpToDate, a synthesized clinical evidence resource. In the present study, we assess the generalizability of the sentence classifier to Medline abstracts. Methods We applied the classification model to an independent gold standard of high quality clinical studies from Medline. Then, the classifier trained on UpToDate sentences was optimized by re-retraining the classifier with Medline abstracts and adding a sentence location feature. Results The previous classifier yielded an F-measure of 58% on Medline versus 67% on UpToDate. Re-training the classifier on Medline improved F-measure to 68%; and to 76% (p<0.01) after adding the sentence location feature. Conclusions The classifier’s model and input features generalized to Medline abstracts, but the classifier needed to be retrained on Medline to achieve equivalent performance. Sentence location provided additional contribution to the overall classification performance. PMID:26958301

  19. MELVYL MEDLINE: a library services perspective.

    PubMed Central

    Horres, M M; Starr, S S; Renford, B L

    1991-01-01

    The MELVYL MEDLINE project resulted in the addition of a full five-year subset of MEDLINE to the University of California's (UC) MELVYL online union catalog. As one of the nation's largest MEDLINE end-user searching systems, MELVYL MEDLINE provides online bibliographic access to the biomedical journal literature for all UC personnel at over seventy library sites or by remote access. This paper summarizes the project's accomplishments, reports MELVYL MEDLINE use and its impact on library services, and provides insights for other end-user search systems. The project serves as a model for adding databases to the MELVYL catalog and demonstrates the potential for use by other disciplines of a specialized database when readily accessible. Evaluation results report high user satisfaction and high usage. However, many advanced searching features of the interface are little used by searchers. Effects on library services include marked increases in reference transactions and interlibrary loans, with significant declines in mediated search services. Future MELVYL MEDLINE enhancements include matching search retrievals to journal locations, linkage to an online document delivery system, and consideration of building a superset of databases by combining MELVYL MEDLINE with citations from another database in the MELVYL catalog. PMID:1884086

  20. Bibliometric analysis of leishmaniasis research in Medline (1945-2010)

    PubMed Central

    2013-01-01

    Background Publications are often used as a measure of success of research work. Leishmaniasis is considered endemic in 98 countries, most of which are developing. This article describes a bibliometric review of the literature on leishmaniasis research indexed in PubMed during a 66-year period. Methods Medline was used via the PubMed online service of the US National Library of Medicine. The search strategy was Leishmania [MeSH] or leishmaniasis [MeSH] from 1 January 1945 until 31 December 2010. Neither language nor document type restrictions were employed. Results A total of 20,780 references were retrieved. The number of publications increased steadily over time, with 3,380 publications from 1945-1980 to 8,267 from 2001-2010. Leishmaniasis documents were published in 1,846 scientific journals, and Transactions of the Royal Society of Tropical Medicine and Hygiene (4.9%) was the top one. The USA was the predominant country by considering the first author’s institutional address (16.8%), followed by Brazil (14.9%), and then India (9.0%), however Brazil leads the scientific output in 2001-2010 period (18.5%), followed by the USA (13.5%) and India (10%). The production ranking changed when the number of publications was normalised by population (Israel and Switzerland), by gross domestic product (Nepal and Tunisia), and by gross national income per capita (India and Ethiopia). For geographical area, Europe led (31.7%), followed by Latin America (24.5%). Conclusions We have found an increase in the number of publications in the field of leishmaniasis. The USA and Brazil led scientific production on leishmaniasis research. PMID:23497410

  1. Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation

    PubMed Central

    Huang, Chung-Chi; Lu, Zhiyong

    2016-01-01

    Identifying relevant papers from the literature is a common task in biocuration. Most current biomedical literature search systems primarily rely on matching user keywords. Semantic search, on the other hand, seeks to improve search accuracy by understanding the entities and contextual relations in user keywords. However, past research has mostly focused on semantically identifying biological entities (e.g. chemicals, diseases and genes) with little effort on discovering semantic relations. In this work, we aim to discover biomedical semantic relations in PubMed queries in an automated and unsupervised fashion. Specifically, we focus on extracting and understanding the contextual information (or context patterns) that is used by PubMed users to represent semantic relations between entities such as ‘CHEMICAL-1 compared to CHEMICAL-2.’ With the advances in automatic named entity recognition, we first tag entities in PubMed queries and then use tagged entities as knowledge to recognize pattern semantics. More specifically, we transform PubMed queries into context patterns involving participating entities, which are subsequently projected to latent topics via latent semantic analysis (LSA) to avoid the data sparseness and specificity issues. Finally, we mine semantically similar contextual patterns or semantic relations based on LSA topic distributions. Our two separate evaluation experiments of chemical-chemical (CC) and chemical–disease (CD) relations show that the proposed approach significantly outperforms a baseline method, which simply measures pattern semantics by similarity in participating entities. The highest performance achieved by our approach is nearly 0.9 and 0.85 respectively for the CC and CD task when compared against the ground truth in terms of normalized discounted cumulative gain (nDCG), a standard measure of ranking quality. These results suggest that our approach can effectively identify and return related semantic patterns in a ranked

  2. Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation.

    PubMed

    Huang, Chung-Chi; Lu, Zhiyong

    2016-01-01

    Identifying relevant papers from the literature is a common task in biocuration. Most current biomedical literature search systems primarily rely on matching user keywords. Semantic search, on the other hand, seeks to improve search accuracy by understanding the entities and contextual relations in user keywords. However, past research has mostly focused on semantically identifying biological entities (e.g. chemicals, diseases and genes) with little effort on discovering semantic relations. In this work, we aim to discover biomedical semantic relations in PubMed queries in an automated and unsupervised fashion. Specifically, we focus on extracting and understanding the contextual information (or context patterns) that is used by PubMed users to represent semantic relations between entities such as 'CHEMICAL-1 compared to CHEMICAL-2' With the advances in automatic named entity recognition, we first tag entities in PubMed queries and then use tagged entities as knowledge to recognize pattern semantics. More specifically, we transform PubMed queries into context patterns involving participating entities, which are subsequently projected to latent topics via latent semantic analysis (LSA) to avoid the data sparseness and specificity issues. Finally, we mine semantically similar contextual patterns or semantic relations based on LSA topic distributions. Our two separate evaluation experiments of chemical-chemical (CC) and chemical-disease (CD) relations show that the proposed approach significantly outperforms a baseline method, which simply measures pattern semantics by similarity in participating entities. The highest performance achieved by our approach is nearly 0.9 and 0.85 respectively for the CC and CD task when compared against the ground truth in terms of normalized discounted cumulative gain (nDCG), a standard measure of ranking quality. These results suggest that our approach can effectively identify and return related semantic patterns in a ranked order

  3. NEMO: Extraction and normalization of organization names from PubMed affiliation strings

    PubMed Central

    Jonnalagadda, Siddhartha; Topham, Philip

    2010-01-01

    Background. We are witnessing an exponential increase in biomedical research citations in PubMed. However, translating biomedical discoveries into practical treatments is estimated to take around 17 years, according to the 2000 Yearbook of Medical Informatics, and much information is lost during this transition. Pharmaceutical companies spend huge sums to identify opinion leaders and centers of excellence. Conventional methods such as literature search, survey, observation, self-identification, expert opinion, and sociometry not only need much human effort, but are also noncomprehensive. Such huge delays and costs can be reduced by “connecting those who produce the knowledge with those who apply it”. A humble step in this direction is large scale discovery of persons and organizations involved in specific areas of research. This can be achieved by automatically extracting and disambiguating author names and affiliation strings retrieved through Medical Subject Heading (MeSH) terms and other keywords associated with articles in PubMed. In this study, we propose NEMO (Normalization Engine for Matching Organizations), a system for extracting organization names from the affiliation strings provided in PubMed abstracts, building a thesaurus (list of synonyms) of organization names, and subsequently normalizing them to a canonical organization name using the thesaurus. Results: We used a parsing process that involves multi-layered rule matching with multiple dictionaries. The normalization process involves clustering based on weighted local sequence alignment metrics to address synonymy at word level, and local learning based on finding connected components to address synonymy. The graphical user interface and java client library of NEMO are available at http://lnxnemo.sourceforge.net . Conclusion: NEMO is developed to associate each biomedical paper and its authors with a unique organization name and the geopolitical location of that organization. This system

  4. Archibald Cochrane (1909–1988): the father of evidence-based medicine

    PubMed Central

    Stavrou, Antonio; Challoumas, Dimitrios; Dimitrakakis, Georgios

    2014-01-01

    Professor Archibald Cochrane (1909–1988) is considered to be the originator of the idea of evidence-based medicine in our era. With his landmark book ‘Effectiveness and Efficiency: Random Reflections on Health services’ he managed to inspire and positively influence the medical society with respect to the proper assessment of reliable evidence for the provision of the best medical care. His vision combined with his scientific achievements can be considered as the foundation of the Cochrane Collaboration; named after him in recognition of and gratitude for his pioneering work. We present the highlights of his adventurous and vibrant personal and academic life in an attempt to honour his contribution to shaping modern medical research. PMID:24140816

  5. Saving the Time of the Library User through Subject Access Innovation: Papers in Honor of Pauline Atherton Cochrane.

    ERIC Educational Resources Information Center

    Wheeler, William J., Ed.

    This book contains the following papers in honor of Pauline Atherton Cochrane on subject access issues in library and information science: (1) "Obstacles in Progress in Mechanized Subject Access and the Necessity of a Paradigm Change" (Robert Fugmann); (2) "On MARC and the Nature of Text Searching: A Review of Pauline Cochrane's Inspirational…

  6. Cluster Randomised Trials in Cochrane Reviews: Evaluation of Methodological and Reporting Practice

    PubMed Central

    Richardson, Marty; Garner, Paul; Donegan, Sarah

    2016-01-01

    Objective Systematic reviews can include cluster-randomised controlled trials (C-RCTs), which require different analysis compared with standard individual-randomised controlled trials. However, it is not known whether review authors follow the methodological and reporting guidance when including these trials. The aim of this study was to assess the methodological and reporting practice of Cochrane reviews that included C-RCTs against criteria developed from existing guidance. Methods Criteria were developed, based on methodological literature and personal experience supervising review production and quality. Criteria were grouped into four themes: identifying, reporting, assessing risk of bias, and analysing C-RCTs. The Cochrane Database of Systematic Reviews was searched (2nd December 2013), and the 50 most recent reviews that included C-RCTs were retrieved. Each review was then assessed using the criteria. Results The 50 reviews we identified were published by 26 Cochrane Review Groups between June 2013 and November 2013. For identifying C-RCTs, only 56% identified that C-RCTs were eligible for inclusion in the review in the eligibility criteria. For reporting C-RCTs, only eight (24%) of the 33 reviews reported the method of cluster adjustment for their included C-RCTs. For assessing risk of bias, only one review assessed all five C-RCT-specific risk-of-bias criteria. For analysing C-RCTs, of the 27 reviews that presented unadjusted data, only nine (33%) provided a warning that confidence intervals may be artificially narrow. Of the 34 reviews that reported data from unadjusted C-RCTs, only 13 (38%) excluded the unadjusted results from the meta-analyses. Conclusions The methodological and reporting practices in Cochrane reviews incorporating C-RCTs could be greatly improved, particularly with regard to analyses. Criteria developed as part of the current study could be used by review authors or editors to identify errors and improve the quality of published

  7. Welcome to NIH MedlinePlus magazine!

    MedlinePlus

    ... Current Issue Past Issues Welcome to NIH MedlinePlus magazine! Past Issues / Winter 2009 Table of Contents For ... Produced by the National Institutes of Health, the magazine and its companion Web site medlineplus.gov are ...

  8. MedlinePlus Connect: How it Works

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    ... it looks depends on how it is implemented. Web Application The Web application returns a formatted response ... for more examples of Web Application response pages. Web Service The MedlinePlus Connect REST-based Web service ...

  9. MedlinePlus Connect: Web Application

    MedlinePlus

    ... nih.gov/medlineplus/connect/application.html MedlinePlus Connect: Web Application To use the sharing features on this ... please see our guidelines and instructions on linking. Web Application Overview The API for the Web application ...

  10. Tutorials for Africa: MedlinePlus

    MedlinePlus

    ... Uganda initiated the MedlinePlus African Tutorials as a teaching tool. Medical students, health workers and staffs of clinics will use the tutorials in both electronic and hard copy formats to educate the general ...

  11. Back Cover: NIH MedlinePlus Salud

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  13. MedlinePlus Milestones: 1998-present

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  15. Child Abuse - Multiple Languages: MedlinePlus

    MedlinePlus

    ... MedlinePlus Site Map FAQs Contact Us Health Topics Drugs & Supplements Videos & Tools You Are Here: Home → Multiple Languages → All Health Topics → Child Abuse URL of this page: https://www.nlm.nih. ...

  16. MedlinePlus Connect: How it Works

    MedlinePlus

    ... medlineplus.gov/connect/howitworks.html MedlinePlus Connect: How it Works To use the sharing features on this ... Web service provide responses in different formats. How it looks depends on how it is implemented. Web ...

  17. Tutorials for Africa: MedlinePlus

    MedlinePlus

    ... NLM created the first MedlinePlus African Tutorial on malaria in collaboration with the Faculty of Medicine and ... meaningful text and illustrations for the tutorials. The malaria tutorial was then field tested in villages by ...

  18. Back Cover: NIH MedlinePlus Salud

    MedlinePlus

    Skip Navigation Bar Home Current Issue Past Issues NIH MedlinePlus Salud Past Issues / Winter 2009 Table of ... su salud! Los Institutos Nacionales de la Salud (NIH, por sus siglas en inglés), la Sociedad de ...

  19. MedlinePlus: Health Problems in Pregnancy

    MedlinePlus

    ... in Spanish Estrogen Test (American Association for Clinical Chemistry) MedlinePlus: Prenatal Testing (National Library of Medicine) Also in Spanish Progesterone Test (American Association for Clinical Chemistry) Prevention and Risk Factors Who Is at Increased ...

  20. PubMed, The New York Times and The Chicago Tribune as Tools for Teaching Genetics

    PubMed Central

    Strauss, Bernard S.

    2005-01-01

    An elementary course in human heredity for students not planning to major in the sciences can be based on current scientific literature and on the popular media. Examinations are constructed from questions on recent abstracts obtained from PubMed. The course is designed to promote writing skills in the sciences, and students write two papers in the course of a quarter. In the first paper, students trace the primary source of media reports on genetics and attempt to evaluate the reporter's translation. In a second paper, students write popular articles on the basis of current primary sources. PMID:16143615

  1. Beyond PubMed: Searching the "Grey Literature" for Clinical Trial Results.

    PubMed

    Citrome, Leslie

    2014-07-01

    Clinical trial results have been traditionally communicated through the publication of scholarly reports and reviews in biomedical journals. However, this dissemination of information can be delayed or incomplete, making it difficult to appraise new treatments, or in the case of missing data, evaluate older interventions. Going beyond the routine search of PubMed, it is possible to discover additional information in the "grey literature." Examples of the grey literature include clinical trial registries, patent databases, company and industrywide repositories, regulatory agency digital archives, abstracts of paper and poster presentations on meeting/congress websites, industry investor reports and press releases, and institutional and personal websites. PMID:25337445

  2. Beyond PubMed: Searching the “Grey Literature” for Clinical Trial Results

    PubMed Central

    2014-01-01

    Clinical trial results have been traditionally communicated through the publication of scholarly reports and reviews in biomedical journals. However, this dissemination of information can be delayed or incomplete, making it difficult to appraise new treatments, or in the case of missing data, evaluate older interventions. Going beyond the routine search of PubMed, it is possible to discover additional information in the “grey literature.” Examples of the grey literature include clinical trial registries, patent databases, company and industrywide repositories, regulatory agency digital archives, abstracts of paper and poster presentations on meeting/congress websites, industry investor reports and press releases, and institutional and personal websites. PMID:25337445

  3. History and Trends of "Personal Health Record" Research in PubMed

    PubMed Central

    Kim, Jeongeun; Bates, David W.

    2011-01-01

    Objectives The purpose of this study was to review history and trends of personal health record research in PubMed and to provide accurate understanding and categorical analysis of expert opinions. Methods For the search strategy, PubMed was queried for 'personal health record, personal record, and PHR' in the title and abstract fields. Those containing different definitions of the word were removed by one-by-one analysis from the results, 695 articles. In the end, total of 229 articles were analyzed in this research. Results The results show that the changes in terms over the years and the shift to patient centeredness and mixed usage. And we identified history and trend of PHR research in some category that the number of publications by year, topic, methodologies and target diseases. Also from analysis of MeSH terms, we can show the focal interest in regards the PHR boundaries and related subjects. Conclusions For PHRs to be efficiently used by general public, initial understanding of the history and trends of PHR research may be helpful. Simultaneously, accurate understanding and categorical analysis of expert opinions that can lead to the development and growth of PHRs will be valuable to their adoption and expansion. PMID:21818452

  4. Geography of Africa biomedical publications: An analysis of 1996–2005 PubMed papers

    PubMed Central

    Uthman, Olalekan A; Uthman, Mubashir B

    2007-01-01

    Background Scientific publications play an important role in scientific process providing a key linkage between knowledge production and use. Scientific publishing activity worldwide over the past decades shows that most countries in Africa have low levels of publication. We sought to examine trends and contribution of different Africa subregions and individual countries as represented by the articles indexed by PubMed between 1996 and 2005. Results Research production in Africa is highly skewed; South Africa, Egypt, and Nigeria make up a striking 60% of the total number of articles indexed by PubMed between 1996 and 2005. When adjusted for population size smaller countries, such as The Gambia, Gabon and Botswana, were more productive than Nigeria and Kenya. The Gambia and Eritrea had better records when total production was adjusted for gross domestic product. The contribution of Africa to global research production was persistently low through the period studied. Conclusion In this study, we found that most populous and rich countries (such as South Africa, Egypt, and Nigeria) have correspondingly higher research production; but smaller countries can be productive. We noted continuous increases and reassuring trends in the production of research articles from all African subregions during the period 1996 – 2005. However, contribution of Africa to global research production was limited. PMID:17927837

  5. Improving efficacy of PubMed Clinical Queries for retrieving scientifically strong studies on treatment.

    PubMed

    Corrao, Salvatore; Colomba, Daniela; Arnone, Sabrina; Argano, Christiano; Di Chiara, Tiziana; Scaglione, Rosario; Licata, Giuseppe

    2006-01-01

    The authors evaluated the retrieval power of PubMed "Clinical Queries," narrow search string, about therapy in comparison with a modified search string to avoid possible retrieval bias. PubMed search strategy was compared to a slightly modified string that included the Britannic English term "randomised." The authors tested the two strings joined onto each of four terms concerning topics of broad interest: hypertension, hepatitis, diabetes, and heart failure. In particular, precision was computed for not-indexed citations. The added word "randomised" improved total citation retrieval in any case. Total retrieval gain for not-indexed citations ranged from 11.1% to 21.4%. A significant number of Randomized Controlled Trial(s) (RCT)s (9.1-18.2%) was retrieved for each of the selected topics. They were often recently published RCTs. The authors think that correction of the Clinical Queries filter (when they focus on therapy and use narrow searches) is necessary to avoid biased search results with loss of relevant and up-to-date scientifically sound information. PMID:16799123

  6. CoPub Mapper: mining MEDLINE based on search term co-publication

    PubMed Central

    Alako, Blaise TF; Veldhoven, Antoine; van Baal, Sjozef; Jelier, Rob; Verhoeven, Stefan; Rullmann, Ton; Polman, Jan; Jenster, Guido

    2005-01-01

    Background High throughput microarray analyses result in many differentially expressed genes that are potentially responsible for the biological process of interest. In order to identify biological similarities between genes, publications from MEDLINE were identified in which pairs of gene names and combinations of gene name with specific keywords were co-mentioned. Results MEDLINE search strings for 15,621 known genes and 3,731 keywords were generated and validated. PubMed IDs were retrieved from MEDLINE and relative probability of co-occurrences of all gene-gene and gene-keyword pairs determined. To assess gene clustering according to literature co-publication, 150 genes consisting of 8 sets with known connections (same pathway, same protein complex, or same cellular localization, etc.) were run through the program. Receiver operator characteristics (ROC) analyses showed that most gene sets were clustered much better than expected by random chance. To test grouping of genes from real microarray data, 221 differentially expressed genes from a microarray experiment were analyzed with CoPub Mapper, which resulted in several relevant clusters of genes with biological process and disease keywords. In addition, all genes versus keywords were hierarchical clustered to reveal a complete grouping of published genes based on co-occurrence. Conclusion The CoPub Mapper program allows for quick and versatile querying of co-published genes and keywords and can be successfully used to cluster predefined groups of genes and microarray data. PMID:15760478

  7. An automated system for retrieving herb-drug interaction related articles from MEDLINE

    PubMed Central

    Lin, Kuo; Friedman, Carol; Finkelstein, Joseph

    2016-01-01

    An automated, user-friendly and accurate system for retrieving herb-drug interaction (HDIs) related articles in MEDLINE can increase the safety of patients, as well as improve the physicians’ article retrieving ability regarding speed and experience. Previous studies show that MeSH based queries associated with negative effects of drugs can be customized, resulting in good performance in retrieving relevant information, but no study has focused on the area of herb-drug interactions (HDI). This paper adapted the characteristics of HDI related papers and created a multilayer HDI article searching system. It achieved a sensitivity of 92% at a precision of 93% in a preliminary evaluation. Instead of requiring physicians to conduct PubMed searches directly, this system applies a more user-friendly approach by employing a customized system that enhances PubMed queries, shielding users from having to write queries, dealing with PubMed, or reading many irrelevant articles. The system provides automated processes and outputs target articles based on the input. PMID:27570662

  8. An automated system for retrieving herb-drug interaction related articles from MEDLINE.

    PubMed

    Lin, Kuo; Friedman, Carol; Finkelstein, Joseph

    2016-01-01

    An automated, user-friendly and accurate system for retrieving herb-drug interaction (HDIs) related articles in MEDLINE can increase the safety of patients, as well as improve the physicians' article retrieving ability regarding speed and experience. Previous studies show that MeSH based queries associated with negative effects of drugs can be customized, resulting in good performance in retrieving relevant information, but no study has focused on the area of herb-drug interactions (HDI). This paper adapted the characteristics of HDI related papers and created a multilayer HDI article searching system. It achieved a sensitivity of 92% at a precision of 93% in a preliminary evaluation. Instead of requiring physicians to conduct PubMed searches directly, this system applies a more user-friendly approach by employing a customized system that enhances PubMed queries, shielding users from having to write queries, dealing with PubMed, or reading many irrelevant articles. The system provides automated processes and outputs target articles based on the input. PMID:27570662

  9. MedlinePlus E-mail Updates | NIH MedlinePlus the Magazine

    MedlinePlus

    ... of this page please turn Javascript on. MedlinePlus E-mail Updates Past Issues / Spring - Summer 2010 Table ... in health and medicine? Sign up for MedlinePlus e-mail updates, and you'll receive alerts whenever ...

  10. MedlinePlus FAQ: What's New on Medline Plus Page and Email Updates

    MedlinePlus

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  11. PubMedMiner: Mining and Visualizing MeSH-based Associations in PubMed.

    PubMed

    Zhang, Yucan; Sarkar, Indra Neil; Chen, Elizabeth S

    2014-01-01

    The exponential growth of biomedical literature provides the opportunity to develop approaches for facilitating the identification of possible relationships between biomedical concepts. Indexing by Medical Subject Headings (MeSH) represent high-quality summaries of much of this literature that can be used to support hypothesis generation and knowledge discovery tasks using techniques such as association rule mining. Based on a survey of literature mining tools, a tool implemented using Ruby and R - PubMedMiner - was developed in this study for mining and visualizing MeSH-based associations for a set of MEDLINE articles. To demonstrate PubMedMiner's functionality, a case study was conducted that focused on identifying and comparing comorbidities for asthma in children and adults. Relative to the tools surveyed, the initial results suggest that PubMedMiner provides complementary functionality for summarizing and comparing topics as well as identifying potentially new knowledge. PMID:25954472

  12. PubMedMiner: Mining and Visualizing MeSH-based Associations in PubMed

    PubMed Central

    Zhang, Yucan; Sarkar, Indra Neil; Chen, Elizabeth S.

    2014-01-01

    The exponential growth of biomedical literature provides the opportunity to develop approaches for facilitating the identification of possible relationships between biomedical concepts. Indexing by Medical Subject Headings (MeSH) represent high-quality summaries of much of this literature that can be used to support hypothesis generation and knowledge discovery tasks using techniques such as association rule mining. Based on a survey of literature mining tools, a tool implemented using Ruby and R – PubMedMiner – was developed in this study for mining and visualizing MeSH-based associations for a set of MEDLINE articles. To demonstrate PubMedMiner’s functionality, a case study was conducted that focused on identifying and comparing comorbidities for asthma in children and adults. Relative to the tools surveyed, the initial results suggest that PubMedMiner provides complementary functionality for summarizing and comparing topics as well as identifying potentially new knowledge. PMID:25954472

  13. [Analysis of the Cochrane Review: Interventions for Improving Upper Limb Function after Stroke. Cochrane Database Syst Rev. 2014,11:CD010820].

    PubMed

    Sousa Nanji, Liliana; Torres Cardoso, André; Costa, João; Vaz-Carneiro, António

    2015-01-01

    Impairment of the upper limbs is quite frequent after stroke, making rehabilitation an essential step towards clinical recovery and patient empowerment. This review aimed to synthetize existing evidence regarding interventions for upper limb function improvement after Stroke and to assess which would bring some benefit. The Cochrane Database of Systematic Reviews, the Database of Reviews of Effects and PROSPERO databases were searched until June 2013 and 40 reviews have been included, covering 503 studies, 18 078 participants and 18 interventions, as well as different doses and settings of interventions. The main results were: 1- Information currently available is insufficient to assess effectiveness of each intervention and to enable comparison of interventions; 2- Transcranial direct current stimulation brings no benefit for outcomes of activities of daily living; 3- Moderate-quality evidence showed a beneficial effect of constraint-induced movement therapy, mental practice, mirror therapy, interventions for sensory impairment, virtual reality and repetitive task practice; 4- Unilateral arm training may be more effective than bilateral arm training; 5- Moderate-quality evidence showed a beneficial effect of robotics on measures of impairment and ADLs; 6- There is no evidence of benefit or harm for technics such as repetitive transcranial magnetic stimulation, music therapy, pharmacological interventions, electrical stimulation and other therapies. Currently available evidence is insufficient and of low quality, not supporting clear clinical decisions. High-quality studies are still needed. PMID:26667856

  14. Nurses' MEDLINE usage and research utilization.

    PubMed

    Prin, P L; Mills, M E

    1997-01-01

    This exploratory study in the field of nursing informatics examined the usage of information technology, namely on-line access to MEDLINE in clinical setting, by a convenience sample of 121 nurses from a large university hospital. A descriptive correlational design was used. Guided by the conceptual frameword of Nurse-Computer Interaction and based on variables set forth in the Theory of Reasoned Action, the study tested hypotheses regarding attitudinal and normative influences on reported use of on-line bibliographic retrieval systems. It was also hypothesized that using MEDLINE coild increase and improve nurses' adoption of nursing research findings. Multiple regression analyses were conducted on nurses' responses to survey questions to test hypotheses-that those who register more favorable attitudes towards nursing research would have a higher reported use of the MEDLINE system. Findings were significant and supported the hypothesis that nurses' attitudes towards research influenced MEDLINE usage. Findings also indicated that MEDLINE usage was significantly related to nurses' research utilization. PMID:10175440

  15. Cochrane corner: psychological interventions for individuals with cystic fibrosis and their families.

    PubMed

    Goldbeck, Lutz; Fidika, Astrid; Herle, Marion; Quittner, Alexandra L

    2015-11-01

    Psychological issues associated with cystic fibrosis may arise from the patients' lifelong disease- and treatment-related burden. This Cochrane Review aimed to determine psychosocial and physical outcomes of psychological interventions. Trial registries, databases and professional networks were used to identify relevant studies. Altogether, 16 studies involving 556 participants were included. They were heterogeneous in their methods, design, target groups, and outcomes. Overall, the current evidence for psychological interventions is insufficient. Preliminary evidence was available for interventions targeting specific aspects of the treatment regimen, such as behavioural nutrition interventions. PMID:26092922

  16. The Impact of Study Size on Meta-analyses: Examination of Underpowered Studies in Cochrane Reviews

    PubMed Central

    Turner, Rebecca M.; Bird, Sheila M.; Higgins, Julian P. T.

