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Sample records for pubmed medline cochrane

  1. Searching MEDLINE free on the Internet using the National Library of Medicine's PubMed.

    PubMed

    Putnam, N C

    1998-09-01

    Searching MEDLINE, the National Library of Medicine's premier bibliographic database covering the fields of medicine, nursing, dental medicine, the healthcare system, veterinary medicine, and the preclinical sciences, is now available free on the Internet through PubMed. This retrieval system allows users of all skill levels to obtain important medical information. Additionally, through the National Network of Libraries of Medicine (NN/LM) program, a division of NLM, user support in the form of phone, e-mail, and training is available free of charge. Those interested in having a training session for PubMed at their facility may contact the NN/LM to make arrangements. PMID:10455581

  2. [Bibliography search in biology and medicine: a tutorial for Medline PubMed use].

    PubMed

    Boudry, Christophe; Bozet, Gérard

    2004-01-01

    To be informed about the last publications recently published or to produce a bibliography in a given thematic field is essential for researchers in the biomedical field. If the use of Internet information searching tools such as "Google" or "Alltheweb" makes possible to discover a great part of the grey literature, bibliographic databases like Embase, Current Contents, Biosis or Medline via PubMed are essential tools to locate scientific articles. Among these bibliographic databases, Medline PubMed, thanks to its free access, is the most used. However, a correct utilization of the various functionalities proposed (thesaurus MeSH, systematization of bibliographic searches...), and consequently the quality of bibliographic researches carried out in this database, requires to master elementary knowledge which are exposed in this article. PMID:15361349

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

    PubMed

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

    2014-10-01

    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

  4. 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

  5. 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...

  6. Cochrane Collaboration w Polsce.

    PubMed

    Ba?a, Ma?gorzata M; Le?niak, Wiktoria; Jaeschke, Roman

    2015-12-22

    Podej?cie oparte na zasadach evidence?based medicine (EBM) w podejmowaniu decyzji w praktyce klinicznej nie jest w Polsce nowe. Pierwsze warsztaty z zakresu EBM odby?y si? w Polsce pod koniec lat 90. Cochrane Collaboration, jedna z g?wnych inicjatyw wywodz?cych si? ze wsplnego pnia EBM, to mi?dzynarodowa organizacja non?for?profit dzia?aj?ca na zasadzie sieci wsp?pracuj?cych ze sob? osb zaanga?owanych w opiek? zdrowotn? (m.in. badaczy, praktykw, pacjentw). Cochrane Collaboration propaguje podejmowanie decyzji, opartych na wiarygodnych i aktualnych informacjach naukowych (EBM) poprzez przygotowywanie przez cz?onkw organizacji wysokiej jako?ci przegl?dw systematycznych Cochrane. Organizacja powsta?a w 1993 roku i od tej pory nieprzerwanie si? rozwija. Nadal niewiele osb w Polsce uczestniczy w pracach nad przegl?dami Cochrane i w innych dzia?aniach organizacji. Dlatego pojawi?a si? potrzeba powo?ania o?rodka, ktry mg?by stymulowa? i wspiera? zaanga?owanie w prace Cochrane Collaboration rwnie? polskich badaczy, lekarzy i innych osb zajmuj?cych si? opiek? zdrowotn?. Artyku? zawiera opis struktury organizacji, jej celw i zasad, na ktrych opiera si? jej dzia?alno?? oraz opis celw i aktywno?ci Filii Cochrane w Polsce. PMID:26794132

  7. Using PubMed effectively to access the orthopaedic literature.

    PubMed

    Clough, J F Myles; Hitchcock, Kristin; Nelson, David L

    2011-01-01

    PubMed is the free public Internet interface to the US National Library of Medicine's MEDLINE database of citations to medical scientific articles. Many orthopaedic surgeons use PubMed on a regular basis, but most orthopaedic surgeons have received little or no training in how to use PubMed effectively and express frustration with the experience. Typical problems encountered are data overload with very large numbers of returns to look through, failure to find a specific article, and a concern that a search has missed important papers. It is helpful to understand the system used to enter journal articles into the database and the classification of the common types of searches and to review suggestions for the best ways to use the PubMed interface and find sources for search teaching and assistance. PMID:21553803

  8. 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...

  9. Automatic Export of PubMed Citations to EndNote.

    PubMed

    London, Sue; Gurdal, Osman; Gall, Carole

    2010-04-01

    The export of MEDLINE references to EndNote can be accomplished in various ways. Unlike Ovid MEDLINE, PubMed does not have a direct export feature to EndNote. Until recently, PubMed references had to be saved as a text file to import into EndNote. Now, the automatic export of PubMed references can be done using Internet Explorer (IE) or Mozilla Firefox Web browsers. The development and teaching of seamless citation management is a value-added service to health professionals. PMID:20432138

  10. 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

  11. Telehealthcare for asthma: a Cochrane review

    PubMed Central

    McLean, Susannah; Chandler, David; Nurmatov, Ulugbek; Liu, Joseph; Pagliari, Claudia; Car, Josip; Sheikh, Aziz

    2011-01-01

    Background: Telehealthcare has the potential to provide care for long-term conditions that are increasingly prevalent, such as asthma. We conducted a systematic review of studies of telehealthcare interventions used for the treatment of asthma to determine whether such approaches to care are effective. Methods: We searched the Cochrane Airways Group Specialised Register of Trials, which is derived from systematic searches of bibliographic databases including CENTRAL (the Cochrane Central Register of Controlled Trials), MEDLINE, Embase, CINAHL (Cumulative Index to Nursing and Allied Health Literature) and PsycINFO, as well as other electronic resources. We also searched registers of ongoing and unpublished trials. We were interested in studies that measured the following outcomes: quality of life, number of visits to the emergency department and number of admissions to hospital. Two reviewers identified studies for inclusion in our meta-analysis. We extracted data and used fixedeffect modelling for the meta-analyses. Results: We identified 21 randomized controlled trials for inclusion in our analysis. The methods of telehealthcare intervention these studies investigated were the telephone and video- and Internet-based models of care. Meta-analysis did not show a clinically important improvement in patients quality of life, and there was no significant change in the number of visits to the emergency department over 12 months. There was a significant reduction in the number of patients admitted to hospital once or more over 12 months (risk ratio 0.25 [95% confidence interval 0.09 to 0.66]). Interpretation: We found no evidence of a clinically important impact on patients quality of life, but telehealthcare interventions do appear to have the potential to reduce the risk of admission to hospital, particularly for patients with severe asthma. Further research is required to clarify the cost-effectiveness of models of care based on telehealthcare. PMID:21746825

  12. Understanding PubMed user search behavior through log analysis.

    PubMed

    Islamaj Dogan, Rezarta; Murray, G Craig; Névéol, Aurélie; Lu, Zhiyong

    2009-01-01

    This article reports on a detailed investigation of PubMed users' needs and behavior as a step toward improving biomedical information retrieval. PubMed is providing free service to researchers with access to more than 19 million citations for biomedical articles from MEDLINE and life science journals. It is accessed by millions of users each day. Efficient search tools are crucial for biomedical researchers to keep abreast of the biomedical literature relating to their own research. This study provides insight into PubMed users' needs and their behavior. This investigation was conducted through the analysis of one month of log data, consisting of more than 23 million user sessions and more than 58 million user queries. Multiple aspects of users' interactions with PubMed are characterized in detail with evidence from these logs. Despite having many features in common with general Web searches, biomedical information searches have unique characteristics that are made evident in this study. PubMed users are more persistent in seeking information and they reformulate queries often. The three most frequent types of search are search by author name, search by gene/protein, and search by disease. Use of abbreviation in queries is very frequent. Factors such as result set size influence users' decisions. Analysis of characteristics such as these plays a critical role in identifying users' information needs and their search habits. In turn, such an analysis also provides useful insight for improving biomedical information retrieval.Database URL:http://www.ncbi.nlm.nih.gov/PubMed. PMID:20157491

  13. Finding query suggestions for PubMed.

    PubMed

    Lu, Zhiyong; Wilbur, W John; McEntyre, Johanna R; Iskhakov, Alexey; Szilagyi, Lee

    2009-01-01

    It is common for PubMed users to repeatedly modify their queries (search terms) before retrieving documents relevant to their information needs. To assist users in reformulating their queries, we report the implementation and usage analysis of a new component in PubMed called Related Queries, which automatically produces query suggestions in response to the original user's input. The proposed method is based on query log analysis and focuses on finding popular queries that contain the initial user search term with a goal of helping users describe their information needs in a more precise manner. This work has been integrated into PubMed since January 2009. Automatic assessment using clickthrough data show that each day, the new feature is used consistently between 6% and 10% of the time when it is shown, suggesting that it has quickly become a popular new feature in PubMed. PMID:20351887

  14. 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

  15. 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

  16. About MedlinePlus

    MedlinePLUS

    ... you can understand. MedlinePlus offers reliable, up-to-date health information, anytime, anywhere, for free. You can ... for information that is authoritative and up-to-date. MedlinePlus has extensive information from the National Institutes ...

  17. 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

  18. The absolute spectrophotometric catalog by Anita Cochran

    NASA Astrophysics Data System (ADS)

    Burnashev, V. I.; Burnasheva, B. A.; Ruban, E. V.; Hagen-Torn, E. I.

    2014-06-01

    The absolute spectrophotometric catalog by Anita Cochran is presented in a machine-readable form. The catalog systematizes observations acquired at the McDonald Observatory in 1977-1978. The data are compared with other sources, in particular, the calculated broadband stellar magnitudes are compared with photometric observations by other authors, to show that the observational data given in the catalog are reliable and suitable for a variety of applications. Observations of variable stars of different types make Cochran's catalog especially valuable.

  19. 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

  20. Materia Socio Medica is Indexed in Pubmed and Archived in PubMed Central

    PubMed Central

    Masic, Izet

    2013-01-01

    Materia Socio Medica Journal has been accepted for archiving in PubMed Central from 2011. The journal started in 1993 as offi cial journal of Social Medicine Association of B&H. During last 3 years Mat Soc Med has included in almost all femous on-line databases (except WoS). All issues of Mat Soc Med published in 2012 are now visible on PubMed/PubMed Central. PMID:23678332

  1. Dialogues with Marilyn Cochran-Smith

    ERIC Educational Resources Information Center

    Fiorentini, Dario; Crecci, Vanessa Moreira

    2015-01-01

    For more than 30years, 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

  2. 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…

  3. 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

  4. A MEDLINE feasibility study.

    PubMed

    McGee, J L

    1980-07-01

    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

  5. 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

  6. 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

  7. Analysis of PubMed User Sessions Using a Full-Day PubMed Query Log: A Comparison of Experienced and Nonexperienced PubMed Users

    PubMed Central

    2015-01-01

    Background PubMed is the largest biomedical bibliographic information source on the Internet. PubMed has been considered one of the most important and reliable sources of up-to-date health care evidence. Previous studies examined the effects of domain expertise/knowledge on search performance using PubMed. However, very little is known about PubMed users’ knowledge of information retrieval (IR) functions and their usage in query formulation. Objective The purpose of this study was to shed light on how experienced/nonexperienced PubMed users perform their search queries by analyzing a full-day query log. Our hypotheses were that (1) experienced PubMed users who use system functions quickly retrieve relevant documents and (2) nonexperienced PubMed users who do not use them have longer search sessions than experienced users. Methods To test these hypotheses, we analyzed PubMed query log data containing nearly 3 million queries. User sessions were divided into two categories: experienced and nonexperienced. We compared experienced and nonexperienced users per number of sessions, and experienced and nonexperienced user sessions per session length, with a focus on how fast they completed their sessions. Results To test our hypotheses, we measured how successful information retrieval was (at retrieving relevant documents), represented as the decrease rates of experienced and nonexperienced users from a session length of 1 to 2, 3, 4, and 5. The decrease rate (from a session length of 1 to 2) of the experienced users was significantly larger than that of the nonexperienced groups. Conclusions Experienced PubMed users retrieve relevant documents more quickly than nonexperienced PubMed users in terms of session length. PMID:26139516

  8. 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

  9. Research, practice and the Cochrane Collaboration.

    PubMed Central

    Robinson, A

    1995-01-01

    The Cochrane Collaboration coordinates the efforts of health care professionals and researchers around the world to prepare, maintain and disseminate systematic reviews of health care research. In carrying out the first two tasks the collaboration employs a rigorous method for analysing the findings of randomized controlled trials; this method was developed in the 1980s and has undergone continual improvement since then. The collaborators believe their work will consolidate and make available the accumulated results of sound research assessing the effectiveness of health care interventions and thus steer health care professionals and consumers toward the right treatments and help guide research into new therapies. Since the collaboration began, in 1993, Cochrane centres have been set up in the British Isles, Canada, Denmark, Italy, the Netherlands and the United States, and many new Cochrane review groups have been registered. Canadian scientists have played an important role in the collaboration. They have prepared and maintained systematic reviews, hosted the collaboration's second annual colloquium and are currently in the vanguard of efforts to facilitate the dissemination of collaboration documents. Although the collaboration uses new modes of communication it has not abandoned traditional ones. Nor has it underestimated the work that remains to be done to bring review findings to the attention of health care providers. Early indications suggest, however, that the collaboration's basic message about the importance of evidence-based practice is getting through. Images p885-a PMID:7697581

  10. 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, ...

  11. MedlinePlus FAQ: MedlinePlus and MEDLINE/PubMed

    MedlinePLUS

    ... Question: What is the difference between MedlinePlus and MEDLINE/PubMed? To use the sharing features on this ... to latest health professional articles on your topic. MEDLINE/PubMed: Is a database of professional biomedical literature ...

  12. pubmed2ensembl: A Resource for Mining the Biological Literature on Genes

    PubMed Central

    Baran, Joachim; Gerner, Martin; Haeussler, Maximilian; Nenadic, Goran; Bergman, Casey M.

    2011-01-01

    Background The last two decades have witnessed a dramatic acceleration in the production of genomic sequence information and publication of biomedical articles. Despite the fact that genome sequence data and publications are two of the most heavily relied-upon sources of information for many biologists, very little effort has been made to systematically integrate data from genomic sequences directly with the biological literature. For a limited number of model organisms dedicated teams manually curate publications about genes; however for species with no such dedicated staff many thousands of articles are never mapped to genes or genomic regions. Methodology/Principal Findings To overcome the lack of integration between genomic data and biological literature, we have developed pubmed2ensembl (http://www.pubmed2ensembl.org), an extension to the BioMart system that links over 2,000,000 articles in PubMed to nearly 150,000 genes in Ensembl from 50 species. We use several sources of curated (e.g., Entrez Gene) and automatically generated (e.g., gene names extracted through text-mining on MEDLINE records) sources of gene-publication links, allowing users to filter and combine different data sources to suit their individual needs for information extraction and biological discovery. In addition to extending the Ensembl BioMart database to include published information on genes, we also implemented a scripting language for automated BioMart construction and a novel BioMart interface that allows text-based queries to be performed against PubMed and PubMed Central documents in conjunction with constraints on genomic features. Finally, we illustrate the potential of pubmed2ensembl through typical use cases that involve integrated queries across the biomedical literature and genomic data. Conclusion/Significance By allowing biologists to find the relevant literature on specific genomic regions or sets of functionally related genes more easily, pubmed2ensembl offers a much-needed genome informatics inspired solution to accessing the ever-increasing biomedical literature. PMID:21980353

  13. 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

  14. 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

  15. 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 ...

  16. MedlinePlus FAQ: Linking to MedlinePlus

    MedlinePLUS

    ... need permission to link to MedlinePlus from my Web site? To use the sharing features on this ... need permission to link to MedlinePlus from your Web site. Please see our guidelines and instructions on ...

  17. 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 ...

  18. Linking to MedlinePlus

    MedlinePLUS

    ... Web sites. MedlinePlus provides XML data via its Web service and XML files . These services are designed for ... to use the MedlinePlus RSS feeds on your web site or information services. For more information on copyrighted materials on MedlinePlus, ...

  19. 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)

  20. Cochrane and non-Cochrane systematic reviews in leading orthodontic journals: a quality paradigm?

    PubMed

    Fleming, Padhraig S; Seehra, Jadbinder; Polychronopoulou, Argy; Fedorowicz, Zbys; Pandis, Nikolaos

    2013-04-01

    The aims of this study were to assess and compare the methodological quality of Cochrane and non-Cochrane systematic reviews (SRs) published in leading orthodontic journals and the Cochrane Database of Systematic Reviews (CDSR) using AMSTAR and to compare the prevalence of meta-analysis in both review types. A literature search was undertaken to identify SRs that consisted of hand-searching five major orthodontic journals [American Journal of Orthodontics and Dentofacial Orthopedics, Angle Orthodontist, European Journal of Orthodontics, Journal of Orthodontics and Orthodontics and Craniofacial Research (February 2002 to July 2011)] and the Cochrane Database of Systematic Reviews from January 2000 to July 2011. Methodological quality of the included reviews was gauged using the AMSTAR tool involving 11 key methodological criteria with a score of 0 or 1 given for each criterion. A cumulative grade was given for the paper overall (0-11); an overall score of 4 or less represented poor methodological quality, 5-8 was considered fair and 9 or greater was deemed to be good. In total, 109 SRs were identified in the five major journals and on the CDSR. Of these, 26 (23.9%) were in the CDSR. The mean overall AMSTAR score was 6.2 with 21.1% of reviews satisfying 9 or more of the 11 criteria; a similar prevalence of poor reviews (22%) was also noted. Multiple linear regression indicated that reviews published in the CDSR (P < 0.01); and involving meta-analysis (? = 0.50, 95% confidence interval 0.72, 2.07, P < 0.001) showed greater concordance with AMSTAR. PMID:22510325

  1. 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 treatment effects. When including these trials in systematic reviews, adequate analysis of their risk of bias is of utmost importance. PMID:23826877

  2. Archie Cochrane and his vision for evidence-based medicine

    PubMed Central

    Shah, Hriday M.; Chung, Kevin C.

    2009-01-01

    Archibald (Archie) Cochrane's most influential mark on healthcare was his 1971 publication, Effectiveness and Efficiency. This book strongly criticized the lack of reliable evidence behind many of the commonly accepted healthcare interventions at the time. His criticisms spurred rigorous evaluations of healthcare interventions and highlighted the need for evidence in medicine. His call for a collection of systematic reviews led to the creation of The Cochrane Collaboration. Archie Cochrane was a visionary person who helped lay down much of the foundation for evidence-based medicine. This paper will introduce evidence-based medicine to Plastic Surgery by tracing its history to the seminal efforts by Archie Cochrane. PMID:19730323

  3. 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

  4. A bibliometric study of scientific literature on obesity research in PubMed (1988-2007).

    PubMed

    Vioque, J; Ramos, J M; Navarrete-Muñoz, E M; García-de-la-Hera, M

    2010-08-01

    This article describes a bibliometric review of the publications on obesity research in PubMed over the last 20 years. We used Medline via the PubMed online service of the US National Library of Medicine from 1988 to 2007. The search strategy was: ([obesity] in MesH). A total of 58,325 references were retrieved, 25.5% in 1988-1997, and 74.5% in 1998-2007. The growth in the number of publications showed an exponential increase. The references were published in 3613 different journals, with 20 journals contributing 25% of obesity literature. The two journals contributing most were the International Journal of Obesity (5.1%), Obesity-Obesity Research (2.9%). North America and Europe were the most productive world areas with 44.1% and 37.9% of the literature, respectively. The US was the predominant country in number of publications, followed by the United Kingdom, Japan and Italy. The ranking of production changed when the number of publications was normalized by population, gross domestic product and obesity prevalence by countries. The great increase of publications on obesity during the period 1988-2007 was particularly evident in the second decade of the period which is concordant with the worldwide obesity epidemic. USA and Europe were leaders in the production of scientific articles on obesity. PMID:19754632

  5. 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. Conclusions The included interventions demonstrated improvements in appropriate polypharmacy based on reductions in inappropriate prescribing. However, it remains unclear if interventions resulted in clinically significant improvements (eg, in terms of hospital admissions). Future intervention studies would benefit from available guidance on intervention development, evaluation and reporting to facilitate replication in clinical practice. PMID:26656020

  6. Telehealthcare for chronic obstructive pulmonary disease: Cochrane Review and meta-analysis

    PubMed Central

    McLean, Susannah; Nurmatov, Ulugbek; Liu, Joseph LY; Pagliari, Claudia; Car, Josip; Sheikh, Aziz

    2012-01-01

    Background Chronic obstructive pulmonary disease (COPD) is common. Telehealthcare, involving personalised health care over a distance, is seen as having the potential to improve care for people with COPD. Aim To systematically review the effectiveness of telehealthcare interventions in COPD to improve clinical and process outcomes. Design and setting Cochrane Systematic Review of randomised controlled trials. Methods The study involved searching the Cochrane Airways Group Register of Trials, which is derived from the Cochrane Central Register of Controlled Trials, MEDLINE, embase, and CINAHL, as well as searching registers of ongoing and unpublished trials. Randomised controlled trials comparing a telehealthcare intervention with a control intervention in people with a clinical diagnosis of COPD were identified. The main outcomes of interest were quality of life and risk of emergency department visit, hospitalisation, and death. Two authors independently selected trials for inclusion and extracted data. Study quality was assessed using the Cochrane Collaborations risk of bias method. Meta-analysis was undertaken using fixed effect and/or random effects modelling. Results Ten randomised controlled trials were included. Telehealthcare did not improve COPD quality of life: mean difference 6.57 (95% confidence interval [CI] = 13.62 to 0.48). However, there was a significant reduction in the odds ratios (ORs) of emergency department attendance (OR = 0.27; 95% CI = 0.11 to 0.66) and hospitalisation (OR = 0.46; 95% CI = 0.33 to 0.65). There was a non-significant change in the OR of death (OR = 1.05; 95% CI = 0.63 to 1.75). Conclusion In COPD, telehealthcare interventions can significantly reduce the risk of emergency department attendance and hospitalisation, but has little effect on the risk of death. PMID:23211177