    2013-01-01

    Background Most meta-analyses include data from one or more small studies that, individually, do not have power to detect an intervention effect. The relative influence of adequately powered and underpowered studies in published meta-analyses has not previously been explored. We examine the distribution of power available in studies within meta-analyses published in Cochrane reviews, and investigate the impact of underpowered studies on meta-analysis results. Methods and Findings For 14,886 meta-analyses of binary outcomes from 1,991 Cochrane reviews, we calculated power per study within each meta-analysis. We defined adequate power as ≥50% power to detect a 30% relative risk reduction. In a subset of 1,107 meta-analyses including 5 or more studies with at least two adequately powered and at least one underpowered, results were compared with and without underpowered studies. In 10,492 (70%) of 14,886 meta-analyses, all included studies were underpowered; only 2,588 (17%) included at least two adequately powered studies. 34% of the meta-analyses themselves were adequately powered. The median of summary relative risks was 0.75 across all meta-analyses (inter-quartile range 0.55 to 0.89). In the subset examined, odds ratios in underpowered studies were 15% lower (95% CI 11% to 18%, P<0.0001) than in adequately powered studies, in meta-analyses of controlled pharmacological trials; and 12% lower (95% CI 7% to 17%, P<0.0001) in meta-analyses of controlled non-pharmacological trials. The standard error of the intervention effect increased by a median of 11% (inter-quartile range −1% to 35%) when underpowered studies were omitted; and between-study heterogeneity tended to decrease. Conclusions When at least two adequately powered studies are available in meta-analyses reported by Cochrane reviews, underpowered studies often contribute little information, and could be left out if a rapid review of the evidence is required. However, underpowered studies made up the

  17. How useful are systematic reviews for informing palliative care practice? Survey of 25 Cochrane systematic reviews

    PubMed Central

    Wee, Bee; Hadley, Gina; Derry, Sheena

    2008-01-01

    Background In contemporary medical research, randomised controlled trials are seen as the gold standard for establishing treatment effects where it is ethical and practical to conduct them. In palliative care such trials are often impractical, unethical, or extremely difficult, with multiple methodological problems. We review the utility of Cochrane reviews in informing palliative care practice. Methods Published reviews in palliative care registered with the Cochrane Pain, Palliative and Supportive Care Group as of December 2007 were obtained from the Cochrane Database of Systematic Reviews, issue 1, 2008. We reviewed the quality and quantity of primary studies available for each review, assessed the quality of the review process, and judged the strength of the evidence presented. There was no prior intention to perform any statistical analyses. Results 25 published systematic reviews were identified. Numbers of included trials ranged from none to 54. Within each review, included trials were heterogeneous with respect to patients, interventions, and outcomes, and the number of patients contributing to any single analysis was generally much lower than the total included in the review. A variety of tools were used to assess trial quality; seven reviews did not use this information to exclude low quality studies, weight analyses, or perform sensitivity analysis for effect of low quality. Authors indicated that there were frequently major problems with the primary studies, individually or in aggregate. Our judgment was that the reviewing process was generally good in these reviews, and that conclusions were limited by the number, size, quality and validity of the primary studies. We judged the evidence about 23 of the 25 interventions to be weak. Two reviews had stronger evidence, but with limitations due to methodological heterogeneity or definition of outcomes. No review provided strong evidence of no effect. Conclusion Cochrane reviews in palliative care are well

  18. [Cochrane Corner: Intra-aortic balloon pump in patients with cardiogenic shock following myocardial infarction].

    PubMed

    Caldeira, Daniel; Pereira, Hélder; Costa, João; Vaz-Carneiro, António

    2016-04-01

    Improvement of hemodynamic parameters is the rationale for the use of intra-aortic balloon pump counterpulsation (IABP) in patients with cardiogenic shock following acute myocardial infarction (MI). This Cochrane systematic review evaluated the impact of this intervention in reducing mortality. Seven randomized controlled trials with a total of 790 patients were included (four using medical therapy as a comparator, and three comparing IABP with other ventricular assist devices). IABP did not reduce mortality in either the short or long term. Therefore, the systematic use of IABP in patients with cardiogenic shock following MI cannot be recommended. PMID:26992744

  19. Publication Productivity of Faculty of Medicine, Mansoura University Indexed in PubMed

    PubMed Central

    Helal, RM; Abou-ElWafa, HS; El-Gilany, AH

    2014-01-01

    Background: Analysis of PubMed publications as an indicator of the research productivity of individual countries, regions, or institutions has recently become a field of interest. Aim: The aim was to assess the past trends in PubMed-indexed medical publications from Mansoura Faculty of Medicine and to have an idea about the current situation in medical research. Materials and Methods: PubMed was searched for publications affiliated to Mansoura from the end of the calendar year 2012 and earlier. Results: Of 2798 papers related to Mansoura, 1756 publications were included in the analysis, and 1042 publications were excluded (false positives). The highest number of publications was in 2011 (10.6%, 187/1756) followed by 2012 (10.2%, 179/1756). There was an increase of the publication rate over 5-years period until it reaches 47.0% (826/1756) during the period from 2008 to 2012. The main high-producing department was Urology and Nephrology, which accounted for 35.9% (631/1756) of the total publications followed by Pediatrics and Parasitology. The median number of authors participated in the researches was four ranging from 1 to 23. Most of the publications were in the form of intervention/clinical trials (38.4%, 662/1756) followed by descriptive/cross-sectional study (38.3%, 659/1756). The median of the impact factor was 1.99 ranging from 0.27 to 53.3. Conclusion: The publication productivity of Mansoura Faculty of Medicine showed fluctuating pattern from the end of the calendar year 2012 and earlier. Future prospects for increasing research productivity should be considered to increase the number and quality of publications and academic staff participating in high-quality international researches. PMID:25364602

  20. A Bibliometric Analysis of PubMed Literature on Middle East Respiratory Syndrome

    PubMed Central

    Wang, Zhengting; Chen, Yongdi; Cai, Gaofeng; Jiang, Zhenggang; Liu, Kui; Chen, Bin; Jiang, Jianmin; Gu, Hua

    2016-01-01

    Middle East Respiratory Syndrome (MERS), a pandemic threat to human beings, has aroused huge concern worldwide, but no bibliometric studies have been conducted on MERS research. The aim of this study was to map research productivity on the disease based on the articles indexed in PubMed. The articles related to MERS dated from 2012 to 2015 were retrieved from PubMed. The articles were classified into three categories according to their focus. Publication outputs were assessed and frequently used terms were mapped using the VOS viewer software. A total of 443 articles were included for analysis. They were published in 162 journals, with Journal of Virology being the most productive (44 articles; 9.9%) and by six types of organizations, with universities being the most productive (276 articles; 62.4%).The largest proportion of the articles focused on basic medical sciences and clinical studies (47.2%) and those on prevention and control ranked third (26.2%), with those on other focuses coming in between (26.6%). The articles on prevention and control had the highest mean rank for impact factor (IF) (226.34), followed by those on basic medical sciences and clinical studies (180.23) and those on other focuses (168.03). The mean rank differences were statistically significant (p = 0.000). Besides, “conronavirus”, “case”, “transmission” and “detection” were found to be the most frequently used terms. The findings of this first bibliometric study on MERS suggest that the prevention and control of the disease has become a big concern and related research should be strengthened. PMID:27304963

  1. A Bibliometric Analysis of PubMed Literature on Middle East Respiratory Syndrome.

    PubMed

    Wang, Zhengting; Chen, Yongdi; Cai, Gaofeng; Jiang, Zhenggang; Liu, Kui; Chen, Bin; Jiang, Jianmin; Gu, Hua

    2016-01-01

    Middle East Respiratory Syndrome (MERS), a pandemic threat to human beings, has aroused huge concern worldwide, but no bibliometric studies have been conducted on MERS research. The aim of this study was to map research productivity on the disease based on the articles indexed in PubMed. The articles related to MERS dated from 2012 to 2015 were retrieved from PubMed. The articles were classified into three categories according to their focus. Publication outputs were assessed and frequently used terms were mapped using the VOS viewer software. A total of 443 articles were included for analysis. They were published in 162 journals, with Journal of Virology being the most productive (44 articles; 9.9%) and by six types of organizations, with universities being the most productive (276 articles; 62.4%).The largest proportion of the articles focused on basic medical sciences and clinical studies (47.2%) and those on prevention and control ranked third (26.2%), with those on other focuses coming in between (26.6%). The articles on prevention and control had the highest mean rank for impact factor (IF) (226.34), followed by those on basic medical sciences and clinical studies (180.23) and those on other focuses (168.03). The mean rank differences were statistically significant (p = 0.000). Besides, "conronavirus", "case", "transmission" and "detection" were found to be the most frequently used terms. The findings of this first bibliometric study on MERS suggest that the prevention and control of the disease has become a big concern and related research should be strengthened. PMID:27304963

  2. An active visual search interface for Medline.

    PubMed

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

    2007-01-01

    Searching the Medline database is almost a daily necessity for many biomedical researchers. However, available Medline search solutions are mainly designed for the quick retrieval of a small set of most relevant documents. Because of this search model, they are not suitable for the large-scale exploration of literature and the underlying biomedical conceptual relationships, which are common tasks in the age of high throughput experimental data analysis and cross-discipline research. We try to develop a new Medline exploration approach by incorporating interactive visualization together with powerful grouping, summary, sorting and active external content retrieval functions. Our solution, PubViz, is based on the FLEX platform designed for interactive web applications and its prototype is publicly available at: http://brainarray.mbni.med.umich.edu/Brainarray/DataMining/PubViz. PMID:17951838

  3. PubMed vs. HighWire Press: a head-to-head comparison of two medical literature search engines.

    PubMed

    Vanhecke, Thomas E; Barnes, Michael A; Zimmerman, Janet; Shoichet, Sandor

    2007-09-01

    PubMed and HighWire Press are both useful medical literature search engines available for free to anyone on the internet. We measured retrieval accuracy, number of results generated, retrieval speed, features and search tools on HighWire Press and PubMed using the quick search features of each. We found that using HighWire Press resulted in a higher likelihood of retrieving the desired article and higher number of search results than the same search on PubMed. PubMed was faster than HighWire Press in delivering search results regardless of search settings. There are considerable differences in search features between these two search engines. PMID:17184763

  4. How to improve your PubMed/MEDLINE searches: 3. advanced searching, MeSH and My NCBI.

    PubMed

    Fatehi, Farhad; Gray, Leonard C; Wootton, Richard

    2014-03-01

    Although the basic PubMed search is often helpful, the results may sometimes be non-specific. For more control over the search process you can use the Advanced Search Builder interface. This allows a targeted search in specific fields, with the convenience of being able to select the intended search field from a list. It also provides a history of your previous searches. The search history is useful to develop a complex search query by combining several previous searches using Boolean operators. For indexing the articles in MEDLINE, the NLM uses a controlled vocabulary system called MeSH. This standardised vocabulary solves the problem of authors, researchers and librarians who may use different terms for the same concept. To be efficient in a PubMed search, you should start by identifying the most appropriate MeSH terms and use them in your search where possible. My NCBI is a personal workspace facility available through PubMed and makes it possible to customise the PubMed interface. It provides various capabilities that can enhance your search performance. PMID:24614997

  5. GLAD4U: deriving and prioritizing gene lists from PubMed literature

    PubMed Central

    2012-01-01

    Background Answering questions such as "Which genes are related to breast cancer?" usually requires retrieving relevant publications through the PubMed search engine, reading these publications, and creating gene lists. This process is not only time-consuming, but also prone to errors. Results We report GLAD4U (Gene List Automatically Derived For You), a new, free web-based gene retrieval and prioritization tool. GLAD4U takes advantage of existing resources of the NCBI to ensure computational efficiency. The quality of gene lists created by GLAD4U for three Gene Ontology (GO) terms and three disease terms was assessed using corresponding "gold standard" lists curated in public databases. For all queries, GLAD4U gene lists showed very high recall but low precision, leading to low F-measure. As a comparison, EBIMed's recall was consistently lower than GLAD4U, but its precision was higher. To present the most relevant genes at the top of a list, we studied two prioritization methods based on publication count and the hypergeometric test, and compared the ranked lists and those generated by EBIMed to the gold standards. Both GLAD4U methods outperformed EBIMed for all queries based on a variety of quality metrics. Moreover, the hypergeometric method allowed for a better performance by thresholding genes with low scores. In addition, manual examination suggests that many false-positives could be explained by the incompleteness of the gold standards. The GLAD4U user interface accepts any valid queries for PubMed, and its output page displays the ranked gene list and information associated with each gene, chronologically-ordered supporting publications, along with a summary of the run and links for file export and functional enrichment and protein interaction network analysis. Conclusions GLAD4U has a high overall recall. Although precision is generally low, the prioritization methods successfully rank truly relevant genes at the top of the lists to facilitate efficient

  6. MedlinePlus Connect: Frequently Asked Questions (FAQs)

    MedlinePlus

    ... the National Library of Medicine's ( NLM ) consumer health Web site. MedlinePlus Connect provides information on diseases and conditions, prescription and over-the-counter medications, and laboratory tests. In some cases, MedlinePlus Connect returns information from ...

  7. Welcome to NIH MedlinePlus, the magazine

    MedlinePlus

    ... Past Issues Welcome to NIH Medline Plus , the magazine Past Issues / Summer 2006 Table of Contents For ... MedlinePlus Web site. Your physician has made this magazine available to you as a free health resource; ...

  8. Mary Tyler Moore Helps Launch NIH MedlinePlus Magazine

    MedlinePlus

    ... Issues Mary Tyler Moore Helps Launch NIH MedlinePlus Magazine Past Issues / Winter 2007 Table of Contents For ... Javascript on. Among those attending the NIH MedlinePlus magazine launch on Capitol Hill were (l-r) NIH ...

  9. MedlinePlus FAQ: Copyrighted and Non-Copyrighted Material

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  10. MedlinePlus FAQ: Easy-to-Read Documents

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  11. MedlinePlus FAQ: Listing Your Web Site

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  12. MedlinePlus FAQ: Listing Your Web Site

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  13. Health Topic XML File Description: MedlinePlus

    MedlinePlus

    ... https://medlineplus.gov/xmldescription.html Health Topic XML File Description: MedlinePlus To use the sharing features on ... Tags Definitions of every possible tag in the file, with examples and their use on MedlinePlus.

  14. MedlinePlus FAQ: Easy-to-Read Documents

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  15. MedlinePlus Marks its 15th Anniversary

    MedlinePlus

    ... top of the American Customer Satisfaction Index for government news sites. In 2010, MedlinePlus introduced the MedlinePlus Connect service that allows electronic health record systems to link from patient diagnoses, ...

  16. MedlinePlus Survey Results 2015

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  17. Open Biomedical Ontology-based Medline exploration

    PubMed Central

    Xuan, Weijian; Dai, Manhong; Mirel, Barbara; Song, Jean; Athey, Brian; Watson, Stanley J; Meng, Fan

    2009-01-01

    Background Effective Medline database exploration is critical for the understanding of high throughput experimental results and the development of novel hypotheses about the mechanisms underlying the targeted biological processes. While existing solutions enhance Medline exploration through different approaches such as document clustering, network presentations of underlying conceptual relationships and the mapping of search results to MeSH and Gene Ontology trees, we believe the use of multiple ontologies from the Open Biomedical Ontology can greatly help researchers to explore literature from different perspectives as well as to quickly locate the most relevant Medline records for further investigation. Results We developed an ontology-based interactive Medline exploration solution called PubOnto to enable the interactive exploration and filtering of search results through the use of multiple ontologies from the OBO foundry. The PubOnto program is a rich internet application based on the FLEX platform. It contains a number of interactive tools, visualization capabilities, an open service architecture, and a customizable user interface. It is freely accessible at: . PMID:19426463

  18. End User Searching of Medline. Final Report.

    ERIC Educational Resources Information Center

    Wildemuth, Barbara M.; Moore, Margaret E.

    One hundred sixty-one MEDLINE searches conducted by third year medical students were analyzed and evaluated to determine which search behaviors were used, whether those individual moves are effective, and whether there is a relationship between specific search behaviors and the effectiveness of the search strategy as a whole. The typical search…

  19. Hepatitis B - Multiple Languages: MedlinePlus

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    ... ung thư gan - Tiếng Việt (Vietnamese) PDF Stanford University, Asian Liver Center Characters not displaying correctly on this page? See language display issues . Return to the MedlinePlus Health Information ...

  20. Liver Cancer - Multiple Languages: MedlinePlus

    MedlinePlus

    ... ung thư gan - Tiếng Việt (Vietnamese) PDF Stanford University, Asian Liver Center Characters not displaying correctly on this page? See language display issues . Return to the MedlinePlus Health Information ...

  1. Child Safety - Multiple Languages: MedlinePlus

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  2. Skin Infections - Multiple Languages: MedlinePlus

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  3. Smokeless Tobacco - Multiple Languages: MedlinePlus

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  4. Circumcision - Multiple Languages: MedlinePlus

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  5. Gallstones - Multiple Languages: MedlinePlus

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  6. Menopause - Multiple Languages: MedlinePlus

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  7. Diabetic Diet - Multiple Languages: MedlinePlus

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  8. Hepatitis - Multiple Languages: MedlinePlus

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  9. Medicines - Multiple Languages: MedlinePlus

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  10. Dentures - Multiple Languages: MedlinePlus

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  11. Tooth Decay - Multiple Languages: MedlinePlus

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  12. Glaucoma - Multiple Languages: MedlinePlus

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  13. Sports Safety - Multiple Languages: MedlinePlus

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  14. Pregnancy - Multiple Languages: MedlinePlus

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  15. Retinal Disorders - Multiple Languages: MedlinePlus

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  16. Rehabilitation - Multiple Languages: MedlinePlus

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  17. Gum Disease - Multiple Languages: MedlinePlus

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  18. Oral Cancer - Multiple Languages: MedlinePlus

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  19. Radiation Emergencies - Multiple Languages: MedlinePlus

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  20. Postpartum Care - Multiple Languages: MedlinePlus

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  1. Colonoscopy - Multiple Languages: MedlinePlus

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  2. Methamphetamine - Multiple Languages: MedlinePlus

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  3. Orthodontia - Multiple Languages: MedlinePlus

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  4. Diabetes Medicines - Multiple Languages: MedlinePlus

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  5. Cataract - Multiple Languages: MedlinePlus

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  6. Hysterectomy - Multiple Languages: MedlinePlus

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  7. Prostate Cancer - Multiple Languages: MedlinePlus

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  8. Mouth Disorders - Multiple Languages: MedlinePlus

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  9. MedlinePlus.gov Turns 10!

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    ... 10 years of bringing trusted health information to people across the country and around the world. What a difference a decade makes. Since its debut in 1998, MedlinePlus.gov has grown to include: Information on hundreds ... Nearly 500 million people in more than 200 countries have turned to ...

  10. MedlinePlus: Islet Cell Transplantation

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  11. Literature in MEDLINE. . . A Bibliographic Anomaly?

    ERIC Educational Resources Information Center

    Robbins, Simone B.

    1985-01-01

    Discusses the inclusion of citations to literary articles that have appeared in medical journals in National Library of Medicine's database, MEDLINE. Highlights include search aids, search strategies, sample references, and five publications that serve as orientations to current status of movement toward interdisciplinary study of medicine and…

  12. MedlinePlus FAQ: Will MedlinePlus work on my mobile device?

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  13. MedlinePlus FAQ: Is audio description available for videos on MedlinePlus?

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  14. A Search Engine to Access PubMed Monolingual Subsets: Proof of Concept and Evaluation in French

    PubMed Central

    Schuers, Matthieu; Soualmia, Lina Fatima; Grosjean, Julien; Kerdelhué, Gaétan; Kergourlay, Ivan; Dahamna, Badisse; Darmoni, Stéfan Jacques

    2014-01-01

    Background PubMed contains numerous articles in languages other than English. However, existing solutions to access these articles in the language in which they were written remain unconvincing. Objective The aim of this study was to propose a practical search engine, called Multilingual PubMed, which will permit access to a PubMed subset in 1 language and to evaluate the precision and coverage for the French version (Multilingual PubMed-French). Methods To create this tool, translations of MeSH were enriched (eg, adding synonyms and translations in French) and integrated into a terminology portal. PubMed subsets in several European languages were also added to our database using a dedicated parser. The response time for the generic semantic search engine was evaluated for simple queries. BabelMeSH, Multilingual PubMed-French, and 3 different PubMed strategies were compared by searching for literature in French. Precision and coverage were measured for 20 randomly selected queries. The results were evaluated as relevant to title and abstract, the evaluator being blind to search strategy. Results More than 650,000 PubMed citations in French were integrated into the Multilingual PubMed-French information system. The response times were all below the threshold defined for usability (2 seconds). Two search strategies (Multilingual PubMed-French and 1 PubMed strategy) showed high precision (0.93 and 0.97, respectively), but coverage was 4 times higher for Multilingual PubMed-French. Conclusions It is now possible to freely access biomedical literature using a practical search tool in French. This tool will be of particular interest for health professionals and other end users who do not read or query sufficiently in English. The information system is theoretically well suited to expand the approach to other European languages, such as German, Spanish, Norwegian, and Portuguese. PMID:25448528

  15. Subscribe to NIH MedlinePlus the Magazine

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  16. Evidence-based management of vitiligo: summary of a Cochrane systematic review.

    PubMed

    Whitton, M; Pinart, M; Batchelor, J M; Leonardi-Bee, J; Gonzalez, U; Jiyad, Z; Eleftheriadou, V; Ezzedine, K

    2016-05-01

    Vitiligo affects around 1% of the world's population. Despite it being relatively common, there is still no effective treatment. The objective of this study was to update the Cochrane systematic review of randomized clinical trials (RCTs) to evaluate the efficacy of treatments for vitiligo. We carried out searches of a range of databases to October 2013 for RCTs of interventions for vitiligo regardless of language or publication status. At least two reviewers independently assessed study eligibility and methodological quality and extracted data using data extraction forms approved by the Cochrane Skin Group. Our primary outcomes of interest were quality of life, > 75% repigmentation and adverse effects. We retrieved 96 studies, of which 39 were new studies, with an overall total of 4512 participants. Repigmentation was assessed in all studies, although only five reported on all three of our primary outcomes. Regarding our two secondary outcomes, six studies measured cessation of spread but none assessed long-term permanence of repigmentation at 2 years' follow-up. Most of the studies evaluated combination treatments, which generally showed better repigmentation than monotherapies. Of the new studies, seven were surgical interventions. The majority of the studies had fewer than 50 participants. The quality of the studies was poor to moderate at best. Very few studies specifically included children or participants with segmental vitiligo. Five years after the last update of this review, there are still important variations in study design and outcome measures in clinical trials for vitiligo, limiting the evidence for the efficacy of different therapeutic options. The best evidence from individual trials showed short-term benefit from topical corticosteroids and various forms of ultraviolet radiation combined with topical preparations. Long-term follow-up and patient-rated outcomes should be incorporated into study design, and more studies should assess psychological

  17. "Is Cybermedicine Killing You?"--The story of a Cochrane disaster.

    PubMed

    Eysenbach, Gunther; Kummervold, Per Egil

    2005-01-01

    This editorial briefly reviews the series of unfortunate events that led to the publication, dissemination, and eventual retraction of a flawed Cochrane systematic review on interactive health communication applications (IHCAs), which was widely reported in the media with headlines such as "Internet Makes Us Sick," "Knowledge May Be Hazardous to Web Consumers' Health," "Too Much Advice Can Be Bad for Your Health," "Click to Get Sick?," and even "Is Cybermedicine Killing You?". While the media attention helped to speed up the identification of errors, leading to a retraction of the review after only 13 days, a paper published in this issue of JMIR by Rada shows that the retraction, in contrast to the original review, remained largely unnoticed by the public. We discuss the three flaws of the review, which include (1) data extraction and coding errors, (2) the pooling of heterogeneous studies, and (3) a problematic and ambiguous scope and, possibly, some overlooked studies. We then discuss "retraction ethics" for researchers, editors/publishers, and journalists. Researchers and editors should, in the case of retractions, match the aggressiveness of the original dissemination campaign if errors are detected. It is argued that researchers and their organizations may have an ethical obligation to track down journalists who reported stories on the basis of a flawed study and to specifically ask them to publish an article indicating the error. Journalists should respond to errors or retractions with reports that have the same prominence as the original story. Finally, we look at some of the lessons for the Cochrane Collaboration, which include (1) improving the peer-review system by routinely sending out pre-prints to authors of the original studies, (2) avoiding downplay of the magnitude of errors if they occur, (3) addressing the usability issues of RevMan, and (4) making critical articles such as retraction notices open access. PMID:15998612

  18. Public accessibility of biomedical articles from PubMed Central reduces journal readership—retrospective cohort analysis

    PubMed Central

    Davis, Philip M.

    2013-01-01

    Does PubMed Central—a government-run digital archive of biomedical articles—compete with scientific society journals? A longitudinal, retrospective cohort analysis of 13,223 articles (5999 treatment, 7224 control) published in 14 society-run biomedical research journals in nutrition, experimental biology, physiology, and radiology between February 2008 and January 2011 reveals a 21.4% reduction in full-text hypertext markup language (HTML) article downloads and a 13.8% reduction in portable document format (PDF) article downloads from the journals' websites when U.S. National Institutes of Health-sponsored articles (treatment) become freely available from the PubMed Central repository. In addition, the effect of PubMed Central on reducing PDF article downloads is increasing over time, growing at a rate of 1.6% per year. There was no longitudinal effect for full-text HTML downloads. While PubMed Central may be providing complementary access to readers traditionally underserved by scientific journals, the loss of article readership from the journal website may weaken the ability of the journal to build communities of interest around research papers, impede the communication of news and events to scientific society members and journal readers, and reduce the perceived value of the journal to institutional subscribers.—Davis, P. M. Public accessibility of biomedical articles from PubMed Central reduces journal readership—retrospective cohort analysis. PMID:23554455

  19. Mining locus tags in PubMed Central to improve microbial gene annotation

    PubMed Central

    2014-01-01

    Background The scientific literature contains millions of microbial gene identifiers within the full text and tables, but these annotations rarely get incorporated into public sequence databases. We propose to utilize the Open Access (OA) subset of PubMed Central (PMC) as a gene annotation database and have developed an R package called pmcXML to automatically mine and extract locus tags from full text, tables and supplements. Results We mined locus tags from 1835 OA publications in ten microbial genomes and extracted tags mentioned in 30,891 sentences in main text and 20,489 rows in tables. We identified locus tag pairs marking the start and end of a region such as an operon or genomic island and expanded these ranges to add another 13,043 tags. We also searched for locus tags in supplementary tables and publications outside the OA subset in Burkholderia pseudomallei K96243 for comparison. There were 168 publications containing 48,470 locus tags and 83% of mentions were from supplementary materials and 9% from publications outside the OA subset. Conclusions B. pseudomallei locus tags within the full text and tables of OA publications represent only a small fraction of the total mentions in the literature. For microbial genomes with very few functionally characterized proteins, the locus tags mentioned in supplementary tables and within ranges like genomic islands contain the majority of locus tags. Significantly, the functions in the R package provide access to additional resources in the OA subset that are not currently indexed or returned by searching PMC. PMID:24499370

  20. Microtask crowdsourcing for disease mention annotation in PubMed abstracts.

    PubMed

    Good, Benjamin M; Nanis, Max; Wu, Chunlei; Su, Andrew I

    2015-01-01

    Identifying concepts and relationships in biomedical text enables knowledge to be applied in computational analyses. Many biological natural language processing (BioNLP) projects attempt to address this challenge, but the state of the art still leaves much room for improvement. Progress in BioNLP research depends on large, annotated corpora for evaluating information extraction systems and training machine learning models. Traditionally, such corpora are created by small numbers of expert annotators often working over extended periods of time. Recent studies have shown that workers on microtask crowdsourcing platforms such as Amazon's Mechanical Turk (AMT) can, in aggregate, generate high-quality annotations of biomedical text. Here, we investigated the use of the AMT in capturing disease mentions in PubMed abstracts. We used the NCBI Disease corpus as a gold standard for refining and benchmarking our crowdsourcing protocol. After several iterations, we arrived at a protocol that reproduced the annotations of the 593 documents in the 'training set' of this gold standard with an overall F measure of 0.872 (precision 0.862, recall 0.883). The output can also be tuned to optimize for precision (max = 0.984 when recall = 0.269) or recall (max = 0.980 when precision = 0.436). Each document was completed by 15 workers, and their annotations were merged based on a simple voting method. In total 145 workers combined to complete all 593 documents in the span of 9 days at a cost of $.066 per abstract per worker. The quality of the annotations, as judged with the F measure, increases with the number of workers assigned to each task; however minimal performance gains were observed beyond 8 workers per task. These results add further evidence that microtask crowdsourcing can be a valuable tool for generating well-annotated corpora in BioNLP. Data produced for this analysis are available at http://figshare.com/articles/Disease_Mention_Annotation_with_Mechanical_Turk/1126402

  1. Trends and topics in eye disease research in PubMed from 2010 to 2014

    PubMed Central

    Denion, Eric; Mortemousque, Bruno; Mouriaux, Fréderic

    2016-01-01

    Background: The purpose of this study is to provide a report on scientific production during the period 2010–2014 in order to identify the major topics as well as the predominant actors (journals, countries, continents) involved in the field of eye disease. Methods: A PubMed search was carried out to extract articles related to eye diseases during the period 2010–2014. Data were downloaded and processed through developed PHP scripts for further analysis. Results: A total of 62,123 articles were retrieved. A total of 3,368 different journals were found, and 19 journals were identified as “core journals” according to Braford’s law. English was by far the predominant language. A total of 853,182 MeSH terms were found, representing an average of 13.73 (SD = 4.98) MeSH terms per article. Among these 853,182 MeSH terms, 14,689 different MeSH terms were identified. Vision Disorders, Glaucoma, Diabetic Retinopathy, Macular Degeneration, and Cataract were the most frequent five MeSH terms related to eye diseases. The analysis of the total number of publications showed that Europe and Asia were the most productive continents, and the USA and China the most productive countries. Interestingly, using the mean Five-Year Impact Factor, the two most productive continents were North America and Oceania. After adjustment for population, the overall ranking positions changed in favor of smaller countries (i.e. Iceland, Switzerland, Denmark, and New Zealand), while after adjustment for Gross Domestic Product (GDP), the overall ranking positions changed in favor of some developing countries (Malawi, Guatemala, Singapore). Conclusions: Due to the large number of articles included and the numerous parameters analyzed, this study provides a wide view of scientific productivity related to eye diseases during the period 2010–2014 and allows us to better understand this field. PMID:26819840

  2. Extracting noun phrases for all of MEDLINE.

    PubMed Central

    Bennett, N. A.; He, Q.; Powell, K.; Schatz, B. R.