  7. Tools for loading MEDLINE into a local relational database

    PubMed Central

    Oliver, Diane E; Bhalotia, Gaurav; Schwartz, Ariel S; Altman, Russ B; Hearst, Marti A

    2004-01-01

    Background Researchers who use MEDLINE for text mining, information extraction, or natural language processing may benefit from having a copy of MEDLINE that they can manage locally. The National Library of Medicine (NLM) distributes MEDLINE in eXtensible Markup Language (XML)-formatted text files, but it is difficult to query MEDLINE in that format. We have developed software tools to parse the MEDLINE data files and load their contents into a relational database. Although the task is conceptually straightforward, the size and scope of MEDLINE make the task nontrivial. Given the increasing importance of text analysis in biology and medicine, we believe a local installation of MEDLINE will provide helpful computing infrastructure for researchers. Results We developed three software packages that parse and load MEDLINE, and ran each package to install separate instances of the MEDLINE database. For each installation, we collected data on loading time and disk-space utilization to provide examples of the process in different settings. Settings differed in terms of commercial database-management system (IBM DB2 or Oracle 9i), processor (Intel or Sun), programming language of installation software (Java or Perl), and methods employed in different versions of the software. The loading times for the three installations were 76 hours, 196 hours, and 132 hours, and disk-space utilization was 46.3 GB, 37.7 GB, and 31.6 GB, respectively. Loading times varied due to a variety of differences among the systems. Loading time also depended on whether data were written to intermediate files or not, and on whether input files were processed in sequence or in parallel. Disk-space utilization depended on the number of MEDLINE files processed, amount of indexing, and whether abstracts were stored as character large objects or truncated. Conclusions Relational database (RDBMS) technology supports indexing and querying of very large datasets, and can accommodate a locally stored version of MEDLINE. RDBMS systems support a wide range of queries and facilitate certain tasks that are not directly supported by the application programming interface to PubMed. Because there is variation in hardware, software, and network infrastructures across sites, we cannot predict the exact time required for a user to load MEDLINE, but our results suggest that performance of the software is reasonable. Our database schemas and conversion software are publicly available at . PMID:15471541

  8. 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 felt to be necessary in selecting literature to read but entirely inadequate for both evaluating and learning from the research. Thus, the restrictions and fees the participants faced in accessing full-text articles were points of frustration. Conclusions The study found strong indications of PubMeds potential value in the professional development of these complementary and alternative medicine practitioners in terms of engaging with and understanding research. It provides support for the various initiatives intended to increase access, including a recommendation that the National Library of Medicine tap into the published research that is being archived by authors in institutional archives and through other websites. PMID:17613489

  9. Cochrane methods - twenty years experience in developing systematic review methods

    PubMed Central

    2013-01-01

    This year, The Cochrane Collaboration reached its 20th anniversary. It has played a pivotal role in the scientific development of systematic reviewing and in the development of review methods to synthesize research evidence, primarily from randomized trials, to answer questions about the effects of healthcare interventions. We introduce a series of articles, which form this special issue describing the development of systematic review methods within The Cochrane Collaboration. We also discuss the impact of Cochrane Review methods, and acknowledge the breadth and depth of methods development within The Cochrane Collaboration as part of the wider context of evidence synthesis. We conclude by considering the future development of methods for Cochrane Reviews. PMID:24050381

  10. 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

  11. 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…

  12. 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 matched pair were cited more frequently. Conclusion Though results between topic-matched Cochrane and non-Cochrane reviews were quite similar, discrepant results were frequent, and the overlap of included studies was surprisingly low. Non-Cochrane reviews report larger effect sizes with lower precision than Cochrane reviews, indicating systematic differences, likely reflective of methodology, between the two types of reviews that could generate different interpretations of the interventions under question. PMID:26671213

  13. 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

  14. Physical rehabilitation for critical illness myopathy and neuropathy: an abridged version of Cochrane Systematic Review.

    PubMed

    Mehrholz, J; Pohl, M; Kugler, J; Burridge, J; Mückel, S; Elsner, B

    2015-10-01

    Intensive care unit (ICU) acquired or generalised weakness due to critical illness myopathy (CIM) and polyneuropathy (CIP) are major causes of chronically impaired motor function that can affect activities of daily living and quality of life. Physical rehabilitation of those affected might help to improve activities of daily living. Our primary objective was to assess the effects of physical rehabilitation therapies and interventions for people with CIP and CIM in improving activities of daily living such as walking, bathing, dressing and eating. Secondary objectives were to assess effects on muscle strength and quality of life, and to assess adverse effects of physical rehabilitation. On 16 July 2014 we searched the Cochrane Neuromuscular Disease Group Specialized Register and on 14 July 2014 we searched CENTRAL, MEDLINE, EMBASE and CINAHL Plus. In July 2014, we searched the Physiotherapy Evidence Database (PEDro) and three trials registries for ongoing trials and further data about included studies with no language restrictions. We also handsearched relevant conference proceedings and screened reference lists to identify further trials. We planned to include randomised controlled trials (RCTs), quasi-RCTs and randomised controlled cross-over trials of any rehabilitation intervention in people with acquired weakness syndrome due to CIP/CIM. We would have extracted data, assessed the risk of bias and classified the quality of evidence for outcomes in duplicate, according to the standard procedures of The Cochrane Collaboration. Outcome data collection would have been for activities of daily living (for example, mobility, walking, transfers and self care). Secondary outcomes included muscle strength, quality of life and adverse events. The search strategy retrieved 3587 references. After examination of titles and abstracts, we retrieved the full text of 24 potentially relevant studies. None of these studies met the inclusion criteria of our review. No data were suitable to be included in a meta-analysis. There are no published RCTs or quasi-RCTs that examine whether physical rehabilitation interventions improve activities of daily living for people with CIP and CIM. Large RCTs, which are feasible, need to be conducted to explore the role of physical rehabilitation interventions for people with CIP and CIM. This paper is based on a Cochrane Review published in in the Cochrane Database of Systematic Reviews (CDSR) 2015, Issue 3, DOI: 10.1002/14651858.CD010942.pub2. (see www.thecochranelibrary.com for information). Cochrane Reviews are regularly updated as new evidence emerges and in response to feedback, and the CDSR should be consulted for the most recent version of the review. PMID:26158919

  15. 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 ...

  16. Evidence-Based Practice: The Cochrane Collaboration, and Occupational Therapy.

    ERIC Educational Resources Information Center

    Hayes, Robyn; McGrath, John

    1998-01-01

    The Cochrane Collaboration is an international project to locate, review, and disseminate information on available randomized controlled trials of health care interventions. Occupational therapists can use it to learn about best practices and evaluate research relevant to their clients. (SK)

  17. Evidence-based treatments for female pattern hair loss: a summary of a Cochrane systematic review.

    PubMed

    van Zuuren, E J; Fedorowicz, Z; Carter, B

    2012-11-01

    Female pattern hair loss (FPHL) or androgenic alopecia is the most common type of hair loss affecting women with reduced hair density and can have a serious psychological impact. It is characterized by progressive replacement of slow cycling terminal hair follicles by miniaturized, rapidly cycling vellus hair follicles. The frontal hair line may or may not be preserved. The aim of this review was to assess the evidence for the effectiveness and safety of the treatments available for FPHL. Searches included: Cochrane Skin Group Specialised Register, Cochrane Central Register of Controlled Clinical Trials in The Cochrane Library, MEDLINE, EMBASE, AMED, PsycINFO, LILACS and several ongoing trials registries (October 2011). Randomized controlled trials in women with FPHL were identified. Twenty-two trials, comprising 2349 participants, were included. A range of interventions was evaluated, with 10 studies examining varying concentrations of minoxidil. Pooled data from four studies indicated that a greater proportion of participants treated with minoxidil reported a moderate increase in their hair regrowth compared with placebo (relative risk 186, 95% confidence interval 142-243). There was no difference between the number of adverse events experienced in the twice daily minoxidil and the placebo intervention groups, except for a reported increase with minoxidil 5% twice daily. Single studies accounted for most of the other comparisons, which were assessed as either having high risk of bias and/or they did not address the prespecified outcomes for this review and provided limited evidence of either the effectiveness or safety of these interventions. Further well-designed, adequately powered randomized controlled trials investigating other treatment options are still required. PMID:23039053

  18. Effective and evidence-based management strategies for rosacea: summary of a Cochrane systematic review.

    PubMed

    van Zuuren, E J; Kramer, S F; Carter, B R; Graber, M A; Fedorowicz, Z

    2011-10-01

    Rosacea is a common chronic skin disease affecting the face. There are numerous treatment options, but it is unclear which are the most effective. The aim of this review was to assess the evidence for the efficacy and safety of treatments for rosacea. Searches included the Cochrane Skin Group Specialised Register, the Cochrane Central Register of Controlled Trials in The Cochrane Library, MEDLINE, EMBASE, Science Citation Index, and Ongoing Trials Registers (updated February 2011). Randomized controlled trials in people with moderate to severe rosacea were included. Fifty-eight trials, including 27 from the original review, comprising 6633 participants were included in this updated review. Interventions included topical metronidazole, oral antibiotics, topical azelaic cream or gel, topical benzoyl peroxide and/or combined with topical antibiotics, sulphacetamide/sulphur, and others. There was some evidence that topical metronidazole and azelaic acid were more effective than placebo. Two trials indicated that doxycycline 40mg was more effective than placebo. There was no statistically significant difference in effectiveness between doxycycline 40mg and 100mg but there were fewer adverse effects. One study reported that ciclosporin ophthalmic emulsion was significantly more effective than artificial tears for treating ocular rosacea. Although the majority of included studies were assessed as being at high or unclear risk of bias, there was some evidence to support the effectiveness of topical metronidazole, azelaic acid and doxycycline (40mg) in the treatment of moderate to severe rosacea, and ciclosporin 005% ophthalmic emulsion for ocular rosacea. Further well-designed, adequately powered randomized controlled trials are required. PMID:21692773

  19. Interventions for rosacea: abridged updated Cochrane systematic review including GRADE assessments.

    PubMed

    van Zuuren, E J; Fedorowicz, Z

    2015-09-01

    Rosacea is a common chronic facial dermatosis. This update of our Cochrane review on interventions for rosacea summarizes the evidence, including Grading of Recommendations Assessment, Development and Evaluation (GRADE) Working Group assessments, of the effects of the currently available treatments. Searches included the following: Cochrane Skin Group Specialised Register, CENTRAL in The Cochrane Library, MEDLINE, EMBASE, LILACS and the Science Citation Index, and ongoing trials registries (July 2014). We included 106 randomized controlled trials (RCTs) with 13631 participants, a more than 80% increase since the last update in 2011. Pooling of data was feasible for a few outcomes, for topical metronidazole and azelaic acid and both appeared to be more effective than placebo (moderate and high-quality evidence, respectively). Topical ivermectin was more effective than placebo based on two studies (high-quality evidence), and slightly more effective than metronidazole in one study. Brimonidine was more effective than vehicle in reducing erythema in rosacea (high-quality evidence). Ciclosporin ophthalmic emulsion was effective for ocular rosacea (low-quality evidence). For oral treatments there was moderate-quality evidence for the effectiveness of tetracycline based on two old studies, and high-quality evidence for doxycycline 40mg compared with placebo according to physician assessments. One study at high risk of bias demonstrated equivalent effectiveness for azithromycin and doxycycline 100mg. Minocycline 45mg may be effective for papulopustular rosacea (low-quality evidence). Low-dose isotretinoin appeared to be slightly more effective than doxycycline 50-100mg (high-quality evidence). Laser and light-based therapies for erythema in rosacea were effective (low-quality evidence). Further RCTs are required for ocular rosacea. PMID:26099423

  20. Information management and complementary alternative medicine: the anatomy of information about CAMs through PubMed.

    PubMed

    Corrao, Salvatore; Argano, Christiano; Colomba, Daniela; Ippolito, Calogero; Gargano, Vincenzo; Arcoraci, Vincenzo; Licata, Giuseppe

    2013-10-01

    In recent years, there has been a growing interest about complementary and alternative medicine (CAM), and the use of CAM interventions has become more common among people. For these reasons, health professionals must be able to effectively manage information in this field of knowledge according to an evidence-based point of view. This study assessed the anatomy of the available information about CAMs using PubMed, to give practical instructions to manage information in this field. We also analyzed the anatomy of information according to each alternative medicine branch, narrow and broad search methods, subset filters for indexed-for-Medline and non-indexed citations, and different publication types including randomized controlled trials (RCTs) and meta-analyses. Our results demonstrated that the use of CAMs subset (supplied by PubMed search engine) leads to a great number of citations determining an information overload. Our data reveal that it would be more useful to search for the CAM separately, identifying specific items and study design. Moreover, we found the largest number of randomized clinical trials and meta-analyses related to herbal medicine and acupuncture, neither RCTs nor meta-analyses were available for bach and flower remedies, auriculoacupuncture, iridology, and pranotherapy. For the first time, our study gives a comprehensive view of the anatomy of information regarding CAMs and each branch of them. We suggest a methodological approach to face with searching information about this emerging issue from an evidence-based point of view. Finally, our data pointed out some "grey zones" since neither RCTs nor meta-analyses were available for some CAMs. PMID:23999987

  1. 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

  2. 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 ...

  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. 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

  5. MedlinePlus FAQ: Framing

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  6. Articles about MedlinePlus

    MedlinePLUS

    ... user interface: studies of design challenges and opportunities. J Med Libr Assoc [Internet]. 2006 [cited 2014 Dec ... N. Analysis of user messages to MedlinePlus.gov. J Med Libr Assoc [Internet]. 2007 [cited 2014 Dec ...

  7. 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 relevancebut 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

  8. 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

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

    PubMed Central

    Rodrguez 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

  10. 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…

  11. 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

  12. 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

  13. 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, underscoring the importance and appropriateness of further research. These preliminary findings should be considered tentative and need to be confirmed with rigorous randomized controlled trials. PMID:19757977

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

    MedlinePLUS

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

  15. 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

  16. 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 SoF tables, the training required to produce SoF tables, and the extent to which the authors of Cochrane Reviews should provide explicit guidance to target audiences of patients, clinicians and policy-makers. PMID:24059250

  17. 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

  18. 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 stories. We argue that our approach can serve as a valuable discovery aid for hypothesis generation and connection exploration in large unstructured biological knowledge bases. PMID:22235301

  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 Amazons 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. PMID:25592589

  20. Depression - Multiple Languages: MedlinePlus

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  1. CT Scans - Multiple Languages: MedlinePlus

    MedlinePLUS

    ... Library of Medicine Menu Health Topics Drugs & Supplements Videos & Tools About MedlinePlus Search Search MedlinePlus GO GO ... Map FAQs Contact Us Health Topics Drugs & Supplements Videos & Tools You Are Here: Home ? Multiple Languages ? All ...

  2. MedlinePlus.gov Turns 10!

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    ... Navigation Bar Home Current Issue Past Issues MedlinePlus.gov Turns 10! Past Issues / Fall 2008 Table of ... Photo courtesy of Michael Spencer, NIH NIH's MedlinePlus.gov , the popular, consumer-friendly health Web site produced ...

  3. Tutorials for Africa: MedlinePlus

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  4. MedlinePlus Connect: Technical Information

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  5. MedlinePlus Connect: Web Service

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  6. Gonadotrophin-releasing hormone antagonists for assisted conception: a Cochrane review.

    PubMed

    Al-Inany, H G; Abou-Setta, A M; Aboulghar, M

    2007-05-01

    Gonadotrophin-releasing hormone (GnRH) antagonists suppress gonadotrophin secretion resulting in dramatic reduction in treatment cycle duration. Assuming comparable clinical outcomes, these benefits may justify changing the standard long GnRH agonist protocol to GnRH antagonist regimens. To evaluate the evidence, databases (e.g. Cochrane Library, MEDLINE, EMBASE) were electronically searched, hand searches were performed, and manufacturers in the field were contacted. Twenty-seven randomized controlled trials (RCT) fulfilled inclusion criteria for comparison of GnRH antagonist with long GnRH agonist protocol. Clinical pregnancy rate and ongoing pregnancy/live-birth rate were significantly lower in the antagonist group (P = 0.009; OR = 0.83, 95% CI 0.72-0.95 and P = 0.02; OR = 0.82, 95% CI 0.68-0.97 respectively). Conversely, incidence of severe OHSS was significantly reduced with the antagonist protocol (P = 0.01; OR = 0.60, 95% CI 0.40-0.88), and interventions to prevent OHSS were administered more frequently in the agonist group (P = 0.03; OR = 0.43, 95% CI 0.20-0.92). Concluding, GnRH antagonist protocols are short, simple, with good clinical outcomes and significant reduction in severe OHSS incidence and gonadotrophin amount; however, the lower pregnancy rate compared with the GnRH agonist long protocol necessitates counselling subfertile couples before recommending change from GnRH agonist to antagonist. PMID:17509210

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. School as Parkland: Re-Storying the Story of Cochrane School

    ERIC Educational Resources Information Center

    Craig, Cheryl J.

    2007-01-01

    The narrative inquiry reported in this study offers a partial view of Cochrane Academy's nuanced landscape. This article elaborates a theoretical frame, then uses different story perspectives to survey Cochrane's professional knowledge landscape over time. It relates what currently is Cochrane Academy to parkland landscape, and it discusses the

  14. Virtual reality for stroke rehabilitation: an abridged version of a Cochrane review.

    PubMed

    Laver, K; George, S; Thomas, S; Deutsch, J E; Crotty, M

    2015-08-01

    Virtual reality and interactive video gaming have emerged as new treatment approaches in stroke rehabilitation settings over the last ten years. The primary objective of this review was to determine the effectiveness of virtual reality on upper limb function and activity after stroke. The impact on secondary outcomes including gait, cognitive function and activities of daily living was also assessed. Randomized and quasi-randomized controlled trials comparing virtual reality with an alternative intervention or no intervention were eligible to be included in the review. The authors searched a number of electronic databases including: the Cochrane Stroke Group Trials Register, the Cochrane Central Register of Controlled Trials, MEDLINE, EMBASE, AMED, CINAHL, PsycINFO, clinical trial registers, reference lists, Dissertation Abstracts and contacted key researchers in the field. Search results were independently examined by two review authors to identify studies meeting the inclusion criteria. A total of 37 randomized or quasi randomized controlled trials with a total of 1019 participants were included in the review. Virtual reality was found to be significantly more effective than conventional therapy in improving upper limb function (standardized mean difference [SMD] 0.28, 95% confidence intervals [CI] 0.08 to 0.49) based on 12 studies and significantly more effective than no therapy in improving upper limber function (SMD 0.44 [95% CI 0.15 to 0.73]) based on nine studies. The use of virtual reality also significantly improved activities of daily living function when compared to more conventional therapy approaches (SMD 0.43 [95% CI 0.18 to 0.69]) based on eight studies. While there are a large number of studies assessing the efficacy of virtual reality they tend to be small and many are at risk of bias. While there is evidence to support the use of virtual reality intervention as part of upper limb training programs, more research is required to determine whether it is beneficial in terms of improving lower limb function and gait and cognitive function. PMID:26158918

  15. Three PubMed skills to support evidence-based dentistry.

    PubMed

    Deahl, S Thomas

    2011-02-01

    The National Library of Medicine's PubMed database can powerfully assist dentists in evidence-based practice. Three useful PubMed skills can improve the efficiency of the clinician's search: (1) Use of MeSH terms; (2) Use of Limits; (3) Use of Clinical Queries. PMID:21473243

  16. Selenium Supplementation for Hashimoto's Thyroiditis: Summary of a Cochrane Systematic Review

    PubMed Central

    van Zuuren, Esther J.; Albusta, Amira Y.; Fedorowicz, Zbys; Carter, Ben; Pijl, Hanno

    2014-01-01

    Selenium supplementation in people with Hashimoto's thyroiditis might reduce antibody levels and result in a decreased dosage of levothyroxine (LT4) and may provide other beneficial effects (e.g. on mood and health-related quality of life). The aim of our systematic review was to assess the effects of selenium supplementation on Hashimoto's thyroiditis. We searched The Cochrane Library, MEDLINE, EMBASE and Web of Science for randomized controlled trials. Study selection, data extraction, assessment of risk of bias and analyses were carried out by two independent review authors. We assessed the quality of the evidence of included studies using GRADE. Four studies rated at unclear to high risk of bias comprising 463 participants were included. One study at high risk of bias showed statistically significant improvement in subjective well-being with sodium selenite 200 ?g plus titrated LT4 compared with placebo plus titrated LT4 (RR 4.67, 95% CI 1.61-13.50). Selenomethionine 200 ?g as a single treatment or combined with LT4 reduced the serum levels of anti-thyroid peroxidase antibodies compared with placebo (or placebo plus LT4) in three studies (p < 0.001). Although the changes from baseline were statistically significant in these three studies, their clinical relevance is unclear. In conclusion, the results of these four studies, assessed at unclear to high risk of bias, show that evidence to support or refute the efficacy of selenium supplementation in people with Hashimoto's thyroiditis is incomplete and not reliable to help inform clinical decision making. PMID:24847462

  17. Selenium Supplementation for Hashimoto's Thyroiditis: Summary of a Cochrane Systematic Review.

    PubMed

    van Zuuren, Esther J; Albusta, Amira Y; Fedorowicz, Zbys; Carter, Ben; Pijl, Hanno

    2014-03-01

    Selenium supplementation in people with Hashimoto's thyroiditis might reduce antibody levels and result in a decreased dosage of levothyroxine (LT4) and may provide other beneficial effects (e.g. on mood and health-related quality of life). The aim of our systematic review was to assess the effects of selenium supplementation on Hashimoto's thyroiditis. We searched The Cochrane Library, MEDLINE, EMBASE and Web of Science for randomized controlled trials. Study selection, data extraction, assessment of risk of bias and analyses were carried out by two independent review authors. We assessed the quality of the evidence of included studies using GRADE. Four studies rated at unclear to high risk of bias comprising 463 participants were included. One study at high risk of bias showed statistically significant improvement in subjective well-being with sodium selenite 200 ?g plus titrated LT4 compared with placebo plus titrated LT4 (RR 4.67, 95% CI 1.61-13.50). Selenomethionine 200 ?g as a single treatment or combined with LT4 reduced the serum levels of anti-thyroid peroxidase antibodies compared with placebo (or placebo plus LT4) in three studies (p < 0.001). Although the changes from baseline were statistically significant in these three studies, their clinical relevance is unclear. In conclusion, the results of these four studies, assessed at unclear to high risk of bias, show that evidence to support or refute the efficacy of selenium supplementation in people with Hashimoto's thyroiditis is incomplete and not reliable to help inform clinical decision making. PMID:24847462

  18. 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

  19. MedlinePlus FAQ: Can you tell me how to cite MedlinePlus pages?

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  1. Overview of Reviews The prevention of eczema in infants and children: an overview of Cochrane and non-Cochrane reviews

    PubMed Central

    Foisy, Michelle; Boyle, Robert J.; Chalmers, Joanne R.; Simpson, Eric L.; Williams, Hywel C.