    1999-01-01

    A natural language parser that could extract noun phrases for all medical texts would be of great utility in analyzing content for information retrieval. We discuss the extraction of noun phrases from MEDLINE, using a general parser not tuned specifically for any medical domain. The noun phrase extractor is made up of three modules: tokenization; part-of-speech tagging; noun phrase identification. Using our program, we extracted noun phrases from the entire MEDLINE collection, encompassing 9.3 million abstracts. Over 270 million noun phrases were generated, of which 45 million were unique. The quality of these phrases was evaluated by examining all phrases from a sample collection of abstracts. The precision and recall of the phrases from our general parser compared favorably with those from three other parsers we had previously evaluated. We are continuing to improve our parser and evaluate our claim that a generic parser can effectively extract all the different phrases across the entire medical literature. PMID:10566444

  3. MEDLINE: the options for health professionals.

    PubMed

    Wood, E H

    1994-01-01

    The bibliographic database MEDLINE, produced by the National Library of Medicine (NLM), is a computerized index to the world's biomedical literature. The database can be searched back to 1966 and contains 6.8 million records. The various means of access are divided, for the purposes of this article, into three categories: logging onto a remote host computer by telephone and modem or by the Internet; subscribing to part or all of the database on compact disc (CD-ROM); and leasing the data on a transport medium such as magnetic tape or CDs for loading on a local host computer. Decisions about which method is preferable in a given situation depend on cost, availability of hardware and software, local expertise, and the size of the intended user population. Trends include increased access to the Internet by health professionals, increased network speed, links from MEDLINE records to full-text databases or online journals, and integration of MEDLINE into wider health information systems. PMID:7850561

  4. Besides Precision & Recall: Exploring Alternative Approaches to Evaluating an Automatic Indexing Tool for MEDLINE

    PubMed Central

    Névéol, Aurélie; Zeng, Kelly; Bodenreider, Olivier

    2006-01-01

    Objective This paper explores alternative approaches for the evaluation of an automatic indexing tool for MEDLINE, complementing the traditional precision and recall method. Materials and methods The performance of MTI, the Medical Text Indexer used at NLM to produce MeSH recommendations for biomedical journal articles is evaluated on a random set of MEDLINE citations. The evaluation examines semantic similarity at the term level (indexing terms). In addition, the documents retrieved by queries resulting from MTI index terms for a given document are compared to the PubMed related citations for this document. Results Semantic similarity scores between sets of index terms are higher than the corresponding Dice similarity scores. Overall, 75% of the original documents and 58% of the top ten related citations are retrieved by queries based on the automatic indexing. Conclusions The alternative measures studied in this paper confirm previous findings and may be used to select particular documents from the test set for a more thorough analysis. PMID:17238409

  5. Discrepancies in Outcome Reporting Exist Between Protocols and Published Oral Health Cochrane Systematic Reviews

    PubMed Central

    Pandis, Nikolaos; Fleming, Padhraig S.; Worthington, Helen; Dwan, Kerry; Salanti, Georgia

    2015-01-01

    Objectives To assess discrepancies in the analyzed outcomes between protocols and published reviews within Cochrane oral health systematic reviews (COHG) on the Cochrane Database of Systematic Reviews (CDSR). Study Design and Setting All COHG systematic reviews on the CDSR and the corresponding protocols were retrieved in November 2014 and information on the reported outcomes was recorded. Data was collected at the systematic review level by two reviewers independently. Results One hundred and fifty two reviews were included. In relation to primary outcomes, 11.2% were downgraded to secondary outcomes, 9.9% were omitted altogether in the final publication and new primary outcomes were identified in 18.4% of publications. For secondary outcomes, 2% were upgraded to primary, 12.5% were omitted and 30.9% were newly introduced in the publication. Overall, 45.4% of reviews had at least one discrepancy when compared to the protocol; these were reported in 14.5% reviews. The number of review updates appears to be associated with discrepancies between final review and protocol (OR: 3.18, 95% CI: 1.77, 5.74, p<0.001). The risk of reporting significant results was lower for both downgraded outcomes [RR: 0.52, 95% CI: 0.17, 1.58, p = 0.24] and upgraded or newly introduced outcomes [RR: 0.77, 95% CI: 0.36, 1.64, p = 0.50] compared to outcomes with no discrepancies. The risk of reporting significant results was higher for upgraded or newly introduced outcomes compared to downgraded outcomes (RR = 1.19, 95% CI: 0.65, 2.16, p = 0.57). None of the comparisons reached statistical significance. Conclusion While no evidence of selective outcome reporting was found in this study, based on the present analysis of SRs published within COHG systematic reviews, discrepancies between outcomes in pre-published protocols and final reviews continue to be common. Solutions such as the use of standardized outcomes to reduce the prevalence of this issue may need to be explored. PMID:26368938

  6. Mentoring programs for medical students - a review of the PubMed literature 2000 - 2008

    PubMed Central

    2010-01-01

    Background Although mentoring is acknowledged as a key to successful and satisfying careers in medicine, formal mentoring programs for medical students are lacking in most countries. Within the framework of planning a mentoring program for medical students at Zurich University, an investigation was carried out into what types of programs exist, what the objectives pursued by such programs are, and what effects are reported. Methods A PubMed literature search was conducted for 2000 - 2008 using the following keywords or their combinations: mentoring, mentoring program, medical student, mentor, mentee, protégé, mentorship. Although a total of 438 publications were identified, only 25 papers met the selection criteria for structured programs and student mentoring surveys. Results The mentoring programs reported in 14 papers aim to provide career counseling, develop professionalism, increase students' interest in research, and support them in their personal growth. There are both one-to-one and group mentorships, established in the first two years of medical school and continuing through graduation. The personal student-faculty relationship is important in that it helps students to feel that they are benefiting from individual advice and encourages them to give more thought to their career choices. Other benefits are an increase in research productivity and improved medical school performance in general. Mentored students also rate their overall well-being as higher. - The 11 surveys address the requirements for being an effective mentor as well as a successful mentee. A mentor should empower and encourage the mentee, be a role model, build a professional network, and assist in the mentee's personal development. A mentee should set agendas, follow through, accept criticism, and be able to assess performance and the benefits derived from the mentoring relationship. Conclusion Mentoring is obviously an important career advancement tool for medical students. In Europe

  7. PSE: A tool for browsing a large amount of MEDLINE/PubMed abstracts with gene names and common words as the keywords

    PubMed Central

    Yoneya, Takashi

    2005-01-01

    Background MEDLINE/PubMed (hereinafter called PubMed) is one of the most important literature databases for the biological and medical sciences, but it is impossible to read all related records due to the sheer size of the repository. We usually have to repeatedly enter keywords in a trial-and-error manner to extract useful records. Software which can reduce such a laborious task is therefore required. Results We developed a web-based software, the PubMed Sentence Extractor (PSE), which parses large number of PubMed abstracts, extracts and displays the co-occurrence sentences of gene names and other keywords, and some information from EntrezGene records. The result links to whole abstracts and other resources such as the Online Mendelian Inheritance in Men and Reference Sequence. While PSE executes at the sentence-level when evaluating the existence of keywords, the popular PubMed operates at the record-level. Therefore, the relationship between the two keywords, a gene name and a common word, is more accurately captured by PSE than PubMed. In addition, PSE shows the list of keywords and considers the synonyms and variations on gene names. Through these functions, PSE would reduce the task of searching through records for gene information. Conclusion We developed PSE in order to extract useful records efficiently from PubMed. This system has four advantages over a simple PubMed search; the reduction in the amount of collected literatures, the showing of keyword lists, the consideration for synonyms and variations on gene names, and the links to external databases. We believe PSE is helpful in collecting necessary literatures efficiently in order to find research targets. PSE is freely available under the GPL licence as additional files to this manuscript. PMID:16336692

  8. Shifting Sands: Science Researchers on Google Scholar, Web of Science, and PubMed, with Implications for Library Collections Budgets

    ERIC Educational Resources Information Center

    Hightower, Christy; Caldwell, Christy

    2010-01-01

    Science researchers at the University of California Santa Cruz were surveyed about their article database use and preferences in order to inform collection budget choices. Web of Science was the single most used database, selected by 41.6%. Statistically there was no difference between PubMed (21.5%) and Google Scholar (18.7%) as the second most…

  9. Public accessibility of biomedical articles from PubMed Central reduces journal readership--retrospective cohort analysis.

    PubMed

    Davis, Philip M

    2013-07-01

    Does PubMed Central--a government-run digital archive of biomedical articles--compete with scientific society journals? A longitudinal, retrospective cohort analysis of 13,223 articles (5999 treatment, 7224 control) published in 14 society-run biomedical research journals in nutrition, experimental biology, physiology, and radiology between February 2008 and January 2011 reveals a 21.4% reduction in full-text hypertext markup language (HTML) article downloads and a 13.8% reduction in portable document format (PDF) article downloads from the journals' websites when U.S. National Institutes of Health-sponsored articles (treatment) become freely available from the PubMed Central repository. In addition, the effect of PubMed Central on reducing PDF article downloads is increasing over time, growing at a rate of 1.6% per year. There was no longitudinal effect for full-text HTML downloads. While PubMed Central may be providing complementary access to readers traditionally underserved by scientific journals, the loss of article readership from the journal website may weaken the ability of the journal to build communities of interest around research papers, impede the communication of news and events to scientific society members and journal readers, and reduce the perceived value of the journal to institutional subscribers. PMID:23554455

  10. The role of The Cochrane Collaboration in support of the WHO Nutrition Guidelines.

    PubMed

    Tovey, David

    2014-01-01

    This article describes the background and contribution of The Cochrane Collaboration to the WHO Nutrition Guidelines program. Systematic reviews, augmented by the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) methodology for assessing the quality of a body of evidence, form the evidence basis for WHO guidelines. Our shared experience of working together has highlighted a number of issues that are challenging, such as decisions made about selecting appropriate questions for evidence synthesis and the nature of study types that are included, in particular the decision on whether or not to extend a search beyond randomized studies. Although the skills and experience required for evidence synthesis are different from those needed to determine recommendations for policy and practice, our experience suggests that some engagement between the two groups is mutually beneficial. Finally, our experience highlights the recognition that evidence of effectiveness is essential but by no means sufficient to guide decisions on recommendations. Programmatic and implementation considerations are important to guide decision making and the evidence basis for this may be limited; therefore, it is essential that groups involved in delivering interventions to populations are also engaged in the guidelines process. PMID:24425720

  11. Tweeting links to Cochrane Schizophrenia Group reviews: a randomised controlled trial

    PubMed Central

    Adams, C E; Bodart, A Y M; Sampson, S; Zhao, S; Montgomery, A A

    2016-01-01

    Objective To assess the effects of using health social media on web activity. Design Individually randomised controlled parallel group superiority trial. Setting Twitter and Weibo. Participants 170 Cochrane Schizophrenia Group full reviews with an abstract and plain language summary web page. Interventions Three randomly ordered slightly different 140 character or less messages, each containing a short URL to the freely accessible summary page sent on specific times on one single day. This was compared with no messaging. Outcome The primary outcome was web page visits at 1 week. Secondary outcomes were other metrics of web activity at 1 week. Results 85 reviews were randomised to each of the intervention and control arms. Google Analytics allowed 100% follow-up within 1 week of completion. Intervention and control reviews received a total of 1162 and 449 visits, respectively (IRR 2.7, 95% CI 2.2 to 3.3). Fewer intervention reviews had single page only visits (16% vs 31%, OR 0.41, 0.19 to 0.88) and users spent more time viewing intervention reviews (geometric mean 76 vs 31 s, ratio 2.5, 1.3 to 4.6). Other secondary metrics of web activity all showed strong evidence in favour of the intervention. Conclusions Tweeting in this limited area of healthcare increases ‘product placement’ of evidence with the potential for that to influence care. Trial registration number ISRCTN84658943. PMID:26956164

  12. Txt2MEDLINE: text-messaging access to MEDLINE/PubMed.

    PubMed

    Fontelo, Paul; Liu, Fang; Muin, Michael; Tolentino, Herman; Ackerman, Michael

    2006-01-01

    We developed a text messaging system for processing incoming Short Message Service (SMS) queries, retrieving medical journal citations from MEDLINE/PubMed and sending them back to the user in the text message format. A database of medical terminology abbreviations and acronyms was developed to reduce the size of text in journal citations and abstracts because of the 160-character per message limit of text messages. Queries may be sent as full-length terms or abbreviations. An algorithm transforms the citations into the SMS format. An abbreviated TBL (the bottom-line) summary instead of the full abstract is sent to the mobile device to shorten the resulting text. The system decreases citation size by 77.5+/-7.9%. Txt2MEDLINE provides physicians and healthcare personnel another rapid and convenient method for searching MEDLINE/PubMed through wireless mobile devices. It is accessible from any location worldwide where GSM wireless service is available. PMID:17238343

  13. Using Cochran's Z Statistic to Test the Kernel-Smoothed Item Response Function Differences between Focal and Reference Groups

    ERIC Educational Resources Information Center

    Zheng, Yinggan; Gierl, Mark J.; Cui, Ying

    2010-01-01

    This study combined the kernel smoothing procedure and a nonparametric differential item functioning statistic--Cochran's Z--to statistically test the difference between the kernel-smoothed item response functions for reference and focal groups. Simulation studies were conducted to investigate the Type I error and power of the proposed…

  14. 77 FR 65545 - Mr. Jesse S. Capel and Mr. Hilton J. Cochran; EWP LLC; Notice of Transfer of Exemption

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-29

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Mr. Jesse S. Capel and Mr. Hilton J. Cochran; EWP LLC; Notice of Transfer of... application.\\2\\ The project is located on the Little River in Montgomery County, North Carolina. The...

  15. 40 CFR Appendix IV to Part 264 - Cochran's Approximation to the Behrens-Fisher Students' t-test

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 26 2014-07-01 2014-07-01 false Cochran's Approximation to the Behrens-Fisher Students' t-test IV Appendix IV to Part 264 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) SOLID WASTES (CONTINUED) STANDARDS FOR OWNERS AND OPERATORS OF HAZARDOUS WASTE TREATMENT, STORAGE, AND DISPOSAL FACILITIES...

  16. Getting evidence into practice: the work of the Cochrane Effective Practice and Organization of care Group (EPOC).

    PubMed

    Mowatt, G; Grimshaw, J M; Davis, D A; Mazmanian, P E

    2001-01-01

    Policy makers and continuing educators often face difficult decisions about which educational and quality assurance interventions to provide. Where possible, such decisions are best informed by rigorous evidence, such as that provided by systematic reviews. The Cochrane Collaboration is an international organization that aims to help people make well-informed decisions about health care by preparing, maintaining, and ensuring the accessibility of systematic reviews of the benefits and risks of health care interventions. International collaborative review groups prepare Cochrane reviews for publication in The Cochrane Library, a collection of databases available on CD-ROM and the World Wide Web and updated quarterly. The Cochrane Effective Practice and Organization of Care Group (EPOC) aims to prepare and maintain systematic reviews of professional, financial, organizational, and regulatory interventions that are designed to improve professional practice and the delivery of effective health services. EPOC has 17 reviews and 20 protocols published in Issue 3, 2000, of the Cochrane Library, with further protocols in development. We also have undertaken an overview of previously published systematic reviews of professional behavior change strategies. Our specialized register contains details of over 1,800 studies that fall within the group's scope. Systematic reviews provide a valuable source of information for policy makers and educators involved in planning continuing education and quality assurance initiatives and organizational change. EPOC will attempt to keep the Journal of Continuing Education in the Health Professions informed on an ongoing basis about new systematic reviews that it produces in the area of continuing medical education and quality assurance. PMID:11291587

  17. Pharmacological treatments for fatigue associated with palliative care: executive summary of a Cochrane Collaboration systematic review

    PubMed Central

    Mochamat; Cuhls, Henning; Peuckmann‐Post, Vera; Minton, Ollie; Stone, Patrick; Radbruch, Lukas

    2016-01-01

    Abstract Background In palliative care patients, fatigue can be severely debilitating and is often not counteracted with rest, thereby impacting daily activity and quality of life. Further complicating issues are the multidimensionality, subjective nature and lack of a consensus definition of fatigue. The review aimed to evaluate the efficacy of pharmacological treatments for fatigue in palliative care, with a focus on patients at an advanced stage of disease, including patients with cancer and other chronic diseases. Methods We considered randomized controlled trials concerning adult palliative care with a focus on pharmacological treatment of fatigue compared with placebo, application of two drugs, usual care or a non‐pharmacological intervention. The primary outcome had to be non‐specific fatigue (or related terms such as asthenia). We searched the CENTRAL, MEDLINE, PsycINFO and EMBASE, and a selection of cancer journals up to 28 April 2014. Two review authors independently assessed trial quality and extracted the data. Results We screened 1645 publications of which 45 met the inclusion criteria. In total, we analysed data from 18 drugs and 4696 participants. There was a very high degree of statistical and clinical heterogeneity in the trials. Meta‐analysis of data was possible for modafinil, pemoline, and methylphenidate. Conclusions Due to the limited evidence, we cannot recommend a specific drug for the treatment of fatigue in palliative care patients. Some drugs, which may be beneficial for the treatment of fatigue associated with palliative care such as amantadine, methylphenidate, and modafinil, should be further researched. PMID:27066315

  18. ω-3 Fatty acids for major depressive disorder in adults: an abridged Cochrane review

    PubMed Central

    Appleton, Katherine M; Sallis, Hannah M; Perry, Rachel; Ness, Andrew R; Churchill, Rachel

    2016-01-01

    Objective To assess the effects of n-3 polyunsaturated fatty acids (n-3PUFAs; also known as ω-3 fatty acids) compared with comparator for major depressive disorder (MDD) in adults. Design Systematic review and meta-analyses. Data sources The Cochrane Depression, Anxiety and Neurosis Review Group's Specialised Registers (CCDANCTR) and International Trial Registries searched to May 2015. CINAHL searched to September 2013. Trial selection Inclusion criteria: a randomised controlled trial (RCT); that provided n-3PUFAs as an intervention; used a comparator; measured depressive symptomology as an outcome; and was conducted in adults with MDD. Outcomes Primary outcomes were depressive symptomology and adverse events. Results 20 trials encompassing 26 relevant studies were found. For n-3PUFAs versus placebo, n-3PUFA supplementation resulted in a small-to-modest benefit for depressive symptomology: SMD=−0.32 (95% CI −0.52 to −0.12; 25 studies, 1373 participants, very low-quality evidence), but this effect is unlikely to be clinically meaningful, is very imprecise and, based on funnel plot inspection, sensitivity analyses and comparison with large well-conducted trials, is likely to be biased. Considerable evidence of heterogeneity between studies was also found, and was not explained by subgroup or sensitivity analyses. Numbers of individuals experiencing adverse events were similar in intervention and placebo groups (OR=1.24, 95% CI 0.95 to 1.62; 19 studies, 1207 participants; very low-quality evidence). For n-3PUFAs versus antidepressants, no differences were found between treatments in depressive symptomology (MD=−0.70 (95% CI −5.88 to 4.48); 1 study, 40 participants, very low-quality evidence). Conclusions At present, we do not have sufficient evidence to determine the effects of n-3PUFAs as a treatment for MDD. Further research in the form of adequately powered RCTs is needed. PMID:26936905

  19. Literature Mapping with PubAtlas — extending PubMed with a ‘BLASTing interface’ *

    PubMed Central

    Parker, D.S.; Chu, W.W.; Sabb, F.W.; Toga, A.W.; Bilder, R.M.

    2009-01-01

    PubAtlas (www.pubatlas.org) is a web service and standalone program providing literature maps for the biomedical research literature. It accepts user-defined sets of terms (PubMed queries) as input, and permits ‘BLASTing’ of one set against another: for all terms x and y in these sets, deriving the results of the pairwise intersections x AND y. This all vs. all capability extends PubMed with a literature analysis interface. Correspondingly, the basic form of literature map that PubAtlas provides for exploring associations among sets of terms is an interactive tabular display, in heatmap/microarray format. PubAtlas supports development of specialized lexica -- hierarchies of controlled terminology that can represent sets of related concepts or a ‘user-defined query language’. PubAtlas also provides historical perspectives on the literature, with temporal query features that highlight historical patterns. Generally, it is a framework for extending the PubMed interface, and an extensible platform for producing interactive literature maps. PMID:21347177

  20. Interventions for hidradenitis suppurativa: a Cochrane systematic review incorporating GRADE assessment of evidence quality.

    PubMed

    Ingram, J R; Woo, P N; Chua, S L; Ormerod, A D; Desai, N; Kai, A C; Hood, K; Burton, T; Kerdel, F; Garner, S E; Piguet, V

    2016-05-01

    More than 50 interventions have been used to treat hidradenitis suppurativa (HS), and so therapy decisions can be challenging. Our objective was to summarize and appraise randomized controlled trial (RCT) evidence for HS interventions in adults. Searches were conducted in Medline, Embase, CENTRAL, LILACS, five trials registers and abstracts from eight dermatology conferences until 13 August 2015. Two review authors independently assessed study eligibility, extracted data and assessed methodological quality. Primary outcomes were quality of life and adverse effects of the interventions. Twelve trials, from 1983 to 2015, investigating 15 different interventions met our inclusion criteria. The median trial duration was 16 weeks and the median number of participants was 27. Adalimumab 40 mg weekly improved the Dermatology Life Quality Index (DLQI) by 4·0 points, which equates to the minimal clinically important difference for the scale, compared with placebo (95% confidence interval -6·5 to -1·5 points). Evidence quality was reduced to 'moderate' because the results are based on only a single study. Adalimumab 40 mg every other week was ineffective in a meta-analysis of two studies comprising 124 participants. Infliximab 5 mg kg(-1) improved the DLQI score by 8·4 points after 8 weeks in a moderate-quality study completed by 33 of 38 participants. Etanercept 50 mg twice weekly was ineffective. Inclusion of a gentamicin sponge prior to primary closure did not improve outcomes. Other interventions, including topical and oral antibiotics, were investigated by relatively small studies, preventing treatment recommendations due to imprecision. More, larger RCTs are required to investigate most HS interventions, particularly oral treatments and surgical therapy. Moderate-quality evidence suggests that adalimumab given weekly and infliximab are effective, whereas adalimumab every other week is ineffective. PMID:26801356

  1. Non-steroidal antiandrogen monotherapy compared with luteinizing hormone-releasing hormone agonists or surgical castration monotherapy for advanced prostate cancer: a Cochrane systematic review.

    PubMed

    Kunath, Frank; Grobe, Henrik R; Rücker, Gerta; Motschall, Edith; Antes, Gerd; Dahm, Philipp; Wullich, Bernd; Meerpohl, Joerg J

    2015-07-01

    To assess the effects of non-steroidal antiandrogen monotherapy compared with luteinizing hormone-releasing hormone agonists or surgical castration monotherapy for treating advanced hormone-sensitive stages of prostate cancer. We searched the Cochrane Prostatic Diseases and Urologic Cancers Group Specialized Register (PROSTATE), the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, Web of Science with Conference Proceedings, three trial registries and abstracts from three major conferences to 23 December 2013, together with reference lists, and contacted selected experts in the field and manufacturers. We included randomized controlled trials comparing non-steroidal antiandrogen monotherapy with medical or surgical castration monotherapy for men in advanced hormone-sensitive stages of prostate cancer. Two review authors independently examined full-text reports, identified relevant studies, assessed the eligibility of studies for inclusion, extracted data and assessed risk of bias as well as quality of evidence according to the GRADE working group guidelines. We used Review Manager 5.2 for data synthesis and the fixed-effect model as primary analysis (when heterogeneity was low with I(2) < 50%); we used a random-effects model when confronted with substantial or considerable heterogeneity (when I(2) ≥50%). A total of 11 studies involving 3060 randomly assigned participants were included in the present review. Use of non-steroidal antiandrogens resulted in lower overall survival times (hazard ratio [HR] 1.24, 95% confidence interval [CI] 1.05-1.48, six studies, 2712 participants) and greater clinical progression (1 year: risk ratio [RR] 1.25, 95% CI 1.08-1.45, five studies, 2067 participants; 70 weeks: RR 1.26, 95% CI 1.08-1.45, six studies, 2373 participants; 2 years: RR 1.14, 95% CI 1.04-1.25, three studies, 1336 participants), as well as treatment failure (1 year: RR 1.19, 95% CI 1.02-1.38, four studies, 1539 participants; 70 weeks: RR 1

  2. Using Noun Phrases for Navigating Biomedical Literature on Pubmed: How Many Updates Are We Losing Track of?

    PubMed Central

    Srikrishna, Devabhaktuni; Coram, Marc A.

    2011-01-01

    Author-supplied citations are a fraction of the related literature for a paper. The “related citations” on PubMed is typically dozens or hundreds of results long, and does not offer hints why these results are related. Using noun phrases derived from the sentences of the paper, we show it is possible to more transparently navigate to PubMed updates through search terms that can associate a paper with its citations. The algorithm to generate these search terms involved automatically extracting noun phrases from the paper using natural language processing tools, and ranking them by the number of occurrences in the paper compared to the number of occurrences on the web. We define search queries having at least one instance of overlap between the author-supplied citations of the paper and the top 20 search results as citation validated (CV). When the overlapping citations were written by same authors as the paper itself, we define it as CV-S and different authors is defined as CV-D. For a systematic sample of 883 papers on PubMed Central, at least one of the search terms for 86% of the papers is CV-D versus 65% for the top 20 PubMed “related citations.” We hypothesize these quantities computed for the 20 million papers on PubMed to differ within 5% of these percentages. Averaged across all 883 papers, 5 search terms are CV-D, and 10 search terms are CV-S, and 6 unique citations validate these searches. Potentially related literature uncovered by citation-validated searches (either CV-S or CV-D) are on the order of ten per paper – many more if the remaining searches that are not citation-validated are taken into account. The significance and relationship of each search result to the paper can only be vetted and explained by a researcher with knowledge of or interest in that paper. PMID:21935487

  3. Methotrexate monotherapy and methotrexate combination therapy with traditional and biologic disease modifying antirheumatic drugs for rheumatoid arthritis: abridged Cochrane systematic review and network meta-analysis

    PubMed Central

    Barnabe, Cheryl; Tomlinson, George; Marshall, Deborah; Devoe, Dan; Bombardier, Claire

    2016-01-01

    Objective To compare methotrexate based disease modifying antirheumatic drug (DMARD) treatments for rheumatoid arthritis in patients naive to or with an inadequate response to methotrexate. Design Systematic review and Bayesian random effects network meta-analysis of trials assessing methotrexate used alone or in combination with other conventional synthetic DMARDs, biologic drugs, or tofacitinib in adult patients with rheumatoid arthritis. Data sources Trials were identified from Medline, Embase, and Central databases from inception to 19 January 2016; abstracts from two major rheumatology meetings from 2009 to 2015; two trial registers; and hand searches of Cochrane reviews. Study selection criteria Randomized or quasi-randomized trials that compared methotrexate with any other DMARD or combination of DMARDs and contributed to the network of evidence between the treatments of interest. Main outcomes American College of Rheumatology (ACR) 50 response (major clinical improvement), radiographic progression, and withdrawals due to adverse events. A comparison between two treatments was considered statistically significant if its credible interval excluded the null effect, indicating >97.5% probability that one treatment was superior. Results 158 trials were included, with between 10 and 53 trials available for each outcome. In methotrexate naive patients, several treatments were statistically superior to oral methotrexate for ACR50 response: sulfasalazine and hydroxychloroquine (“triple therapy”), several biologics (abatacept, adalimumab, etanercept, infliximab, rituximab, tocilizumab), and tofacitinib. The estimated probability of ACR50 response was similar between these treatments (range 56-67%), compared with 41% with methotrexate. Methotrexate combined with adalimumab, etanercept, certolizumab, or infliximab was statistically superior to oral methotrexate for inhibiting radiographic progression, but the estimated mean change over one year with all

  4. Mary Tyler Moore Helps Launch NIH MedlinePlus Magazine

    MedlinePlus

    ... Javascript on. Among those attending the NIH MedlinePlus magazine launch on Capitol Hill were (l-r) NIH Director Dr. Elias Zerhouni, Rep. Ralph Regula (R-OH), Mary Tyler Moore, former Rep. Paul Rogers, and NLM ... issue of NIH MedlinePlus magazine. In September, the FNLM was fortunate to have ...

  5. MedlinePlus FAQ: Copyrighted and Non-Copyrighted Material

    MedlinePlus

    ... https://www.nlm.nih.gov/medlineplus/faq/copyrightfaq.html Question: Is the material on MedlinePlus copyrighted? To use the sharing features on this page, please enable JavaScript. Answer: MedlinePlus contains both copyrighted and non-copyrighted material. Please see our copyright information page . ...

  6. Red blood cell transfusion to treat or prevent complications in sickle cell disease: an overview of Cochrane reviews

    PubMed Central

    Estcourt, Lise J; Fortin, Patricia M; Hopewell, Sally; Trivella, Marialena

    2016-01-01

    This is the protocol for a review and there is no abstract. The objectives are as follows: To summarize the evidence in Cochrane reviews of the effectiveness and safety of red cell transfusions versus no transfusion, or restrictive (to increase the total haemoglobin) versus liberal (to decrease the haemoglobin S level below a specified percentage) transfusion, for treatment or prevention of complications experienced by people with SCD. PMID:27069421

  7. Update of strategies to translate evidence from cochrane musculoskeletal group systematic reviews for use by various audiences.

    PubMed

    Rader, Tamara; Pardo Pardo, Jordi; Stacey, Dawn; Ghogomu, Elizabeth; Maxwell, Lara J; Welch, Vivian A; Singh, Jasvinder A; Buchbinder, Rachelle; Légaré, France; Santesso, Nancy; Toupin April, Karine; O'Connor, Annette M; Wells, George A; Winzenberg, Tania M; Johnston, Renea; Tugwell, Peter

    2014-02-01

    For rheumatology research to have a real influence on health and well-being, evidence must be tailored to inform the decisions of various audiences. The Cochrane Musculoskeletal Group (CMSG), one of 53 groups of the not-for-profit international Cochrane Collaboration, prepares, maintains, and disseminates systematic reviews of treatments for musculoskeletal diseases. While systematic reviews provided by the CMSG fill a major gap in meeting the need for high-quality evidence syntheses, our work does not end at the completion of a review. The term "knowledge translation" (KT) refers to the activities involved in bringing research evidence to various audiences in a useful form so it can be used to support decision making and improve practices. Systematic reviews give careful consideration to research methods and analysis. Because the review is often long and detailed, the clinically relevant results may not be apparent or in the optimal form for use by patients and their healthcare practitioners. This paper describes 10 formats, many of them new, for ways that evidence from Cochrane Reviews can be translated with the intention of meeting the needs of various audiences, including patients and their families, practitioners, policy makers, the press, and members of the public (the "5 Ps"). Current and future knowledge tools include summary of findings tables, patient decision aids, plain language summaries, press releases, clinical scenarios in general medical journals, frequently asked questions (Cochrane Clinical Answers), podcasts, Twitter messages, Journal Club materials, and the use of storytelling and narratives to support continuing medical education. Future plans are outlined to explore ways of improving the influence and usefulness of systematic reviews by providing results in formats suitable to our varied audiences. PMID:24293571

  8. Does Syndrome Differentiation Matter? A Meta-Analysis of Randomized Controlled Trials in Cochrane Reviews of Acupuncture

    PubMed Central

    Cao, Huijuan; Bourchier, Suzannah

    2012-01-01

    Abstract Background One of the basic and important principles of Traditional Chinese Medicine theory is syndrome differentiation, which is widely utilized for individual diagnosis and in the application of acupuncture treatment. However, the impact of syndrome differentiation on therapeutic effect is unclear because of insufficient supportive clinical evidence. Objective The aim of this study was to analyze current Cochrane Database systematic reviews of acupuncture and to evaluate differences in therapeutic effects of acupuncture treatment when syndrome differentiation is utilized, compared to when this approach is not utilized. Methods Cochrane Database systematic reviews of acupuncture were included if the reviews had sufficient data to perform subgroup analyses by syndrome differentiation applied during acupoints' selection. Searching was conducted across all available articles of the Cochrane Library, and the search concluded in July 2011. Results Forty-four trials from five Cochrane reviews were included in 10 subgroup meta-analyses. Seven meta-analyses showed that there were no differences between trials using fixed acupoints prescriptions and trials using individualized treatment based on relevant symptom improvements in cases of acute stroke, depression, epilepsy, migraine, and peripheral joint osteoarthritis (OA). The remaining 3 meta-analyses showed that acupuncture with fixed prescriptions was superior to individualized acupuncture for pain relief of peripheral joint OA, compared to sham control. Conclusions The available evidence showed no significant difference between acupuncture treatment with or without syndrome differentiation. Large, well-designed trials are warranted to address the use of syndrome differentiation for specific diseases or conditions in order to confirm if there are any advantages of using syndrome differentiation to achieve better therapeutic effects with acupuncture. PMID:24761164

  9. Finding Good Health Information on the Internet | NIH MedlinePlus the Magazine

    MedlinePlus

    ... page please turn JavaScript on. Feature: MedlinePlus Advantage The MedlinePlus Advantage Past Issues / Winter 2015 Table of Contents MedlinePlus is the National Institutes of Health's website for patients and ...

  10. [Cochrane EPOC group: closing the gap between quality assurance and organization of care research and front line professionals].

    PubMed

    Moja, P L; Castelli, B; McCauley, L; Grilli, R; Auxilia, F

    2005-01-01

    Keeping physicians informed on an ongoing basis is a new challenge for continuing medical education and quality assurance. In Italy over the last 5 years interest in evidence based literature is growing. This is demonstrated by the launch of an Italian edition of Clinical Evidence and by the growing number of guidelines and systematic reviews produced by Italian authors and institutions. However, there is some uncertainty concerning the familiarity of Italian policy makers and public health physicians with the evidence-based resources, including also how to access them. This article attempts to close this gap, by describing the activities of the Cochrane Collaboration and, within it, of the Cochrane Effective Practice and Organisation of Care Group (EPOC), both aim to prepare and maintaining SR of health care interventions. Specifically, the EPOC group develops systematic reviews of professional, financial, organisational and regulatory interventions that are designed to improve professional practice and the delivery of effective health services. EPOC has 31 reviews and 24 protocols published in Issue 4, 2004 of the Cochrane Library and has developed standard methods to assist people, such as quality criteria for study design specific to health services research. The EPOC specialized register contains details of over 2200 studies that fall within the group's scope. Systematic reviews provide a valuable and efficient source of information for policy makers and health care professionals aimed at implementing effective and efficient strategies to encourage medical behavioural change and deliver of high quality services. PMID:16523717

  11. Automated knowledge extraction from MEDLINE citations.

    PubMed

    Mendonça, E A; Cimino, J J

    2000-01-01

    As part of preliminary studies for the development of a digital library, we have studied the possibility of using the co-occurrence of MeSH terms in MEDLINE citations associated with the search strategies optimal for evidence-based medicine to automate construction of a knowledge base. We use the UMLS semantic types in order to analyze search results to determine which semantic types are most relevant for different types of questions (etiology, diagnosis, therapy, and prognosis). The automated process generated a large amount of information. Seven to eight percent of the semantic pairs generated in each clinical task group co-occur significantly more often than can be accounted for by chance. A pilot study showed good specificity and sensitivity for the intended purposes of this project in all groups. PMID:11079949

  12. A qualitative study into the difficulties experienced by healthcare decision makers when reading a Cochrane diagnostic test accuracy review

    PubMed Central

    2013-01-01

    Background Cochrane reviews are one of the best known and most trusted sources of evidence-based information in health care. While steps have been taken to make Cochrane intervention reviews accessible to a diverse readership, little is known about the accessibility of the newcomer to the Cochrane library: diagnostic test accuracy reviews (DTARs). The current qualitative study explored how healthcare decision makers, who varied in their knowledge and experience with test accuracy research and systematic reviews, read and made sense of DTARs. Methods A purposive sample of clinicians, researchers and policy makers (n = 21) took part in a series of think-aloud interviews, using as interview material the first three DTARs published in the Cochrane library. Thematic qualitative analysis of the transcripts was carried out to identify patterns in participants’ ‘reading’ and interpretation of the reviews and the difficulties they encountered. Results Participants unfamiliar with the design and methodology of DTARs found the reviews largely inaccessible and experienced a range of difficulties stemming mainly from the mismatch between background knowledge and level of explanation provided in the text. Experience with systematic reviews of interventions did not guarantee better understanding and, in some cases, led to confusion and misinterpretation. These difficulties were further exacerbated by poor layout and presentation, which affected even those with relatively good knowledge of DTARs and had a negative impact not only on their understanding of the reviews but also on their motivation to engage with the text. Comparison between the readings of the three reviews showed that more accessible presentation, such as presenting the results as natural frequencies, significantly increased participants’ understanding. Conclusions The study demonstrates that authors and editors should pay more attention to the presentation as well as the content of Cochrane DTARs

  13. Automated Patent Categorization and Guided Patent Search using IPC as Inspired by MeSH and PubMed

    PubMed Central

    2013-01-01

    Document search on PubMed, the pre-eminent database for biomedical literature, relies on the annotation of its documents with relevant terms from the Medical Subject Headings ontology (MeSH) for improving recall through query expansion. Patent documents are another important information source, though they are considerably less accessible. One option to expand patent search beyond pure keywords is the inclusion of classification information: Since every patent is assigned at least one class code, it should be possible for these assignments to be automatically used in a similar way as the MeSH annotations in PubMed. In order to develop a system for this task, it is necessary to have a good understanding of the properties of both classification systems. This report describes our comparative analysis of MeSH and the main patent classification system, the International Patent Classification (IPC). We investigate the hierarchical structures as well as the properties of the terms/classes respectively, and we compare the assignment of IPC codes to patents with the annotation of PubMed documents with MeSH terms. Our analysis shows a strong structural similarity of the hierarchies, but significant differences of terms and annotations. The low number of IPC class assignments and the lack of occurrences of class labels in patent texts imply that current patent search is severely limited. To overcome these limits, we evaluate a method for the automated assignment of additional classes to patent documents, and we propose a system for guided patent search based on the use of class co-occurrence information and external resources. PMID:23734562

  14. SLIM: an alternative Web interface for MEDLINE/PubMed searches – a preliminary study

    PubMed Central

    Muin, Michael; Fontelo, Paul; Liu, Fang; Ackerman, Michael

    2005-01-01

    Background With the rapid growth of medical information and the pervasiveness of the Internet, online search and retrieval systems have become indispensable tools in medicine. The progress of Web technologies can provide expert searching capabilities to non-expert information seekers. The objective of the project is to create an alternative search interface for MEDLINE/PubMed searches using JavaScript slider bars. SLIM, or Slider Interface for MEDLINE/PubMed searches, was developed with PHP and JavaScript. Interactive slider bars in the search form controlled search parameters such as limits, filters and MeSH terminologies. Connections to PubMed were done using the Entrez Programming Utilities (E-Utilities). Custom scripts were created to mimic the automatic term mapping process of Entrez. Page generation times for both local and remote connections were recorded. Results Alpha testing by developers showed SLIM to be functionally stable. Page generation times to simulate loading times were recorded the first week of alpha and beta testing. Average page generation times for the index page, previews and searches were 2.94 milliseconds, 0.63 seconds and 3.84 seconds, respectively. Eighteen physicians from the US, Australia and the Philippines participated in the beta testing and provided feedback through an online survey. Most users found the search interface user-friendly and easy to use. Information on MeSH terms and the ability to instantly hide and display abstracts were identified as distinctive features. Conclusion SLIM can be an interactive time-saving tool for online medical literature research that improves user control and capability to instantly refine and refocus search strategies. With continued development and by integrating search limits, methodology filters, MeSH terms and levels of evidence, SLIM may be useful in the practice of evidence-based medicine. PMID:16321145

  15. How Twitter Is Studied in the Medical Professions: A Classification of Twitter Papers Indexed in PubMed

    PubMed Central

    2013-01-01

    Background Since their inception, Twitter and related microblogging systems have provided a rich source of information for researchers and have attracted interest in their affordances and use. Since 2009 PubMed has included 123 journal articles on medicine and Twitter, but no overview exists as to how the field uses Twitter in research. Objective This paper aims to identify published work relating to Twitter within the fields indexed by PubMed, and then to classify it. This classification will provide a framework in which future researchers will be able to position their work, and to provide an understanding of the current reach of research using Twitter in medical disciplines. Methods Papers on Twitter and related topics were identified and reviewed. The papers were then qualitatively classified based on the paper’s title and abstract to determine their focus. The work that was Twitter focused was studied in detail to determine what data, if any, it was based on, and from this a categorization of the data set size used in the studies was developed. Using open coded content analysis additional important categories were also identified, relating to the primary methodology, domain, and aspect. Results As of 2012, PubMed comprises more than 21 million citations from biomedical literature, and from these a corpus of 134 potentially Twitter related papers were identified, eleven of which were subsequently found not to be relevant. There were no papers prior to 2009 relating to microblogging, a term first used in 2006. Of the remaining 123 papers which mentioned Twitter, thirty were focused on Twitter (the others referring to it tangentially). The early Twitter focused papers introduced the topic and highlighted the potential, not carrying out any form of data analysis. The majority of published papers used analytic techniques to sort through thousands, if not millions, of individual tweets, often depending on automated tools to do so. Our analysis demonstrates that

  16. Down the Block... Around the World...MedlinePlus.gov

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  8. Aggregator: A machine learning approach to identifying MEDLINE articles that derive from the same underlying clinical trial

    PubMed Central

    Shao, Weixiang; Adams, Clive E.; Cohen, Aaron M.; Davis, John M.; McDonagh, Marian S.; Thakurta, Sujata; Yu, Philip S.; Smalheiser, Neil R.

    2014-01-01

    Objective It is important to identify separate publications that report outcomes from the same underlying clinical trial, in order to avoid over-counting these as independent pieces of evidence. Methods We created positive and negative training sets (comprised of pairs of articles reporting on the same condition and intervention) that were, or were not, linked to the same clinicaltrials.gov trial registry number. Features were extracted from MEDLINE and PubMed metadata; pairwise similarity scores were modeled using logistic regression. Results Article pairs from the same trial were identified with high accuracy (F1 score = 0.843). We also created a clustering tool, Aggregator, that takes as input a PubMed user query for RCTs on a given topic, and returns article clusters predicted to arise from the same clinical trial. Discussion Although painstaking examination of full-text may be needed to be conclusive, metadata are surprisingly accurate in predicting when two articles derive from the same underlying clinical trial. PMID:25461812

  9. Bibliometric Analysis of the Korean Journal of Parasitology: Measured from SCI, PubMed, Scopus, and Synapse Databases

    PubMed Central

    2009-01-01

    The Korean Journal of Parasitology (KJP) is the official journal of the Korean Society for Parasitology which is celebrating its 50th anniversary in 2009. To assess the contributions and achievements of the KJP, bibliometric analysis was conducted based on the citation data retrieved from 4 major databases; SCI, PubMed, Synapse, and Scopus. It was found that the KJP articles were constantly cited by the articles published in major international journals represented in these databases. More than 60% of 1,370 articles published in the KJP from 1963 to June 2009 were cited at least once by SCI articles. The overall average times cited by SCI articles are 2.6. The rate is almost 3 times higher for the articles published in the last 10 years compared to 1.0 for the articles of the 1960s. The SCI journal impact factor for 2008 is calculated as 0.871. It is increasing and it is expected to increase further with the introduction of the KJP in the database in 2008. The more realistic h-indixes were measured from the study data set covering all the citations to the KJP; 17 for SCI, 6 for PubMed, 19 for Synapse, and 17 for Scopus. Synapse extensively picked up the citations to the earlier papers not retrievable from the other 3 databases. It identified many papers published in the 1960s and in the 1980s which have been cited heavily, proving the central role of the KJP in the dissemination of the important research findings over the last 5 decades. PMID:19885331

  10. Identifying observational studies of surgical interventions in MEDLINE and EMBASE

    PubMed Central

    Fraser, Cynthia; Murray, Alison; Burr, Jennifer

    2006-01-01

    Background Health technology assessments of surgical interventions frequently require the inclusion of non-randomised evidence. Literature search strategies employed to identify this evidence often exclude a methodological component because of uncertainty surrounding the use of appropriate search terms. This can result in the retrieval of a large number of irrelevant records. Methodological filters would help to minimise this, making literature searching more efficient. Methods An objective approach was employed to develop MEDLINE and EMBASE filters, using a reference standard derived from screening the results of an electronic literature search that contained only subject-related terms. Candidate terms for MEDLINE (N = 37) and EMBASE (N = 35) were derived from examination of the records of the reference standard. The filters were validated on two sets of studies that had been included in previous health technology assessments. Results The final filters were highly sensitive (MEDLINE 99.5%, EMBASE 100%, MEDLINE/EMBASE combined 100%) with precision ranging between 16.7% – 21.1%, specificity 35.3% – 43.5%, and a reduction in retrievals of over 30%. Against the validation standards, the individual filters retrieved 85.2% – 100% of records. In combination, however, the MEDLINE and EMBASE filters retrieved 100% against both validation standards with a reduction in retrieved records of 28.4% and 30.1% Conclusion The MEDLINE and EMBASE filters were highly sensitive and substantially reduced the number of records retrieved, indicating that they are useful tools for efficient literature searching. PMID:16919159

  11. Report from the kick-off meeting of the Cochrane Skin Group Core Outcome Set Initiative (CSG-COUSIN).

    PubMed

    Schmitt, J; Deckert, S; Alam, M; Apfelbacher, C; Barbaric, J; Bauer, A; Chalmers, J; Chosidow, O; Delamere, F; Doney, E; Eleftheriadou, V; Grainge, M; Johannsen, L; Kottner, J; Le Cleach, L; Mayer, A; Pinart, M; Prescott, L; Prinsen, C A C; Ratib, S; Schlager, J G; Sharma, M; Thomas, K S; Weberschock, T; Weller, K; Werner, R N; Wild, T; Wilkes, S R; Williams, H C

    2016-02-01

    A major obstacle of evidence-based clinical decision making is the use of nonstandardized, partly untested outcome measurement instruments. Core Outcome Sets (COSs) are currently developed in different medical fields to standardize and improve the selection of outcomes and outcome measurement instruments in clinical trials, in order to pool results of trials or to allow indirect comparison between interventions. A COS is an agreed minimum set of outcomes that should be measured and reported in all clinical trials of a specific disease or trial population. The international, multidisciplinary Cochrane Skin Group Core Outcome Set Initiative (CSG-COUSIN) aims to develop and implement COSs in dermatology, thus making trial evidence comparable and, herewith, more useful for clinical decision making. The inaugural meeting of CSG-COUSIN was held on 17-18 March 2015 in Dresden, Germany, as the exclusive theme of the Annual Cochrane Skin Group Meeting. In total, 29 individuals representing a broad mix of different stakeholder groups, professions, skills and perspectives attended. This report provides a description of existing COS initiatives in dermatology, highlights current methodological challenges in COS development, and presents the concept, aims and structure of CSG-COUSIN. PMID:26779929

  12. MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline

    PubMed Central

    Kim, Jung-jae; Pȩzik, Piotr; Rebholz-Schuhmann, Dietrich

    2008-01-01

    Summary: Search engines running on MEDLINE abstracts have been widely used by biologists to find publications that are related to their research. The existing search engines such as PubMed, however, have limitations when applied for the task of seeking textual evidence of relations between given concepts. The limitations are mainly due to the problem that the search engines do not effectively deal with multi-term queries which may imply semantic relations between the terms. To address this problem, we present MedEvi, a novel search engine that imposes positional restriction on occurrences matching multi-term queries, based on the observation that terms with semantic relations which are explicitly stated in text are not found too far from each other. MedEvi further identifies additional keywords of biological and statistical significance from local context of matching occurrences in order to help users reformulate their queries for better results. Availability: http://www.ebi.ac.uk/tc-test/textmining/medevi/ Contact: kim@ebi.ac.uk PMID:18400773

  13. Commentary on a Cochrane Review of Early Additional Food and Fluids for Healthy Breastfed Full-Term Infants.

    PubMed

    Maslin, Kate

    2016-01-01

    The World Health Organization recommends that infants should be exclusively breastfed for the first 6 months of life. A Cochrane Review assessed the benefits and harms of additional foods and fluids for full-term healthy breastfed infants. The review included randomized or quasirandomized controlled trials of full-term healthy breastfed infants up to the age of 6 months. Six studies met the inclusion criteria. Trials from early days after birth did not indicate that giving additional fluids was beneficial. Trials with 4- to 6-month-old infants did not indicate any benefit to supplementing with food at 4 months. This review did not find any evidence for disagreement with the recommendation that exclusive breastfeeding should be recommended for 6 months after birth. PMID:27520599

  14. Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data

    PubMed Central

    2013-01-01

    Background The World Wide Web has become a dissemination platform for scientific and non-scientific publications. However, most of the information remains locked up in discrete documents that are not always interconnected or machine-readable. The connectivity tissue provided by RDF technology has not yet been widely used to support the generation of self-describing, machine-readable documents. Results In this paper, we present our approach to the generation of self-describing machine-readable scholarly documents. We understand the scientific document as an entry point and interface to the Web of Data. We have semantically processed the full-text, open-access subset of PubMed Central. Our RDF model and resulting dataset make extensive use of existing ontologies and semantic enrichment services. We expose our model, services, prototype, and datasets at http://biotea.idiginfo.org/ Conclusions The semantic processing of biomedical literature presented in this paper embeds documents within the Web of Data and facilitates the execution of concept-based queries against the entire digital library. Our approach delivers a flexible and adaptable set of tools for metadata enrichment and semantic processing of biomedical documents. Our model delivers a semantically rich and highly interconnected dataset with self-describing content so that software can make effective use of it. PMID:23734622

  15. A drug-adverse event extraction algorithm to support pharmacovigilance knowledge mining from PubMed citations.

    PubMed

    Wang, Wei; Haerian, Krystl; Salmasian, Hojjat; Harpaz, Rave; Chase, Herbert; Friedman, Carol

    2011-01-01

    Adverse drug events (ADEs) create a serious problem causing substantial harm to patients. An executable standardized knowledgebase of drug-ADE relations which is publicly available would be valuable so that it could be used for ADE detection. The literature is an important source that could be used to generate a knowledgebase of drug-ADE pairs. In this paper, we report on a method that automatically determines whether a specific adverse event (AE) is caused by a specific drug based on the content of PubMed citations. A drug-ADE classification method was initially developed to detect neutropenia based on a pre-selected set of drugs. This method was then applied to a different set of 76 drugs to determine if they caused neutropenia. For further proof of concept this method was applied to 48 drugs to determine whether they caused another AE, myocardial infarction. Results showed that AUROC was 0.93 and 0.86 respectively. PMID:22195210

  16. An experimental search strategy retrieves more precise results than PubMed and Google for questions about medical interventions

    PubMed Central

    Dylla, Daniel P.; Megison, Susan D.

    2015-01-01

    Objective. We compared the precision of a search strategy designed specifically to retrieve randomized controlled trials (RCTs) and systematic reviews of RCTs with search strategies designed for broader purposes. Methods. We designed an experimental search strategy that automatically revised searches up to five times by using increasingly restrictive queries as long at least 50 citations were retrieved. We compared the ability of the experimental and alternative strategies to retrieve studies relevant to 312 test questions. The primary outcome, search precision, was defined for each strategy as the proportion of relevant, high quality citations among the first 50 citations retrieved. Results. The experimental strategy had the highest median precision (5.5%; interquartile range [IQR]: 0%–12%) followed by the narrow strategy of the PubMed Clinical Queries (4.0%; IQR: 0%–10%). The experimental strategy found the most high quality citations (median 2; IQR: 0–6) and was the strategy most likely to find at least one high quality citation (73% of searches; 95% confidence interval 68%–78%). All comparisons were statistically significant. Conclusions. The experimental strategy performed the best in all outcomes although all strategies had low precision. PMID:25922798

  17. Matching references with MEDLINE via TCP/IP.

    PubMed Central

    Guidi, J. N.

    1993-01-01

    Bibliographic references are an important part of databases and information resources used by clinicians and biomedical researchers. In addition to the obvious clerical advantages of standard references, bibliographic references can also be used as links to related items in different data sets. This paper describes an effort that involved matching references from a variety of disparate databases to canonical MEDLINE references. The references matched were those involved in a database unification project which is part of the Mouse Genome Informatics effort at The Jackson Laboratory. Software was developed to take advantage of a commercially available retrieval engine which accesses MEDLINE on CD-ROM disks. The software permits client programs on UNIX/C, and potentially other environments, to access unabridged MEDLINE via networks supporting the TCP/IP protocols. The matching process described can be used as a model for similar efforts with different research or clinical data sets, as well as different hardware or software environments. PMID:8130546

  18. Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts

    PubMed Central

    Li, Jiao; Zhu, Xiaoyan; Chen, Jake Yue

    2009-01-01

    The recently proposed concept of molecular connectivity maps enables researchers to integrate experimental measurements of genes, proteins, metabolites, and drug compounds under similar biological conditions. The study of these maps provides opportunities for future toxicogenomics and drug discovery applications. We developed a computational framework to build disease-specific drug-protein connectivity maps. We integrated gene/protein and drug connectivity information based on protein interaction networks and literature mining, without requiring gene expression profile information derived from drug perturbation experiments on disease samples. We described the development and application of this computational framework using Alzheimer's Disease (AD) as a primary example in three steps. First, molecular interaction networks were incorporated to reduce bias and improve relevance of AD seed proteins. Second, PubMed abstracts were used to retrieve enriched drug terms that are indirectly associated with AD through molecular mechanistic studies. Third and lastly, a comprehensive AD connectivity map was created by relating enriched drugs and related proteins in literature. We showed that this molecular connectivity map development approach outperformed both curated drug target databases and conventional information retrieval systems. Our initial explorations of the AD connectivity map yielded a new hypothesis that diltiazem and quinidine may be investigated as candidate drugs for AD treatment. Molecular connectivity maps derived computationally can help study molecular signature differences between different classes of drugs in specific disease contexts. To achieve overall good data coverage and quality, a series of statistical methods have been developed to overcome high levels of data noise in biological networks and literature mining results. Further development of computational molecular connectivity maps to cover major disease areas will likely set up a new model for

  19. Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts.