    2012-01-01

    Background Eczema is the most common inflammatory skin disease of childhood, characterized by an itchy red rash that usually involves the face and skin folds. There is currently no curative treatment for eczema, so the reduction of eczema incidence through disease prevention is a desirable goal. Potential interventions for preventing eczema include exclusive breastfeeding, hydrolysed protein formulas and soy formulas when bottle feeding, maternal antigen avoidance, omega oil supplementation, prebiotics and probiotics. Objectives This overview of reviews aims to present the current body of data from Cochrane and non-Cochrane reviews to provide the most up-to-date evidence on the efficacy and safety of interventions to prevent eczema in infants and children at different risk levels for developing allergic disease. Methods Our pool of Cochrane and non-Cochrane reviews came from the 2010 United Kingdom National Health Service (NHS) Evidence Skin Disorders Annual Evidence Updates Mapping Exercise on Atopic Eczema. This group used a comprehensive search strategy last conducted in August 2010 to identify all systematic reviews on eczema prevention. We identified all reviews that met our pre-specified inclusion criteria, and data were extracted, analysed, compiled into tables and synthesized using quantitative and qualitative methods. Main results Seven systematic reviews containing 39 relevant trials with 11 897 participants were included in this overview. Overall, there was no clear evidence that any of the main interventions reviewed reduced eczema incidence. In subgroup analyses of infants at high risk of allergic disease, an observational study found that exclusive breastfeeding for at least six months compared with introduction of solids at three to six months decreased the incidence of eczema by 60% (risk ratio (RR): 0.40; 95% confidence interval (CI): 0.21, 0.78), and a randomized controlled trial found that prebiotics compared with no prebiotics decreased incidence by 58% (RR: 0.42; 95% CI: 0.21, 0.84). However, each of these findings was based on the results of a single small trial, and no intervention reduced eczema incidence beyond the first two years of life. Although we pre-specified incidence of atopic eczema (i.e. eczema associated with immunoglobulin E (IgE) sensitization) as a primary outcome, data on whether participants diagnosed with eczema were truly atopic were largely lacking from systematic reviews. Similarly, data on atopy, measured using skin prick tests or specific IgE tests to allergens, were not reported in many reviews. No interventions were found to decrease atopy when reported. Adverse events data were generally lacking, but data from a trial of probiotics versus no probiotics showed significantly more spitting up in the first one (RR: 1.88; 95% CI: 1.03, 3.45) and two (RR: 1.69; 95% CI: 1.02, 2.80) months of life, but no overall increase in risk of gastrointestinal symptoms in the first year. Authors conclusions Although there is currently no clear evidence showing that any of the interventions examined in this overview prevent eczema in participants not selected for risk of allergic disease, there is some evidence that exclusive breastfeeding for at least six months and prebiotics might reduce eczema incidence in high-risk participants. However, these conclusions are based on limited evidence with methodological shortcomings. Future research on prevention of eczema is needed and should examine different types of hydrolysed formulas, prebiotics and probiotics, as well as enhancement of the skin barrier and other novel approaches in infants at different risk levels for developing allergic disease. PMID:22822349

  2. A Cochrane Systematic Review finds no significant difference in outcome or risk of postoperative complications between day care and in-patient cataract surgery.

    PubMed

    Fedorowicz, Zbigniew; Lawrence, David J; Gutierrez, Peter

    2006-09-01

    This review was conducted to determine reliable evidence regarding the safety, feasibility, effectiveness, and cost-effectiveness of cataract extraction performed as a day care versus in-patient procedure. The search to identify randomized controlled trials comparing day care and in-patient surgery for age-related cataract included the Cochrane Eyes and Vision Group Trials Register, the Cochrane Central Register of Controlled Trials, MEDLINE, EMBASE and LILACS Latin American and Caribbean Literature on Health Sciences. Assessment of methodological quality was based on criteria defined by the Cochrane Collaboration. The primary outcome was the achievement of a satisfactory visual acuity 6 weeks after operation. Two trials, involving a total of 1284 people, are included. One trial reported statistically significant differences in early postoperative complication rates in the day care group, which had no clinical relevance to visual outcomes 4 months postoperatively. Mean change in visual acuity Snellen lines of the operated eye 4 months postoperatively was 4.1 standard deviation SD 2.3 for the day care group and 4.1 SD 2.2 for the in-patient group. Costs were 20% more for the in-patient group attributable to higher costs for overnight stay. PMID:16951761

  3. MedlinePlus.gov on Twitter

    MedlinePLUS

    ... page please turn Javascript on. MedlinePlus.gov on Twitter Past Issues / Fall 2009 Table of Contents You can now follow MedlinePlus.gov on Twitter: twitter.com/medlineplus4you The medlineplus4you Twitter feed provides ...

  4. PubMed enhancements: fulfilling the promise of a great product.

    PubMed

    Schott, Michael J

    2004-01-01

    There have been many recent changes to PubMed to enhance its usefulness. Those changes include: LinkOut Libraries (local holding field), PubMed Central (full-text articles archived by the National Library of Medicine), and LinkOut (access to full-text articles right from the PubMed citation). Medical librarians should be aware of how these features work to best assist their clients. These new features offer the possibility of true desktop access for library patrons. Not only will patrons appreciate these new features, but their use in libraries will literally change what we do, who does it, and how it is done. PMID:15778178

  5. Quertle and KNALIJ: searching PubMed has never been so easy and effective.

    PubMed

    Giglia, E

    2011-12-01

    Quertle and KNALIJ are two innovative tools created to search PubMed in a easier and more effective way. They dramatically reduce time to discover meaningful results. Quertle allows a semantic search in multiple biomedical databases (PubMed included) and runs a query via relationships between concepts, so that you retrieve at ease more pertinent results and can navigate them by "key concepts". KNALIJ is a visualization tool which searches PubMed and presents the results in the form of visual, interactive maps you can zoom, scale, and explore according to new paths. PMID:22222966

  6. Automatic inference of indexing rules for MEDLINE

    PubMed Central

    Nvol, Aurlie; Shooshan, Sonya E; Claveau, Vincent

    2008-01-01

    Background: Indexing is a crucial step in any information retrieval system. In MEDLINE, a widely used database of the biomedical literature, the indexing process involves the selection of Medical Subject Headings in order to describe the subject matter of articles. The need for automatic tools to assist MEDLINE indexers in this task is growing with the increasing number of publications being added to MEDLINE. Methods: In this paper, we describe the use and the customization of Inductive Logic Programming (ILP) to infer indexing rules that may be used to produce automatic indexing recommendations for MEDLINE indexers. Results: Our results show that this original ILP-based approach outperforms manual rules when they exist. In addition, the use of ILP rules also improves the overall performance of the Medical Text Indexer (MTI), a system producing automatic indexing recommendations for MEDLINE. Conclusion: We expect the sets of ILP rules obtained in this experiment to be integrated into MTI. PMID:19025687

  7. [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

  8. GOClonto: an ontological clustering approach for conceptualizing PubMed abstracts.

    PubMed

    Zheng, Hai-Tao; Borchert, Charles; Kim, Hong-Gee

    2010-02-01

    Concurrent with progress in biomedical sciences, an overwhelming of textual knowledge is accumulating in the biomedical literature. PubMed is the most comprehensive database collecting and managing biomedical literature. To help researchers easily understand collections of PubMed abstracts, numerous clustering methods have been proposed to group similar abstracts based on their shared features. However, most of these methods do not explore the semantic relationships among groupings of documents, which could help better illuminate the groupings of PubMed abstracts. To address this issue, we proposed an ontological clustering method called GOClonto for conceptualizing PubMed abstracts. GOClonto uses latent semantic analysis (LSA) and gene ontology (GO) to identify key gene-related concepts and their relationships as well as allocate PubMed abstracts based on these key gene-related concepts. Based on two PubMed abstract collections, the experimental results show that GOClonto is able to identify key gene-related concepts and outperforms the STC (suffix tree clustering) algorithm, the Lingo algorithm, the Fuzzy Ants algorithm, and the clustering based TRS (tolerance rough set) algorithm. Moreover, the two ontologies generated by GOClonto show significant informative conceptual structures. PMID:19635585

  9. 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

  10. Evidence-based topical treatments for tinea cruris and tinea corporis: a summary of a Cochrane systematic review.

    PubMed

    van Zuuren, E J; Fedorowicz, Z; El-Gohary, M

    2015-03-01

    Tinea cruris and tinea corporis are common fungal infections. Most can be treated with a variety of topical antifungals. This review aimed to assess the evidence for the effectiveness and safety of topical treatments for tinea cruris and tinea corporis. Searches included the Cochrane Skin Group Specialised Register, CENTRAL in The Cochrane Library, Medline, Embase, LILACS and ongoing trials registries (August 2013). One hundred and twenty-nine randomized controlled trials (RCTs) with 18086 participants evaluated a range of interventions - mostly azoles. Pooling of data for several outcomes was only possible for two individual treatments. In five studies, terbinafine showed a statistically significant higher clinical cure rate compared with placebo [risk ratio (RR) 451, 95% confidence interval (CI) 310-656]. Data for mycological cure could not be pooled owing to substantial heterogeneity. Across three studies, mycological cure rates favoured naftifine (1%) compared with placebo (RR 238, 95% CI 180-314) but the quality of the evidence was low. Combinations of azoles with corticosteroids were slightly more effective than azoles for clinical cure, but there was no statistically significant difference with regard to mycological cure. Sixty-five studies were assessed as 'unclear' and 64 as being at 'high risk' of bias; many were over 20years old, and most were poorly designed and inadequately reported. Although most active interventions showed sufficient therapeutic effect, this review highlights the need for further, high-quality, adequately powered RCTs to evaluate the effects of these interventions, which can ultimately provide reliable evidence to inform clinical decision making. PMID:25294700

  11. A short guide to peer-reviewed, MEDLINE-indexed complementary and alternative medicine journals.

    PubMed

    Morgan, Sherry; Littman, Lynn; Palmer, Christina; Singh, Gurneet; LaRiccia, Patrick J

    2012-01-01

    Complementary and alternative medicine (CAM) comprises a multitude of disciplines, for example, acupuncture, ayurvedic medicine, biofeedback, herbal medicine, and homeopathic medicine. While research on CAM interventions has increased and the CAM literature has proliferated since the mid-1990s, a number of our colleagues have expressed difficulties in deciding where to publish CAM articles. In response, we created a short guide to peer-reviewed MEDLINE-indexed journals that publish CAM articles. We examined numerous English-language sources to identify titles that met our criteria, whether specific to or overlapping CAM. A few of the resources in which we found the journal titles that we included are Alternative Medicine Foundation, American Holistic Nurses Association, CINAHL/Nursing Database, Journal Citation Reports database, MEDLINE, PubMed, and Research Council for Complementary Medicine. We organized the 69 selected titles for easy use by creating 2 user-friendly tables, one listing titles in alphabetical order and one listing them in topical categories. A few examples of the topical categories are Acupuncture, CAM (general), Chinese Medicine, Herbal/Plant/Phytotherapy, Neuroscience/Psychology, Nursing/Clinical Care. Our study is the first to list general CAM journals, specialty CAM journals, and overlapping mainstream journals that are peer reviewed, in English, and indexed in MEDLINE. Our goal was to assist both authors seeking publication and mainstream journal editors who receive an overabundance of publishable articles but must recommend that authors seek publication elsewhere due to space and priority issues. Publishing in journals indexed by and included in MEDLINE (or PubMed) ensures that citations to articles will be found easily. PMID:22517352

  12. 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

  13. Improving accuracy for identifying related PubMed queries by an integrated approach.

    PubMed

    Lu, Zhiyong; Wilbur, W John

    2009-10-01

    PubMed is the most widely used tool for searching biomedical literature online. As with many other online search tools, a user often types a series of multiple related queries before retrieving satisfactory results to fulfill a single information need. Meanwhile, it is also a common phenomenon to see a user type queries on unrelated topics in a single session. In order to study PubMed users' search strategies, it is necessary to be able to automatically separate unrelated queries and group together related queries. Here, we report a novel approach combining both lexical and contextual analyses for segmenting PubMed query sessions and identifying related queries and compare its performance with the previous approach based solely on concept mapping. We experimented with our integrated approach on sample data consisting of 1539 pairs of consecutive user queries in 351 user sessions. The prediction results of 1396 pairs agreed with the gold-standard annotations, achieving an overall accuracy of 90.7%. This demonstrates that our approach is significantly better than the previously published method. By applying this approach to a one day query log of PubMed, we found that a significant proportion of information needs involved more than one PubMed query, and that most of the consecutive queries for the same information need are lexically related. Finally, the proposed PubMed distance is shown to be an accurate and meaningful measure for determining the contextual similarity between biological terms. The integrated approach can play a critical role in handling real-world PubMed query log data as is demonstrated in our experiments. PMID:19162232

  14. MedlinePlus FAQ: Spelling Assistance

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  15. Back Cover: NIH MedlinePlus Salud

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  20. Tutorials for Africa: MedlinePlus

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  1. MedlinePlus Connect: Email List

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  2. MedlinePlus Survey Results 2015

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  3. Mercury - Multiple Languages: MedlinePlus

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  4. Hazardous Waste - Multiple Languages: MedlinePlus

    MedlinePLUS

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  5. Streptococcal Infections - Multiple Languages: MedlinePlus

    MedlinePLUS

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  6. MEDLINE services to the developing countries.

    PubMed Central

    Weitzel, R

    1976-01-01

    Supplying MEDLINE services to a widely dispersed user population in the developing countries creates numerous problems not encountered by other MEDLINE centres. The inability to interact with the user complicates system promotion and makes search formulation sometimes a gamble. Nevertheless, an evaluation survey has shown high user satisfaction. Of great concern is the still inadequate solution of document delivery. Near-term objectives are the broadening of geographic coverage and the integration of search processing with supporting hard copy supply. PMID:1247707

  7. 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

  8. Cochrane methods--twenty years experience in developing systematic review methods.

    PubMed

    Chandler, Jackie; Hopewell, Sally

    2013-01-01

    This year, The Cochrane Collaboration reached its 20th anniversary. It has played a pivotal role in the scientific development of systematic reviewing and in the development of review methods to synthesize research evidence, primarily from randomized trials, to answer questions about the effects of healthcare interventions. We introduce a series of articles, which form this special issue describing the development of systematic review methods within The Cochrane Collaboration. We also discuss the impact of Cochrane Review methods, and acknowledge the breadth and depth of methods development within The Cochrane Collaboration as part of the wider context of evidence synthesis. We conclude by considering the future development of methods for Cochrane Reviews. PMID:24050381

  9. 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

  10. Telerehabilitation for persons with multiple sclerosis. A Cochrane review.

    PubMed

    Khan, F; Amatya, B; Kesselring, J; Galea, M P

    2015-06-01

    A wide range of telerehabilitation interventions are trialled in persons with multiple sclerosis (pwMS). However, the evidence for their effectiveness is unclear. Aim of the review was to systematically assess the effectiveness and safety of telerehabilitation intervention in pwMS, the types of approaches that are effective (setting, type, intensity) and the outcomes (impairment, activity limitation and participation) that are affected. The search strategy comprised: Cochrane Multiple Sclerosis and Rare Diseases of the Central Nervous System Review Group Specialised Register (up to 9 July, 2014). Relevant journals and reference lists of identified studies were screened for additional data. Selected studies included randomized and controlled clinical trials that compared telerehabilitation intervention/s in pwMS with a control intervention (such as lower level or different types of intervention, minimal intervention; waiting-list controls, no treatment or usual care; interventions given in different settings). Best evidence synthesis was based on methodological quality using the GRADEpro software. Nine RCTs (N.=531 participants, 469 included in analyses) investigated a variety of telerehabilitation interventions in adults with MS. The interventions evaluated were complex, with more than one rehabilitation component and included physical activity, educational, behavioural and symptom management programmes. All studies scored "low" on the methodological quality assessment. Evidence from included studies provides 'low-level' evidence for reduction in short-term disability (and symptoms) such as fatigue. There was also "low-level" evidence supporting telerehabilitation in the longer term for improved functional activities, impairments (such as fatigue, pain, insomnia); and participation. There were limited data on process evaluation (participants'/therapists' satisfaction) and no data available for cost effectiveness. There were no adverse events reported as a result of telerehabilitation intervention. There is limited evidence to date, on the efficacy of telerehabilitation in improving functional activities, fatigue and quality of life in adults with MS. There is also insufficient evidence to support what types of telerehabilitation interventions are effective, and in which setting. More robust trials are needed to build evidence for the clinical and cost effectiveness of these interventions. PMID:25943744

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

    PubMed Central

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

    2007-01-01

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

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

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

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  14. 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

  15. The impact of Cochrane Reviews: a mixed-methods evaluation of outputs from Cochrane Review Groups supported by the National Institute for Health Research.

    PubMed Central

    Bunn, Frances; Trivedi, Daksha; Alderson, Phil; Hamilton, Laura; Martin, Alice; Pinkney, Emma; Iliffe, Steve

    2015-01-01

    BACKGROUND The last few decades have seen a growing emphasis on evidence-informed decision-making in health care. Systematic reviews, such as those produced by Cochrane, have been a key component of this movement. The National Institute for Health Research (NIHR) Systematic Review Programme currently supports 20 Cochrane Review Groups (CRGs) in the UK and it is important that this funding represents value for money. AIMS AND OBJECTIVES The overall aim was to identify the impacts and likely impacts on health care, patient outcomes and value for money of Cochrane Reviews published by 20 NIHR-funded CRGs during the years 2007-11. DESIGN We sent questionnaires to CRGs and review authors, undertook interviews with guideline developers (GDs) 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. The evaluation was guided by a framework with four categories (knowledge production, research targeting, informing policy development and impact on practice/services). RESULTS A total of 3187 new and updated reviews were published on the Cochrane Database of Systematic Reviews between 2007 and 2011, 1502 (47%) of which were produced by the 20 CRGs funded by the NIHR. We found 40 examples where reviews appeared to have influenced primary research and reviews had contributed to the creation of new knowledge and stimulated debate. Twenty-seven of the 60 reviews had 100 or more citations in Google Scholar™ (Google, CA, USA). Overall, 483 systematic reviews had been cited in 247 sets of guidance. This included 62 sets of international guidance, 175 sets of national guidance (87 from the UK) and 10 examples of local guidance. Evidence from the interviews suggested that Cochrane Reviews often play an instrumental role in informing guidance, although reviews being a poor fit with guideline scope or methods, reviews being out of date and a lack of communication between CRGs and GDs were barriers to their use. Cochrane Reviews appeared to have led to a number of benefits to the health service including safer or more appropriate use of medication or other health technologies or the identification of new effective drugs or treatments. However, whether or not these changes were directly as a result of the Cochrane Review and not the result of subsequent clinical guidance was difficult to judge. Potential benefits of Cochrane Reviews included economic benefits through budget savings or the release of funds, improvements in clinical quality, the reduction in the use of unproven or unnecessary procedures and improvements in patient and carer experiences. CONCLUSIONS This study identified a number of impacts and likely impacts of Cochrane Reviews. The clearest impacts of Cochrane Reviews are on research targeting and health-care policy, with less evidence of a direct impact on clinical practice and the organisation and delivery of NHS services. Although it is important for researchers to consider how they might increase the influence of their work, such impacts are difficult to measure. More work is required to develop suitable methods for defining and quantifying the impact of research. FUNDING The NIHR Health Technology Assessment programme. PMID:25875129

  16. 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

  17. 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. PMID:23071826

  18. Challenges and strategies of increasing the production and use of Cochrane reviews: the Argentinean experience.

    PubMed

    Ciapponi, Agustn

    2008-01-01

    The Cochrane Collaboration (CC), established in 1993, is an internationally renowned initiative dedicated to improving health care for the world's population. In the late 1990 s, the Iberoamerican Cochrane Centre (IbCC) was created to promote the CC in Latin America. Because the production and use of Cochrane reviews were still low in 2002, Argentina implemented specific strategies and a model to expand the IbCC. The objective of this article was to describe strategies to increase the production and use of Cochrane reviews in Argentina. Methods used included surveys delivered to primary health care workers to provide data about their knowledge and use of the CC, and about the production of titles, protocols, and systematic reviews published in the Cochrane Library. Our survey showed that only 51% of a selected population of primary healthcare workers knew about the CC and only 23% knew about the Argentine Cochrane centre. In the previous year, 60% had never used the CC. To overcome these challenges, we used seven types of complementary strategies: (1) networking, (2) dissemination, (3) training, (4) support to Cochrane members, (5) strategic alliances, (6) research, and (7) fund-raising. An improvement in the production and use of Cochrane reviews was seen in Argentina, and the set of aforementioned strategies could be partly responsible for this increase. Multi-level networking, training and an appropriate centre's mother institution could be the most important interventions. More research is needed to explore this hypothesis. Lessons learned on this first evaluation will help us to continue with the development of the CC in Argentina. PMID:18237346

  19. 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…

  20. MedlinePlus FAQ: News Coverage

    MedlinePLUS

    ... medlineplus/faq/news.html Question: I saw a news article on MedlinePlus but now I can't find ... stories are also displayed on health topic pages . News articles come from the HealthDay news services. NLM does ...

  1. 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

  2. PubMedAlertMe - Standalone Windows-based PubMed SDI Software Application

    PubMed Central

    Maayan, Avi

    2008-01-01

    PubMedAlertMe is a Windows-based software system for automatically receiving e-mail alert messages about recent publications listed on PubMed. The e-mail messages contain links to newly available abstracts listed on PubMed describing publications that were selectively returned from a specified list of queries. Links are also provided to directly export citations to EndNote, and links are provided to directly forward articles to colleagues. The program is standalone. Thus, it does not require a remote mail server or user registration. PubMedAlertMe is free software, and can be downloaded from: http://amp.pharm.mssm.edu/PubMedAlertMe/PubMedAlertMe_setup.zip PMID:18402930

  3. PubMed and beyond: a survey of web tools for searching biomedical literature.

    PubMed

    Lu, Zhiyong

    2011-01-01

    The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement. Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications. These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed. In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development. Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search. Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search. PMID:21245076

  4. PubMed and beyond: a survey of web tools for searching biomedical literature

    PubMed Central

    Lu, Zhiyong

    2011-01-01

    The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement. Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications. These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed. In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development. Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search. Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search PMID:21245076

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

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  8. MedlinePlus Marks 15th Anniversary | NIH MedlinePlus the Magazine

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  10. 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 order covering diverse bio-entity relations. To assess the potential utility of our automated top-ranked patterns of a given relation in semantic search, we performed a pilot study on frequently sought semantic relations in PubMed and observed improved literature retrieval effectiveness based on post-hoc human relevance evaluation. Further investigation in larger tests and in real-world scenarios is warranted. PMID:27016698

  11. 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 provides more accurate information about organizations than the raw affiliation strings provided in PubMed abstracts. It can be used for : a) bimodal social network analysis that evaluates the research relationships between individual researchers and their institutions; b) improving author name disambiguation; c) augmenting National Library of Medicine (NLM)s Medical Articles Record System (MARS) system for correcting errors due to OCR on affiliation strings that are in small fonts; and d) improving PubMed citation indexing strategies (authority control) based on normalized organization name and country. PMID:20922666

  12. 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 theCCandCD taskwhen 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 covering diverse bio-entity relations. To assess the potential utility of our automated top-ranked patterns of a given relation in semantic search, we performed a pilot study on frequently sought semantic relations in PubMed and observed improved literature retrieval effectiveness based on post-hoc human relevance evaluation. Further investigation in larger tests and in real-world scenarios is warranted. PMID:27016698

  13. Diabetic Nerve Problems - Multiple Languages: MedlinePlus

    MedlinePLUS

    ... Library of Medicine Menu Health Topics Drugs & Supplements Videos & Tools About MedlinePlus Search Search MedlinePlus GO GO ... Map FAQs Contact Us Health Topics Drugs & Supplements Videos & Tools You Are Here: Home ? Multiple Languages ? All ...

  14. Diabetes and Pregnancy - Multiple Languages: MedlinePlus

    MedlinePLUS

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  15. Diabetic Kidney Problems - Multiple Languages: MedlinePlus

    MedlinePLUS

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  16. Diabetic Eye Problems - Multiple Languages: MedlinePlus

    MedlinePLUS

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  17. MedlinePlus FAQ: Listing Your Web Site

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  18. MedlinePlus Connect: Frequently Asked Questions (FAQs)

    MedlinePLUS

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  19. MedlinePlus Marks its 15th Anniversary

    MedlinePLUS

    ... or near the 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 ...

  20. MedlinePlus FAQ: Copyrighted and Non-Copyrighted Material

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  1. MedlinePlus FAQ: Easy-to-Read Documents

    MedlinePLUS

    ... faq/easytoread.html Question: How can I locate materials on MedlinePlus that are easy to read and ... public, not for health professionals. But, not all materials on MedlinePlus are at the same reading level. ...

  2. Misunderstandings about Q and 'Cochran's Q test' in meta-analysis.

    PubMed

    Hoaglin, David C

    2016-02-20

    Many meta-analyses report using 'Cochran's Q test' to assess heterogeneity of effect-size estimates from the individual studies. Some authors cite work by W.G. Cochran, without realizing that Cochran deliberately did not use Q itself to test for heterogeneity. Further, when heterogeneity is absent, the actual null distribution of Q is not the chi-squared distribution assumed for 'Cochran's Q test'. This paper reviews work by Cochran related to Q. It then discusses derivations of the asymptotic approximation for the null distribution of Q, as well as work that has derived finite-sample moments and corresponding approximations for the cases of specific measures of effect size. Those results complicate implementation and interpretation of the popular heterogeneity index I(2) . Also, it turns out that the test-based confidence intervals used with I(2) are based on a fallacious approach. Software that outputs Q and I(2) should use the appropriate reference value of Q for the particular measure of effect size and the current meta-analysis. Q is a key element of the popular DerSimonian-Laird procedure for random-effects meta-analysis, but the assumptions of that procedure and related procedures do not reflect the actual behavior of Q and may introduce bias. The DerSimonian-Laird procedure should be regarded as unreliable. Copyright 2015 John Wiley & Sons, Ltd. PMID:26303773

  3. Intervention for replacing missing teeth: Partially absent dentition-Evidence summary of Cochrane review

    PubMed Central

    Jayaraman, Srinivasan

    2015-01-01

    Cochrane reviews are systematic reviews with meta analysis published by the Cochrane collaboration, in the Cochrane Database of Systematic Reviews (CDSR). These reviews provide the clinicians with the highest level of evidence as they use a highly structured and transparent systematic review model to address a specific research question. The management of partially absent dentition is routinely under taken by general dentist and Prosthodontist but clinical practice guidelines based on evidence to this common problem is yet to be summarized. This Cochrane systematic review aims to address the effect of different prosthesis for the treatment of partially absent dentition in the terms of, Long-term success, function, morbidity, and patient satisfaction. All randomized controlled trials were searched till March 18, 2011, based on the inclusion and exclusion criteria, 21 trials were included and 32 trials were excluded and, it was critically appraised using the Cochrane methodology for interventions. The summary of evidence from the study concludes that there is insufficient evidence to state the effectiveness of removable and fixed prosthesis in partially edentulous subjects in the following four outcomes. There were insufficient trials to perform a meta-analysis and sensitivity analysis. This evidence-based summary emphasizes and reinforces the need to reassess the quality of research currently pursued in our profession, to address the need to provide higher level of evidence for common conditions like partial edentulousness. The included studies are basically not from our population too, hence the urgency to address this critical issue.

  4. Cochrane summary of findings: horse chestnut seed extract for chronic venous insufficiency.

    PubMed

    Underland, Vigdis; Sæterdal, Ingvil; Nilsen, Elin Strømme

    2012-03-01

    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

  5. Strategies to improve retention in randomised trials: a Cochrane systematic review and meta-analysis

    PubMed Central

    Brueton, V C; Tierney, J F; Stenning, S; Meredith, S; Harding, S; Nazareth, I; Rait, G

    2014-01-01

    Objective To quantify the effect of strategies to improve retention in randomised trials. Design Systematic review and meta-analysis. Data sources Sources searched: MEDLINE, EMBASE, PsycINFO, DARE, CENTRAL, CINAHL, C2-SPECTR, ERIC, PreMEDLINE, Cochrane Methodology Register, Current Controlled Trials metaRegister, WHO trials platform, Society for Clinical Trials (SCT) conference proceedings and a survey of all UK clinical trial research units. Review methods Included trials were randomised evaluations of strategies to improve retention embedded within host randomised trials. The primary outcome was retention of trial participants. Data from trials were pooled using the fixed-effect model. Subgroup analyses were used to explore the heterogeneity and to determine whether there were any differences in effect by the type of strategy. Results 38 retention trials were identified. Six broad types of strategies were evaluated. Strategies that increased postal questionnaire responses were: adding, that is, giving a monetary incentive (RR 1.18; 95% CI 1.09 to 1.28) and higher valued incentives (RR 1.12; 95% CI 1.04 to 1.22). Offering a monetary incentive, that is, an incentive given on receipt of a completed questionnaire, also increased electronic questionnaire response (RR 1.25; 95% CI 1.14 to 1.38). The evidence for shorter questionnaires (RR 1.04; 95% CI 1.00 to 1.08) and questionnaires relevant to the disease/condition (RR 1.07; 95% CI 1.01 to 1.14) is less clear. On the basis of the results of single trials, the following strategies appeared effective at increasing questionnaire response: recorded delivery of questionnaires (RR 2.08; 95% CI 1.11 to 3.87); a package of postal communication strategies (RR 1.43; 95% CI 1.22 to 1.67) and an open trial design (RR 1.37; 95% CI 1.16 to 1.63). There is no good evidence that the following strategies impact on trial response/retention: adding a non-monetary incentive (RR=1.00; 95% CI 0.98 to 1.02); offering a non-monetary incentive (RR=0.99; 95% CI 0.95 to 1.03); enhanced letters (RR=1.01; 95% CI 0.97 to 1.05); monetary incentives compared with offering prize draw entry (RR=1.04; 95% CI 0.91 to 1.19); priority postal delivery (RR=1.02; 95% CI 0.95 to 1.09); behavioural motivational strategies (RR=1.08; 95% CI 0.93 to 1.24); additional reminders to participants (RR=1.03; 95% CI 0.99 to 1.06) and questionnaire question order (RR=1.00, 0.97 to 1.02). Also based on single trials, these strategies do not appear effective: a telephone survey compared with a monetary incentive plus questionnaire (RR=1.08; 95% CI 0.94 to 1.24); offering a charity donation (RR=1.02, 95% CI 0.78 to 1.32); sending sites reminders (RR=0.96; 95% CI 0.83 to 1.11); sending questionnaires early (RR=1.10; 95% CI 0.96 to 1.26); longer and clearer questionnaires (RR=1.01, 0.95 to 1.07) and participant case management by trial assistants (RR=1.00; 95% CI 0.97 to 1.04). Conclusions Most of the trials evaluated questionnaire response rather than ways to improve participants return to site for follow-up. Monetary incentives and offers of monetary incentives increase postal and electronic questionnaire response. Some strategies need further evaluation. Application of these results would depend on trial context and follow-up procedures. PMID:24496696

  6. Mining MEDLINE for the treatment of osteoporosis.

    PubMed

    Yildirim, Pinar; Ceken, Cinar; Hassanpour, Reza; Esmelioglu, Sadik; Tolun, Mehmet Resit

    2012-08-01

    In this paper, we consider the importance of osteoporosis disease in terms of medical research and pharmaceutical industry and we introduce a knowledge discovery approach regarding the treatment of osteoporosis from a historical perspective. Osteoporosis is a systemic skeletal disease in which osteoporotic fractures are associated with substantial morbidity and mortality and impaired quality of life. Osteoporosis has also higher costs, for example, longer hospital stays than many other diseases such as diabetes and heart attack and it is an attractive market for pharmaceutical companies. We use a freely available biomedical search engine leveraging text-mining technology to extract the drug names used in the treatment of osteoporosis from MEDLINE articles. We conclude that alendronate (Fosamax) and raloxifene (Evista) have the highest number of articles in MEDLINE and seem the dominating drugs for the treatment of osteoporosis in the last decade. PMID:21494854

  7. 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

  8. 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

  9. MedlinePlus FAQ: Disease or Condition Information

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  10. Subscribe to NIH MedlinePlus the Magazine

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  11. 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. Impacts on knowledge production and clinical guidance were easier to identify and substantiate than those on clinical practice. Questions remain about how we define and measure impact, and more work is needed to develop suitable methods for impact analysis. PMID:25348511

  12. Systematic Reviews Published in the July 2015 Issue of the Cochrane Library.

    PubMed

    Wiffen, Philip J

    2015-12-01

    The Cochrane Library of Systematic Reviews is published quarterly as a DVD and monthly online ( http://www.thecochranelibrary.com ). The July 2015 issue (third DVD for 2015) contains 6506 complete reviews, 2431 protocols for reviews in production, and 36,600 short summaries of systematic reviews published in the general medical literature. In addition, there are citations of 871,000 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 seven new reviews have been published in the previous 3 months, of which seven 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:26654419

  13. Antenatal interventions to reduce preterm birth: an overview of Cochrane systematic reviews

    PubMed Central

    2014-01-01

    Background Several factors are associated with an increased risk of preterm birth (PTB); therefore, various interventions might have the potential to influence it. Due to the large number of interventions that address PTB, the objective of this overview is to summarise evidence from Cochrane reviews regarding the effects and safety of these different interventions. Methods We conducted a systematic literature search in the Cochrane Database of Systematic Reviews. Included reviews should be based on randomised controlled trials comparing antenatal non-pharmacological and pharmacological interventions that directly or indirectly address PTB with placebo/no treatment or routine care in pregnant women at less than 37 completed weeks of gestation without signs of threatened preterm labour. We considered PTB at less than 37 completed weeks of gestation as the primary outcome. Results We included 56 Cochrane systematic reviews. Three interventions increased PTB risk significantly. Twelve interventions led to a statistically significant lower incidence of PTBs. However, this reduction was mostly observed in defined at-risk subgroups of pregnant women. The remaining antenatal interventions failed to prove a significant effect on PTB?Cochrane reviews which intended to report on PTB?Cochrane systematic reviews. Few interventions have been demonstrated to be effective and a small number have been found to be harmful. For around half of the interventions evaluated, the Cochrane review concluded that there was insufficient evidence to provide sound recommendations for clinical practice. No RCT evidence is available for a number of potentially relevant interventions. PMID:24758148

  14. 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

  15. Automatic Summarization of Mouse Gene Information by Clustering and Sentence Extraction from MEDLINE Abstracts

    PubMed Central

    Yang, Jianji; Cohen, Aaron M.; Hersh, William

    2007-01-01

    Tools to automatically summarize gene information from the literature have the potential to help genomics researchers better interpret gene expression data and investigate biological pathways. The task of finding information on sets of genes is common for genomic researchers, and PubMed is still the first choice because the most recent and original information can only be found in the unstructured, free text biomedical literature. However, finding information on a set of genes by manually searching and scanning the literature is a time-consuming and daunting task for scientists. We built and evaluated a query-based automatic summarizer of information on mouse genes studied in microarray experiments. The system clusters a set of genes by MeSH, GO and free text features and presents summaries for each gene by ranked sentences extracted from MEDLINE abstracts. Evaluation showed that the system seems to provide meaningful clusters and informative sentences are ranked higher by the algorithm. PMID:18693953

  16. 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

  17. Txt2MEDLINE: Text-Messaging Access to MEDLINE/PubMed

    PubMed Central

    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 77.57.9%. 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

  18. 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…

  19. 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

  20. 78 FR 62678 - Morris W. Cochran, M.D.; Decision and Order

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-22

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF JUSTICE Drug Enforcement Administration Morris W. Cochran, M.D.; Decision and Order On July 9, 2013, Administrative Law Judge Gail A. Randall (hereinafter, ALJ) issued the attached Recommended Decision. Therein, the ALJ found that there was no dispute over...

  1. 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…

  2. Benchmarking the dental implant evidence on MEDLINE.

    PubMed

    Russo, S P; Fiorellini, J P; Weber, H P; Niederman, R

    2000-01-01

    The purpose of this study was to estimate the quantity of dental implant literature available on MEDLINE for evidence-based clinical decision-making and to identify its location. A search strategy based on Medical Subject Headings for dental implants was developed to examine MEDLINE using the Ovid Web Gateway search engine. Sensitive and specific methodologic search filters identified 4 categories of information: etiology, diagnosis, therapy, and prognosis. The results were then subdivided by year to identify trends and sorted to identify the sources of publications. The searches identified 4,655 articles published in English between 1989 and 1999 on human dental implants on MEDLINE. The mean number of articles (+/- SD) per year ranged from 15 +/- 11 for specific searches to 107 +/- 50 for sensitive searches. The number of articles increased by 14% to 43% each year for the sensitive search. When subdivided by clinical category, the mean numbers of articles per year for sensitive and specific searches were, respectively: diagnosis 12 +/- 7.5 and 1.5 +/- 1.6, etiology 58 +/- 33 and 1.9 +/- 2.5, therapy 23 +/- 15 and 0.3 +/- 0.5, and prognosis 67 +/- 33 and 12 +/- 8.3. Four dental journals account for approximately half of these publications. These results provide 6 key central findings: (1) there appears to be a substantial literature of clinically relevant information on implants upon which to base clinical decisions; (2) the implant literature is significantly biased toward articles addressing prognosis; (3) to stay current, one would need to read between 1 and 2 articles per week 52 weeks per year, and this number increases significantly each year; (4) approximately 50% of the articles were published in 4 journals, whereas the remainder reside in approximately 97 other journals, making it difficult to stay current; (5) these trends reaffirm the need for lifelong learning; (6) these trends also suggest the need for computer-based clinical knowledge systems. PMID:11151577

  3. Summarizing drug information in Medline citations.

    PubMed

    Fiszman, Marcelo; Rindflesch, Thomas C; Kilicoglu, Halil

    2006-01-01

    Adverse drug events and drug-drug interactions are a major concern in patient care. Although databases exist to provide information about drugs, they are not always up-to-date and complete (particularly regarding pharmacogenetics). We propose a methodology based on automatic summarization to identify drug information in Medline citations and present results to the user in a convenient form. We evaluate the method on a selection of citations discussing ten drugs ranging from the proton pump inhibitor lansoprazole to the vasoconstrictor sumatriptan. We suggest that automatic summarization can provide a valuable adjunct to curated drug databases in supporting quality patient care. PMID:17238342

  4. Books for free? How can this be? - A PubMed resource you may be overlooking.

    PubMed

    Corsi, Ann K

    2006-07-01

    The NCBI (National Center for Biotechnology Information) at the National Institutes of Health collects a wide range of molecular biological data, and develops tools and databases to analyse and disseminate this information. Many life scientists are familiar with the website maintained by the NCBI (http://www.ncbi.nlm.nih.gov), because they use it to search GenBank for homologues of their genes of interest or to search the PubMed database for scientific literature of interest. There is also a database called the Bookshelf that includes searchable popular life science textbooks, medical and research reference books and NCBI reference materials. The Bookshelf can be useful for researchers and educators to find basic biological information. This article includes a representative list of the resources currently available on the Bookshelf, as well as instructions on how to access the information in these resources. PMID:16776646

  5. Developing Topic-Specific Search Filters for PubMed with Click-Through Data

    PubMed Central

    Li, Jiao; Lu, Zhiyong

    2013-01-01

    Summary Objectives Search filters have been developed and demonstrated for better information access to the immense and ever-growing body of publications in the biomedical domain. However, to date the number of filters remains quite limited because the current filter development methods require significant human efforts in manual document review and filter term selection. In this regard, we aim to investigate automatic methods for generating search filters. Methods We present an automated method to develop topic-specific filters on the basis of users search logs in PubMed. Specifically, for a given topic, we first detect its relevant user queries and then include their corresponding clicked articles to serve as the topic-relevant document set accordingly. Next, we statistically identify informative terms that best represent the topic-relevant document set using a background set composed of topic irrelevant articles. Lastly, the selected representative terms are combined with Boolean operators and evaluated on benchmark datasets to derive the final filter with the best performance. Results We applied our method to develop filters for four clinical topics: nephrology, diabetes, pregnancy, and depression. For the nephrology filter, our method obtained performance comparable to the state of the art (sensitivity of 91.3%, specificity of 98.7%, precision of 94.6%, and accuracy of 97.2%). Similarly, high-performing results (over 90% in all measures) were obtained for the other three search filters. Conclusion Based on PubMed click-through data, we successfully developed a high-performance method for generating topic-specific search filters that is significantly more efficient than existing manual methods. All data sets (topic-relevant and irrelevant document sets) used in this study and a demonstration system are publicly available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/downloads/CQ_filter/ PMID:23666447

  6. 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

  7. Identifying Clinical Study Types from PubMed Metadata: The Active (Machine) Learning Approach.

    PubMed

    Dunn, Adam G; Arachi, Diana; Bourgeois, Florence T

    2015-01-01

    We examined a process for automating the classification of articles in MEDLINE aimed at minimising manual effort without sacrificing accuracy. From 22,808 articles pertaining to 19 antidepressants, 1000 were randomly selected and manually labelled according to article type (including, randomised controlled trials, editorials, etc.). We applied a machine learning approach termed 'active learning', where the learner (machine) selects the order in which the user (human) labels examples. Via simulation, we determined the number of articles a user needed to label to produce a classifier with at least 95% recall and 90% precision in three scenarios related to evidence synthesis. We found that the active learning process reduced the number of training instances required by 70%, 19%, and 14% in the three scenarios. The results show that the active learning method may be used in some scenarios to produce accurate classifiers that meet the needs of evidence synthesis tasks and reduce manual effort. PMID:26262175

  8. 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 PubMedMiners 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

  9. PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm

    PubMed Central

    Plikus, Maksim V; Zhang, Zina; Chuong, Cheng-Ming

    2006-01-01

    Background Understanding research activity within any given biomedical field is important. Search outputs generated by MEDLINE/PubMed are not well classified and require lengthy manual citation analysis. Automation of citation analytics can be very useful and timesaving for both novices and experts. Results PubFocus web server automates analysis of MEDLINE/PubMed search queries by enriching them with two widely used human factor-based bibliometric indicators of publication quality: journal impact factor and volume of forward references. In addition to providing basic volumetric statistics, PubFocus also prioritizes citations and evaluates authors' impact on the field of search. PubFocus also analyses presence and occurrence of biomedical key terms within citations by utilizing controlled vocabularies. Conclusion We have developed citations' prioritisation algorithm based on journal impact factor, forward referencing volume, referencing dynamics, and author's contribution level. It can be applied either to the primary set of PubMed search results or to the subsets of these results identified through key terms from controlled biomedical vocabularies and ontologies. NCI (National Cancer Institute) thesaurus and MGD (Mouse Genome Database) mammalian gene orthology have been implemented for key terms analytics. PubFocus provides a scalable platform for the integration of multiple available ontology databases. PubFocus analytics can be adapted for input sources of biomedical citations other than PubMed. PMID:17014720