    PubMed

    Li, Jiao; Zhu, Xiaoyan; Chen, Jake Yue

    2009-07-01

    The recently proposed concept of molecular connectivity maps enables researchers to integrate experimental measurements of genes, proteins, metabolites, and drug compounds under similar biological conditions. The study of these maps provides opportunities for future toxicogenomics and drug discovery applications. We developed a computational framework to build disease-specific drug-protein connectivity maps. We integrated gene/protein and drug connectivity information based on protein interaction networks and literature mining, without requiring gene expression profile information derived from drug perturbation experiments on disease samples. We described the development and application of this computational framework using Alzheimer's Disease (AD) as a primary example in three steps. First, molecular interaction networks were incorporated to reduce bias and improve relevance of AD seed proteins. Second, PubMed abstracts were used to retrieve enriched drug terms that are indirectly associated with AD through molecular mechanistic studies. Third and lastly, a comprehensive AD connectivity map was created by relating enriched drugs and related proteins in literature. We showed that this molecular connectivity map development approach outperformed both curated drug target databases and conventional information retrieval systems. Our initial explorations of the AD connectivity map yielded a new hypothesis that diltiazem and quinidine may be investigated as candidate drugs for AD treatment. Molecular connectivity maps derived computationally can help study molecular signature differences between different classes of drugs in specific disease contexts. To achieve overall good data coverage and quality, a series of statistical methods have been developed to overcome high levels of data noise in biological networks and literature mining results. Further development of computational molecular connectivity maps to cover major disease areas will likely set up a new model for

  20. False-positive findings in Cochrane meta-analyses with and without application of trial sequential analysis: an empirical review

    PubMed Central

    Imberger, Georgina; Thorlund, Kristian; Gluud, Christian; Wetterslev, Jørn

    2016-01-01

    Objective Many published meta-analyses are underpowered. We explored the role of trial sequential analysis (TSA) in assessing the reliability of conclusions in underpowered meta-analyses. Methods We screened The Cochrane Database of Systematic Reviews and selected 100 meta-analyses with a binary outcome, a negative result and sufficient power. We defined a negative result as one where the 95% CI for the effect included 1.00, a positive result as one where the 95% CI did not include 1.00, and sufficient power as the required information size for 80% power, 5% type 1 error, relative risk reduction of 10% or number needed to treat of 100, and control event proportion and heterogeneity taken from the included studies. We re-conducted the meta-analyses, using conventional cumulative techniques, to measure how many false positives would have occurred if these meta-analyses had been updated after each new trial. For each false positive, we performed TSA, using three different approaches. Results We screened 4736 systematic reviews to find 100 meta-analyses that fulfilled our inclusion criteria. Using conventional cumulative meta-analysis, false positives were present in seven of the meta-analyses (7%, 95% CI 3% to 14%), occurring more than once in three. The total number of false positives was 14 and TSA prevented 13 of these (93%, 95% CI 68% to 98%). In a post hoc analysis, we found that Cochrane meta-analyses that are negative are 1.67 times more likely to be updated (95% CI 0.92 to 2.68) than those that are positive. Conclusions We found false positives in 7% (95% CI 3% to 14%) of the included meta-analyses. Owing to limitations of external validity and to the decreased likelihood of updating positive meta-analyses, the true proportion of false positives in meta-analysis is probably higher. TSA prevented 93% of the false positives (95% CI 68% to 98%). PMID:27519923

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  17. Language and country preponderance trends in MEDLINE and its causes

    PubMed Central

    Loria, Alvar; Arroyo, Pedro

    2005-01-01

    Objective: The authors characterized the output of MEDLINE papers by language and country of publication during a thirty-four-year time period. Methods: We classified MEDLINE's journal articles by country of publication (Anglos/Non-Anglos) and language (English/Non-English) for the years 1966 and from 1970 to 2000 at five-year intervals. Eight English-speaking countries were considered Anglos. Linear regression analysis of number of papers versus time was performed. Results: The global number of papers increased linearly at a rate of 8,142 papers per year. Anglo and English papers also increased linearly (6,740 and 9,199, respectively). Journals of Non-Anglo countries accounted for 25% of the English language increase (2,438 per year). Only Non-English papers decreased at a rate of 1,056 fewer papers per year. These trends have led to overwhelming shares of English and Anglo papers in MEDLINE. In 2000, 68% of all papers were published in the 8 Anglo countries and 90% were written in English. Conclusions: The Anglo and English preponderances appear to be a consequence of at least two phenomena: (1) editorial policy changes in MEDLINE and in some journals from Non-Anglo countries and (2) factors affecting Non-Anglo researchers in the third world (publication constraints, migration, and undersupport). These are tentative conclusions that need confirmation. PMID:16059428

  18. Use of positive and negative words in scientific PubMed abstracts between 1974 and 2014: retrospective analysis

    PubMed Central

    Tijdink, Joeri K; Otte, Willem M

    2015-01-01

    Objective To investigate whether language used in science abstracts can skew towards the use of strikingly positive and negative words over time. Design Retrospective analysis of all scientific abstracts in PubMed between 1974 and 2014. Methods The yearly frequencies of positive, negative, and neutral words (25 preselected words in each category), plus 100 randomly selected words were normalised for the total number of abstracts. Subanalyses included pattern quantification of individual words, specificity for selected high impact journals, and comparison between author affiliations within or outside countries with English as the official majority language. Frequency patterns were compared with 4% of all books ever printed and digitised by use of Google Books Ngram Viewer. Main outcome measures Frequencies of positive and negative words in abstracts compared with frequencies of words with a neutral and random connotation, expressed as relative change since 1980. Results The absolute frequency of positive words increased from 2.0% (1974-80) to 17.5% (2014), a relative increase of 880% over four decades. All 25 individual positive words contributed to the increase, particularly the words “robust,” “novel,” “innovative,” and “unprecedented,” which increased in relative frequency up to 15 000%. Comparable but less pronounced results were obtained when restricting the analysis to selected journals with high impact factors. Authors affiliated to an institute in a non-English speaking country used significantly more positive words. Negative word frequencies increased from 1.3% (1974-80) to 3.2% (2014), a relative increase of 257%. Over the same time period, no apparent increase was found in neutral or random word use, or in the frequency of positive word use in published books. Conclusions Our lexicographic analysis indicates that scientific abstracts are currently written with more positive and negative words, and provides an insight into the

  19. Critique of the review of 'Water fluoridation for the prevention of dental caries' published by the Cochrane Collaboration in 2015.

    PubMed

    Rugg-Gunn, A J; Spencer, A J; Whelton, H P; Jones, C; Beal, J F; Castle, P; Cooney, P V; Johnson, J; Kelly, M P; Lennon, M A; McGinley, J; O'Mullane, D; Sgan-Cohen, H D; Sharma, P P; Thomson, W M; Woodward, S M; Zusman, S P

    2016-04-01

    The Cochrane Review on water fluoridation for the prevention of dental caries was published in 2015 and attracted considerable interest and comment, especially in countries with extensive water fluoridation programmes. The Review had two objectives: (i) to evaluate the effects of water fluoridation (artificial or natural) on the prevention of dental caries, and (ii) to evaluate the effects of water fluoridation (artificial or natural) on dental fluorosis. The authors concluded, inter alia, that there was very little contemporary evidence, meeting the Review's inclusion criteria, that evaluated the effectiveness of water fluoridation for the prevention of dental caries. The purpose of this critique is to examine the conduct of the above Review, and to put it into context in the wider body of evidence regarding the effectiveness of water fluoridation. While the overall conclusion that water fluoridation is effective in caries prevention agrees with previous reviews, many important public health questions could not be answered by the Review because of the restrictive criteria used to judge adequacy of study design and risk of bias. The potential benefits of using wider criteria in order to achieve a fuller understanding of the effectiveness of water fluoridation are discussed. PMID:27056513

  20. MedlinePlus - Health Information from the National Library of Medicine

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    ... Health Information in Multiple Languages MedlinePlus Connect for EHRs About MedlinePlus Site Map FAQs Contact Us Get ... Accessibility Quality Guidelines Viewers & Players MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 ...

  1. Twelve Years of Scientific Production on Medline by Latin American Spine Surgeons

    PubMed Central

    Falavigna, Asdrubal; Botelho, Ricardo Vieira; Teles, Alisson Roberto; Guarise da Silva, Pedro; Martins, Delio; Guyot, Juan Pablo; Gonzalez, Alvaro Silva; Avila, José Maria Jiménez; Defino, Helton Luiz Aparecido

    2014-01-01

    Background Despite the small contribution of LA in the Science Citation Index (SCI), a growing contribution by LA research to international literature has been observed in recent years. Study Design Systematic review. Purpose To evaluate the scientific contribution of Latin American (LA) Spine Surgeons in the last decade. Methods A literature search of publications by LA spinal surgeons on topics concerning the spine or spinal cord was performed using an online database; Pubmed.gov. The results were limited to articles published from January 2000 to December 2011. The quality of the publication was evaluated with the journal impact factor (IF), Oxford classification and number of citations. Results This study comprised 320 articles published in the Medline database by LA spine surgeons from 2000 to 2011. In recent years, there has been an increase in the number of publications by LA spine surgeons. It was observed that 38.4% of LA papers were published in LA journals. 46.6% of the articles were published in journals with an IF lower than 1, and there was no statistically significant difference in the number of articles published in journals with a higher IF during the period. Linear-by-linear association analysis demonstrated an improvement in the level of evidence provided by LA articles published in recent years. Conclusions This study showed a growth in the number of publications in last 12 years by LA spinal surgeons. It is necessary to discuss a way to increase quantity and quality of scientific publications, mainly through a better education in research. PMID:24505336

  2. Preliminary comparison of the Essie and PubMed search engines for answering clinical questions using MD on Tap, a PDA-based program for accessing biomedical literature.

    PubMed

    Sutton, Victoria R; Hauser, Susan E

    2005-01-01

    MD on Tap, a PDA application that searches and retrieves biomedical literature, is specifically designed for use by mobile healthcare professionals. With the goal of improving the usability of the application, a preliminary comparison was made of two search engines (PubMed and Essie) to determine which provided most efficient path to the desired clinically-relevant information. PMID:16779415

  3. Preliminary comparison of the Essie and PubMed search engines for answering clinical questions using MD on Tap, a PDA-based program for accessing biomedical literature

    PubMed Central

    Sutton, Victoria R.; Hauser, Susan E.

    2005-01-01

    MD on Tap, a PDA application that searches and retrieves biomedical literature, is specifically designed for use by mobile healthcare professionals. With the goal of improving the usability of the application, a preliminary comparison was made of two search engines (PubMed and Essie) to determine which provided most efficient path to the desired clinically-relevant information. PMID:16779415

  4. NIH Quickfinder and NIH MedlinePlus Advisory Group - Fall 2010 | NIH MedlinePlus the Magazine

    MedlinePlus

    ... 1770 NIH MedlinePlus Advisory Group Marin P. Allen, Ph.D., Office of Communications and Public Liaison, NIH ... of Allergy and Infectious Diseases Richard E. Manrow, Ph.D., National Cancer Institute John McGrath, Ph.D., ...

  5. NIH Quickfinder and NIH MedlinePlus Advisory Group - Winter 2010 | NIH MedlinePlus the Magazine

    MedlinePlus

    ... 1770 NIH MedlinePlus Advisory Group Marin P. Allen, Ph.D., Office of Communications and Public Liaison, NIH ... of Allergy and Infectious Diseases Richard E. Manrow, Ph.D., National Cancer Institute John McGrath, Ph.D., ...

  6. ClinicalTrials.gov Turns 10! | NIH MedlinePlus the Magazine

    MedlinePlus

    ... On the ClinicalTrials.gov Web site, you can search for a trial by the name of the ... incidence of breast cancer. Also, it lets you search medical journal references via NLM's PubMed ( www.pubmed. ...

  7. Service Engagement in Interventions for Street-Connected Children and Young People: A Summary of Evidence Supplementing a Recent Cochrane-Campbell Review

    ERIC Educational Resources Information Center

    Hossain, Rosa; Coren, Esther

    2015-01-01

    Background: This paper builds on a Cochrane-Campbell systematic review of interventions that reduce harms and promote reintegration in street-connected children and young people focusing on intervention outcomes. The aim of the present analysis is to explore questions raised in the systematic review over the potential role of service engagement in…

  8. Information Literacy for Users at the National Medical Library of Cuba: Cochrane Library Course for the Search of Best Evidence for Clinical Decisions

    ERIC Educational Resources Information Center

    Santana Arroyo, Sonia; del Carmen Gonzalez Rivero, Maria

    2012-01-01

    The National Medical Library of Cuba is currently developing an information literacy program to train users in the use of biomedical databases. This paper describes the experience with the course "Cochrane Library: Evidence-Based Medicine," which aims to teach users how to make the best use of this database, as well as the evidence-based medicine…

  9. Are mass-media campaigns effective in preventing drug use? A Cochrane systematic review and meta-analysis

    PubMed Central

    Allara, Elias; Ferri, Marica; Bo, Alessandra; Gasparrini, Antonio; Faggiano, Fabrizio

    2015-01-01

    Objective To determine whether there is evidence that mass-media campaigns can be effective in reducing illicit drug consumption and the intent to consume. Design Systematic review of randomised and non-randomised studies. Methods We searched four electronic databases (MEDLINE, EMBASE, ProQuest Dissertations & Theses A&I and CENTRAL) and further explored seven additional resources to obtain both published and unpublished materials. We appraised the quality of included studies using standardised tools. We carried out meta-analyses of randomised controlled trials and a pooled analysis of interrupted time-series and controlled before-and-after studies. Results We identified 19 studies comprising 184 811 participants. Pooled analyses and narrative synthesis provided mixed evidence of effectiveness. Eight interventions evaluated with randomised controlled trials leaned towards no evidence of an effect, both on drug use (standardised mean difference (SMD) −0.02; 95% CI −0.15 to 0.12) and the intention to use drugs (SMD −0.07; 95% CI −0.19 to 0.04). Four campaigns provided some evidence of beneficial effects in preventing drug use and two interventions provided evidence of iatrogenic effects. Conclusions Studies were considerably heterogeneous in type of mass-media intervention, outcome measures, underlying theory, comparison groups and design. Such factors can contribute to explaining the observed variability in results. Owing to the risk of adverse effects, caution is needed in disseminating mass-media campaigns tackling drug use. Large studies conducted with appropriate methodology are warranted to consolidate the evidence base. PMID:26338836

  10. Author Disambiguation in PubMed: Evidence on the Precision and Recall of Author-ity among NIH-Funded Scientists

    PubMed Central

    Lerchenmueller, Marc J.; Sorenson, Olav

    2016-01-01

    We examined the usefulness (precision) and completeness (recall) of the Author-ity author disambiguation for PubMed articles by associating articles with scientists funded by the National Institutes of Health (NIH). In doing so, we exploited established unique identifiers—Principal Investigator (PI) IDs—that the NIH assigns to funded scientists. Analyzing a set of 36,987 NIH scientists who received their first R01 grant between 1985 and 2009, we identified 355,921 articles appearing in PubMed that would allow us to evaluate the precision and recall of the Author-ity disambiguation. We found that Author-ity identified the NIH scientists with 99.51% precision across the articles. It had a corresponding recall of 99.64%. Precision and recall, moreover, appeared stable across common and uncommon last names, across ethnic backgrounds, and across levels of scientist productivity. PMID:27367860

  11. Author Disambiguation in PubMed: Evidence on the Precision and Recall of Author-ity among NIH-Funded Scientists.

    PubMed

    Lerchenmueller, Marc J; Sorenson, Olav

    2016-01-01

    We examined the usefulness (precision) and completeness (recall) of the Author-ity author disambiguation for PubMed articles by associating articles with scientists funded by the National Institutes of Health (NIH). In doing so, we exploited established unique identifiers-Principal Investigator (PI) IDs-that the NIH assigns to funded scientists. Analyzing a set of 36,987 NIH scientists who received their first R01 grant between 1985 and 2009, we identified 355,921 articles appearing in PubMed that would allow us to evaluate the precision and recall of the Author-ity disambiguation. We found that Author-ity identified the NIH scientists with 99.51% precision across the articles. It had a corresponding recall of 99.64%. Precision and recall, moreover, appeared stable across common and uncommon last names, across ethnic backgrounds, and across levels of scientist productivity. PMID:27367860

  12. Early Childhood Dental Caries: A Rising Dental Public Health Crisis

    ERIC Educational Resources Information Center

    Gomez, Grace Felix

    2013-01-01

    The aim of this article is to examine the literature and review the risk factors and disparities contributing to early childhood caries (ECC), which is a major health problem among preschoolers in the United States of America. A search was conducted using MEDLINE, PubMed, Google Scholar, and the Cochrane Library databases and the key terms…

  13. Physical Activity Measurement Instruments for Children with Cerebral Palsy: A Systematic Review

    ERIC Educational Resources Information Center

    Capio, Catherine M.; Sit, Cindy H. P.; Abernethy, Bruce; Rotor, Esmerita R.

    2010-01-01

    Aim: This paper is a systematic review of physical activity measurement instruments for field-based studies involving children with cerebral palsy (CP). Method: Database searches using PubMed Central, MEDLINE, CINAHL Plus, PsycINFO, EMBASE, Cochrane Library, and PEDro located 12 research papers, identifying seven instruments that met the inclusion…

  14. Weight change and all-cause mortality in older adults: A meta-analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This meta-analysis of observational cohort studies examined the association between weight change (weight loss, weight gain, and weight fluctuation) and all-cause mortality among older adults. We used PubMed (MEDLINE), Web of Science, and Cochrane Library to identify prospective studies published in...

  15. The Relationship between Sugar-Containing Methadone and Dental Caries: A Systematic Review

    ERIC Educational Resources Information Center

    Tripathee, Sheela; Akbar, Tahira; Richards, Derek; Themessl-Huber, Markus; Freeman, Ruth

    2013-01-01

    Objectives: To review the evidence of a relationship between sugar-containing methadone and dental caries. Data sources: A systematic search of Cochrane Library, PubMed, PsychINFO, EMBASE, MEDLINE, Current Controlled Trials, WHO, OHRN, SIGLE and ERIC databases was conducted from January 1978 up to June 2010. Study selection: Articles were assessed…

  16. Anne O'Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results

    PubMed Central

    Smalheiser, Neil R; Zhou, Wei; Torvik, Vetle I

    2008-01-01

    Background PubMed is designed to provide rapid, comprehensive retrieval of papers that discuss a given topic. However, because PubMed does not organize the search output further, it is difficult for users to grasp an overview of the retrieved literature according to non-topical dimensions, to drill-down to find individual articles relevant to a particular individual's need, or to browse the collection. Results In this paper, we present Anne O'Tate, a web-based tool that processes articles retrieved from PubMed and displays multiple aspects of the articles to the user, according to pre-defined categories such as the "most important" words found in titles or abstracts; topics; journals; authors; publication years; and affiliations. Clicking on a given item opens a new window that displays all papers that contain that item. One can navigate by drilling down through the categories progressively, e.g., one can first restrict the articles according to author name and then restrict that subset by affiliation. Alternatively, one can expand small sets of articles to display the most closely related articles. We also implemented a novel cluster-by-topic method that generates a concise set of topics covering most of the retrieved articles. Conclusion Anne O'Tate is an integrated, generic tool for summarization, drill-down and browsing of PubMed search results that accommodates a wide range of biomedical users and needs. It can be accessed at [4]. Peer review and editorial matters for this article were handled by Aaron Cohen. PMID:18279519

  17. Relative Citation Ratio of Top Twenty Macedonian Biomedical Scientists in PubMed: A New Metric that Uses Citation Rates to Measure Influence at the Article Level

    PubMed Central

    Spiroski, Mirko

    2016-01-01

    AIM: The aim of this study was to analyze relative citation ratio (RCR) of top twenty Macedonian biomedical scientists with a new metric that uses citation rates to measure influence at the article level. MATERIAL AND METHODS: Top twenty Macedonian biomedical scientists were identified by GoPubMed on the base of the number of deposited abstracts in PubMed, corrected with the data from previously published paper, and completed with the Macedonian biomedical scientists working in countries outside the Republic of Macedonia, but born or previously worked in the country. iCite was used as a tool to access a dashboard of bibliometrics for papers associated with a portfolio. RESULTS: The biggest number of top twenty Macedonian biomedical scientists has RCR lower than one. Only four Macedonian biomedical scientists have bigger RCR in comparison with those in PubMed. The most prominent RCR of 2.29 has Rosoklija G. RCR of the most influenced individual papers deposited in PubMed has shown the biggest value for the paper of Efremov D (35.19). This paper has the biggest number of authors (860). CONCLUSION: It is necessary to accept top twenty Macedonian biomedical scientists as an example of new metric that uses citation rates to measure influence at the article level, rather than qualification of the best Macedonian biomedical scientists. PMID:27335586

  18. Compared with what? An analysis of control-group types in Cochrane and Campbell reviews of psychosocial treatment efficacy with substance use disorders

    PubMed Central

    Karlsson, Patrik; Bergmark, Anders

    2015-01-01

    Abstract Background and Aims A crucial, but under-appreciated, aspect in experimental research on psychosocial treatments of substance use disorders concerns what kinds of control groups are used. This paper examines how the distinction between different control-group designs have been handled by the Cochrane and the Campbell Collaborations in their systematic reviews of psychosocial treatments of substance abuse disorders. Methods We assessed Cochrane and Campbell reviews (n = 8) that were devoted to psychosocial treatments of substance use disorders. We noted what control groups were considered and analysed the extent to which the reviews provided a rationale for chosen comparison conditions. We also analysed whether type of control group in the primary studies influenced how the reviews framed the effects discussed and whether this was related to conclusions drawn. Results The reviews covered studies involving widely different control conditions. Overall, little attention was paid to the use of different control groups (e.g. head-to-head comparisons versus untreated controls) and what this implies when interpreting effect sizes. Seven of eight reviews did not provide a rationale for the choice of comparison conditions. Conclusions Cochrane and Campbell reviews of the efficacy of psychosocial interventions with substance use disorders seem to underappreciate that the use of different control-group types yields different effect estimates. Most reviews have not distinguished between different control-group designs and therefore have provided a confused picture regarding absolute and relative treatment efficacy. A systematic approach to treating different control-group designs in research reviews is necessary for meaningful estimates of treatment efficacy. PMID:25393504

  19. Step 4: Get Routine Care to Avoid Problems | NIH MedlinePlus the Magazine

    MedlinePlus

    ... plan to address relevant challenges for type 2 diabetes. Read Part 1 on lupus in MedlinePlus magazine , Spring 2014 issue: medlineplus.gov/magazine/ Read Part 2 on rheumatoid arthritis in MedlinePlus magazine, Summer 2014 issue: medlineplus.gov/ ...

  20. MedlinePlus FAQ: Can I play videos on my phone or tablet?

    MedlinePlus

    ... medlineplus/faq/mobilevideo.html Question: Can I play videos on my phone or tablet? To use the ... this page, please enable JavaScript. Answer: MedlinePlus has video content in different formats. MedlinePlus also links to ...

  1. Polio and Post-Polio Syndrome - Multiple Languages: MedlinePlus

    MedlinePlus

    ... Search Search MedlinePlus GO GO About MedlinePlus Site Map FAQs Contact Us Health Topics Drugs & Supplements Videos & ... Korean (한국어) Laotian (Lao) Polish (polski) Portuguese (português) Romanian (Română) Russian (Русский) Samoan (Gagana Samoa) Somali (af ...

  2. Health Information in Romanian (Română): MedlinePlus

    MedlinePlus

    ... Search Search MedlinePlus GO GO About MedlinePlus Site Map FAQs Contact Us Health Topics Drugs & Supplements Videos & Tools You Are Here: Home → Multiple Languages → Romanian (Română) URL of this page: https://www.nlm. ...

  3. To Your Health: NLM update transcript - NIH MedlinePlus magazine Summer 2016

    MedlinePlus

    ... National Library of Medicine (NLM). Here is what's new this week in To Your Health, a consumer health oriented podcast from NLM, that helps you use MedlinePlus to follow up on weekly topics. The new edition of NIH MedlinePlus magazine covers the Zika ...

  4. MedlinePlus en español marks its 10th anniversary

    MedlinePlus

    ... medlineplus.gov/spanishanniversary.html MedlinePlus en español Marks its 10 th Anniversary To use the sharing features ... Spanish greatly expands NIH's ability to carry out its mission to communicate with the public.” MedlinePlus en ...

  5. MedlinePlus FAQ: Can I play videos on my phone or tablet?

    MedlinePlus

    ... MedlinePlus also links to video content on the Internet. Some videos might not play on your mobile device. Text alternatives are available for video content licensed by MedlinePlus: Access closed captioning for health videos with the CC ...

  6. CAM on PubMed

    MedlinePlus

    ... Grants & Funding What Will NCCIH Fund? Overview Funding Strategy Funding Opportunities Grantee Policies Application Resources Program Directors Clinical Research Toolbox Types of Grants and Contracts General Award Mechanisms Small Business Research Grant Program (SBIR) All Grant Information Training ...

  7. Cochrane Reviews of non-medication-based psychotherapeutic and other interventions for schizophrenia, psychosis, and bipolar disorder: A systematic literature review.

    PubMed

    Jung, Xenia Tricia; Newton, Richard

    2009-08-01

    Mental health-care professionals are striving to keep up to date with health interventions that are effective and beneficial to patients. The Cochrane Reviews make available a systematic and up-to-date review of a comprehensive range of health interventions. We identified a total of 28 interventions from a systematic search and review of the Cochrane Reviews for either schizophrenia, psychosis, schizoaffective, or bipolar disorder. These interventions have been graded into tables of: strong support that merits application, moderate support that warrants consideration of application, not supported, and data that is deemed inconclusive. The tables provide a comprehensive summary and classification of evidence-based practices. This information is presented in a way to enable nurses and other health-care professionals to analyze their own practices to improve mental health services and outcomes for patients. Of the 28 interventions identified in this review, four had strong support and five had moderate support meriting application. Limitations of this review are discussed. PMID:19594644

  8. Low-molecular-weight heparins for managing vasoocclusive crises in people with sickle cell disease: a summary of a cochrane systematic review.

    PubMed

    van Zuuren, Esther J; Fedorowicz, Zbys

    2014-01-01

    We summarize a Cochrane systematic review that was conducted to assess the effects of low-molecular-weight heparins (LMWH) for managing vasoocclusive crises (VOC) in people with sickle cell disease. Sickle cell disease is one of the most common and severe genetic disorders in the world. It can be divided into three broadly distinct clinical phenotypes characterized by either hemolysis, pain syndromes or organ damage. Pain is the most prominent symptom of vasoocclusion, and hypercoagulability is a well-established pathogenic phenomenon in people with sickle cell disease. Searches included the Cochrane Cystic Fibrosis and Genetic Disorders Group Haemoglobinopathies Trials Register, abstract books of conference proceedings and several online trials registries (December 2012). One study (with an overall unclear to high risk of bias) comprising 253 participants was included. This study provided limited data, but concluded that tinzaparin resulted in a more rapid resolution of pain, and in a statistically significant lower number of hospitalization days compared to a placebo. Two minor bleeding events were reported as adverse events in the tinzaparin group. Based on the results from this single study, there is incomplete evidence to either support or refute the effectiveness of LMWH in people with sickle cell disease. PMID:24826795

  9. Influence of a vertical subject on research in biomedicine and activities of The Cochrane Collaboration branch on medical students' knowledge and attitudes toward evidence-based medicine

    PubMed Central

    Balajić, Karolina; Barac-Latas, Vesna; Drenjančević, Ines; Ostojić, Marko; Fabijanić, Damir; Puljak, Livia

    2012-01-01

    Aim To investigate whether the introduction of a vertical subject on research in biomedicine and founding of The Cochrane Collaboration branch at the University of Split School of Medicine influenced students’ knowledge and attitudes toward evidence-based medicine (EBM), including the use of research literature. Methods We used a 26-item questionnaire on EBM knowledge and attitudes to survey 1232 medical students of all study years in 3 medical schools in Croatia (Split, Rijeka, Osijek) and the Croatian-speaking medical school in Mostar (Bosnia and Herzegovina). Results Students from the University of Split School of Medicine who had been exposed to the vertical subject on research in biomedicine and activities of The Cochrane Collaboration at the school had better knowledge and more positive attitudes toward EBM. In general, students rarely searched for evidence; 28% of students searched for evidence more than once a month and 96% of students used only textbooks in Croatian and teachers’ handouts, even though 74% of students agreed that articles from scholarly journals were an important supplement for textbooks. Conclusion Building up an environment that fosters EBM may be beneficial for students’ knowledge and attitudes toward EBM. Teachers should encourage and require using evidence during all the courses in medical school. PMID:22911530

  10. Using Clinical Data, Hypothesis Generation Tools and PubMed Trends to Discover the Association between Diabetic Retinopathy and Antihypertensive Drugs

    SciTech Connect

    Senter, Katherine G; Sukumar, Sreenivas R; Patton, Robert M; Chaum, Ed

    2015-01-01

    Diabetic retinopathy (DR) is a leading cause of blindness and common complication of diabetes. Many diabetic patients take antihypertensive drugs to prevent cardiovascular problems, but these drugs may have unintended consequences on eyesight. Six common classes of antihypertensive drug are angiotensin converting enzyme (ACE) inhibitors, alpha blockers, angiotensin receptor blockers (ARBs), -blockers, calcium channel blockers, and diuretics. Analysis of medical history data might indicate which of these drugs provide safe blood pressure control, and a literature review is often used to guide such analyses. Beyond manual reading of relevant publications, we sought to identify quantitative trends in literature from the biomedical database PubMed to compare with quantitative trends in the clinical data. By recording and analyzing PubMed search results, we found wide variation in the prevalence of each antihypertensive drug in DR literature. Drug classes developed more recently such as ACE inhibitors and ARBs were most prevalent. We also identified instances of change-over-time in publication patterns. We then compared these literature trends to a dataset of 500 diabetic patients from the UT Hamilton Eye Institute. Data for each patient included class of antihypertensive drug, presence and severity of DR. Graphical comparison revealed that older drug classes such as diuretics, calcium channel blockers, and -blockers were much more prevalent in the clinical data than in the DR and antihypertensive literature. Finally, quantitative analysis of the dataset revealed that patients taking -blockers were statistically more likely to have DR than patients taking other medications, controlling for presence of hypertension and year of diabetes onset. This finding was concerning given the prevalence of -blockers in the clinical data. We determined that clinical use of -blockers should be minimized in diabetic patients to prevent retinal damage.

  11. Coverage and overlaps in bibliographic databases relevant to forensic medicine: a comparative analysis of MEDLINE.

    PubMed Central

    Yonker, V A; Young, K P; Beecham, S K; Horwitz, S; Cousin, K

    1990-01-01

    This study was designed to make a comparative evaluation of the performance of MEDLINE in covering serial literature. Forensic medicine was chosen because it is an interdisciplinary subject area that would test MEDLARS at the periphery of the system. The evaluation of database coverage was based upon articles included in the bibliographies of scholars in the field of forensic medicine. This method was considered appropriate for characterizing work used by researchers in this field. The results of comparing MEDLINE to other databases evoked some concerns about the selective indexing policy of MEDLINE in serving the interests of those working in forensic medicine. PMID:2403829

  12. The Effect of Feature Representation on MEDLINE Document Classification

    PubMed Central

    Yetisgen-Yildiz, Meliha; Pratt, Wanda

    2005-01-01

    This work explores the effect of text representation techniques on the overall performance of medical text classification. To accomplish this goal, we developed a text classification system that supports the very basic word representation (bag-of-words) and the more complex medical phrase representation (bag-of-phrases). We also combined word and phrase representations (hybrid) for further analysis. Our system extracts medical phrases from text by incorporating a medical knowledge base and natural language processing techniques. We conducted experiments to evaluate the effects of different representations by measuring the change in classification performance with MEDLINE documents from the OHSUMED dataset. We measured classification performance with information retrieval metrics; precision (p), recall (r), and F1-score (F1). In our experiments, we achieved better classification performance with the hybrid approach (p=0.87, r=0.46, F1=0.60) compared to the bag-of-words approach (p=0.85, r=0.44, F1=0.58) and the bag-of-phrases approach (p=0.87, r=0.42, F1=0.57). PMID:16779160

  13. An evolution of experts: MEDLINE in the library school

    PubMed Central

    Arnott Smith, Catherine

    2005-01-01

    Question: What is the real value that medical librarians bring to the health care environment? How have library science educators, frequently former practitioners themselves, responded to the challenge of expert searching? Methods: In this paper, I give an historical introduction to the landscape of medical information retrieval through the development of MEDLINE. I then look at the evolution of training in online searching and its place in the context of library school education and particularly the effect of generalist education on future specialists. Finally, I acknowledge the new role of the informationist as another assertion of our professional expertise. Conclusions: The three interdependent subsystems of our professional machine—our schools, our association, and our professional peers— must all respond to this challenge by asserting our expertise in our curricula, in our continuing education, and in our dialogues with each other. Only by acknowledging the interaction of these subsystems will real and positive changes be effected to benefit our profession and our constituencies. PMID:15685275

  14. MedlinePlus Connect: Linking Patient Portals and Electronic Health Records to Health Information

    MedlinePlus

    ... information on diagnoses (problem codes), medications , and lab tests , and returns related information from MedlinePlus . This API is available as a Web application or a Web service . A patient portal, ...

  15. Finding Good Health Information on the Internet | NIH MedlinePlus the Magazine

    MedlinePlus

    ... turn JavaScript on. Feature: MedlinePlus Advantage Finding Good Health Information on the Internet Past Issues / Winter 2015 ... do with your information. 8. Consult with your health professional —Patient/provider partnerships lead to the best ...

  16. Globetrotting to a Good Night's Sleep | NIH MedlinePlus the Magazine

    MedlinePlus

    ... is one of the most common and troubling sleep disorders. At least 1 in 10 older adults, and ... have sleep apnea. To Find Out More MedlinePlus Sleep Disorders www.nlm.nih.gov/medlineplus/sleepdisorders.html NHLBI ...

  17. Finding Good Health Information on the Internet | NIH MedlinePlus the Magazine

    MedlinePlus

    ... issues in language you can understand. MedlinePlus offers reliable, up-to-date health information, anytime, anywhere—for ... will provide you with a gold standard of reliable, up-to-date health information in a very ...

  18. What Research is being done? | NIH MedlinePlus the Magazine

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    ... this page please turn Javascript on. Feature: Stroke Rehabilitation What Research is Being Done? Past Issues / Spring ... of Contents To Find Out More MedlinePlus: Stroke Rehabilitation www.nlm.nih.gov/medlineplus/strokerehabilitation.html National ...

  19. Cancer Survivor Eric Dishman Is On a Precision Medicine Mission | NIH MedlinePlus the Magazine

    MedlinePlus

    ... devices can encourage healthy behaviors Lay the scientific foundation for precision medicine for many diseases Find Out More National Center for Advancing Translational Sciences (NCATS) : https://ncats.nih.gov MedlinePlus: (search for ...

  20. Seasonal Allergy Research at NIH | NIH MedlinePlus the Magazine

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    ... page please turn Javascript on. Feature: Managing Allergies Seasonal Allergy Research at NIH Past Issues / Summer 2011 Table ... www.nlm.nih.gov/medlineplus/allergy.html MedlinePlus: Hay Fever www.nlm.nih.gov/medlineplus/hayfever.html National ...

  1. Seasonal Allergy Research at NIH | NIH MedlinePlus the Magazine

    MedlinePlus

    ... page please turn Javascript on. Feature: Managing Allergies Seasonal Allergy Research at NIH Past Issues / Spring 2013 Table ... www.nlm.nih.gov/medlineplus/allergy.html MedlinePlus: Hay Fever www.nlm.nih.gov/medlineplus/hayfever.html National ...

  2. Saying "Yes!" to Careers in Health Care | NIH MedlinePlus Magazine

    MedlinePlus

    ... of Medicine The e-Patient: Digital and Genomic Technologies for Personalized Health Care April 6-7, 2010 To find out more, visit www.fnlm.org Mobile MedlinePlus! On the go! Find trusted health information ...

  3. Cholesterol Levels: What You Need to Know | NIH MedlinePlus the Magazine

    MedlinePlus

    ... please turn Javascript on. Feature: High Cholesterol Cholesterol Levels: What You Need to Know Past Issues / Summer 2012 Table of Contents Measuring Cholesterol Levels Learn more at MedlinePlus: https://medlineplus.gov/cholesterol. ...

  4. For Distinguished Public Service: Medical Library Association Honors FNLM and NIH MedlinePlus Magazine | NIH ...

    MedlinePlus

    ... turn Javascript on. For Distinguished Public Service: Medical Library Association Honors FNLM and NIH MedlinePlus Magazine Past ... hearing from you. The Friends of the National Library of Medicine has a warm and mutually appreciative ...

  5. Publishing Biomedical Predication Repository About MeSH Co-Occurrences in MEDLINE.

    PubMed

    Miñarro-Giménez, Jose Antonio; Martínez, Manuel Quesada; Fernández-Breis, Jesualdo Tomás; Schulz, Stefan

    2016-01-01

    The construction and publication of predications form scientific literature databases like MEDLINE is necessary due to the large amount of resources available. The main goal is to infer meaningful predicates between relevant co-occurring MeSH concepts manually annotated from MEDLINE records. The resulting predications are formed as subject-predicate-object triples. We exploit the content of MRCOC file to extract the MeSH indexing terms (main headings and subheadings) of MEDLINE. The predications were inferred by combining the semantic predicates from SemMedDB, the clustering of MeSH terms by their associated MeSH subheadings and the frequency of relevant terms in the abstracts of MEDLINE records. The inferring process also obtains and associates a weight to each generated predication. As a result, we published the generated dataset of predications using the Linked Data principles to make it available for future projects. PMID:27577489

  6. Cholesterol Levels: What You Need to Know | NIH MedlinePlus the Magazine

    MedlinePlus

    ... please turn Javascript on. Feature: High Cholesterol Cholesterol Levels: What You Need to Know Past Issues / Summer 2012 Table of Contents Measuring Cholesterol Levels Learn more at MedlinePlus: https://www.nlm.nih. ...

  7. For Distinguished Public Service: Medical Library Association Honors FNLM and NIH MedlinePlus Magazine | NIH ...

    MedlinePlus

    ... page please turn Javascript on. For Distinguished Public Service: Medical Library Association Honors FNLM and NIH MedlinePlus ... Dr. Donald West King with the Distinguished Public Service Award at the MLA’s recent national conference. Let ...

  8. Preliminary comparison of three search engines for point of care access to MEDLINE citations.

    PubMed

    Hauser, Susan E; Demner-Fushman, Dina; Ford, Glenn M; Jacobs, Joshua L; Thoma, George

    2006-01-01

    Medical resident physicians used MD on Tap in real time to search for MEDLINE citations relevant to clinical questions using three search engines: Essie, Entrez and Google, in order of performance. PMID:17238564

  9. MedlinePlus en español marks its 10th anniversary

    MedlinePlus

    ... of authoritative, reliable consumer-level health information in Spanish from the National Institutes of Health and national ... public can use. Making MedlinePlus information available in Spanish greatly expands NIH's ability to carry out its ...

  10. Methylphenidate for attention-deficit/hyperactivity disorder in children and adolescents: Cochrane systematic review with meta-analyses and trial sequential analyses of randomised clinical trials

    PubMed Central

    Krogh, Helle B; Ramstad, Erica; Moreira-Maia, Carlos R; Holmskov, Mathilde; Skoog, Maria; Nilausen, Trine Danvad; Magnusson, Frederik L; Zwi, Morris; Gillies, Donna; Rosendal, Susanne; Groth, Camilla; Rasmussen, Kirsten Buch; Gauci, Dorothy; Kirubakaran, Richard; Forsbøl, Bente; Simonsen, Erik; Gluud, Christian

    2015-01-01

    Study question Is methylphenidate beneficial or harmful for the treatment of attention-deficit/hyperactivity disorder (ADHD) in children and adolescents? Methods Electronic databases were searched up to February 2015 for parallel and crossover randomised clinical trials comparing methylphenidate with placebo or no intervention in children and adolescents with ADHD. Meta-analyses and trial sequential analyses (TSA) were conducted. Quality was assessed using GRADE. Teachers, parents, and observers rated ADHD symptoms and general behaviour. Study answer and limitations The analyses included 38 parallel group trials (n=5111, median treatment duration 49 days) and 147 crossover trials (n=7134, 14 days). The average age across all studies was 9.7 years. The analysis suggested a beneficial effect of methylphenidate on teacher rated symptoms in 19 parallel group trials (standardised mean difference (SMD) −0.77, n=1698), corresponding to a mean difference of −9.6 points on the ADHD rating scale. There was no evidence that methylphenidate was associated with an increase in serious adverse events (risk ratio 0.98, nine trials, n=1532; TSA adjusted intervention effect RR 0.91). Methylphenidate was associated with an increased risk of non-serious adverse events (1.29, 21 trials, n=3132; TSA adjusted RR 1.29). Teacher rated general behaviour seemed to improve with methylphenidate (SMD −0.87, five trials, n=668) A change of 7 points on the child health questionnaire (CHQ) has been deemed a minimal clinically relevant difference. The change reported in a meta-analysis of three trials corresponds to a mean difference of 8.0 points on the CHQ (range 0-100 points), which suggests that methylphenidate may improve parent reported quality of life (SMD 0.61, three trials, n=514). 96.8% of trials were considered high risk of bias trials according to the Cochrane guidelines. All outcomes were assessed very low quality according to GRADE. What this study adds The results suggest that

  11. Identifying gaps in research prioritization: The global burden of neglected tropical diseases as reflected in the Cochrane database of systematic reviews

    PubMed Central

    Bhaumik, Soumyadeep; Karimkhani, Chante; Czaja, Christopher A.; Williams, Hywel C.; Rani, Monica; Nasser, Mona; Boyers, Lindsay N.; Dmitruk, Sergei; Dellavalle, Robert P.

    2015-01-01

    Background: Neglected tropical diseases (NTDs) impact disadvantaged populations in resource-scarce settings. Availability of synthesized evidence is paramount to end this disparity. The aim of the study was to determine whether NTD systematic reviews or protocols in the Cochrane Database of Systematic Reviews (CDSR) reflect disease burden. Methods: Two authors independently searched the CDSR for reviews/protocols regarding the NTDs diseases. Each review or protocol was classified to a single NTD category. Any discrepancy was solved by consensus with third author. NTD systematic review or protocol from CDSR were matched with disability-adjusted life year (DALY) metrics from the Global Burden of Disease 2010 Study. Spearman's rank correlation coefficient and associated P values were used to assess for correlation between the number of systematic reviews and protocols and the %2010 DALY associated with each NTD. Results: Overall, there was poor correlation between CDSR representation and DALYs. Yellow fever, echinococcus, onchocerciasis, and schistosomiasis representation was well-aligned with DALY. Leprosy, trachoma, dengue, leishmaniasis, and Chagas disease representation was greater, while cysticercosis, human African trypanosomiasis, ascariasis, lymphatic filariasis, and hookworm representation was lower than DALY. Three of the 18 NTDs had reviews/protocols of diagnostic test accuracy. Conclusions: Our results indicate the need for increased prioritization of systematic reviews on NTDs, particularly diagnostic test accuracy reviews. PMID:26985407

  12. Extracting rate changes in transcriptional regulation from MEDLINE abstracts

    PubMed Central

    2014-01-01

    Background Time delays are important factors that are often neglected in gene regulatory network (GRN) inference models. Validating time delays from knowledge bases is a challenge since the vast majority of biological databases do not record temporal information of gene regulations. Biological knowledge and facts on gene regulations are typically extracted from bio-literature with specialized methods that depend on the regulation task. In this paper, we mine evidences for time delays related to the transcriptional regulation of yeast from the PubMed abstracts. Results Since the vast majority of abstracts lack quantitative time information, we can only collect qualitative evidences of time delays. Specifically, the speed-up or delay in transcriptional regulation rate can provide evidences for time delays (shorter or longer) in GRN. Thus, we focus on deriving events related to rate changes in transcriptional regulation. A corpus of yeast regulation related abstracts was manually labeled with such events. In order to capture these events automatically, we create an ontology of sub-processes that are likely to result in transcription rate changes by combining textual patterns and biological knowledge. We also propose effective feature extraction methods based on the created ontology to identify the direct evidences with specific details of these events. Our ontologies outperform existing state-of-the-art gene regulation ontologies in the automatic rule learning method applied to our corpus. The proposed deterministic ontology rule-based method can achieve comparable performance to the automatic rule learning method based on decision trees. This demonstrates the effectiveness of our ontology in identifying rate-changing events. We also tested the effectiveness of the proposed feature mining methods on detecting direct evidence of events. Experimental results show that the machine learning method on these features achieves an F1-score of 71.43%. Conclusions The manually

  13. Evaluating CD-ROM versions of the MEDLINE database: a checklist.

    PubMed

    Hewison, N S

    1989-10-01

    The emergence of CD-ROM (compact disc/read-only memory) versions of the MEDLINE database requires experienced MEDLINE searchers to examine assumptions about searching MEDLINE, since some expectations may not be fulfilled by this new technology. When applied to a particular CD-ROM MEDLINE product, the evaluation procedure involves testing assumptions concerning database contents; mechanics of searching; display, print, and download capabilities; and user-friendly features. The extent to which a CD-ROM product preserves and exploits important MEDLINE strengths should be assessed, e.g., the MeSH controlled vocabulary, the designation of major and minor MeSH emphasis, and the use of subheadings. Search software characteristics that affect ease of searching and quality of results also need to be examined, e.g., the ability to truncate search terms and the order of precedence in which Boolean operators are evaluated. A checklist to assist in the evaluation process is presented, including search examples for use in testing search functions. PMID:2676046

  14. Knowledge Extraction from MEDLINE by Combining Clustering with Natural Language Processing

    PubMed Central

    Miñarro-Giménez, Jose A.; Kreuzthaler, Markus; Schulz, Stefan

    2015-01-01

    The identification of relevant predicates between co-occurring concepts in scientific literature databases like MEDLINE is crucial for using these sources for knowledge extraction, in order to obtain meaningful biomedical predications as subject-predicate-object triples. We consider the manually assigned MeSH indexing terms (main headings and subheadings) in MEDLINE records as a rich resource for extracting a broad range of domain knowledge. In this paper, we explore the combination of a clustering method for co-occurring concepts based on their related MeSH subheadings in MEDLINE with the use of SemRep, a natural language processing engine, which extracts predications from free text documents. As a result, we generated sets of clusters of co-occurring concepts and identified the most significant predicates for each cluster. The association of such predicates with the co-occurrences of the resulting clusters produces the list of predications, which were checked for relevance. PMID:26958228

  15. MEDLINE on CD-ROM: end user searching in a medical school library.

    PubMed

    Miller, N; Kirby, M; Templeton, E

    1988-01-01

    End users at the Medical College of Pennsylvania enjoyed searching CD-ROM versions of MEDLINE and judged such searches "extremely useful." To assess the effectiveness of their searches, a sample of 500 search statements from Compact Cambridge (CC) MEDLINE was examined. A high proportion of search statements (224, or 45 percent) retrieved no documents. Over one-third of search statements (185, or 37 percent) contained at least one error, which usually resulted in zero retrieval for that search statement. Searchers attempting to enter Medical Subject Headings were frequently defeated by the elaborate punctuation requirement of CC MEDLINE. "Missed opportunities" were evident in over three-fourths of search statements. One-on-one instruction and library classes may increase search success, but these measures reach a limited audience. Improvement in the search software itself is needed to help searchers improve the effectiveness of their searches. PMID:10303159

  16. Prophylactic cranial irradiation for preventing brain metastases in patients undergoing radical treatment for non-small-cell lung cancer: A Cochrane Review

    SciTech Connect

    Lester, Jason Francis . E-mail: jason.lester@velindre-tr.wales.nhs.uk; MacBeth, Fergus R.; Coles, Bernadette

    2005-11-01

    Purpose: To investigate whether prophylactic cranial irradiation (PCI) has a role in the management of patients with non-small-cell lung cancer (NSCLC) treated with curative intent. Methods and Materials: A search strategy was designed to identify randomized controlled trials (RCTs) comparing PCI with no PCI in NSCLC patients treated with curative intent. The electronic databases MEDLINE, EMBASE, LILACS, and Cancerlit were searched, along with relevant journals, books, and review articles to identify potentially eligible trials. Four RCTs were identified and reviewed. A total of 951 patients were randomized in these RCTs, of whom 833 were evaluable and reported. Forty-two patients with small-cell lung cancer were excluded, leaving 791 patients in total. Because of the small patient numbers and trial heterogeneity, no meta-analysis was attempted. Results: Prophylactic cranial irradiation did significantly reduce the incidence of brain metastases in three trials. No trial reported a survival advantage with PCI over observation. Toxicity data were poorly collected and no quality of life assessments were carried out in any trial. Conclusion: Prophylactic cranial irradiation may reduce the incidence of brain metastases, but there is no evidence of a survival benefit. It was not possible to evaluate whether any radiotherapy regimen is superior, and the effect of PCI on quality of life is not known. There is insufficient evidence to support the use of PCI in clinical practice. Where possible, patients should be offered entry into a clinical trial.

  17. Identifying gaps for research prioritisation: Global burden of external causes of injury as reflected in the Cochrane Database of Systematic Reviews☆

    PubMed Central

    Karimkhani, Chante; Trikha, Ritika; Aksut, Baran; Jones, Trevor; Boyers, Lindsay N.; Schlichte, Megan; Pederson, Hannah; Okland, Tyler; DiGuiseppi, Carolyn; Nasser, Mona; Naghavi, Mohsen; Vos, Theo; Yoong, Sze Lin; Wolfenden, Luke; Murray, Christopher J.L.; Dellavalle, Robert P.

    2016-01-01

    Importance Burden of disease should impact research prioritisation. Objective To analyse the Cochrane Database of Systematic Reviews (CDSR) and determine whether systematic reviews and protocols accurately represent disease burden, as measured by disability-adjusted life years (DALYs) from the Global Burden of Disease (GBD) 2010 Study. Methods Two investigators collected GBD disability metrics for 12 external causes of injury in the GBD 2010 Study. These external causes were then assessed for systematic review and protocol representation in CDSR. Data was collected during the month of April 2015. There were no study participants aside from the researchers. Percentage of total 2010 DALYs, 2010 DALY rank, and median DALY percent change from 1990 to 2010 of the 12 external causes of injury were compared with CDSR representation of systematic reviews and protocols. Data were analysed for correlation using Spearman rank correlation. Results Eleven of the 12 causes were represented by at least one systematic review or protocol in CDSR; the category collective violence and legal intervention had no representation in CDSR. Correlation testing revealed a strong positive correlation that was statistically significant. Representation of road injury; interpersonal violence; fire, heat, and hot substances; mechanical forces; poisonings, adverse effect of medical treatment, and animal contact was well aligned with respect to DALY. Representation of falls was greater compared to DALY, while self-harm, exposure to forces of nature, and other transport injury representation was lower compared to DALY. Conclusions and relevance CDSR representation of external causes of injury strongly correlates with disease burden. The number of systematic reviews and protocols was well aligned for seven out of 12 causes of injury. These results provide high-quality and transparent data that may guide future prioritisation decisions. PMID:26804937

  18. Systematic review and meta-analysis of skin substitutes in the treatment of diabetic foot ulcers: Highlights of a Cochrane systematic review.

    PubMed

    Santema, T B Katrien; Poyck, Paul P C; Ubbink, Dirk T

    2016-07-01

    Skin substitutes are increasingly used in the treatment of various types of acute and chronic wounds. The aim of this study was to perform a systematic review and meta-analysis to evaluate the effectiveness of skin substitutes on ulcer healing and limb salvage in the treatment of diabetic foot ulcers. Randomized clinical trials were searched and assessed following the methodology of The Cochrane Collaboration. We included 17 trials, totaling 1655 randomized participants. Risk of bias was variable among included trials. Thirteen trials compared the skin substitutes with standard care. The pooled results showed that that skin substitutes can, in addition to standard care, increase the likelihood of achieving complete ulcer closure compared with standard care alone after 6-16 weeks (risk ratio 1.55, 95% confidence interval [CI] 1.30-1.85). Four of the included trials compared two types of skin substitutes but no particular product showed a superior effect over another. Two trials reported on total incidence of lower limb amputations. Pooling the results of these two trials yielded a statistically significantly lower amputation rate among patients treated with skin substitutes (risk ratio 0.43, 95% CI 0.23-0.81), although the absolute risk difference was small (-0.06, 95% CI -0.10 to -0.01). This systematic review provides evidence that skin substitutes can, in addition to standard care, increase the likelihood of achieving complete ulcer closure compared with standard care alone in the treatment of diabetic foot ulcers. However, effectiveness on the long term, including lower limb salvage and recurrence, is currently lacking and cost-effectiveness is unclear. PMID:27062201

  19. Analysis of the Acceptance Behaviour of Medical Librarians and Their Patrons with Regards to Medline on CD-ROM.

    ERIC Educational Resources Information Center

    Eger, A. J.

    1988-01-01

    Two questionnaires sent to medical librarians and users of the Core Medline/Ebsco CD-ROM disc in the Netherlands gathered data on librarians' attitudes toward the various forms in which Medline is offered--i.e., printed, online, and CD-ROM. Tables and graphs present data on product attributes, availability, use, relevance, subjects searched,…

  20. NIH Quickfinder and NIH MedlinePlus Advisory Group - Winter 2011

    MedlinePlus

    ... 1770 NIH MedlinePlus Advisory Group Marin P. Allen, Ph.D., Office of Communications and Public Liaison, NIH ... of Allergy and Infectious Diseases Richard E. Manrow, Ph.D., National Cancer Institute John McGrath, Ph.D., ...

  1. On the Front Lines of Rare Disease Research | NIH MedlinePlus the Magazine

    MedlinePlus

    ... and Translational Science Awards Program. Find Out More National Center for Advancing Translational Sciences (NCATS): https://ncats.nih.gov/ MedlinePlus: www.nlm.nih.gov/medlineplus/rarediseases.html Rare Disease United Foundation: rarediseaseunited.org How important is medical research on ...

  2. A Study on the Selection and Utilization of MEDLINE Search Systems.

    ERIC Educational Resources Information Center

    Bader, Shelley A.; Piemme, Thomas E.

    This report presents the objectives, methodology, and results of a study which assessed the selection and utilization of four MEDLINE search systems by faculty and medical residents at the George Washington University Medical Center. The four systems, which were provided or sponsored by the Himmelfarb Health Sciences Library, offer a wide range of…

  3. A novel algorithm for analyzing drug-drug interactions from MEDLINE literature.

    PubMed

    Lu, Yin; Shen, Dan; Pietsch, Maxwell; Nagar, Chetan; Fadli, Zayd; Huang, Hong; Tu, Yi-Cheng; Cheng, Feng

    2015-01-01

    Drug-drug interaction (DDI) is becoming a serious clinical safety issue as the use of multiple medications becomes more common. Searching the MEDLINE database for journal articles related to DDI produces over 330,000 results. It is impossible to read and summarize these references manually. As the volume of biomedical reference in the MEDLINE database continues to expand at a rapid pace, automatic identification of DDIs from literature is becoming increasingly important. In this article, we present a random-sampling-based statistical algorithm to identify possible DDIs and the underlying mechanism from the substances field of MEDLINE records. The substances terms are essentially carriers of compound (including protein) information in a MEDLINE record. Four case studies on warfarin, ibuprofen, furosemide and sertraline implied that our method was able to rank possible DDIs with high accuracy (90.0% for warfarin, 83.3% for ibuprofen, 70.0% for furosemide and 100% for sertraline in the top 10% of a list of compounds ranked by p-value). A social network analysis of substance terms was also performed to construct networks between proteins and drug pairs to elucidate how the two drugs could interact. PMID:26612138

  4. Measuring Information through Topical Subheadings of the Medline Database: A Case Study.

    ERIC Educational Resources Information Center

    Alvarez, P.; Pulgarin, A.

    1999-01-01

    Describes a method for measuring research information from thematic references such as headings and subheadings that are used in indexing, cataloging, and online searching, using the Rasch model as the measuring instrument. Discusses results of a search of anesthesiology in the Medline database that was used as a case study. (Author/LRW)

  5. Choosing a Doctor or Health Care Service - Multiple Languages: MedlinePlus

    MedlinePlus

    ... Tìm Nơi Chữa Trị Y Tế - Tiếng Việt (Vietnamese) Bilingual PDF Health Information Translations Characters not displaying correctly on this page? See language display issues . Return to the MedlinePlus Health Information ...

  6. A novel algorithm for analyzing drug-drug interactions from MEDLINE literature

    PubMed Central

    Lu, Yin; Shen, Dan; Pietsch, Maxwell; Nagar, Chetan; Fadli, Zayd; Huang, Hong; Tu, Yi-Cheng; Cheng, Feng

    2015-01-01

    Drug–drug interaction (DDI) is becoming a serious clinical safety issue as the use of multiple medications becomes more common. Searching the MEDLINE database for journal articles related to DDI produces over 330,000 results. It is impossible to read and summarize these references manually. As the volume of biomedical reference in the MEDLINE database continues to expand at a rapid pace, automatic identification of DDIs from literature is becoming increasingly important. In this article, we present a random-sampling-based statistical algorithm to identify possible DDIs and the underlying mechanism from the substances field of MEDLINE records. The substances terms are essentially carriers of compound (including protein) information in a MEDLINE record. Four case studies on warfarin, ibuprofen, furosemide and sertraline implied that our method was able to rank possible DDIs with high accuracy (90.0% for warfarin, 83.3% for ibuprofen, 70.0% for furosemide and 100% for sertraline in the top 10% of a list of compounds ranked by p-value). A social network analysis of substance terms was also performed to construct networks between proteins and drug pairs to elucidate how the two drugs could interact. PMID:26612138

  7. High school peer tutors teach MedlinePlus: a model for Hispanic outreach*

    PubMed Central

    Warner, Debra G.; Olney, Cynthia A.; Wood, Fred B.; Hansen, Lucille; Bowden, Virginia M.

    2005-01-01

    Objectives: The objective was to introduce the MedlinePlus Website to the predominantly Hispanic residents of the Lower Rio Grande Valley region of Texas by partnering with a health professions magnet high school (known as Med High). Methods: Community assessment was used in the planning stages and included pre-project focus groups with students and teachers. Outreach methods included peer tutor selection, train-the-trainer sessions, school and community outreach, and pre- and posttests of MedlinePlus training sessions. Evaluation methods included Web statistics; end-of-project interviews; focus groups with students, faculty, and librarians; and end-of-project surveys of students and faculty. Results: Four peer tutors reached more than 2,000 people during the project year. Students and faculty found MedlinePlus to be a useful resource. Faculty and librarians developed new or revised teaching methods incorporating MedlinePlus. The project enhanced the role of school librarians as agents of change at Med High. The project continues on a self-sustaining basis. Conclusions: Using peer tutors is an effective way to educate high school students about health information resources and, through the students, to reach families and community members. PMID:15858628

  8. Parkinson's Disease Research at NIH | NIH MedlinePlus the Magazine

    MedlinePlus

    ... of this page please turn JavaScript on. Feature: Parkinson's Disease Parkinson's Disease Research at NIH Past Issues / Winter 2014 Table ... of its research: MedlinePlus . www.medlineplus.gov . Type "Parkinson's disease" in the Search box. NIHSeniorHealth —Parkinson's Disease http:// ...