  10. 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

  11. Psychosocial interventions for men with prostate cancer: a Cochrane systematic review.

    PubMed

    Parahoo, Kader; McDonough, Suzanne; McCaughan, Eilis; Noyes, Jane; Semple, Cherith; Halstead, Elizabeth J; Neuberger, Molly M; Dahm, Philipp

    2015-08-01

    To evaluate the effectiveness of psychosocial interventions for men with prostate cancer in improving quality of life (QoL), self-efficacy and knowledge and in reducing distress, uncertainty and depression. We searched for trials using a range of electronic databases including the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE and PsycINFO to October 2013, together with hand searching of journals and reference lists. Randomised controlled trials were eligible if they included psychosocial interventions that explicitly used one or a combination of the following approaches: cognitive behavioural, psycho-educational, supportive and counselling. Interventions had to be delivered or facilitated by trained or lay personnel. Our outcomes were an improvement in QoL, self-efficacy and knowledge and a reduction in distress, uncertainty and depression. Pairs of review authors independently extracted data and assessed risk of bias. We analysed data using standardised mean differences (SMDs), random-effects models and 95% confidence intervals (CIs). In all, 19 studies with a total of 3204 men, with a diagnosis of prostate cancer, comparing psychosocial interventions vs usual care were included in this review. Men in the psychosocial intervention group had a small, statistically significant improvement in the physical component of general health-related QoL (GHQoL) at end of intervention (SMD 0.12, 95% CI 0.01-0.22) based on low quality evidence. There was no clear evidence of benefit associated with psychosocial interventions for the mental component of GHQoL at end of intervention (SMD -0.04, 95% CI -0.15 to 0.06) based on moderate quality evidence. At end of intervention, cancer-related QoL showed a small improvement after psychosocial interventions (SMD 0.21, 95% CI 0.04-0.39). For prostate cancer-specific and symptom-related QoL, the differences between intervention and control groups were not significant. There was no clear evidence that psychosocial interventions were beneficial in improving self-efficacy at end of intervention (SMD 0.16, 95% CI -0.05 to 0.38) based on very low quality evidence. Men in the psychosocial intervention group had a moderate increase in prostate cancer knowledge at end of intervention (SMD 0.51, 95% CI 0.32-0.71) based on very low quality evidence. A small increase in knowledge with psychosocial interventions was noted at 3months after intervention (SMD 0.31, 95% CI 0.04-0.58). The results for uncertainty (SMD -0.05, 95% CI -0.35 to 0.26) and distress (SMD 0.02, 95% CI -0.11 to 0.15) at end of intervention were compatible with both benefit and harm based on very low quality evidence. Finally, there was no clear evidence of benefit associated with psychosocial interventions for depression at end of intervention (SMD -0.18, 95% CI -0.51 to 0.15) based on very low quality evidence. The overall risk of bias in the included studies was unclear or high, primarily as the result of performance bias. No data about stage of disease or treatment with androgen-deprivation therapy were extractable for subgroup analysis. Only one study addressed adverse effects. Overall, this review shows that psychosocial interventions may have small, short-term beneficial effects on certain domains of wellbeing, as measured by the physical component of GHQoL and cancer-related QoL when compared with usual care. Prostate cancer knowledge was also increased. However, this review failed to show a statistically significant effect on other domains such as symptom-related QoL, self-efficacy, uncertainty, distress or depression. Moreover, when beneficial effects were seen, it remained uncertain whether the magnitude of effect was large enough to be considered clinically important. The quality of evidence for most outcomes was rated as very low according to the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) system, reflecting study limitations, loss to follow-up, study heterogeneity and small sample sizes. We were unable to perform meaningful subgroup analyses based on disease s

  12. 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

  13. 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

    ... Energy Regulatory Commission Mr. Jesse S. Capel and Mr. Hilton J. Cochran; EWP LLC; Notice of Transfer of... and Mr. Hilton J. Cochran and EWP LLC informed the Commission that its exemption from licensing for... Exemption to Project 4815, filed July 30, 2012 and supplemented on August 14, 2012. 2. EWP LLC, Mr. J....

  14. 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

  15. 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 systematic reviews incorporating C-RCTs. PMID:26982697

  16. How relevant is the Cochrane Database of Systematic Reviews to nursing care?

    PubMed

    Geurden, Bart J G; Stern, Cindy; Piron, Ccile; Gobert, Micheline

    2012-12-01

    Barriers obstructing evidence-based nursing have been explored in many countries. Lack of resources and evidence has been noted as one of these barriers. We aimed to identify nursing care-related systematic reviews published in the Cochrane Database of Systematic Reviews from 1996 until 2009. Using a broad search strategy we identified titles of Cochrane systematic reviews and protocols that focused on nursing care. The abstract of each title was examined and predetermined data were collected and analysed. 1249 titles out of a possible 6244 records were identified as being relevant to nursing care. Most of them focused on newborn and adult populations and related to comparing one intervention with another, and management strategies. The most common nursing specialties represented were internal medicine (34%) and mother and child care (25%). Twenty one percent of reviews published in the Cochrane Database of Systematic Reviews are of direct interest to those involved in nursing care however their relevance was not always obvious. PMID:23181952

  17. 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

  18. Stochastic Gradient Descent and the Prediction of MeSH for PubMed Records.

    PubMed

    Wilbur, W John; Kim, Won

    2014-01-01

    Stochastic Gradient Descent (SGD) has gained popularity for solving large scale supervised machine learning problems. It provides a rapid method for minimizing a number of loss functions and is applicable to Support Vector Machine (SVM) and Logistic optimizations. However SGD does not provide a convenient stopping criterion. Generally an optimal number of iterations over the data may be determined using held out data. Here we compare stopping predictions based on held out data with simply stopping at a fixed number of iterations and show that the latter works as well as the former for a number of commonly studied text classification problems. In particular fixed stopping works well for MeSH() predictions on PubMed() records. We also surveyed the published algorithms for SVM learning on large data sets, and chose three for comparison: PROBE, SVMperf, and Liblinear and compared them with SGD with a fixed number of iterations. We find SGD with a fixed number of iterations performs as well as these alternative methods and is much faster to compute. As an application we made SGD-SVM predictions for all MeSH terms and used the Pool Adjacent Violators (PAV) algorithm to convert these predictions to probabilities. Such probabilistic predictions lead to ranked MeSH term predictions superior to previously published results on two test sets. PMID:25954431

  19. Enhancing search efficiency by means of a search filter for finding all studies on animal experimentation in PubMed

    PubMed Central

    Hooijmans, Carlijn R; Tillema, Alice; Leenaars, Marlies; Ritskes-Hoitinga, Merel

    2010-01-01

    Collecting and analysing all available literature before starting an animal experiment is important and it is indispensable when writing a systematic review (SR) of animal research. Writing such review prevents unnecessary duplication of animal studies and thus unnecessary animal use (Reduction). One of the factors currently impeding the production of high-quality SRs in laboratory animal science is the fact that searching for all available literature concerning animal experimentation is rather difficult. In order to diminish these difficulties, we developed a search filter for PubMed to detect all publications concerning animal studies. This filter was compared with the method most frequently used, the PubMed Limit: Animals, and validated further by performing two PubMed topic searches. Our filter performs much better than the PubMed limit: it retrieves, on average, 7% more records. Other important advantages of our filter are that it also finds the most recent records and that it is easy to use. All in all, by using our search filter in PubMed, all available literature concerning animal studies on a specific topic can easily be found and assessed, which will help in increasing the scientific quality and thereby the ethical validity of animal experiments. PMID:20551243

  20. Benchmarking the clinical orthodontic evidence on Medline.

    PubMed

    Sun, R L; Conway, S; Zawaideh, S; Niederman, D R

    2000-12-01

    The purpose of this study was to identify and quantify the availability of orthodontic literature for evidence-based clinical decision-making (ie, sound clinical studies of etiology, diagnosis, treatment, or prognosis meeting basic methodologic criteria for direct clinical use). This is a first step toward developing online decision analysis systems. A search strategy based on Medical Subject Headings (MeSH) for orthodontics was developed to examine MEDLINE using the Ovid Web Gateway search engine. Sensitive and specific methodologic search filters were then employed to identify the 4 categories of information. The results were then subdivided by year to identify trends and sorted to identify source of publications. In the period 1990 to 1998, the MEDLINE searches identified 6938 English-language articles about orthodontics. The mean number of articles (+/-SD) per year ranged from 42+/-25 for specific searches to 314+/-214 for sensitive searches. The number of articles identified by the specific or sensitive searches increased 14% to 21% annually. When subdivided by clinical category, the mean numbers of articles per year for specific and sensitive searches were respectively: etiology 19+/-15 and 91+/-37, diagnosis 11+/-5 and 80+/-35, therapy 3+/-1 and 50+/-23, and prognosis 10+/-7 and 93+/-33. Five dental journals accounted for nearly half of these publications. These results provide several key findings: (1) there is a substantial literature of clinically relevant information in orthodontics upon which to base clinical decisions; (2) the information appears to be balanced between etiology, diagnosis, treatment, and prognosis; (3) approximately 45% of the articles reside in 5 journals, whereas the remainder reside in approximately 66 other journals, making it difficult to stay current; (4) the number of articles is increasing significantly each year; (5) to stay current, one would need to read between 1 and 6 articles per week, 52 weeks per year; (6) these trends suggest the need for computer-based clinical knowledge systems; and (7) the methods used here can be immediately employed to identify the best and most current clinical orthodontic evidence. PMID:11138650

  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. Celebrating 20 years of evidence from the Cochrane Collaboration: what has been the impact of systematic reviews on nephrology?

    PubMed

    Palmer, Suetonia C; Craig, Jonathan C; Jones, Ann; Higgins, Gail; Willis, Narelle; Strippoli, Giovanni F M

    2015-06-01

    It has been 20 years since the Cochrane Collaboration started the global effort to synthesize evidence to improve healthcare. Since 1997, the Cochrane Renal Group has produced over 100 systematic reviews that have collectively had an important impact on nephrology care, guidelines and policy. In this article, we reflect on the ongoing need for randomized trials and systematic reviews in contemporary nephrology and the achievements of the Cochrane Collaboration so far. We also describe some of the challenges in clinical research still faced by the nephrology community today. PMID:25016606

  3. Progressing towards standard outcomes in gestational diabetes Cochrane reviews and randomised trials.

    PubMed

    Bain, Emily; Middleton, Philippa; Crowther, Caroline A

    2016-02-01

    Outcomes in gestational diabetes Cochrane protocols and reviews before and after development of 'standard outcomes' by WOMBAT (WOMen and Babies health and well-being: Action through Trials) were surveyed. An increase in 'common' outcomes (those prespecified by ?50% of the protocols and reviews) over time was observed (2001-2009: 27 vs 2010-2014: 46). There were discrepancies in outcomes prespecified in reviews and reported by randomised trials. Efforts are needed to develop a core outcome set, to reduce research waste and improve health outcomes. PMID:26757351

  4. 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 performed, but fail to provide good evidence for clinical practice because the primary studies are few in number, small, clinically heterogeneous, and of poor quality and external validity. They are useful in highlighting the weakness of the evidence base and problems in performing trials in palliative care. PMID:18715496

  5. 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

  6. [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 asdifferent 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 realityand 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

  7. [Analysis of the Cochrane Review: Vitamin D supplementation for prevention of cancer in adults. Cochrane Database Syst Rev. 2014, 6:CD007469].

    PubMed

    Cardoso, Andr Torres; Nanji, Liliana; Costa, Joo; Vaz-Carneiro, Antnio

    2014-01-01

    Vitamin D has been mentioned in the literature has a potentially important agent for preventing the development of tumors, namely breast, colon, prostate and ovary tumors. However, the currently available evidence on the subject is contradictory and inconclusive. In this Cochrane systematic review, patients taking supplemental vitamin D on its various forms (cholecalciferol, ergocalciferol, alfacalcidol or calcitriol), regardless the dose, duration and route of administration, were compared with placebo, healthy adults without any intervention or adults with a disease in a stable phase, non-related with vitamin D metabolism. The results showed that currently, there is no firm evidence that vitamin D supplementation increases or decreases the risk of cancer occurrence, mainly in elderly community-dwelling women. Though at risk of type I errors due to small samples and substantial dropout of participants during the trials, the administration of supplemental cholecalciferol led to a 12% (CI 95%: 2 a 22%) decreased in cancer mortality, while the administration of supplemental vitamin D decreased all-cause mortality by 7% (CI 95%: 2 a 12%). The combined administration of supplements of cholecalciferol and calcium induced an increased incidence of nephrolithiasis. PMID:25203945

  8. Evaluating the impact of MEDLINE using the Critical Incident Technique.

    PubMed

    Siegel, E R; Rapp, B A; Lindberg, D A

    1991-01-01

    An adaptation of the Critical Incident Technique for the evaluation of an online information system is described. 552 users of the National Library of Medicine's MEDLINE database, interviewed by telephone and responding to a highly structured set of open-ended questions, reported 1,158 incidents in which the results of a MEDLINE search was especially helpful (or not helpful) in carrying out professional activities. Systematic analysis of these "critical incidents" produced three comprehensive and detailed views of the purposes and outcomes of MEDLINE searches: (1) why information is sought from MEDLINE; (2) the impact of MEDLINE-derived information on medical decision-making; and (3) the ultimate outcome of having (or not having) the desired information on medical situations prompting a MEDLINE search. Results revealed that MEDLINE is used to satisfy a diversity of medical needs concerning patient care, the progress of biomedical research, the quality of education received by health professionals in training, the safety and effectiveness of health care institutions, the operation of the system of third-party reimbursement, for legal decisions, and for the knowledge of the public. PMID:1807723

  9. Do trialists endorse clinical trial registration? Survey of a Pubmed sample

    PubMed Central

    Reveiz, Ludovic; Krleža-Jerić, Karmela; Chan, An-Wen; De Aguiar, Sylvia

    2007-01-01

    Introduction Despite intense interest in trial registration, there is a wide gap between theoretical postulates on trial registration and its implementation worldwide. Objective We aimed to evaluate trialists views about current international guidelines on trial registration, including the World Health Organization's (WHO) International Clinical Trials Registry Platform (ICTRP) policies and the Ottawa Statement, as well as their intention to register any future clinical trials they conduct. Methods We identified all 40,158 PUBMED-indexed clinical trials published from May 2005 to May 2006 using an advanced search strategy. From a random sample of 500 confirmed clinical trials, corresponding authors with e-mail contact addresses were surveyed. Results A total of 275 (60%) questionnaires from 45 countries were completed. 31% of the respondents had received only nonindustry funding during the past ten years, while 5% and 61% had received only industry or mixed funding respectively. Approximately two third of participants supported registration of all 20 WHO Data Set items, and endorsed the Ottawa Statement part 1 and part 2. Delayed public disclosure of some essential data in instances where they may be considered sensitive for competitive commercial reasons was supported by 30% of the participants, whereas immediate disclosure was supported by 53%. Only 21% of participants had registered all of their ongoing trials since 2005, while 47% stated that they would provide the 20 WHO Data Set items to a publicly accessible register for all their future clinical trials; a significantly higher proportion of participants who received only nonindustry funding (62%) was found among those who would always provide the 20 WHO items for future trials, compared to 42% of participants who received mixed or only industry funding. Among those who were undecided about endorsing registration. One third of participants expressed a lack of sufficient knowledge as the primary reason. Conclusion Although disagreement was apparent on certain issues, our findings illustrate that trial registration is gradually becoming part of the current research paradigm internationally. Our results also suggest that researchers require more knowledge to inform their decision to comply with the International standards at this early stage of voluntary trial registration. PMID:17956618

  10. 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…

  11. 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

  12. 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

  13. Intervention for replacing missing teeth: Different types of implants - evidence summary of updated Cochrane review.

    PubMed

    Singh, Balendra Pratap; Jivanani, Hemant

    2015-01-01

    Around 1300 different types of dental implants are available worldwide and the implant manufacturers are resorting to aggressive marketing strategies; claiming their implants to provide a superior outcome. The clinician is left with a constant dilemma on which implant to choose for better clinical outcome and welfare of the patient. Moreover, in India, economical consideration is a concern too. The dentist has to select an implant that provides a good result and is economical. Cochrane systematic reviews provide the gold standard evidence for intervention, diagnosis, etc., and follow a strict quality control. A Cochrane systematic review was done to shed light on whether the different implant surface modifications, shapes or materials significantly influence clinical outcomes. All randomized controlled trials (RCTs) till January 17, 2014 were searched and out of the 81 trials, only 27 met the inclusion criteria. This evidence summary from the review concludes that based on the available literature; there is no evidence of any one type of implant being superior to another. There is weak evidence showing roughened dental implants are more prone to bone loss due to periimplantitis. This review indicated that there is a need for well-designed RCTs, with long-term follow-up and low bias. Moreover, none of the included studies was from India, which also points out the need for improving the quality of RCTs conducted in India. PMID:26929524

  14. Evidence-based clinical practice, [corrected] evidence-based medicine and the Cochrane collaboration.

    PubMed

    Gambrill, E

    1999-03-01

    Encouraging professionals in training and later to consider practice-related research findings when making important clinical decisions is an on-going concern. Evidenced-Based Medicine (EBM) and the Cochrane Collaboration (CC) provide a source of tools and ideas for doing so, as well as a roster of colleagues who share this interest. Evidenced-based medicine involves integrating clinical expertise with the best available external evidence from systematic research as well as considering the values and expectations of patients/clients. Advantage can be taken of educational formats developed in EBM, such as problem-based learning and critical-appraisal workshops in which participants learn how to ask key answerable questions related to important clinical practice questions (e.g., regarding effectiveness, accuracy of assessment measures, prediction, prevention, and quality of clinical practice guidelines) and to access and critically appraise related research. The Cochrane Collaboration is a world-wide network of centers that prepare, maintain, and disseminate high-quality systematic reviews on the efficacy of healthcare. These databases allow access to evidence related to clinical practice decisions. Forging reciprocal working relationships with those involved in EBM reciprocal and the CC should contribute to the pursuit of shared goals such as basing clinical decisions on the best-available evidence and involving clients as informed consumers. PMID:10365860

  15. To Your Health: NLM update—MedlinePlus

    MedlinePLUS

    ... page, please enable JavaScript. NLM presents a weekly audio update that highlights consumer health news and accompanying information from MedlinePlus. Title Date Audio Text Version Dementia rates decline March 28 2016 ...

  16. Rethinking Drinking | NIH MedlinePlus the Magazine

    MedlinePLUS

    ... gov ) and publication from the National Institute on Alcohol Abuse and Alcoholism (NIAAA). It is designed to help ... More MedlinePlus www.medlineplus.gov National Institute on Alcohol Abuse and Alcoholism (NIAAA) www.niaaa.nih.gov Alcoholics ...

  17. Get Updated on your health with MedlinePlus

    MedlinePLUS

    ... Current Issue Past Issues Get Updated on your health with MedlinePlus Past Issues / Summer 2007 Table of ... on. A free, comprehensive, authoritative, up-to-date health information Website from the world's largest medical library, ...

  18. Treating Cataracts | NIH MedlinePlus the Magazine

    MedlinePLUS

    ... her experience recently with NIH MedlinePlus magazine. What did you notice about your vision that told you ... how long it would take to recover. Where did you go for information about cataracts and surgery? ...

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

    MedlinePLUS

    ... Issue Past Issues Down the Block... Around the World...MedlinePlus.gov Past Issues / Spring 2008 Table of ... on. No matter where you are in the world, www.medlineplus.gov is your best global source ...

  20. NIH MedlinePlus the Magazine: Health, Medical & Wellness Articles

    MedlinePLUS

    ... all, we hope that you take out a free subscription. NIH MedlinePlus is produced by NIH, the ... the National Library of Medicine. Subscriptions are available free of charge. With the best of good health ...

  1. Mary Tyler Moore Helps Launch NIH MedlinePlus Magazine

    MedlinePLUS

    ... R-OH), Mary Tyler Moore, former Rep. Paul Rogers, and NLM Director Dr. Donald Lindberg. Photo courtesy ... free subscription to NIH MedlinePlus . Sincerely, Paul G. Rogers Chairman Friends of the National Library of Medicine ...

  2. 2011 Awards Gala | NIH MedlinePlus the Magazine

    MedlinePLUS

    ... 20814. The FNLM is classified as a 501(c)(3) nonprofit organization for federal tax purposes. Web site: www.fnlm.org Mobile MedlinePlus! On the go! Find trusted health information from the experts at ...

  3. Welcome to NIH MedlinePlus, the magazine

    MedlinePLUS

    ... world's largest medical library, NIH's National Library of Medicine. MedlinePlus has extensive information from the NIH and other trusted sources on more than 700 diseases and conditions. There ...

  4. What's New on MedlinePlus: Announcements and Special Features

    MedlinePLUS

    ... www.nlm.nih.gov/medlineplus/whatsnew.html What's New: Announcements and Special Features To use the sharing ... New England Journal of Medicine. March 23, 2016 New Topic Page: Chikungunya Visit the new MedlinePlus Health ...