  9. An Investigation of the Optimization of Search Logic for the MEDLINE Database.

    ERIC Educational Resources Information Center

    Heine, M. H.; Tague, J. M.

    1991-01-01

    Discussion of the role of Boolean logic in the information retrieval process focuses on a study that investigated the optimization of search logic for the MEDLINE database. Measures of retrieval effectiveness are discussed, the relationship of weighting schema and the logical schema is considered, and further investigations are suggested. (17…

  10. Evaluating MEDLINE on CD-ROM: An Overview of Field Tests in Library and Clinical Settings.

    ERIC Educational Resources Information Center

    Rapp, Barbara A.; And Others

    1990-01-01

    Presents an overview of the National Library of Medicine's 1988 field test and evaluation project on the use of MEDLINE products on CD-ROM. Results are summarized in the areas of user characteristics, search characteristics, user satisfaction, product features and costs, and impact on online searching. (10 references) (LRW)

  11. A Zipfian Model of an Automatic Bibliographic System: An Application to MEDLINE.

    ERIC Educational Resources Information Center

    Fedorowicz, Jane

    1982-01-01

    Derives the underlying structure of the Zipf distribution, with emphasis on its application to word frequencies in the inverted files of automatic bibliographic systems, and applies the Zipfian model to the National Library of Medicine's MEDLINE database. An appendix on the Zipfian mean and 12 references are included. (Author/JL)

  12. [MEDLINE on compact disk as an information source at the Medical School Library in Novi Sad].

    PubMed

    Brkić, S; Pejić, M; Ninković, S

    1996-01-01

    The transformation of the Library at the Medical Faculty of Novi Sad into a modern information center necessitated the introduction of an up-to-date technology and enforced the use of the latest information sources among which MEDLINE medical database is the most famous one. In the studied period, January 1993-current, 200 searches have been performed on the basis of which the following parameters were analyzed: institution, occupation, and degree of the user, purpose and accuracy of the order, relevant period, number and format of the references, assessment of the search quality and the quality of the library staff services. The analysis proved the initial belief that MEDLINE is a remarkably valuable data base necessary for medical libraries. PMID:8692082

  13. MEDLINE training within the library school curriculum: quality control and future trends.

    PubMed Central

    Berk, R A; Davidson, R W

    1978-01-01

    In order to assess the current status of MEDLINE training provided by schools of library science, a survey was conducted of those schools having an educational identification code issued by the National Library of Medicine. Information was gathered on such variables as the instructors' background and preparation, the course objectives and content, and the amount of on-line experience provided to students in each of eleven programs. An evaluation of these measures indicates that more opportunities to gain experience in using MEDLINE should be initiated by library schools and that current efforts should be continued and expanded. Specific recommendations for accomplishing these goals are outlined; they are addressed to health sciences librarians, library school educators, the Medical Library Association, and the National Library of Medicine. PMID:354705

  14. A Study of the Morpho-Semantic Relationship in Medline1

    PubMed Central

    Wilbur, W. John; Smith, Larry

    2014-01-01

    Morphological analysis as applied to English has generally involved the study of rules for inflections and derivations. Recent work has attempted to derive such rules from automatic analysis of corpora. Here we study similar issues, but in the context of the biological literature. We introduce a new approach which allows us to assign probabilities of the semantic relatedness of pairs of tokens that occur in text in consequence of their relatedness as character strings. Our analysis is based on over 84 million sentences from the MEDLINE database, over 2.3 million token types that occur in MEDLINE, and enables us to identify over 36 million token type pairs which have assigned probabilities of semantic relatedness of at least 0.7 based on their similarity as strings. The quality of these predictions is tested by two different manual evaluations and found to be good. PMID:24976874

  15. Operationalizing Semantic Medline for meeting the information needs at point of care

    PubMed Central

    Rastegar-Mojarad, Majid; Li, Dingcheng; Liu, Hongfang

    2015-01-01

    Scientific literature is one of the popular resources for providing decision support at point of care. It is highly desirable to bring the most relevant literature to support the evidence-based clinical decision making process. Motivated by the recent advance in semantically enhanced information retrieval, we have developed a system, which aims to bring semantically enriched literature, Semantic Medline, to meet the information needs at point of care. This study reports our work towards operationalizing the system for real time use. We demonstrate that the migration of a relational database implementation to a NoSQL (Not only SQL) implementation significantly improves the performance and makes the use of Semantic Medline at point of care decision support possible. PMID:26306259

  16. Operationalizing Semantic Medline for meeting the information needs at point of care.

    PubMed

    Rastegar-Mojarad, Majid; Li, Dingcheng; Liu, Hongfang

    2015-01-01

    Scientific literature is one of the popular resources for providing decision support at point of care. It is highly desirable to bring the most relevant literature to support the evidence-based clinical decision making process. Motivated by the recent advance in semantically enhanced information retrieval, we have developed a system, which aims to bring semantically enriched literature, Semantic Medline, to meet the information needs at point of care. This study reports our work towards operationalizing the system for real time use. We demonstrate that the migration of a relational database implementation to a NoSQL (Not only SQL) implementation significantly improves the performance and makes the use of Semantic Medline at point of care decision support possible. PMID:26306259

  17. French MeSH Browser: a cross-language tool to access MEDLINE/PubMed.

    PubMed

    Thirion, Benoit; Pereira, Susanne; Névéol, Aurélie; Dahamna, Badisse; Darmoni, Stéfan

    2007-01-01

    When searching the medical literature, health professionals and lay people strongly prefer to use their native language. Therefore, Medical Subject Headings (MeSH) translations would be helpful to those who are not fluent in English to access scientific papers indexed in the MEDLINE bibliographic database. Furthermore, medical terminologies such as MeSH are challenging in any language. In this context, a French MeSH Browser was developed. PMID:18694229

  18. Welcome from Library Director Donald A.B. Lindberg, M.D. | NIH MedlinePlus the Magazine

    MedlinePlus

    ... turn Javascript on. Welcome to the NIH MedlinePlus Magazine. Past Issues / Spring 2013 Table of Contents Donald ... about their efforts to cure disease. Lastly, the magazine's lively graphics, fun quizzes and practical tips have ...

  19. [Medline criteria for scientific journals selection. Methodology and indicators. Application to Spanish medical journals paying special attention to public health].

    PubMed

    Delgado López-Cózar, Emilio; Ruiz-Pérez, Rafael; Jiménez-Contreras, Evaristo

    2006-01-01

    Due to the strict selection process applied to its indexed journals, Medline is the most prestigious database in the Health and medicine field. The aim of this paper is both to analyze its selection criteria and translate into indicators that can be applied to Spanish medical journals willing to enter the Index Medicus. Analysis samples and methodology to apply obtained from the five groups of criteria considered by Medline (namely, Scope and coverage, Quality of contents, Quality of editorial work, Production quality and Audience) are proposed. A list of qualitative and quantitative indicators related to the five groups of criteria used by Medline is presented; namely, journal scientific output in the national and international context of the discipline, citation, analysis of the editorial committees, the editorial process and the peer-review system, indicators on compliance with the Vancouver guidelines, journal layout and informational quality, attractiveness, audience, journal visibility and interest as regards Medline goals. PMID:17193815

  20. Assigning categorical information to Japanese medical terms using MeSH and MEDLINE.

    PubMed

    Onogi, Yuzo

    2007-01-01

    This paper reports on the assigning of MeSH (Medical Subject Headings) categories to Japanese terms in an English-Japanese dictionary using the titles and abstracts of articles indexed in MEDLINE. In a previous study, 30,000 of 80,000 terms in the dictionary were mapped to MeSH terms by normalized comparison. It was reasoned that if the remaining dictionary terms appeared in MEDLINE-indexed articles that are indexed using MeSH terms, then relevancies between the dictionary terms and MeSH terms could be calculated, and thus MeSH categories assigned. This study compares two approaches for calculating the weight matrix. One is the TF*IDF method and the other uses the inner product of two weight matrices. About 20,000 additional dictionary terms were identified in MEDLINE-indexed articles published between 2000 and 2004. The precision and recall of these algorithms were evaluated separately for MeSH terms and non-MeSH terms. Unfortunately, the precision and recall of the algorithms was not good, but this method will help with manual assignment of MeSH categories to dictionary terms. PMID:17911806

  1. MEDLINE demand profiles: an analysis of requests for clinical and research information.

    PubMed

    Greenberg, B; Breedlove, R; Berger, W

    1977-01-01

    When a medical library serves both research scientists and practicing physicians, it may be predicted from the results of previous studies that computerized bibliographic search services will show more research and less clinical activity. The present paper reports the results of a statistical analysis of professional use of the National Library of Medicine's bibliographic retrieval system. MEDLINE (Medical Literature Analysis and Retrieval System on-Line), at a large medical school library. Results indicate that (1) demand for MEDLINE service is primarily research oriented; (2) frequency of use bears a relationship to rank and departmental affiliation; (3) broad and comprehensive searches are requested more frequently than searches for specific information; (4) usage shows an interesting curvilinear relationship with age and status of the user; and (5) grant funds and support correlate with the number of searches requested. Implication of these findings are that since clinicians' use of MEDLINE was found to be minimal, information services should be reevaluated in order to assist in meeting their information needs more effectively. PMID:831884

  2. Combining MEDLINE and publisher data to create parallel corpora for the automatic translation of biomedical text

    PubMed Central

    2013-01-01

    Background Most of the institutional and research information in the biomedical domain is available in the form of English text. Even in countries where English is an official language, such as the United States, language can be a barrier for accessing biomedical information for non-native speakers. Recent progress in machine translation suggests that this technique could help make English texts accessible to speakers of other languages. However, the lack of adequate specialized corpora needed to train statistical models currently limits the quality of automatic translations in the biomedical domain. Results We show how a large-sized parallel corpus can automatically be obtained for the biomedical domain, using the MEDLINE database. The corpus generated in this work comprises article titles obtained from MEDLINE and abstract text automatically retrieved from journal websites, which substantially extends the corpora used in previous work. After assessing the quality of the corpus for two language pairs (English/French and English/Spanish) we use the Moses package to train a statistical machine translation model that outperforms previous models for automatic translation of biomedical text. Conclusions We have built translation data sets in the biomedical domain that can easily be extended to other languages available in MEDLINE. These sets can successfully be applied to train statistical machine translation models. While further progress should be made by incorporating out-of-domain corpora and domain-specific lexicons, we believe that this work improves the automatic translation of biomedical texts. PMID:23631733

  3. Efficacy of black cohosh (Cimicifuga racemosa) medicines for treatment of menopausal symptoms - comments on major statements of the Cochrane Collaboration report 2012 "black cohosh (Cimicifuga spp.) for menopausal symptoms (review)".

    PubMed

    Beer, André-M; Osmers, Rüdiger; Schnitker, Jörg; Bai, Wenpei; Mueck, Alfred O; Meden, Harald

    2013-12-01

    Menopausal symptoms management with high-quality plant extracts from Actaea (Cimicifuga. racemosa rootstock is well-established. Efficacy and safety are supported by research and clinical trials since several decades and backed up by official monographs. However, the recent published Cochrane review on black cohosh neglects major evidence for beneficial effects. The authors' negative conclusions are questionable and call for reply and clarification. Our careful reconsideration of all appropriate placebo-controlled clinical studies reveals a standardized mean difference of 0.385 in favor of black cohosh (p < 0.0001). PMID:23992293

  4. Extraction of gene-disease relations from Medline using domain dictionaries and machine learning.

    PubMed

    Chun, Hong-Woo; Tsuruoka, Yoshimasa; Kim, Jin-Dong; Shiba, Rie; Nagata, Naoki; Hishiki, Teruyoshi; Tsujii, Jun'ichi

    2006-01-01

    We describe a system that extracts disease-gene relations from Medline. We constructed a dictionary for disease and gene names from six public databases and extracted relation candidates by dictionary matching. Since dictionary matching produces a large number of false positives, we developed a method of machine learning-based named entity recognition (NER) to filter out false recognitions of disease/gene names. We found that the performance of relation extraction is heavily dependent upon the performance of NER filtering and that the filtering improves the precision of relation extraction by 26.7% at the cost of a small reduction in recall. PMID:17094223

  5. Modular Semantic Tagging of Medline Abstracts and its Use in Inferring Regulatory Networks

    SciTech Connect

    Verhagen, Marc; Pustejovsky, James; Taylor, Ronald C.; Sanfilippo, Antonio P.

    2011-09-19

    We describe MedstractPlus, a resource for mining relations from the Medline bibliographic database that is currently under construction. It was built on the remains of Medstract, a previously created resource that included a biorelation server and an acronym database. MedstractPlus uses simple and scalable natural language processing modules to structure text, is designed with reusability and extendibility in mind, and adheres to the philosophy of the Linguistic Annotation Framework. We show how MedstractPlus has been used to provide seeds for a novel approach to inferring transcriptional regulatory networks from gene expression data.

  6. BabelMeSH: development of a cross-language tool for MEDLINE/PubMed.

    PubMed

    Liu, Fang; Ackerman, Michael; Fontelo, Paul

    2006-01-01

    BabelMeSH is a cross-language tool for searching MEDLINE/PubMed. Queries can be submitted as single terms or complex phrases in French, Spanish and Portuguese. Citations will be sent to the user in English. It uses a smart parser interface with a medical terms database in MySQL. Preliminary evaluation using compound key words in foreign language medical journals showed an accuracy of 68%, 60% and 51% for French, Spanish and Portuguese, respectively. Development is continuing. PMID:17238631

  7. Factors Associated with Success in Searching medline and Applying Evidence to Answer Clinical Questions

    PubMed Central

    Hersh, William R.; Crabtree, M. Katherine; Hickam, David H.; Sacherek, Lynetta; Friedman, Charles P.; Tidmarsh, Patricia; Mosbaek, Craig; Kraemer, Dale

    2002-01-01

    Objectives: This study sought to assess the ability of medical and nurse practitioner students to use medline to obtain evidence for answering clinical questions and to identify factors associated with the successful answering of questions. Methods: A convenience sample of medical and nurse practitioner students was recruited. After completing instruments measuring demographic variables, computer and searching attitudes and experience, and cognitive traits, the subjects were given a brief orientation to medline searching and the techniques of evidence-based medicine. The subjects were then given 5 questions (from a pool of 20) to answer in two sessions using the Ovid medline system and the Oregon Health & Science University library collection. Each question was answered using three possible responses that reflected the quality of the evidence. All actions capable of being logged by the Ovid system were captured. Statistical analysis was performed using a model based on generalized estimating equations. The relevance-based measures of recall and precision were measured by defining end queries and having relevance judgments made by physicians who were not associated with the study. Results: Forty-five medical and 21 nurse practitioner students provided usable answers to 324 questions. The rate of correctness increased from 32.3 to 51.6 percent for medical students and from 31.7 to 34.7 percent for nurse practitioner students. Ability to answer questions correctly was most strongly associated with correctness of the answer before searching, user experience with medline features, the evidence-based medicine question type, and the spatial visualization score. The spatial visualization score showed multi-collinearity with student type (medical vs. nurse practitioner). Medical and nurse practitioner students obtained comparable recall and precision, neither of which was associated with correctness of the answer. Conclusions: Medical and nurse practitioner students in this

  8. Generating MEDLINE search strategies using a librarian knowledge-based system.

    PubMed Central

    Peng, P.; Aguirre, A.; Johnson, S. B.; Cimino, J. J.

    1993-01-01

    We describe a librarian knowledge-based system that generates a search strategy from a query representation based on a user's information need. Together with the natural language parser AQUA, the system functions as a human/computer interface, which translates a user query from free text into a BRS Onsite search formulation, for searching the MEDLINE bibliographic database. In the system, conceptual graphs are used to represent the user's information need. The UMLS Metathesaurus and Semantic Net are used as the key knowledge sources in building the knowledge base. PMID:8130544

  9. Survey of individual users of MEDLINE on the NLM system (Summary)

    NASA Astrophysics Data System (ADS)

    Fukushima, Translated By Isao; Kawano, Koreni

    In the past three years the number of individual health professionals who search with MEDLINE on the NLM system has increased dramatically. It is continuing to grow at the rate of over 200 users per month. In order to provide them with an online information retrieval service that individuals can use easily and effectively, NLM surveyed this growing end-user population by the questionnaire including 35 items such as their demographic characteristics, methods of access to the system, frequency of searching, search purpose, number of citations retrieved, use of information retrieved, and level of satisfaction with current system. This paper describes the results of this survey.

  10. BMExpert: Mining MEDLINE for Finding Experts in Biomedical Domains Based on Language Model.

    PubMed

    Wang, Beichen; Chen, Xiaodong; Mamitsuka, Hiroshi; Zhu, Shanfeng

    2015-01-01

    With the rapid development of biomedical sciences, a great number of documents have been published to report new scientific findings and advance the process of knowledge discovery. By the end of 2013, the largest biomedical literature database, MEDLINE, has indexed over 23 million abstracts. It is thus not easy for scientific professionals to find experts on a certain topic in the biomedical domain. In contrast to the existing services that use some ad hoc approaches, we developed a novel solution to biomedical expert finding, BMExpert, based on the language model. For finding biomedical experts, who are the most relevant to a specific topic query, BMExpert mines MEDLINE documents by considering three important factors: relevance of documents to the query topic, importance of documents, and associations between documents and experts. The performance of BMExpert was evaluated on a benchmark dataset, which was built by collecting the program committee members of ISMB in the past three years (2012-2014) on 14 different topics. Experimental results show that BMExpert outperformed three existing biomedical expert finding services: JANE, GoPubMed, and eTBLAST, with respect to both MAP (mean average precision) and P@50 (Precision). BMExpert is freely accessed at http://datamining-iip.fudan.edu.cn/service/BMExpert/. PMID:26671801

  11. Study of style effects on OCR errors in the MEDLINE database

    NASA Astrophysics Data System (ADS)

    Garrison, Penny; Davis, Diane L.; Andersen, Tim L.; Barney Smith, Elisa H.

    2005-01-01

    The National Library of Medicine has developed a system for the automatic extraction of data from scanned journal articles to populate the MEDLINE database. Although the 5-engine OCR system used in this process exhibits good performance overall, it does make errors in character recognition that must be corrected in order for the process to achieve the requisite accuracy. The correction process works by feeding words that have characters with less than 100% confidence (as determined automatically by the OCR engine) to a human operator who then must manually verify the word or correct the error. The majority of these errors are contained in the affiliation information zone where the characters are in italics or small fonts. Therefore only affiliation information data is used in this research. This paper examines the correlation between OCR errors and various character attributes in the MEDLINE database, such as font size, italics, bold, etc. and OCR confidence levels. The motivation for this research is that if a correlation between the character style and types of errors exists it should be possible to use this information to improve operator productivity by increasing the probability that the correct word option is presented to the human editor. We have determined that this correlation exists, in particular for the case of characters with diacritics.

  12. Study of style effects on OCR errors in the MEDLINE database

    NASA Astrophysics Data System (ADS)

    Garrison, Penny; Davis, Diane L.; Andersen, Tim L.; Barney Smith, Elisa H.

    2004-12-01

    The National Library of Medicine has developed a system for the automatic extraction of data from scanned journal articles to populate the MEDLINE database. Although the 5-engine OCR system used in this process exhibits good performance overall, it does make errors in character recognition that must be corrected in order for the process to achieve the requisite accuracy. The correction process works by feeding words that have characters with less than 100% confidence (as determined automatically by the OCR engine) to a human operator who then must manually verify the word or correct the error. The majority of these errors are contained in the affiliation information zone where the characters are in italics or small fonts. Therefore only affiliation information data is used in this research. This paper examines the correlation between OCR errors and various character attributes in the MEDLINE database, such as font size, italics, bold, etc. and OCR confidence levels. The motivation for this research is that if a correlation between the character style and types of errors exists it should be possible to use this information to improve operator productivity by increasing the probability that the correct word option is presented to the human editor. We have determined that this correlation exists, in particular for the case of characters with diacritics.

  13. Separate but equal? A system comparison study of MEDLINE's controlled vocabulary MeSH.

    PubMed Central

    Hallett, K S

    1998-01-01

    This study tested the effect of controlled vocabulary search feature implementation on two online systems. Specifically, the study examined retrieval rates using four unique controlled vocabulary search features (explode, major descriptor, descriptor, subheadings). Each search feature was applied to nine search queries obtained from a medical reference librarian. The same queries were searched in the complete MEDLINE file on the Dialog and Ovid systems. The unique records, i.e., those records retrieved in only one of the two systems, were identified and analyzed. Dialog produced equal or more records than Ovid in nearly 20% of the queries. The study demonstrated that users need to be aware of system-specific designs that may require differing input strategies across different systems for the same unique controlled vocabulary search features. The paper concludes by making recommendations and suggestions for future research. PMID:9803290

  14. Addition of Japanese terms to MEDLINE File-Service through JOIS-III

    NASA Astrophysics Data System (ADS)

    Hosoe, Takao; Sakagami, Yasuhiko; Kawano, Koreni

    This paper describes new service through JOIS-III(JICST Online Information System-III) which enabled English databases, MEDLINE, TOXLINE, and CANCERLIT, to search and output both with Japanese MeSH terms and with English MeSH terms by adding terms of MeSH translated into Japanese to these three files. In this paper, circumstances and background of this plan, cooperation of the work between JICST and The Japan Medical Library Association(JMLA) , fundamental conception and rules for translation of MeSH thesaurus terms into Japanese, practical translation work, search and output by JOIS-III using Japanese MeSH terms translated, relation between JOIS-III and Japanese version of MeSH in book style published by JMLA, and future issues are also described.

  15. Automatic Summarization of MEDLINE Citations for Evidence–Based Medical Treatment: A Topic-Oriented Evaluation

    PubMed Central

    Fiszman, Marcelo; Demner-Fushman, Dina; Kilicoglu, Halil; Rindflesch, Thomas C.

    2009-01-01

    As the number of electronic biomedical textual resources increases, it becomes harder for physicians to find useful answers at the point of care. Information retrieval applications provide access to databases; however, little research has been done on using automatic summarization to help navigate the documents returned by these systems. After presenting a semantic abstraction automatic summarization system for MEDLINE citations, we concentrate on evaluating its ability to identify useful drug interventions for fifty-three diseases. The evaluation methodology uses existing sources of evidence-based medicine as surrogates for a physician-annotated reference standard. Mean average precision (MAP) and a clinical usefulness score developed for this study were computed as performance metrics. The automatic summarization system significantly outperformed the baseline in both metrics. The MAP gain was 0.17 (p < 0.01) and the increase in the overall score of clinical usefulness was 0.39 (p < 0.05). PMID:19022398

  16. Journal searching in non-MEDLINE resources on Internet Web sites.

    PubMed

    Lingle, V A

    1997-01-01

    Internet access to the medical journal literature is absorbing the attention of all relevant parties, i.e., publishers, journal vendors, librarians, commercial providers, government agencies, and end users. Journal content on the Web sites spans the range from advertising and ordering information for the print version, to table of contents and abstracts, to downloadable full text and graphics of articles. The searching parameters for systems other than MEDLINE also differ extensively with a wide variety of features and resulting retrieval. This discussion reviews a selection of providers of medical information (particularly the journal literature) on the Internet, making a comparison of what is available on Web sites and how it can be searched. PMID:10173597

  17. Publications indexed in Medline and Embase originating from the Syrian Arab Republic: a survey.

    PubMed

    Matar, H E; Almerie, M Q; Adams, C E; Essali, A

    2009-01-01

    Health research in the Syrian Arab Republic faces many difficulties, including limited funds, infrastructure and means of dissemination. In a search of Medline and Embase databases in March 2006 we extracted data on 386 biomedical papers originating from the Syrian Arab Republic. Embase had the superior coverage. A total of 64% were published in journals from Europe, 22% from North American journals and 12% in periodicals from the Middle East. Output of papers increased by 1.4 articles/year since 1979. The topics of 57% of papers were biomedical, with the remainder being pure science or agricultural/veterinarian issues. Dentistry, public health and surgery were the commonest subjects of the biomedical papers. Funding was largely from government. PMID:19731781

  18. Risk of Bias in Systematic Reviews of Non-Randomized Studies of Adverse Cardiovascular Effects of Thiazolidinediones and Cyclooxygenase-2 Inhibitors: Application of a New Cochrane Risk of Bias Tool

    PubMed Central

    Bilandzic, Anja; Fitzpatrick, Tiffany; Rosella, Laura; Henry, David

    2016-01-01

    Background Systematic reviews of the effects of healthcare interventions frequently include non-randomized studies. These are subject to confounding and a range of other biases that are seldom considered in detail when synthesizing and interpreting the results. Our aims were to assess the reliability and usability of a new Cochrane risk of bias (RoB) tool for non-randomized studies of interventions and to determine whether restricting analysis to studies with low or moderate RoB made a material difference to the results of the reviews. Methods and Findings We selected two systematic reviews of population-based, controlled non-randomized studies of the relationship between the use of thiazolidinediones (TZDs) and cyclooxygenase-2 (COX-2) inhibitors and major cardiovascular events. Two epidemiologists applied the Cochrane RoB tool and made assessments across the seven specified domains of bias for each of 37 component studies. Inter-rater agreement was measured using the weighted Kappa statistic. We grouped studies according to overall RoB and performed statistical pooling for (a) all studies and (b) only studies with low or moderate RoB. Kappa scores across the seven bias domains ranged from 0.50 to 1.0. In the COX-2 inhibitor review, two studies had low overall RoB, 14 had moderate RoB, and five had serious RoB. In the TZD review, six studies had low RoB, four had moderate RoB, four had serious RoB, and two had critical RoB. The pooled odds ratios for myocardial infarction, heart failure, and death for rosiglitazone versus pioglitazone remained significantly elevated when analyses were confined to studies with low or moderate RoB. However, the estimate for myocardial infarction declined from 1.14 (95% CI 1.07–1.24) to 1.06 (95% CI 0.99–1.13) when analysis was confined to studies with low RoB. Estimates of pooled relative risks of cardiovascular events with COX-2 inhibitors compared with no nonsteroidal anti-inflammatory drug changed little when analyses were

  19. Clinical practice: between Aristotle and Cochrane.

    PubMed

    Fugelli, P

    1998-02-01

    Health and disease consist of amino acids and self image, cell membranes and human ideals, muscles and politics. Only to a limited extent can clinical practice be based on science. It can never be carried on in isolation from political, and cultural forces that influence patients' health behaviour. Evidence-based medicine is essential but not sufficient. A continuous relationship with patients is a conditio sine qua non for general practice. The general practitioner must be a master of pragmatic medicine. Rationality, the dominant modern trend, may be dangerous for patients and doctors: (1) advances in technology can give patients and doctors the illusion of mastering the universe; (2) patients complain of being treated like biomachines, without human touch. Another symptom of modernity is the decline of religion. But patients and doctors are by no means rational beings. God, destiny and hope are replaced by modern medico-scientific megalomania. Modern medicine is also strongly influenced by commercialization and invasion by bureaucrats. Instead of becoming a biomedical robot, the general practitioner must learn to value the Aristotelian concept of phronesis. It means practical wisdom and can only be gained by personal experience; a form of learning by doing. Good clinical practice cannot come from science alone, or from personal experience alone. It is an amalgam of scientia and phronesis. PMID:9540138

  20. MeSHSim: An R/Bioconductor package for measuring semantic similarity over MeSH headings and MEDLINE documents.

    PubMed

    Zhou, Jing; Shui, Yuxuan; Peng, Shengwen; Li, Xuhui; Mamitsuka, Hiroshi; Zhu, Shanfeng

    2015-12-01

    Currently, all MEDLINE documents are indexed by medical subject headings (MeSH). Computing semantic similarity between two MeSH headings as well as two documents has become very important for many biomedical text mining applications. We develop an R package, MeSHSim, which can compute nine similarity measures between MeSH nodes, by which similarity between MeSH headings as well as MEDLINE documents can be easily computed. Also, MeSHSim supports querying hierarchy information of a MeSH heading and retrieving MeSH headings of a query document, and can be easily integrated into pipelines for any biomedical text analysis tasks. MeSHSim is released under general public license (GPL), and available through Bioconductor and from Github at https://github.com/JingZhou2015/MeSHSim. PMID:26471719

  1. User support for a library-managed online database search service: the BMA Library free MEDLINE service.

    PubMed

    Rowlands, J; Yeadon, J; Forrester, W; McSeán, T

    1997-07-01

    This paper discusses user support in the context of a library-managed online database search service. Experience is drawn from the British Medical Association (BMA) Library's Free MEDLINE Service. More than 9,600 BMA members, who are largely unfamiliar with computer communications and database searching, have registered as users of the service. User support has played a significant role in the development of the service and has comprised four main aspects: an information pack, a help desk, online help, and MEDLINE courses. The paper includes an analysis of help desk usage statistics collected from January 1996 through June 1996, and highlights other relevant research. Plans for further service enhancements and their implications in terms of future user support are discussed. PMID:9285124

  2. CiteGraph: a citation network system for MEDLINE articles and analysis.

    PubMed

    Zhang, Qing; Yu, Hong

    2013-01-01

    This paper details the development and implementation of CiteGraph, a system for constructing large-scale citation and co-authorship networks from full-text biomedical articles. CiteGraph represents articles and authors by uniquely identified nodes, and connects those nodes through citation and co-authorship relations. CiteGraph network encompasses over 1.65 million full-text articles and 6.35 million citations by 1.37 million unique authors from the Elsevier full-text articles. Our evaluation shows 98% 99% F1-score for mapping a citation to the corresponding article and identifying MEDLINE articles. We further analyzed the characteristics of CiteGraph and found that they are consistent with assumptions made using small-scale bibliometric analysis. We also developed several novel network-based methods for analyzing publication, citation and collaboration patterns. This is the first work to develop a completely automated system for the creation of a large-scale citation network in the biomedical domain, and also to introduce novel findings in researcher publication histories. CiteGraph can be a useful resource to both the biomedical community, and bibliometric research. PMID:23920674

  3. Mining connections between chemicals, proteins, and diseases extracted from Medline annotations

    PubMed Central

    Baker, Nancy C.; Hemminger, Bradley M.