  5. Proces przygotowywania przegl?dw systematycznych, z uwzgl?dnieniem przegl?dw Cochrane.

    PubMed

    Ba?a, Ma?gorzata M; Le?niak, Wiktoria; Jaeschke, Roman

    2015-12-22

    Przegl?d systematyczny jest istotny z punktu widzenia zarwno badacza, jak i klinicysty czy osb odpowiedzialnychza podejmowanie decyzji w ochronie zdrowia, poniewa? przedstawia bardziej wiarygodn? informacj? na dany temat ni? pojedyncze badania kliniczne, ktrych wyniki mog? si? mi?dzy sob? znacznie r?ni? lub by? wr?cz sprzeczne. Taki przegl?d pozwala podsumowa? dost?pne informacje o danym problemie klinicznym. Przegl?dy systematyczne s? wykorzystywane przez lekarzy na ca?ym ?wiecie w codziennej praktyce klinicznej. S? wa?nym elementem procesu tworzenia wytycznych praktyki klinicznej oraz podstaw? analiz ekonomicznych technologii medycznych. Przygotowanie przegl?du systematycznego jest procesem wieloetapowym, wymagaj?cym zastosowania okre?lonych metod i starannego udokumentowania wraz z rozwa?nym zastosowaniem wiedzy i oceny klinicznej. W artykule opisano elementy procesu przygotowania przegl?du systematycznego z uwzgl?dnieniem kolejnych krokw, jakie nale?y podj?? tak?e w przypadku przegl?du systematycznego Cochrane. PMID:26794237

  6. 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

  7. Celebrating methodological challenges and changes: reflecting on the emergence and importance of the role of qualitative evidence in Cochrane reviews

    PubMed Central

    2013-01-01

    Cochrane systematic reviews have proven to be beneficial for decision making processes, both on a practitioner and a policy level, and there are current initiatives to extend the types of evidence used by them, including qualitative research. In this article we outline the major achievements of the Cochrane Qualitative and Implementation Methods Group. Although the Group has encountered numerous challenges in dealing with the evolution of qualitative evidence synthesis, both outside and within the Cochrane Collaboration, it has successfully responded to the challenges posed in terms of incorporating qualitative evidence in systematic reviews. The Methods Group will continue to advocate for more flexible and inclusive approaches to evidence synthesis in order to meet the exciting challenges and opportunities presented by mixed methods systematic reviews and reviews of complex interventions. PMID:24135194

  8. 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

  9. 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

  10. Pharmacy journal abstracts published in PubMed that abide by the CONsolidated Standards Of Reporting Trials (CONSORT) guidelines

    PubMed Central

    Blair, Daniel A.; Woolley, Thomas W.

    2014-01-01

    The purpose of this research was to determine the proportion of abstracts in pharmacy journals that are prepared according to the CONsolidated Standards Of Reporting Trials (CONSORT) criteria for abstracts. Certain abstracts for randomized controlled clinical trials (RCTs) indexed in PubMed were eligible for inclusion, with the primary endpoint being median overall compliance to CONSORT recommendations for abstracts. A total of 63 RCT abstracts were included in the analysis, with only 56% of the recommended CONSORT items represented in the sample. It is recommended that pharmacy journals encourage authors to follow CONSORT recommendations for abstracts when submitting RCTs for publication. PMID:24860268

  11. Interventions for the treatment of trachoma: an overview of Cochrane systematic reviews.

    PubMed

    Lockwood, Craig; Stern, Cindy

    2014-12-01

    Trachoma is an infectious disease caused by the bacterium Chlamydia trachomatis. Infection with C.?trachomatis produces characteristic changes to the inner surface of the eyelids, resulting in sequela that when left untreated, leads to vision impairment and blindness. Repeated trachoma infections can cause severe scarring of the inside of the eyelid and can cause the eyelashes to scratch the cornea (trichiasis). The objective of this overview was to synthesize the evidence from Cochrane systematic reviews regarding the treatment of trachoma, and to provide a brief and user-friendly front end for health professionals, researchers and policy makers. Face washing plus topical tetracycline eye ointment gave no additional protective benefit against active trachoma when compared with topical tetracycline eye ointment alone. Nor was any benefit conferred in the presence of severe trachoma. Primary health-care education was found to be effective in reducing the odds of active trachoma. Evidence of benefit from insecticide spray or provision of latrines away from living areas was inconclusive for active trachoma. Surgical interventions that involve full-thickness incision with tarsal rotation are more effective than alternate surgical procedures. PMID:25532886

  12. 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

  13. Cochrane corner: is integrated disease management for patients with COPD effective?

    PubMed Central

    Kruis, Annemarije L; Smidt, Nynke; Assendelft, Willem J J; Gussekloo, Jacobijn; Boland, Melinde R S; Rutten-van Mlken, Maureen; Chavannes, Niels H

    2014-01-01

    Patients with COPD experience respiratory symptoms, impairments of daily living and recurrent exacerbations. The aim of integrated disease management (IDM) is to establish a programme of different components of care (ie, self-management, exercise, nutrition) in which several healthcare providers (ie, nurses, general practitioners, physiotherapists, pulmonologists) collaborate to provide efficient and good quality of care. The aim of this Cochrane systematic review was to evaluate the effectiveness of IDM on quality of life, exercise tolerance and exacerbation related outcomes. Searches for all available evidence were carried out in various databases. Included randomised controlled trials (RCTs) consisted of interventions with multidisciplinary (?2 healthcare providers) and multitreatment (?2 components) IDM interventions with duration of at least 3?months. Two reviewers independently searched, assessed and extracted data of all RCTs. A total of 26 RCTs were included, involving 2997 patients from 11 different countries with a follow-up varying from 3 to 24?months. In all 68% of the patients were men, with a mean age of 68?years and a mean forced expiratory volume in 1?s (FEV1) predicted value of 44.3%. Patients treated with an IDM programme improved significantly on quality of life scores and reported a clinically relevant improvement of 44?m on 6?min walking distance, compared to controls. Furthermore, the number of patients with ?1 respiratory related hospital admission reduced from 27 to 20 per 100 patients. Duration of hospitalisation decreased significantly by nearly 4?days. PMID:24415716

  14. 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

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

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 27 2013-07-01 2013-07-01 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. NIH Quickfinder | NIH MedlinePlus the Magazine

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  18. Health Information in Italian (italiano): MedlinePlus

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  19. Health Information in Multiple Languages: MedlinePlus

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  20. 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

  1. Distribution of Country of Origin in Studies Used in Cochrane Reviews

    PubMed Central

    Wolff, Robert F.; Reinders, Stefan; Barth, Michael; Antes, Gerd

    2011-01-01

    Background and Objective Inclusion in systematic reviews is one important component in judging the potential impact of clinical studies upon practice and hence the value for money of spending for clinical research. This study aims to quantify the distribution of countries of origin of clinical studies used in Cochrane Reviews (CRs), and to link these data to the size of a country and to its spending on research. Methods Random sample of publications used for CRs published in Issue 1 2008 and of publications used in CRs in the field of complementary and alternative medicine (CAM). Publications without original data were excluded. Likely countries of origin determined based on abstracts/full texts. CIA World Factbook (population data) and OECD database (economic data) were used. Results 1,000 random entries out of 140,005 references available in all specialities. In 876 (91.4%) of 959 eligible studies, country of origin was determined. The USA was the leading contributor (36.0% of the studies), followed by UK (13.4%), Canada (5.3%), Australia and Sweden (3.7%). In the CAM sample, country of origin was determined in 458 (93.5%) of 497 assessed studies. Again, the USA was the leading contributor (24.9%), with China also emerging as a significant contributor (24.7%) in this field. For both samples, the contribution of smaller countries (especially Scandinavian countries, Greece, and Ireland) became more noteworthy when considered in relation to population size and research spending. Conclusions Our results support the leading roles of both the USA and the UK in publishing clinical papers. The emerging role of China can be seen, particularly related to CAM studies. Taking into account size of population and economic power, countries like France, Germany, Italy, and Spain provide small contributions. In contrast, smaller countries like Australia, Denmark, Finland, Ireland, New Zealand, and Sweden also play major roles. PMID:21526195

  2. 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

  3. 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 researchers are starting to use knowledge discovery methods and data mining techniques to understand vast quantities of tweets: the study of Twitter is becoming quantitative research. Conclusions This work is to the best of our knowledge the first overview study of medical related research based on Twitter and related microblogging. We have used 5 dimensions to categorize published medical related research on Twitter. This classification provides a framework within which researchers studying development and use of Twitter within medical related research, and those undertaking comparative studies of research, relating to Twitter in the area of medicine and beyond, can position and ground their work. PMID:25075237

  4. 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; Rcker, 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 1.27, 95% CI 1.05-1.52, five studies, 1845 participants; 2 years: RR 1.14, 95% CI 1.05-1.24, two studies, 808 participants), compared with medical or surgical castration. The quality of evidence for overall survival, clinical progression and treatment failure was rated as moderate according to GRADE. Use of non-steroidal antiandrogens increased the risk for treatment discontinuation as a result of adverse events (RR 1.82, 95% CI 1.13-2.94, eight studies, 1559 participants), including events such as breast pain (RR 22.97, 95% CI 14.79- 35.67, eight studies, 2670 participants) and gynaecomastia (RR 8.43, 95% CI 3.19-22.28, nine studies, 2774 participants) The risk of other adverse events, such as hot flushes (RR 0.23, 95% CI 0.19-0.27, nine studies, 2774 participants) was decreased when non-steroidal antiandrogens were used. The quality of evidence for breast pain, gynaecomastia and hot flushes was rated as moderate according to GRADE. The effects of non-steroidal antiandrogens on cancer-specific survival and biochemical progression remained unclear. Non-steroidal antiandrogen monotherapy compared with medical or surgical castration monotherapy for advanced prostate cancer is less effective in terms of overall survival, clinical progression, treatment failure and treatment discontinuation resulting from adverse events. Evidence quality was rated as moderate according to GRADE; therefore, further research is likely to have an important impact on results for patients with advanced but non-metastatic prostate cancer treated with non-steroidal antiandrogen monotherapy. PMID:25523493

  5. The Use of Transarterial Chemoembolization in the Treatment of Unresectable Hepatocellular Carcinoma: A Response to the Cochrane Collaboration Review of 2011

    PubMed Central

    Ray, Charles E.; Haskal, Ziv J; Geschwind, Jean-Francois H.; Funaki, Brian S.

    2015-01-01

    This commentary is written in response to a recent Cochrane Collaboration review published in March 2011 (1). The authors of this commentary would like to express their concerns over the conclusions of the Cochrane review, which state, There is no firm evidence to support or refute transarterial chemoembolization (TACE) or transarterial embolization (TAE) for patients with unresectable hepatocellular carcinoma (HCC). PMID:22035882

  6. The use of transarterial chemoembolization in the treatment of unresectable hepatocellular carcinoma: a response to the Cochrane Collaboration review of 2011.

    PubMed

    Ray, Charles E; Haskal, Ziv J; Geschwind, Jean-Francois H; Funaki, Brian S

    2011-12-01

    This commentary is written in response to a recent Cochrane Collaboration review published in March 2011 (1). The authors of this commentary would like to express their concerns over the conclusions of the Cochrane review, which state, "There is no firm evidence to support or refute transarterial chemoembolization (TACE) or transarterial embolization (TAE) for patients with unresectable hepatocellular carcinoma (HCC)." PMID:22035882

  7. To Your Health: NLM update transcript - NIH MedlinePlus Magazine Fall 2015

    MedlinePLUS

    ... edition of NIH MedlinePlus magazine covers precision medicine, delirium in hospitals, as well as migraines. The cover ... magazine highlights the symptoms, causes, and prevention of delirium in hospitals. NIH MedlinePlus magazine explains more than ...

  8. Finding Answers in a Beauty Shop | NIH MedlinePlus the Magazine

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    ... customers the MedlinePlus website. Dexter Waiters uses the computer at MaFlo's to access the MedlinePlus consumer health ... A waiting area offers several comfortable chairs, three computers, and a printer. On a typical day, the ...

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

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    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 You Are Here: ...

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

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  11. MedlinePlus® Everywhere: Access from Your Phone, Tablet or Desktop

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  12. 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, Jos Maria Jimnez; 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

  13. Antiemetic treatment for acute gastroenteritis in children: an updated Cochrane systematic review with meta-analysis and mixed treatment comparison in a Bayesian framework

    PubMed Central

    Fedorowicz, Zbys

    2012-01-01

    Objective To assess the evidence for the safety and effectiveness of antiemetics on gastroenteritis-induced vomiting in children and adolescents. Design Systematic review. Data Sources The Cochrane Central Register of Controlled Trials, MEDLINE and EMBASE searched from 1980 to March 2012. Methods Methods included comprehensive searches, data synthesis, meta-analysis and mixed treatment comparisons (MTC). Review methods Reference lists were checked, and missing or inconsistent data were sought from trial investigators. Randomised controlled trials comparing antiemetics in participants younger than 18?years and who were vomiting due to acute gastroenteritis. Four meta-analyses and three MTC were carried out. Results 10 trials (1479 participants) and five treatments were included: dexamethasone, dimenhydrinate, granisetron, metoclopramide and ondansetron. There was clear evidence that ondansetron (oral or intravenous) compared with placebo increased the proportion of patients with cessation of vomiting (orally administered) (RR 1.44, 95% CI 1.29 to 1.61), reduced the immediate hospital admission rate (orally administered) (RR 0.40, 95% CI 0.19 to 0.83) and the need for intravenous rehydration therapy (orally administered) (RR 0.41, 95% CI 0.29 to 0.59). No significant difference was noted in the revisit rates, but ondansetron was associated with an increase in episodes of diarrhoea. There was no evidence for the use of dexamethasone or metoclopramide and limited evidence that dimenhydrinate or granisetron increased the cessation of vomiting. The MTC analysis suggested that ondansetron was the most likely treatment to stop the child vomiting. Nine studies were carried out in secondary care and one in primary care. Conclusions This systematic review used a method novel to this clinical area and found clear evidence that ondansetron was the most likely treatment to allow oral rehydration therapy to commence. Given the significance of these results, the authors urge healthcare policy makers to consider the wider use of ondansetron in secondary care. Furthermore, randomised controlled trials are needed to investigate the effectiveness of antiemetic treatment in primary care (including ambulatory care interventions). PMID:22815462

  14. A MedlinePlus Kiosk Promoting Health Literacy

    PubMed Central

    TEOLIS, MARILYN G.

    2010-01-01

    As an ongoing community outreach project, a pictorial touch-screen kiosk and Web site was developed for 48 MedlinePlus tutorials. This learning experience serves Davidson County, Tennessees uninsured patients at the University of Tennessee/Baptist Hospitals Internal Medicine Clinic. The availability of a health information kiosk at the University of Tennessee/Baptist Hospital primary care clinic significantly increases health literacy for patients by providing reliable, physician-recommended information in an appropriate formatinformation these patients did not previously find readily available. Participants report they have a greater understanding of their health issues, and the project is introducing hundreds of patients to MedlinePlus. PMID:20808715

  15. Evidence based palaeopathology: meta-analysis of Pubmed-listed scientific studies on pre-Columbian, South American mummies.

    PubMed

    Dagefrde, K L; Vennemann, M; Rhli, F J

    2014-06-01

    The aim of this study was to review all Pubmed()-listed palaeopathological studies performed on pre-Columbian South American mummies. A total of 61 studies were found (1977-2005). Review criteria included e.g. method of examination, method of mummification, palaeopathological diagnoses and individual age of mummies as well as dating, which ranged from 7500 to 500 years BP, mainly (if reported) originating from the Chiribaya and Chinchorro cultures. The average age of the 99 individually reported mummies was about 25 years. Only six studies included computed tomography, thirteen studies used classical radiography as an examination method. Three studies analysed parasite related diseases, especially caused by Trypanosoma cruzi. Among all of the reported infectious diseases (n=9), there were seven studies presenting cases of tuberculosis. The results were also compared inter-culturally. In 61 studies (37 epidemiological and 24 case reports) more than 6400 mummified individuals were analysed. By contrast, meta-analytic data for ancient Egyptian mummies (Zweifel et al., 2009) included about 3000 analysed individuals in 131 studies (85 case reports and 46 epidemiological studies). In general, ancient Egyptian mummies were shown to be intentionally mummified, whereas the Pre-Columbian American mummies showed a great diversity of spontaneous mummification. However, ritualistic mummification methods were also practised (n=2). This study's results shall assist to improve evidence-based research in palaeopathology. PMID:24721560

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

    PubMed

    Badgett, Robert G; Dylla, Daniel P; Megison, Susan D; Harmon, E Glynn

    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. 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: 06) 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

  18. 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

  19. Factor Analytic Approach to Transitive Text Mining using Medline Descriptors

    NASA Astrophysics Data System (ADS)

    Stegmann, J.; Grohmann, G.

    Matrix decomposition methods were applied to examples of noninteractive literature sets sharing implicit relations. Document-by-term matrices were created from downloaded PubMed literature sets, the terms being the Medical Subject Headings (MeSH descriptors) assigned to the documents. The loadings of the factors derived from singular value or eigenvalue matrix decomposition were sorted according to absolute values and subsequently inspected for positions of terms relevant to the discovery of hidden connections. It was found that only a small number of factors had to be screened to find key terms in close neighbourhood, being separated by a small number of terms only.

  20. Using Topic Models to Interpret MEDLINE's Medical Subject Headings

    NASA Astrophysics Data System (ADS)

    Newman, David; Karimi, Sarvnaz; Cavedon, Lawrence

    We consider the task of interpreting and understanding a taxonomy of classification terms applied to documents in a collection. In particular, we show how unsupervised topic models are useful for interpreting and understanding MeSH, the Medical Subject Headings applied to articles in MEDLINE. We introduce the resampled author model, which captures some of the advantages of both the topic model and the author-topic model. We demonstrate how topic models complement and add to the information conveyed in a traditional listing and description of a subject heading hierarchy.

  1. Making the rough places plain: designing MEDLINE end user training.

    PubMed

    Snow, B

    1984-01-01

    Library personnel are frequently asked to design user education programs for orientation to medical databases online. These programs aim at promoting judicious use of online resources via searches conducted by librarian intermediaries or, more recently, at preparing end users to perform online searches themselves. This discussion will focus on factors considered in designing MEDLINE training for medical practitioners, including problems end users may encounter in extant user aids, and how these problems have been addressed in the new DIALOG Seminar for Medical professionals. PMID:10299957

  2. Evidence for non-communicable diseases: analysis of Cochrane reviews and randomised trials by World Bank classification

    PubMed Central

    Heneghan, C; Blacklock, C; Perera, R; Davis, R; Banerjee, A; Gill, P; Liew, S; Chamas, L; Hernandez, J; Mahtani, K; Hayward, G; Harrison, S; Lasserson, D; Mickan, S; Sellers, C; Carnes, D; Homer, K; Steed, L; Ross, J; Denny, N; Goyder, C; Thompson, M; Ward, A

    2013-01-01

    Introduction Prevalence of non-communicable diseases (NCDs) is increasing globally, with the greatest projected increases in low-income and middle-income countries. We sought to quantify the proportion of Cochrane evidence relating to NCDs derived from such countries. Methods We searched the Cochrane database of systematic reviews for reviews relating to NCDs highlighted in the WHO NCD action plan (cardiovascular, cancers, diabetes and chronic respiratory diseases). We excluded reviews at the protocol stage and those that were repeated or had been withdrawn. For each review, two independent researchers extracted data relating to the country of the corresponding author and the number of trials and participants from countries, using the World Bank classification of gross national income per capita. Results 797 reviews were analysed, with a reported total number of 12?340 trials and 10?937?306 participants. Of the corresponding authors 90% were from high-income countries (41% from the UK). Of the 746 reviews in which at least one trial had met the inclusion criteria, only 55% provided a summary of the country of included trials. Analysis of the 633 reviews in which country of trials could be established revealed that almost 90% of trials and over 80% of participants were from high-income countries. 438 (5%) trials including 1?145?013 (11.7%) participants were undertaken in low-middle income countries. We found that only 13 (0.15%) trials with 982 (0.01%) participants were undertaken in low-income countries. Other than the five Cochrane NCD corresponding authors from South Africa, only one other corresponding author was from Africa (Gambia). Discussion The overwhelming body of evidence for NCDs pertains to high-income countries, with only a small number of review authors based in low-income settings. As a consequence, there is an urgent need for research infrastructure and funding for the undertaking of high-quality trials in this area. PMID:23833146

  3. User experiences of evidence-based online resources for health professionals: User testing of The Cochrane Library

    PubMed Central

    Rosenbaum, Sarah E; Glenton, Claire; Cracknell, Jane

    2008-01-01

    Background Evidence-based decision making relies on easy access to trustworthy research results. The Cochrane Library is a key source of evidence about the effect of interventions and aims to "promote the accessibility of systematic reviews to anyone wanting to make a decision about health care". We explored how health professionals found, used and experienced The Library, looking at facets of user experience including findability, usability, usefulness, credibility, desirability and value. Methods We carried out 32 one-hour usability tests on participants from Norway and the UK. Participants both browsed freely and attempted to perform individually tailored tasks while "thinking aloud". Sessions were recorded and viewed in real time by researchers. Transcriptions and videos were reviewed by one researcher and one designer. Findings reported here reflect issues receiving a high degree of saturation and that we judge to be critical to the user experience of evidence-based web sites, based on principles for usability heuristics, web guidelines and evidence-based practice. Results Participants had much difficulty locating both the site and its contents. Non-native English speakers were at an extra disadvantage when retrieving relevant documents despite high levels of English-language skills. Many participants displayed feelings of ineptitude, alienation and frustration. Some made serious mistakes in correctly distinguishing between different information types, for instance reviews, review protocols, and individual studies. Although most expressed a high regard for the site's credibility, some later displayed a mistrust of the independence of the information. Others were overconfident, thinking everything on The Cochrane Library site shared the same level of quality approval. Conclusion Paradoxically, The Cochrane Library, established to support easy access to research evidence, has its own problems of accessibility. Health professionals' experiences of this and other evidence-based online resources can be improved by applying existing principles for web usability, prioritizing the development of simple search functionality, emitting "researcher" jargon, consistent marking of site ownership, and clear signposting of different document types and different content quality. PMID:18662382

  4. 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

  5. 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 evolution of scientific writing. Apparently scientists look on the bright side of research results. But whether this perception fits reality should be questioned. PMID:26668206

  6. 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

  7. 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

  8. The comparative recall of Google Scholar versus PubMed in identical searches for biomedical systematic reviews: a review of searches used in systematic reviews

    PubMed Central

    2013-01-01

    Background The usefulness of Google Scholar (GS) as a bibliographic database for biomedical systematic review (SR) searching is a subject of current interest and debate in research circles. Recent research has suggested GS might even be used alone in SR searching. This assertion is challenged here by testing whether GS can locate all studies included in 21 previously published SRs. Second, it examines the recall of GS, taking into account the maximum number of items that can be viewed, and tests whether more complete searches created by an information specialist will improve recall compared to the searches used in the 21 published SRs. Methods The authors identified 21 biomedical SRs that had used GS and PubMed as information sources and reported their use of identical, reproducible search strategies in both databases. These search strategies were rerun in GS and PubMed, and analyzed as to their coverage and recall. Efforts were made to improve searches that underperformed in each database. Results GS overall coverage was higher than PubMed (98% versus 91%) and overall recall is higher in GS: 80% of the references included in the 21 SRs were returned by the original searches in GS versus 68% in PubMed. Only 72% of the included references could be used as they were listed among the first 1,000 hits (the maximum number shown). Practical precision (the number of included references retrieved in the first 1,000, divided by 1,000) was on average 1.9%, which is only slightly lower than in other published SRs. Improving searches with the lowest recall resulted in an increase in recall from 48% to 66% in GS and, in PubMed, from 60% to 85%. Conclusions Although its coverage and precision are acceptable, GS, because of its incomplete recall, should not be used as a single source in SR searching. A specialized, curated medical database such as PubMed provides experienced searchers with tools and functionality that help improve recall, and numerous options in order to optimize precision. Searches for SRs should be performed by experienced searchers creating searches that maximize recall for as many databases as deemed necessary by the search expert. PMID:24360284

  9. MedlinePlus en español marks its 10th anniversary

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

    MedlinePLUS

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  11. PCorral--interactive mining of protein interactions from MEDLINE.