    2010-01-01

    The biomedical literature is an important source of information about the biological activity and effects of chemicals. We present an application that extracts terms indicating biological activity of chemicals from Medline records, associates them with chemical name and stores the terms in a repository called ChemoText. We describe the construction of ChemoText and then demonstrate its utility in drug research by employing Swanson’s ABC discovery paradigm. We reproduce Swanson’s discovery of a connection between magnesium and migraine in a novel approach that uses only proteins as the intermediate B terms. We validate our methods by using a cutoff date and evaluate them by calculating precision and recall. In addition to magnesium, we have identified valproic acid and nitric oxide as chemicals which developed links to migraine. We hypothesize, based on protein annotations, that zinc and retinoic acid may play a role in migraine. The ChemoText repository has promise as a data source for drug discovery. PMID:20348023

  4. Mining characteristics of epidemiological studies from Medline: a case study in obesity

    PubMed Central

    2014-01-01

    Background The health sciences literature incorporates a relatively large subset of epidemiological studies that focus on population-level findings, including various determinants, outcomes and correlations. Extracting structured information about those characteristics would be useful for more complete understanding of diseases and for meta-analyses and systematic reviews. Results We present an information extraction approach that enables users to identify key characteristics of epidemiological studies from MEDLINE abstracts. It extracts six types of epidemiological characteristic: design of the study, population that has been studied, exposure, outcome, covariates and effect size. We have developed a generic rule-based approach that has been designed according to semantic patterns observed in text, and tested it in the domain of obesity. Identified exposure, outcome and covariate concepts are clustered into health-related groups of interest. On a manually annotated test corpus of 60 epidemiological abstracts, the system achieved precision, recall and F-score between 79-100%, 80-100% and 82-96% respectively. We report the results of applying the method to a large scale epidemiological corpus related to obesity. Conclusions The experiments suggest that the proposed approach could identify key epidemiological characteristics associated with a complex clinical problem from related abstracts. When integrated over the literature, the extracted data can be used to provide a more complete picture of epidemiological efforts, and thus support understanding via meta-analysis and systematic reviews. PMID:24949194

  5. Biomedical text summarization to support genetic database curation: using Semantic MEDLINE to create a secondary database of genetic information

    PubMed Central

    Fiszman, Marcelo; Hurdle, John F; Rindflesch, Thomas C

    2010-01-01

    Objective: This paper examines the development and evaluation of an automatic summarization system in the domain of molecular genetics. The system is a potential component of an advanced biomedical information management application called Semantic MEDLINE and could assist librarians in developing secondary databases of genetic information extracted from the primary literature. Methods: An existing summarization system was modified for identifying biomedical text relevant to the genetic etiology of disease. The summarization system was evaluated on the task of identifying data describing genes associated with bladder cancer in MEDLINE citations. A gold standard was produced using records from Genetics Home Reference and Online Mendelian Inheritance in Man. Genes in text found by the system were compared to the gold standard. Recall, precision, and F-measure were calculated. Results: The system achieved recall of 46%, and precision of 88% (F-measure = 0.61) by taking Gene References into Function (GeneRIFs) into account. Conclusion: The new summarization schema for genetic etiology has potential as a component in Semantic MEDLINE to support the work of data curators. PMID:20936065

  6. Evaluation and management of hemorrhoids: Italian society of colorectal surgery (SICCR) consensus statement.

    PubMed

    Trompetto, M; Clerico, G; Cocorullo, G F; Giordano, P; Marino, F; Martellucci, J; Milito, G; Mistrangelo, M; Ratto, C

    2015-10-01

    Hemorrhoids are one of the most common medical and surgical diseases and the main reason for a visit to a coloproctologist. This consensus statement was drawn up by the Italian society of colorectal surgery in order to provide practice parameters for an accurate assessment of the disease and consequent appropriate treatment. The authors made a careful search in the main databases (MEDLINE, PubMed, Embase and Cochrane), and all results were classified on the basis of the grade of recommendation (A-C) of the American College of Chest Physicians. PMID:26403234

  7. Impacted valgus fractures of the proximal humerus.

    PubMed

    Ribeiro, Fabiano Rebouças; Takesian, Fernando Hovaguim; Bezerra, Luiz Eduardo Pimentel; Filho, Rômulo Brasil; Júnior, Antonio Carlos Tenor; da Costa, Miguel Pereira

    2016-01-01

    Impacted valgus fractures of the proximal humerus are considered to be a special type fracture, since impaction of the humeral head on the metaphysis with maintenance of the posteromedial periosteum improves the prognosis regarding occurrences of avascular necrosis. This characteristic can also facilitate the reduction maneuver and increase the consolidation rate of these fractures, even in more complex cases. The studies included were obtained by searching the Bireme, Medline, PubMed, Cochrane Library and Google Scholar databases for those published between 1991 and 2013. The objective of this study was to identify the most common definitions, classifications and treatment methods used for these fractures in the orthopedic medical literature. PMID:27069878

  8. Local Anesthetic Adjuvants Providing the Longest Duration of Analgesia for Single- Injection Peripheral Nerve Blocks in Orthopedic Surgery: A Literature Review.

    PubMed

    Patacsil, Jason A; McAuliffe, Maura S; Feyh, Leah S; Sigmon, Lorie L

    2016-04-01

    Inadequate pain relief after surgery may delay surgical recovery, decrease patient satisfaction, increase length of stay, raise the risk of hospital readmissions, and increase overall healthcare costs. One way to decrease postoperative pain for patients undergoing orthopedic surgery is through the use of peripheral nerve blocks. Anesthesia providers can add many adjuvants to local anesthetics to improve quality and prolong duration of analgesia. The purpose of this literature review is to evaluate local anesthetic adjuvants to peripheral nerve blocks. A review of published studies using PubMed, MEDLINE, and Cochrane search engines was performed using predefined data fields. Based on this literature review, recommendations for practice are provided. PMID:27311150

  9. Impacted valgus fractures of the proximal humerus☆

    PubMed Central

    Ribeiro, Fabiano Rebouças; Takesian, Fernando Hovaguim; Bezerra, Luiz Eduardo Pimentel; Filho, Rômulo Brasil; Júnior, Antonio Carlos Tenor; da Costa, Miguel Pereira

    2016-01-01

    Impacted valgus fractures of the proximal humerus are considered to be a special type fracture, since impaction of the humeral head on the metaphysis with maintenance of the posteromedial periosteum improves the prognosis regarding occurrences of avascular necrosis. This characteristic can also facilitate the reduction maneuver and increase the consolidation rate of these fractures, even in more complex cases. The studies included were obtained by searching the Bireme, Medline, PubMed, Cochrane Library and Google Scholar databases for those published between 1991 and 2013. The objective of this study was to identify the most common definitions, classifications and treatment methods used for these fractures in the orthopedic medical literature. PMID:27069878

  10. Impact of a low-intensity pedagogical model for integrating MedlinePlus exercises into middle school nutrition lessons*†

    PubMed Central

    Rankins, Jenice; Kirksey, Otis; Bogan, Yolanda; Brown, Betty

    2007-01-01

    Objective: The research developed and pilot-tested MedlinePlus exercises in a diet-related chronic disease prevention (DCDP) middle school lesson unit called “Live.” Methods: MedlinePlus exercises were jointly developed by two middle school family and consumer sciences (FCS) teachers and integrated into the “Live” DCDP lesson unit. FCS classes (n = 4) who had participated in a prior “Live” study were chosen to pilot-test the MedlinePlus-supplemented exercises. Evaluation measures included student satisfaction (assessed using an 8-item pre- and posttest questionnaire), knowledge gained, and attitudinal changes (assessed with an abridged version of a previously developed “Live” questionnaire). Statistical analyses were performed using SPSS. Results: Of 62 total study participants, 56 (92.3%) said that they were either “somewhat” or “clearly”: (a) more likely to use MedlinePlus as a future source for answering questions about their personal health and (b) more knowledgeable about how eating habits can help prevent disease. Selected parameters were improved for nutrition knowledge (P < 0.01) and attitudes (P < 0.01) related to healthy eating. Conclusions: MedlinePlus has good potential for efficiently communicating trustworthy diet-related disease-prevention behaviors to adolescents in an existing classroom curriculum. PMID:17971886

  11. Use of statistical tests and statistical software choice in 2014: tale from three Medline indexed Pakistani journals.

    PubMed

    Shaikh, Masood Ali

    2016-04-01

    Statistical tests help infer meaningful conclusions from studies conducted and data collected. This descriptive study analyzed the type of statistical tests used and the statistical software utilized for analysis reported in the original articles published in 2014 by the three Medline-indexed journals of Pakistan. Cumulatively, 466 original articles were published in 2014. The most frequently reported statistical tests for original articles by all three journals were bivariate parametric and non-parametric tests i.e. involving comparisons between two groups e.g. Chi-square test, t-test, and various types of correlations. Cumulatively, 201 (43.1%) articles used these tests. SPSS was the primary choice for statistical analysis, as it was exclusively used in 374 (80.3%) original articles. There has been a substantial increase in the number of articles published, and in the sophistication of statistical tests used in the articles published in the Pakistani Medline indexed journals in 2014, compared to 2007. PMID:27122277

  12. Sharing MedlinePlus®/MEDLINE® for information literacy education (SMILE): a dental public health information project.

    PubMed

    Gaines, Julie K; Levy, Linda S; Cogdill, Keith W

    2011-01-01

    The SMILE project represented a partnership among the University of Texas Health Science Center at San Antonio Libraries, the Gateway Clinic in Laredo, and the San Antonio Metropolitan Health District. The project focused on improving dental practitioners' access to reliable information resources and integrating the best evidence into public health dental practice. Through its training program, SMILE cultivated a set of "power information users" among the dentists, dental hygienists, and community health workers (promotores) who provided public health preventive care and oral health education. The dental public health practitioners gained information literacy skills and increased their knowledge about reliable sites such as blogs, PubMed®, and MedlinePlus®. This project fostered opportunities for expanded partnerships with public health personnel. PMID:22040242

  13. How to do a quick search for evidence.

    PubMed

    Isaacs, David

    2014-08-01

    Doctors quote lack of time and lack of knowledge as major obstacles to searching the literature for evidence. This article argues that it is possible to do a literature search in 10-15 minutes with little specialist knowledge, using the Clinical Queries option of Medline (PubMed). PubMed is a free, user friendly service available to anyone with access to the internet and designed by librarians for use by clinicians who are not skilled in electronic searching. Numerous hidden search filters built into Clinical Queries facilitate targeted searches and find all published systematic reviews (including Cochrane Reviews). If no systematic reviews are available, the clinician can find randomised controlled trials and observational studies. PMID:24612231

  14. Academic Scientists' Reaction to End-User Services: Observations on a Trial Service Giving Access to MEDLINE Using the GRATEFUL MED Software.

    ERIC Educational Resources Information Center

    Tilson, Yvette; East, Harry

    1994-01-01

    Conducted at two British universities in 1993, a year-long trial service study of 20 bio-scientists using GRATEFUL MED software access to National Library of Medicine databases, principally MEDLINE, found that the users approved most of the service's ease, convenience, and time saving features and disapproved of its susceptibility to network…

  15. From Shakespeare to Star Trek and beyond: a Medline search for literary and other allusions in biomedical titles

    PubMed Central

    Goodman, Neville W

    2005-01-01

    Objectives To document biomedical paper titles containing literary and other allusions. Design Retrospective survey. Setting Medline (1951 to mid-2005) through Dialog Datastar. Main outcome measure Allusions to Shakespeare, Hans Christian Andersen, proverbs, the Bible, Lewis Carroll, and movie titles, corrected and scaled for five year periods 1950-4 to 2000-4. Results More than 1400 Shakespearean allusions exist, a third of them to “What's in a name” and another third to Hamlet—mostly to “To be or not to be.” The trend of increasing use of allusive titles, identified from Shakespeare and Andersen, is paralleled by allusions to Carroll and proverbs; the trend of biblical allusions is also upward but is more erratic. Trends for newer allusions are also upwards, including the previously surveyed “paradigm shift.” Allusive titles are likely to be to editorial or comment rather than to original research. Conclusions The similar trends are presumably a mark of a particular learnt author behaviour. Newer allusions may be becoming more popular than older ones. Allusive titles can be unhelpful to reviewers and researchers, and many are now clichés. Whether they attract readers or citations is unknown, but better ways of gaining attention exist. PMID:16373745

  16. Self-Service Computerized Bibliographic Retrieval: A Comparison of Colleague and PaperChase, Programs That Search the MEDLINE Database

    PubMed Central

    Porter, Douglas; Wigton, Robert S.; Reidelbach, Marie A.; Bleich, Howard L.; Slack, Warner V.

    1988-01-01

    Colleague and PaperChase are the two most widely used computer systems designed for clinicians and scientists who wish to search the National Library of Medicine's MEDLINE data base of biomedical references. The present study compares the performance of these two systems. Two matched groups of second-year medical students each received three hours of instruction, one group in Colleague, the other in PaperChase. Each student then attempted 10 test searches. The next day the groups were reversed, and each student attempted five additional searches. During the 3.5 hours allocated for searching, users of Colleague attempted 64 test searches and retrieved 326 target references; users of PaperChase attempted 78 searches and retrieved 496. Users of Colleague took a mean of 2.2 minutes and spent a mean of $1.20 to find each target reference; users of PaperChase took 1.6 minutes and spent $0.92. We conclude that after limited training, medical students find more references faster and at lower cost with PaperChase than with Colleague.

  17. Integrating CD-ROM Medline with electronic mail: first step in implementing new strategy for online reference library.

    PubMed

    Ribitzky, R

    1991-01-01

    Simultaneous ACCESS to and DISSEMINATION of electronically available PROFESSIONAL KNOWLEDGE, in a productive, Cost-of-Ownership effective, and affordable manner are now achievable. Emerging MANAGEMENT-OF-INFORMATION and SYSTEMS-INTEGRATION disciplines are essential contributing factors to devising and implementing NEW STRATEGIES for ONLINE REFERENCE LIBRARIES. Bringing integrated information closer to the ultimate user and RESHAPING the electronic databases and full-text management systems MARKETPLACE are the most significant outcomes. Key technology attributes are advancements in CD-ROM, Networking, and office automation. We have proven this concept by developing an INTERFACE between MEDLINE from COMPACT CAMBRIDGE and ALL-IN-1 from DIGITAL EQUIPMENT CORPORATION. Saved search results are automatically routed to the individual's ALL-IN-1 account where further DOCUMENT MANAGEMENT and electronic mail functions may be performed. A 486Ware system from Logicraft and a five-members VAX-Cluster (respectively), are linked in a DECNet environment that is the foundation of Children's Integrated Hospital Information System. In phase one of the project up to 8 SIMULTANEOUS USERS may access the 8 RECENT YEARS, from any one of 1500 ACCESS POINTS (local and remote), and utilize any one of 150 NETWORKED PRINTERS. Opportunities are now within reach to expand the electronic library services while utilizing progressive methods and taking advantage of the best available technologies. PMID:1807668

  18. Evolution of Cooperation Patterns in Psoriasis Research: Co-Authorship Network Analysis of Papers in Medline (1942–2013)

    PubMed Central

    González-Alcaide, Gregorio; Park, Jinseo; Huamaní, Charles; Belinchón, Isabel; Ramos, José M.

    2015-01-01

    Background Although researchers have worked in collaboration since the origins of modern science and the publication of the first scientific journals in the eighteenth century, this phenomenon has acquired exceptional importance in the last several decades. Since the mid-twentieth century, new knowledge has been generated from within an ever-growing network of investigators, working cooperatively in research groups across countries and institutions. Cooperation is a crucial determinant of academic success. Objective The aim of the present paper is to analyze the evolution of scientific collaboration at the micro level, with regard to the scientific production generated on psoriasis research. Methods A bibliographic search in the Medline database containing the MeSH terms “psoriasis” or “psoriatic arthritis” was carried out. The search results were limited to articles, reviews and letters. After identifying the co-authorships of documents on psoriasis indexed in the Medline database (1942–2013), various bibliometric indicators were obtained, including the average number of authors per document and degree of multi-authorship over time. In addition, we performed a network analysis to study the evolution of certain features of the co-authorship network as a whole: average degree, size of the largest component, clustering coefficient, density and average distance. We also analyzed the evolution of the giant component to characterize the changing research patterns in the field, and we calculated social network indicators for the nodes, namely betweenness and closeness. Results The main active research clusters in the area were identified, along with their authors of reference. Our analysis of 28,670 documents sheds light on different aspects related to the evolution of scientific collaboration in the field, including the progressive increase in the mean number of co-authors (which stood at 5.17 in the 2004–2013 decade), and the rise in multi-authored papers

  19. MedlinePlus: Endoscopy

    MedlinePlus

    ... What Is Endoscopy? (American Cancer Society) Also in Spanish Related Issues Ensuring the Safety of Your Endoscopic Procedure (American Society for Gastrointestinal Endoscopy) Also in Spanish Sedation for Your Endoscopy (American College of Gastroenterology) ...

  20. MedlinePlus: Disclaimers

    MedlinePlus

    ... and Human Services, or federal policy. Pop-Up Advertisements: When visiting our Web site, your Web browser may produce pop-up advertisements. These advertisements were most likely produced by other ...

  1. MedlinePlus: Statins

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    ... Clinical Trials. Article: Perioperative Rosuvastatin in Cardiac Surgery. Article: In primary prevention, the ACC/AHA risk-based approach predicted ASCVD better... Statins -- see more articles Find an Expert American Heart Association Food and ...

  2. MedlinePlus: Chiropractic

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    ... Many people visit chiropractors for treatment of low back pain , neck pain, and headaches . NIH: National Center for ... Chiropractic Association) - PDF Specifics Spinal Manipulation for Low-Back Pain (National Center for Complementary and Integrative Health) Tips ...

  3. MedlinePlus: Antibiotics

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    ... or not using them properly, can add to antibiotic resistance . This happens when bacteria change and become able ... ports Pseudomembranous colitis Sensitivity analysis Related Health Topics Antibiotic Resistance Bacterial Infections Medicines National Institutes of Health The ...

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  6. MedlinePlus: Antidepressants

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  7. MedlinePlus: Nutrition

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  8. MedlinePlus: Colonoscopy

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    ... Institute) What Is a Colonoscopy (OR-Live) - Broward Health Medical Center, Fort Lauderdale, FL, 12/06/2011 What to Expect During a Colonoscopy (American College of Gastroenterology) Your Radiologist Explains CT Colonography (Radiological Society of North America, ...

  9. MedlinePlus: Mammography

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    ... Radiological Society of North America, American College of Radiology) What Is a Mammogram and When Should I ... Radiological Society of North America, American College of Radiology) Mammogram: Can It Find Cancer in Dense Breasts? ( ...

  10. MedlinePlus: Gas

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    ... International Foundation for Functional Gastrointestinal Disorders) Living With Foods That May Cause Gas (International Foundation for Functional Gastrointestinal Disorders) Health Check Tools Excessive Gas (DSHI ...

  11. MedlinePlus: Mastectomy

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  12. About MedlinePlus

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    ... Guidelines Want to learn more? Guide to Healthy Web Surfing Sign Up for Email Updates Training Materials ... Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, ...

  13. MedlinePlus: Prediabetes

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    ... National Diabetes Statistics Report, 2014 (Centers for Disease Control and Prevention) - PDF Also in Spanish Patient Access to Research (American Diabetes Association) Clinical Trials ClinicalTrials. ...

  14. MedlinePlus: Creatinine

    MedlinePlus

    ... Kidney Diseases Resources Creatinine (American Association for Clinical Chemistry) Creatinine - blood Also in Spanish Creatinine - urine Also ... and Albumin/ Creatinine Ratio (American Association for Clinical Chemistry) Urine Protein and Urine Protein to Creatinine Ratio ( ...

  15. Comparing the Precision of Information Retrieval of MeSH-Controlled Vocabulary Search Method and a Visual Method in the Medline Medical Database

    PubMed Central

    Hariri, Nadjla; Ravandi, Somayyeh Nadi

    2014-01-01

    Background: Medline is one of the most important databases in the biomedical field. One of the most important hosts for Medline is Elton B. Stephens CO. (EBSCO), which has presented different search methods that can be used based on the needs of the users. Visual search and MeSH-controlled search methods are among the most common methods. The goal of this research was to compare the precision of the retrieved sources in the EBSCO Medline base using MeSH-controlled and visual search methods. Methods: This research was a semi-empirical study. By holding training workshops, 70 students of higher education in different educational departments of Kashan University of Medical Sciences were taught MeSH-Controlled and visual search methods in 2012. Then, the precision of 300 searches made by these students was calculated based on Best Precision, Useful Precision, and Objective Precision formulas and analyzed in SPSS software using the independent sample T Test, and three precisions obtained with the three precision formulas were studied for the two search methods. Results: The mean precision of the visual method was greater than that of the MeSH-Controlled search for all three types of precision, i.e. Best Precision, Useful Precision, and Objective Precision, and their mean precisions were significantly different (P <0.001). Sixty-five percent of the researchers indicated that, although the visual method was better than the controlled method, the control of keywords in the controlled method resulted in finding more proper keywords for the searches. Fifty-three percent of the participants in the research also mentioned that the use of the combination of the two methods produced better results. Conclusion: For users, it is more appropriate to use a natural, language-based method, such as the visual method, in the EBSCO Medline host than to use the controlled method, which requires users to use special keywords. The potential reason for their preference was that the visual

  16. Knowledge for Knowledge Translation: The Role of the Cochrane Collaboration

    ERIC Educational Resources Information Center

    Grimshaw, Jeremy M.; Santesso, Nancy; Cumpston, Miranda; Mayhew, Alain; McGowan, Jessie

    2006-01-01

    Knowledge-translation (KT) activities, including continuing education, should be informed by the totality of available research evidence. Systematic reviews are a generic methodology used to synthesize evidence from a broad range of research methods addressing different questions. Over the past decade, there has been a dramatic increase in the…

  17. RetroMine, or how to provide in-depth retrospective studies from Medline in a glance: the hepcidin use-case.

    PubMed

    Ameline de Cadeville, Bertrand; Loréal, Olivier; Moussouni-Marzolf, Fouzia

    2015-01-01

    The rapid expansion of biomedical literature has provoked an increased development of advanced text mining tools to rapidly extract relevant events from the continuously increasing amount of knowledge published periodically in PubMed. However, bioinvestigators are still reluctant to use these tools for two reasons: i) a large volume of events is often extracted upon a query, and this volume is hard to manage, and ii) background events dominate search results and overshadow more pertinent published information, especially for domain experts. In this paper, we propose an approach that incorporates the temporal dimension of published events to the process of information extraction to improve data selection and prioritize more pertinent periodically published knowledge for scientists. Indeed, instead of providing the total knowledge associated with a PubMed query, which is usually a mix of trivial background information and non-background information, we propose a method that incorporates time and selects non background and highly relevant biological entities and events published over time for bioinvestigators. Before excluding background events from the total knowledge extracted, a quantification of their amount is also provided. This work is illustrated by a case study regarding Hepcidin gene publications over a decade, a duration that is sufficiently long enough to generate alternative views on the overall data extracted. PMID:26673791

  18. [Systematic review of diagnostic tests accuracy: a narrative review].

    PubMed

    de Oliveira, Glória Maria; Camargo, Fábio Trinca; Gonçalves, Eduardo Costa; Duarte, Carlos Vinicius Nascimento; Guimarães, Carlos Alberto

    2010-04-01

    The aim of this study is to perform a narrative review of systematic reviews of diagnostic tests accuracy. We undertook a search using The Cochrane Methodology Reviews (Cochrane Reviews of Diagnostic Test Accuracy), Medline and LILACS up to October 2009. Reference lists of included studies were also hand searched. The following search strategy was constructed by using a combination of subject headings and text words: 1. Cochrane Methodology Reviews: accuracy study "Methodology" 2. In Pubmed "Meta-Analysis" [Publication Type] AND "Evidence-Based Medicine" [Mesh]) AND "Sensitivity and Specificity" [Mesh] 3. LILACS (revisao sistematica) or "literatura de REVISAO como assunto" [Descritor de assunto] and (sistematica) or "SISTEMATICA" [Descritor de assunto] and (acuracia) or "SENSIBILIDADE e especificidade" [Descritor de assunto]. In summary, the methodological planning and preparation of systematic reviews of therapeutic interventions are prior to that used in systematic reviews of diagnostic tests accuracy. There are more sources of heterogeneity in design of diagnostic test studies, which impair the synthesis - meta-analysis - of the results. To work around this problem, there are currently uniform requirements for diagnostic test manuscripts submitted to leading biomedical journals. PMID:20549106

  19. Meta analysis of efficacy and safety between Mammotome vacuum-assisted breast biopsy and open excision for benign breast tumor

    PubMed Central

    Ding, Boni; Chen, Daojin; Li, Xiaorong; Zhang, Hongyan

    2013-01-01

    Objective To compare the efficacy and safety between Mammotome vacuum-assisted breast biopsy (Mammotome VABB) and conventional open excision for benign breast tumor. Methods A computer-based online search of Medline, PubMed, Embase, Ovid, Cochrane Library, VIP, Wanfang, CNKI and Chinese Biological Medicine Database was performed, and conference references were manually searched. With the Cochrane Collaboration Guidelines, all randomized controlled trials comparing mammotome minimally invasive operation and conventional open excision were systematically reviewed. The Cochrane Collaboration’s RevMan 5.0 software was used for data analysis. Results A total of 15 studies involving 5,256 patients was included. Meta-analyses showed no significant difference in the size of tumor, postoperative hematomas, ecchymosis, ecchymoma and residual disease between Mammotome VABB and conventional open excision. Mammotome VABB was superior to open excision as to the size of incision, intraoperative blood loss, operative time, healing time, size of scar, wound infection and breast deformation. Conclusions Mammotome VABB is an ideal method for benign breast tumor. PMID:25083462

  20. Fenestrated and Chimney Technique for Juxtarenal Aortic Aneurysm: A Systematic Review and Pooled Data Analysis

    PubMed Central

    Li, Yue; Hu, Zhongzhou; Bai, Chujie; Liu, Jie; Zhang, Tao; Ge, Yangyang; Luan, Shaoliang; Guo, Wei

    2016-01-01

    Juxtarenal aortic aneurysms (JAA) account for approximately 15% of abdominal aortic aneurysms. Fenestrated endovascular aneurysm repair (FEVAR) and chimney endovascular aneurysm repair (CH-EVAR) are both effective methods to treat JAAs, but the comparative effectiveness of these treatment modalities is unclear. We searched the PubMed, Medline, Embase, and Cochrane databases to identify English language articles published between January 2005 and September 2013 on management of JAA with fenestrated and chimney techniques to conduct a systematic review to compare outcomes of patients with juxtarenal aortic aneurysm (JAA) treated with the two techniques. We compared nine F-EVAR cohort studies including 542 JAA patients and 8 CH-EVAR cohorts with 158 JAA patients regarding techniques success rates, 30-day mortality, late mortality, endoleak events and secondary intervention rates. The results of this systematic review indicate that both fenestrated and chimney techniques are attractive options for JAAs treatment with encouraging early and mid-term outcomes. PMID:26869488