    PubMed

    Li, Chen; Jimeno-Yepes, Antonio; Arregui, Miguel; Kirsch, Harald; Rebholz-Schuhmann, Dietrich

    2013-01-01

    The extraction of information from the scientific literature is a complex task-for researchers doing manual curation and for automatic text processing solutions. The identification of protein-protein interactions (PPIs) requires the extraction of protein named entities and their relations. Semi-automatic interactive support is one approach to combine both solutions for efficient working processes to generate reliable database content. In principle, the extraction of PPIs can be achieved with different methods that can be combined to deliver high precision and/or high recall results in different combinations at the same time. Interactive use can be achieved, if the analytical methods are fast enough to process the retrieved documents. PCorral provides interactive mining of PPIs from the scientific literature allowing curators to skim MEDLINE for PPIs at low overheads. The keyword query to PCorral steers the selection of documents, and the subsequent text analysis generates high recall and high precision results for the curator. The underlying components of PCorral process the documents on-the-fly and are available, as well, as web service from the Whatizit infrastructure. The human interface summarizes the identified PPI results, and the involved entities are linked to relevant resources and databases. Altogether, PCorral serves curator at both the beginning and the end of the curation workflow for information retrieval and information extraction. Database URL: http://www.ebi.ac.uk/Rebholz-srv/pcorral. PMID:23640984

  12. Mining MEDLINE for problems associated with vitamin D

    PubMed Central

    Demner-Fushman, Dina; Mork, James G.; Aronson, Alan R.

    2013-01-01

    This paper presents a two-step approach to generating comprehensive abstractive overviews for biomedical topics. It starts with a sensitivity-maximizing search of MEDLINE/PubMed and MeSH-based filtering of the results that are then processed using NLP methods to extract relations between entities of interest. We evaluate this approach in a case study based on the IOM report on the role of vitamin D in human health. The report defines disorders that serve as health indicators for the role of vitamin D. We evaluate the abstractive overviews generated using MeSH indexing and the extracted relations using the disorders listed in the IOM report as reference standard. We conclude that MeSH-based aggregation and filtering of the results is a useful and easy step in the generation of abstractive overviews. Although our relation extraction achieved 83.6% recall and 92.8% precision, only half of the disorders of interest participated in these relations. PMID:24551339

  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 machineour 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. ALICE: An Algorithm to Extract Abbreviations from MEDLINE

    PubMed Central

    Ao, Hiroko; Takagi, Toshihisa

    2005-01-01

    Objective: To help biomedical researchers recognize dynamically introduced abbreviations in biomedical literature, such as gene and protein names, we have constructed a support system called ALICE (Abbreviation LIfter using Corpus-based Extraction). ALICE aims to extract all types of abbreviations with their expansions from a target paper on the fly. Methods: ALICE extracts an abbreviation and its expansion from the literature by using heuristic pattern-matching rules. This system consists of three phases and potentially identifies valid 320 abbreviation-expansion patterns as combinations of the rules. Results: It achieved 95% recall and 97% precision on randomly selected titles and abstracts from the MEDLINE database. Conclusion: ALICE extracted abbreviations and their expansions from the literature efficiently. The subtly compiled heuristics enabled it to extract abbreviations with high recall without significantly reducing precision. ALICE does not only facilitate recognition of an undefined abbreviation in a paper by constructing an abbreviation database or dictionary, but also makes biomedical literature retrieval more accurate. This system is freely available at http://uvdb3.hgc.jp/ALICE/ALICE_index.html. PMID:15905486

  15. PCorral—interactive mining of protein interactions from MEDLINE

    PubMed Central

    Li, Chen; Arregui, Miguel; Kirsch, Harald; Rebholz-Schuhmann, Dietrich

    2013-01-01

    The extraction of information from the scientific literature is a complex task—for researchers doing manual curation and for automatic text processing solutions. The identification of protein–protein interactions (PPIs) requires the extraction of protein named entities and their relations. Semi-automatic interactive support is one approach to combine both solutions for efficient working processes to generate reliable database content. In principle, the extraction of PPIs can be achieved with different methods that can be combined to deliver high precision and/or high recall results in different combinations at the same time. Interactive use can be achieved, if the analytical methods are fast enough to process the retrieved documents. PCorral provides interactive mining of PPIs from the scientific literature allowing curators to skim MEDLINE for PPIs at low overheads. The keyword query to PCorral steers the selection of documents, and the subsequent text analysis generates high recall and high precision results for the curator. The underlying components of PCorral process the documents on-the-fly and are available, as well, as web service from the Whatizit infrastructure. The human interface summarizes the identified PPI results, and the involved entities are linked to relevant resources and databases. Altogether, PCorral serves curator at both the beginning and the end of the curation workflow for information retrieval and information extraction. Database URL: http://www.ebi.ac.uk/Rebholz-srv/pcorral. PMID:23640984

  16. 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

  17. 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…

  18. 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…

  19. 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…

  20. 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

  1. 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

  2. Long and short time variability of the global and the hemisphere temperature anomalies -Application of the Cochrane-Orcutt method

    NASA Astrophysics Data System (ADS)

    Werner, Rolf; Valev, Dimitare; Danov, Dimitar; Goranova, M.

    Climate change holds a key position in science and policy today. A central issue to discuss in the scientific publications is the question how much humans contribute to the climate warming. To get answers in the last decades a lot of efforts were made to model the processes determining the climate, to make forecasts under defined conditions for the development of the society (climate projections). Another scientific tendency to find a more probable right answer consists in the application and development of the statistics to study responses of different climate forcings. Here a classical statistical method -the linear regression -is applied to examine the parts of the global and hemisphere warming due to different radiation forcings, by the use of their long and short time variabilities. The residuals of the regressions are significantly auto-correlated. Therefore the Cochrane-Orcutt method is applied to test the statistical significances. By multiple regression it is found that the main part of the temperature variability is caused by CO2. The impact of the total solar irradiance during the examined time period of 1866 up to 2000 is at the critical level of significance.

  3. Evidence-based dentistry: Part II. Searching for answers to clinical questions: how to use MEDLINE.

    PubMed

    Sutherland, S E

    2001-05-01

    The ability to conduct efficient literature searches is fundamental to the practice of evidence-based dentistry. In the second part of this series on evidence-based dentistry, strategic literature search techniques are discussed. MEDLINE, because of its breadth, depth and continuous maintenance by the U.S. National Library of Medicine (NLM), is the best source of evidence for health care. Although there are many gateways to MEDLINE, this paper highlights the user-friendly versions of MEDLINE offered free on the Internet by the NLM. The use of well-established search tactics and the unique features of the NLM sites facilitate rapid, effective literature searches. PMID:11398391

  4. 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

  5. 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…

  6. 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…

  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. Helping people make well-informed decisions about health care: old and new challenges to achieving the aim of the Cochrane Collaboration.

    PubMed

    Oxman, Andrew D

    2013-01-01

    The aim of the Cochrane Collaboration is to help people make well-informed decisions about health care by preparing, maintaining and promoting the accessibility of systematic reviews of the effects of health care interventions. This aim is as relevant now as it was 20 years ago, when the Cochrane Collaboration was established. Substantial progress has been made toward addressing challenges to achieving the Collaboration's aim. At the same time, a huge amount of work remains to be done. Current challenges include improving the quality of reviews, methodological challenges, meeting the needs of contributors and users and taking on new challenges while staying focused on the Collaboration's aim. Radical thinking and substantial change may be needed to identify and implement pragmatic strategies to ensure that reviews are up-to-date and informative. Methodological challenges include the development and application of better methods for addressing explanatory factors, incorporating non-randomized evidence and making comparisons across multiple interventions. Innovations in editorial processes and strategies to meet the needs of low- and middle-income countries and diverse users of Cochrane reviews are needed. Finally, although it is important to consider broadening the aims of the Collaboration to include types of questions other than the effects of interventions and types of products other than the Cochrane Library, we should not lose sight of the aim of the Cochrane Collaboration. Addressing that aim is still a major challenge that requires the collaboration of thousands of people around the world and continuing improvements in the methods used to achieve that aim. PMID:24050439

  9. Semi-automated population of an online database of neuronal models (ModelDB) with citation information, using PubMed for validation.

    PubMed

    Davison, Andrew P; Morse, Thomas M; Migliore, Michele; Shepherd, Gordon M; Hines, Michael L

    2004-01-01

    Citations play an important role in medical and scientific databases by indicating the authoritative source of the data. Manual citation entry is tedious and prone to errors. We describe a method and make available computer scripts which automate the process of citation entry. We use an open citation project PERL module (PARSER) for parsing citation data that is then used to retrieve PubMed records to supply the (validated) reference. Our PERL scripts are available via a link in the web references section of this article. PMID:15365194

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

    MedlinePLUS

    ... on our Stress page. MedlinePlus is now on Facebook! Find us for the latest ... with Advanced Colon Cancer Often Get Costly, Dubious Treatments Mom's Smoking May Put Kids at Higher Risk of COPD ...

  11. 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 ...

  12. 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

  13. Preliminary Comparison of Three Search Engines for Point of Care Access to MEDLINE Citations

    PubMed Central

    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

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

    MedlinePLUS

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

    MedlinePLUS

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  16. Are men difficult to find? Identifying male-specific studies in MEDLINE and Embase

    PubMed Central

    2014-01-01

    Background Systematic reviews often investigate the effectiveness of interventions for one sex. However, identifying interventions with data presented according to the sex of study participants can be challenging due to suboptimal indexing in bibliographic databases and poor reporting in titles and abstracts. The purposes of this study were to develop a highly sensitive search filter to identify literature relevant to men's health and to assess the performance of a range of sex-specific search terms used individually and in various combinations. Methods Comprehensive electronic searches were undertaken across a range of databases to inform a series of systematic reviews investigating obesity management for men. The included studies formed a reference standard set. A set of sex-specific search terms, identified from database-specific controlled vocabularies and from natural language used in the titles and abstracts of relevant papers, was investigated in MEDLINE and Embase. Sensitivity, precision, number needed to read (NNR) and percent reduction in results compared to searching without sex-specific terms were calculated. Results The reference standard set comprised 57 papers in MEDLINE and 63 in Embase. Seven sex-specific search terms were identified. Searching without sex-specific terms returned 31,897 results in MEDLINE and 37,351 in Embase and identified 84% (MEDLINE) and 83% (Embase) of the reference standard sets. The best performing individual sex-specific term achieved 100%/98% sensitivity (MEDLINE/Embase), NNR 544/609 (MEDLINE/Embase) and reduced the number of results by 18%/17% (MEDLINE/Embase), relative to searching without sex-specific terms. The best performing filter, compromising different combinations of controlled vocabulary terms and natural language, achieved higher sensitivity (MEDLINE and Embase 100%), greater reduction in number of results (MEDLINE/Embase 24%/20%) and greater reduction in NNR (MEDLINE/Embase 506/578) than the best performing individual sex-specific term. Conclusions The proposed MEDLINE and Embase filters achieved high sensitivity and a reduction in the number of search results and NNR, indicating that they are useful tools for efficient, comprehensive literature searching but their performance is partially dependent on the appropriate use of database controlled vocabularies and index terms. PMID:25033713

  17. Pharmacological interventions for self-injurious behaviour in adults with intellectual disabilities: Abridged republication of a Cochrane systematic review.

    PubMed

    Gormez, A; Rana, F; Varghese, S

    2014-04-30

    We aimed to determine clinical effectiveness of pharmacological interventions for self-injurious behaviour in adults with intellectual disability. We searched the following databases: CENTRAL; MEDLINE; EMBASE; PsycINFO; CINAHL; SCI; SSCI; Conference Proceedings Citation Index - Science; Conference Proceedings Citation Index - Social Science and Humanities; ZETOC; World Cat .We also searched ClinicalTrials.gov,ICTRP and the reference lists of included trials. We included randomised controlled trials that examined drug interventions versus placebo for self-injurious behaviour. We found five double-blind, placebo-controlled trials, which included a total of 50 people. Four trials compared the effects of naltrexone versus placebo and one trial clomipramine versus placebo. We did not identify any relevant placebo-controlled trials for other drugs. We presented a narrative summary, as meta-analysis was not appropriate due to differences in study designs, differences between interventions and heterogeneous outcome measures. There was weak evidence in included trials that any active drug was more effective than placebo for people with intellectual disability demonstrating self-injurious behaviour. Due to sparse data, an absence of power and statistical significance, and high risk of bias for four of the included trials, we are unable to reach any definite conclusions about the relative benefits of naltrexone or clomipramine compared to placebo. PMID:24785762

  18. 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

  19. 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.

  20. MeSH Speller + askMEDLINE: auto-completes MeSH terms then searches MEDLINE/PubMed via free-text, natural language queries.

    PubMed

    Fontelo, Paul; Liu, Fang; Ackerman, Michael

    2005-01-01

    Medical terminology is challenging even for healthcare personnel. Spelling errors can make searching MEDLINE/PubMed ineffective. We developed a utility that provides MeSH term and Specialist Lexicon Vocabulary suggestions as it is typed on a search page. The correctly spelled term can be incorporated into a free-text, natural language search or used as a clinical queries search. PMID:16779244

  1. The MedlinePlus public user interface: studies of design challenges and opportunities

    PubMed Central

    Marill, Jennifer L.; Miller, Naomi; Kitendaugh, Paula

    2006-01-01

    Question: What are the challenges involved in designing, modifying, and improving a major health information portal that serves over sixty million page views a month? Setting: MedlinePlus, the National Library of Medicine's (NLM's) consumer health Website, is examined. Method: Challenges are presented as six studies, which describe selected design issues and how NLM staff resolved them. Main Result: Improving MedlinePlus is an iterative process. Changes in the public user interface are ongoing, reflecting Web design trends, usability testing recommendations, user survey results, new technical requirements, and the need to grow the site in an orderly way. Conclusion: Testing and analysis should accompany Website design modifications. New technologies may enhance a site but also introduce problems. Further modifications to MedlinePlus will be informed by the experiences described here. PMID:16404467

  2. 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

  3. 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

  4. Evaluation of the Cochrane Collaboration’s tool for assessing the risk of bias in randomized trials: focus groups, online survey, proposed recommendations and their implementation

    PubMed Central

    2014-01-01

    Background In 2008, the Cochrane Collaboration introduced a tool for assessing the risk of bias in clinical trials included in Cochrane reviews. The risk of bias (RoB) tool is based on narrative descriptions of evidence-based methodological features known to increase the risk of bias in trials. Methods To assess the usability of this tool, we conducted an evaluation by means of focus groups, online surveys and a face-to-face meeting. We obtained feedback from a range of stakeholders within The Cochrane Collaboration regarding their experiences with, and perceptions of, the RoB tool and associated guidance materials. We then assessed this feedback in a face-to-face meeting of experts and stakeholders and made recommendations for improvements and further developments of the RoB tool. Results The survey attracted 380 responses. Respondents reported taking an average of between 10 and 60 minutes per study to complete their RoB assessments, which 83% deemed acceptable. Most respondents (87% of authors and 95% of editorial staff) thought RoB assessments were an improvement over past approaches to trial quality assessment. Most authors liked the standardized approach (81%) and the ability to provide quotes to support judgements (74%). A third of participants disliked the increased workload and found the wording describing RoB judgements confusing. The RoB domains reported to be the most difficult to assess were incomplete outcome data and selective reporting of outcomes. Authors expressed the need for more guidance on how to incorporate RoB assessments into meta-analyses and review conclusions. Based on this evaluation, recommendations were made for improvements to the RoB tool and the associated guidance. The implementation of these recommendations is currently underway. Conclusions Overall, respondents identified positive experiences and perceptions of the RoB tool. Revisions of the tool and associated guidance made in response to this evaluation, and improved provision of training, may improve implementation. PMID:24731537

  5. 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)

  6. 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

  7. 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 ... of its research: MedlinePlus . www.medlineplus.gov . Type "Parkinson's disease" in the Search box. NIHSeniorHealth —Parkinson's Disease ...

  8. 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

  9. 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)

  10. Where should the pharmacy researcher look first? Comparing International Pharmaceutical Abstracts and MEDLINE.

    PubMed Central

    Fishman, D L; Stone, V L; DiPaula, B A

    1996-01-01

    This study compared the usefulness of various CD-ROM versions of International Pharmaceutical Abstracts (IPA) and MEDLINE for pharmacy research. Journal coverage as well as the strengths and weaknesses of database structure and contents were considered. The journals indexed in each database were compared to those identified in a survey of the research journals most important to University of Maryland at Baltimore pharmacy faculty and in a similar North Carolina study rating pharmacy journals. In addition, indexed journals were checked against the Institute for Scientific Information's most recent list of high-impact journals in pharmacology and pharmacy. Searches representing a variety of topics relevant to pharmacy were conducted in both databases, and the number and relevance of citations located were analyzed. Results showed that IPA indexed a greater number of pharmacy titles, but that MEDLINE indexed more pharmacy journals designated in studies as significant to the field. There was little overlap in coverage between the two databases. MEDLINE produced larger retrievals for the majority of questions, but many citations retrieved in IPA did not appear in MEDLINE. PMID:8883989

  11. 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

  12. 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

  13. Testing the New Technology: MEDLINE on CD-ROM in an Academic Health Sciences Library.

    ERIC Educational Resources Information Center

    Glitz, Beryl

    1988-01-01

    Describes the experiences of the University of Southern California at Los Angeles (UCLA) Biomedical Library in testing MEDLINE on CD-ROM. Preparations for testing are discussed, as well as patron response to the system, measured by evaluation forms, and implications for libraries providing new technological tools for patrons. (MES)

  14. An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology

    PubMed Central

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

    2007-01-01

    Background Identifying relevant research in an ever-growing body of published literature is becoming increasingly difficult. Establishing domain-specific knowledge bases may be a more effective and efficient way to manage and query information within specific biomedical fields. Adopting controlled vocabulary is a critical step toward data integration and interoperability in any information system. We present an open source infrastructure that provides a powerful capacity for managing and mining data within a domain-specific knowledge base. As a practical application of our infrastructure, we presented two applications Literature Finder and Investigator Browser as well as a tool set for automating the data curating process for the human genome published literature database. The design of this infrastructure makes the system potentially extensible to other data sources. Results Information retrieval and usability tests demonstrated that the system had high rates of recall and precision, 90% and 93% respectively. The system was easy to learn, easy to use, reasonably speedy and effective. Conclusion The open source system infrastructure presented in this paper provides a novel approach to managing and querying information and knowledge from domain-specific PubMed data. Using the controlled vocabulary UMLS enhanced data integration and interoperability and the extensibility of the system. In addition, by using MVC-based design and Java as a platform-independent programming language, this system provides a potential infrastructure for any domain-specific knowledge base in the biomedical field. PMID:17996092

  15. 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,…

  16. 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

  17. Use of the Cochrane electronic library in complementary and alternative medicine courses in medical schools: is the giant lost in cyberspace?

    PubMed

    Ezzo, Jeanette; Wright, Katherine; Hadhazy, Victoria; Bahr-Robertson, Mary; Mac Beckner, William; Covington, Maggie; Berman, Brian

    2002-10-01

    Courses in complementary and alternative medicine (CAM) are increasing in medical schools in the United States and, currently, approximately two thirds of U.S. medical schools offer at least one such course. As these courses grow in popularity, however, concerns are also growing that these courses lack an evidence-based perspective. We propose that one interesting and easy way to bring an evidence-based perspective to the CAM classroom is to utilize the Cochrane Electronic Library (CLIB), which is available in many medical libraries, as a teaching tool. The CLIB currently houses more than 80 CAM-related, full-text systematic reviews and approximately 5000 CAM-related clinical trials, making it a valued resource for people who seek CAM evidence. Moreover, the CLIB commitment to publishing reviews regardless of the results make it a resource where one can find reviews concluding there is strong evidence of benefit or no evidence of benefit. In addition to the access to CAM evidence which the CLIB provides, students can learn basic critical appraisal skills by learning the rationale behind Cochrane systematic reviews. A survey of CAM course directors, however, shows that almost one half of these directors have never used the CLIB. For those who have never used the CLIB, this editorial explains the four main databases within the CLIB and presents ideas for using them in CAM school courses. PMID:12470450

  18. Applying MetaMap to Medline for identifying novel associations in a large clinical dataset: a feasibility analysis

    PubMed Central

    Hanauer, David A; Saeed, Mohammed; Zheng, Kai; Mei, Qiaozhu; Shedden, Kerby; Aronson, Alan R; Ramakrishnan, Naren

    2014-01-01

    Objective We describe experiments designed to determine the feasibility of distinguishing known from novel associations based on a clinical dataset comprised of International Classification of Disease, V.9 (ICD-9) codes from 1.6 million patients by comparing them to associations of ICD-9 codes derived from 20.5 million Medline citations processed using MetaMap. Associations appearing only in the clinical dataset, but not in Medline citations, are potentially novel. Methods Pairwise associations of ICD-9 codes were independently identified in both the clinical and Medline datasets, which were then compared to quantify their degree of overlap. We also performed a manual review of a subset of the associations to validate how well MetaMap performed in identifying diagnoses mentioned in Medline citations that formed the basis of the Medline associations. Results The overlap of associations based on ICD-9 codes in the clinical and Medline datasets was low: only 6.6% of the 3.1 million associations found in the clinical dataset were also present in the Medline dataset. Further, a manual review of a subset of the associations that appeared in both datasets revealed that co-occurring diagnoses from Medline citations do not always represent clinically meaningful associations. Discussion Identifying novel associations derived from large clinical datasets remains challenging. Medline as a sole data source for existing knowledge may not be adequate to filter out widely known associations. Conclusions In this study, novel associations were not readily identified. Further improvements in accuracy and relevance for tools such as MetaMap are needed to realize their expected utility. PMID:24928177

  19. The mini MEDLINE SYSTEM: a library-based end-user search system.

    PubMed

    Broering, N C

    1985-04-01

    The mini MEDLINE SYSTEM, a user-friendly search system developed in 1981 at the Georgetown University Medical Center, has been operational since 1982. The system is designed to meet the immediate educational and clinical information needs of students, residents, and faculty. This article focuses on system planning and design, database creation through "downloading," hardware adaptation, and system use. The database is a subset of the NLM's MEDLINE file; it includes over 180,000 citations to articles indexed in over 160 journals from 1982 to the present. With only a few keystrokes in a two-step process it allows users to conduct bibliographic searches. The system is being replicated at eight other medical libraries. PMID:3888329

  20. 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

  1. 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

  2. [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

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

    PubMed

    Thirion, Benoit; Pereira, Susanne; Nvol, Aurlie; Dahamna, Badisse; Darmoni, Stfan

    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

  4. An update on Uniform Resource Locator (URL) decay in MEDLINE abstracts and measures for its mitigation

    PubMed Central

    Ducut, Erick; Liu, Fang; Fontelo, Paul

    2008-01-01

    Background For years, Uniform Resource Locator (URL) decay or "link rot" has been a growing concern in the field of biomedical sciences. This paper addresses this issue by examining the status of the URLs published in MEDLINE abstracts, establishing current availability and estimating URL decay in these records from 1994 to 2006. We also reviewed the information provided by the URL to determine if the context that the author cited in writing the paper is the same information presently available in the URL. Lastly, with all the documented recommended methods to preserve URL links, we determined which among them have gained acceptance among authors and publishers. Methods MEDLINE records from 1994 to 2006 from the National Library of Medicine in Extensible Mark-up Language (XML) format were processed yielding 10,208 URL addresses. These were accessed once daily at random times for 30 days. Titles and abstracts were also searched for the presence of archival tools such as WebCite, Persistent URL (PURL) and Digital Object Identifier (DOI). Results Results showed that the average URL length ranged from 13 to 425 characters with a mean length of 35 characters [Standard Deviation (SD) = 13.51; 95% confidence interval (CI) 13.25 to 13.77]. The most common top-level domains were ".org" and ".edu", each with 34%. About 81% of the URL pool was available 90% to 100% of the time, but only 78% of these contained the actual information mentioned in the MEDLINE record. "Dead" URLs constituted 16% of the total. Finally, a survey of archival tool usage showed that since its introduction in 1998, only 519 of all abstracts reviewed had incorporated DOI addresses in their MEDLINE abstracts. Conclusion URL persistence parallels previous studies which showed approximately 81% general availability during the 1-month study period. As peer-reviewed literature remains to be the main source of information in biomedicine, we need to ensure the accuracy and preservation of these links. PMID:18547428

  5. 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

  6. MedlinePlus and the challenge of low health literacy: findings from the Colonias project*

    PubMed Central

    Olney, Cynthia A.; Warner, Debra G.; Reyna, Greysi; Wood, Fred B.; Siegel, Elliot R.

    2007-01-01

    Objective: To explore the potential of a community-based health information outreach project to overcome problems associated with health literacy in low-income Hispanic communities along the Texas-Mexico border. Methods: Using a train-the-trainer approach, community outreach workers known as promotoras were trained by a health information outreach team to search English and Spanish versions of MedlinePlus. These 15 promotoras submitted written examples on a weekly basis of the topics they helped residents explore on MedlinePlus and the ways in which the residents used the information. These weekly reports, along with verbal interviews with promotoras and others in the communities, allowed development of a database of 161 incidents (“stories”) demonstrating how community residents used MedlinePlus. These stories were thematically analyzed to explore how the program benefited participants. Results: The database of stories included examples of community residents becoming better informed about their illnesses, resolving to visit doctors, making decisions about recommended treatments, reducing their anxiety about health conditions, committing to healthy or preventive behavior, and assisting family members. Conclusion: With the help of paraprofessionals like promotoras, community-based health information outreach projects may improve the ability of community residents to understand their health conditions and to participate actively in their health care. PMID:17252064

  7. 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

  8. 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.

  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. 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

  11. BabelMeSH: Development of a Cross-Language Tool for MEDLINE/PubMed

    PubMed Central

    Liu, Fang; Fontelo, Paul; Ackerman, Michael

    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

  12. 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

  13. Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation

    PubMed Central

    2011-01-01

    Background Evaluation of Word Sense Disambiguation (WSD) methods in the biomedical domain is difficult because the available resources are either too small or too focused on specific types of entities (e.g. diseases or genes). We present a method that can be used to automatically develop a WSD test collection using the Unified Medical Language System (UMLS) Metathesaurus and the manual MeSH indexing of MEDLINE. We demonstrate the use of this method by developing such a data set, called MSH WSD. Methods In our method, the Metathesaurus is first screened to identify ambiguous terms whose possible senses consist of two or more MeSH headings. We then use each ambiguous term and its corresponding MeSH heading to extract MEDLINE citations where the term and only one of the MeSH headings co-occur. The term found in the MEDLINE citation is automatically assigned the UMLS CUI linked to the MeSH heading. Each instance has been assigned a UMLS Concept Unique Identifier (CUI). We compare the characteristics of the MSH WSD data set to the previously existing NLM WSD data set. Results The resulting MSH WSD data set consists of 106 ambiguous abbreviations, 88 ambiguous terms and 9 which are a combination of both, for a total of 203 ambiguous entities. For each ambiguous term/abbreviation, the data set contains a maximum of 100 instances per sense obtained from MEDLINE. We evaluated the reliability of the MSH WSD data set using existing knowledge-based methods and compared their performance to that of the results previously obtained by these algorithms on the pre-existing data set, NLM WSD. We show that the knowledge-based methods achieve different results but keep their relative performance except for the Journal Descriptor Indexing (JDI) method, whose performance is below the other methods. Conclusions The MSH WSD data set allows the evaluation of WSD algorithms in the biomedical domain. Compared to previously existing data sets, MSH WSD contains a larger number of biomedical terms/abbreviations and covers the largest set of UMLS Semantic Types. Furthermore, the MSH WSD data set has been generated automatically reusing already existing annotations and, therefore, can be regenerated from subsequent UMLS versions. PMID:21635749

  14. 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 among children and adolescents with a diagnosis of ADHD, methylphenidate may improve teacher reported symptoms of ADHD and general behaviour and parent reported quality of life. However, given the risk of bias in the included studies, and the very low quality of outcomes, the magnitude of the effects is uncertain. Methylphenidate is associated with an increased risk of non-serious but not serious adverse events. Funding, competing interests, data sharing Region Zealand Research Foundation and Copenhagen Trial Unit. Competing interests are given in the full paper on bmj.com. Full data are available in the version of this review published in The Cochrane Library. PMID:26608309

  15. 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

  16. 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.

  17. 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.

  18. Querying parse tree database of Medline text to synthesize user-specific biomolecular networks.

    PubMed

    Tari, Luis; Hakenberg, Jrg; Gonzalez, Graciela; Baral, Chitta

    2009-01-01

    Curated biological knowledge of interactions and pathways is largely available from various databases, and network synthesis is a popular method to gain insight into the data. However, such data from curated databases presents a single view of the knowledge to the biologists, and it may not be suitable to researchers' specific needs. On the other hand, Medline abstracts are publicly accessible and encode the necessary information to synthesize different kinds of biological networks. In this paper, we propose a new paradigm in synthesizing biomolecular networks by allowing biologists to create their own networks through queries to a specialized database of Medline abstracts. With this approach, users can specify precisely what kind of information they want in the resulting networks. We demonstrate the feasibility of our approach in the synthesis of gene-drug, gene-disease and protein-protein interaction networks. We show that our approach is capable of synthesizing these networks with high precision and even finds relations that have yet to be curated in public databases. In addition, we demonstrate a scenario of recovering a drug-related pathway using our approach. PMID:19209697

  19. A performance and failure analysis of SAPHIRE with a MEDLINE test collection.

    PubMed Central

    Hersh, W R; Hickam, D H; Haynes, R B; McKibbon, K A

    1994-01-01

    OBJECTIVE: Assess the performance of the SAPHIRE automated information retrieval system. DESIGN: Comparative study of automated and human searching of a MEDLINE test collection. MEASUREMENTS: Recall and precision of SAPHIRE were compared with those attributes of novice physicians, expert physicians, and librarians for a test collection of 75 queries and 2,334 citations. Failure analysis assessed the efficacy of the Metathesaurus as a concept vocabulary; the reasons for retrieval of nonrelevant articles and nonretrieval of relevant articles; and the effect of changing the weighting formula for relevance ranking of retrieved articles. RESULTS: Recall and precision of SAPHIRE were comparable to those of both physician groups, but less than those of librarians. CONCLUSION: The current version of the Metathesaurus, as utilized by SAPHIRE, was unable to represent the conceptual content of one-fourth of physician-generated MEDLINE queries. The most likely cause for retrieval of nonrelevant articles was the presence of some or all of the search terms in the article, with frequencies high enough to lead to retrieval. The most likely cause for nonretrieval of relevant articles was the absence of the actual terms from the query, with synonyms or hierarchically related terms present instead. There were significant variations in performance when SAPHIRE's concept-weighing formulas were modified. PMID:7719787

  20. Automatic identification of comparative effectiveness research from Medline citations to support clinicians treatment information needs

    PubMed Central

    Zhang, Mingyuan; Fiol, Guilherme Del; Grout, Randall W.; Jonnalagadda, Siddhartha; Medlin, Richard; Mishra, Rashmi; Weir, Charlene; Liu, Hongfang; Mostafa, Javed; Fiszman, Marcelo

    2014-01-01

    Online knowledge resources such as Medline can address most clinicians patient care information needs. Yet, significant barriers, notably lack of time, limit the use of these sources at the point of care. The most common information needs raised by clinicians are treatment-related. Comparative effectiveness studies allow clinicians to consider multiple treatment alternatives for a particular problem. Still, solutions are needed to enable efficient and effective consumption of comparative effectiveness research at the point of care. Objective Design and assess an algorithm for automatically identifying comparative effectiveness studies and extracting the interventions investigated in these studies. Methods The algorithm combines semantic natural language processing, Medline citation metadata, and machine learning techniques. We assessed the algorithm in a case study of treatment alternatives for depression. Results Both precision and recall for identifying comparative studies was 0.83. A total of 86% of the interventions extracted perfectly or partially matched the gold standard. Conclusion Overall, the algorithm achieved reasonable performance. The method provides building blocks for the automatic summarization of comparative effectiveness research to inform point of care decision-making. PMID:23920677

  1. 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

  2. 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.

  3. A Zipfian model of an automatic bibliographic system: an application to MEDLINE.

    PubMed

    Fedorowicz, J

    1982-07-01

    A Zipfian model of an automatic bibliographic system is developed using parameters describing the contents of it database and its inverted file. The underlying structure of the Zipf distribution is derived, with particular emphasis on its application to work frequencies, especially with regard to the inverted flies of an automatic bibliographic system. Andrew Booth developed a form of Zipf's law which estimates the number of words of a particular frequency for a given author and text. His formulation has been adopted as the basis of a model of term dispersion in an inverted file system. The model is also distinctive in its consideration of the proliferation of spelling errors in free text, and the inclusion of all searchable elements from the system's inverted file. This model is applied to the National Library of Medicine's MEDLINE. The model carries implications for the determination of database storage requirements, search response time, and search exhaustiveness. PMID:10298621

  4. 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.

  5. Automatic Summarization of MEDLINE Citations for EvidenceBased 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

  6. 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

  7. SPIRS, WinSPIRS, and OVID: a comparison of three MEDLINE-on-CD-ROM interfaces.

    PubMed Central

    Schoonbaert, D

    1996-01-01

    Three MEDLINE-on-CD-ROM interfaces are compared: SPIRS (version 3.11) and WinSPIRS (version 1.0) from SilverPlatter and OVID (version 3.0, DOS and Windows interfaces) from CD Plus Technologies. Though the database is the same, there are substantial differences among the interfaces in the way these data are presented and can be searched. These different approaches are discussed, and a detailed comparative table is included. It is obvious that all three interfaces are quite good yet none of them is perfect; each has desirable and unfortunate features. Together, they offer an enormous range of possibilities. Users would benefit if most of the better features (e.g., easy menu, free-text retrieval, pre-exploded thesaurus terms) were implemented in future versions of these interfaces and if system operators were given greater latitude to determine the system defaults appropriate to their specific situations and customers. PMID:8938331

  8. Knowledge-based Methods to Help Clinicians Find Answers in MEDLINE

    PubMed Central

    Sneiderman, Charles A.; Demner-Fushman, Dina; Fiszman, Marcelo; Ide, Nicholas C.; Rindflesch, Thomas C.

    2007-01-01

    Objectives Large databases of published medical research can support clinical decision making by providing physicians with the best available evidence. The time required to obtain optimal results from these databases using traditional systems often makes accessing the databases impractical for clinicians. This article explores whether a hybrid approach of augmenting traditional information retrieval with knowledge-based methods facilitates finding practical clinical advice in the research literature. Design Three experimental systems were evaluated for their ability to find MEDLINE citations providing answers to clinical questions of different complexity. The systems (SemRep, Essie, and CQA-1.0), which rely on domain knowledge and semantic processing to varying extents, were evaluated separately and in combination. Fifteen therapy and prevention questions in three categories (general, intermediate, and specific questions) were searched. The first 10 citations retrieved by each system were randomized, anonymized, and evaluated on a three-point scale. The reasons for ratings were documented. Measurements Metrics evaluating the overall performance of a system (mean average precision, binary preference) and metrics evaluating the number of relevant documents in the first several presented to a physician were used. Results Scores (mean average precision = 0.57, binary preference = 0.71) for fusion of the retrieval results of the three systems are significantly (p < 0.01) better than those for any individual system. All three systems present three to four relevant citations in the first five for any question type. Conclusion The improvements in finding relevant MEDLINE citations due to knowledge-based processing show promise in assisting physicians to answer questions in clinical practice. PMID:17712086

  9. Randomized Controlled Trials of HIV/AIDS Prevention and Treatment in Africa: Results from the Cochrane HIV/AIDS Specialized Register

    PubMed Central

    Zani, Babalwa; Pienaar, Elizabeth D.; Oliver, Joy; Siegfried, Nandi

    2011-01-01

    Introduction To effectively address HIV/AIDS in Africa, evidence on preventing new infections and providing effective treatment is needed. Ideally, decisions on which interventions are effective should be based on evidence from randomized controlled trials (RCTs). Our previous research described African RCTs of HIV/AIDS reported between 1987 and 2003. This study updates that analysis with RCTs published between 2004 and 2008. Objectives To describe RCTs of HIV/AIDS conducted in Africa and reported between 2004 and 2008. Methods We searched the Cochrane HIV/AIDS Specialized Register in September 2009. Two researchers independently evaluated studies for inclusion and extracted data using standardized forms. Details included location of trials, interventions, methodological quality, location of principal investigators and funders. Results Our search identified 834 RCTs, with 68 conducted in Africa. Forty-three assessed prevention-interventions and 25 treatment-interventions. Fifteen of the 43 prevention RCTs focused on preventing mother-to-child HIV transmission. Thirteen of the 25 treatment trials focused on opportunistic infections. Trials were conducted in 16 countries with most in South Africa (20), Zambia (12) and Zimbabwe (9). The median sample size was 628 (range 33-9645). Methods used for the generation of the allocation sequence and allocation concealment were adequate in 38 and 32 trials, respectively, and 58 reports included a CONSORT recommended flow diagram. Twenty-nine principal investigators resided in the United States of America (USA) and 18 were from African countries. Trials were co-funded by different agencies with most of the funding obtained from USA governmental and non-governmental agencies. Nineteen pharmaceutical companies provided partial funding to 15 RCTs and African agencies co-funded 17 RCTs. Ethical approval was reported in 65 trials and informed consent in 61 trials. Conclusion Prevention trials dominate the trial landscape in Africa. Of note, few principal investigators and funders are from Africa. These findings mirror our previous work and continue to indicate a need for strengthening trial research capacity in Africa. PMID:22194905

  10. Using MEDLINE Elemental Similarity to Assist in the Article Screening Process for Systematic Reviews

    PubMed Central

    Ji, Xiaonan

    2015-01-01

    Background Systematic reviews and their implementation in practice provide high quality evidence for clinical practice but are both time and labor intensive due to the large number of articles. Automatic text classification has proven to be instrumental in identifying relevant articles for systematic reviews. Existing approaches use machine learning model training to generate classification algorithms for the article screening process but have limitations. Objective We applied a network approach to assist in the article screening process for systematic reviews using predetermined article relationships (similarity). The article similarity metric is calculated using the MEDLINE elements title (TI), abstract (AB), medical subject heading (MH), author (AU), and publication type (PT). We used an article network to illustrate the concept of article relationships. Using the concept, each article can be modeled as a node in the network and the relationship between 2 articles is modeled as an edge connecting them. The purpose of our study was to use the article relationship to facilitate an interactive article recommendation process. Methods We used 15 completed systematic reviews produced by the Drug Effectiveness Review Project and demonstrated the use of article networks to assist article recommendation. We evaluated the predictive performance of MEDLINE elements and compared our approach with existing machine learning model training approaches. The performance was measured by work saved over sampling at 95% recall (WSS95) and the F-measure (F1). We also used repeated analysis over variance and Hommels multiple comparison adjustment to demonstrate statistical evidence. Results We found that although there is no significant difference across elements (except AU), TI and AB have better predictive capability in general. Collaborative elements bring performance improvement in both F1 and WSS95. With our approach, a simple combination of TI+AB+PT could achieve a WSS95 performance of 37%, which is competitive to traditional machine learning model training approaches (23%-41% WSS95). Conclusions We demonstrated a new approach to assist in labor intensive systematic reviews. Predictive ability of different elements (both single and composited) was explored. Without using model training approaches, we established a generalizable method that can achieve a competitive performance. PMID:26323593

  11. Hybrid approach combining contextual and statistical information for identifying MEDLINE citation terms

    NASA Astrophysics Data System (ADS)

    Kim, In Cheol; Le, Daniel X.; Thoma, George R.

    2008-01-01

    There is a strong demand for developing automated tools for extracting pertinent information from the biomedical literature that is a rich, complex, and dramatically growing resource, and is increasingly accessed via the web. This paper presents a hybrid method based on contextual and statistical information to automatically identify two MEDLINE citation terms: NIH grant numbers and databank accession numbers from HTML-formatted online biomedical documents. Their detection is challenging due to many variations and inconsistencies in their format (although recommended formats exist), and also because of their similarity to other technical or biological terms. Our proposed method first extracts potential candidates for these terms using a rule-based method. These are scored and the final candidates are submitted to a human operator for verification. The confidence score for each term is calculated using statistical information, and morphological and contextual information. Experiments conducted on more than ten thousand HTML-formatted online biomedical documents show that most NIH grant numbers and databank accession numbers can be successfully identified by the proposed method, with recall rates of 99.8% and 99.6%, respectively. However, owing to the high false alarm rate, the proposed method yields F-measure rates of 86.6% and 87.9% for NIH grants and databanks, respectively.

  12. Characteristics of project management at institutions sponsoring National Library of Medicine MedlinePlus Go Local*

    PubMed Central

    Olney, Cynthia A.; Backus, Joyce E. B.; Klein, Lori J.

    2010-01-01

    Objectives: Through interviews with the National Library of Medicine's MedlinePlus Go Local collaborators, an evaluation team sought to identify process characteristics that are critical for long-term sustainability of Go Local projects and to describe the impact that Go Local projects have on sponsoring institutions. Methods: Go Local project coordinators (n?=?44) at 31 sponsor institutions participated in semi-structured interviews about their experiences developing and maintaining Go Local sites. Interviews were summarized, checked for accuracy by the participating librarians, and analyzed using a general inductive methodology. Results: Institutional factors that support Go Local projects were identified through the interviews, as well as strategies for staffing and partnerships with external organizations. Positive outcomes for sponsoring institutions also were identified. Conclusions: The findings may influence the National Library of Medicine team's decisions about improvements to its Go Local system and the support it provides to sponsoring institutions. The findings may benefit current sponsoring institutions as well as those considering or planning a Go Local project. PMID:20098657

  13. The relationship between term specificity in MeSH and online postings in MEDLINE.

    PubMed Central

    Weinberg, B H; Cunningham, J A

    1985-01-01

    Hierarchically structured thesauri--including MeSH--were studied to test the assumption of an inverse relationship between term specificity and the number of postings in online databases. It was suggested that this assumption holds only for peripheral terms and that the opposite is true for the central terms of a discipline. The Environment tree structure of MeSH was used to test the "peripheral" hypothesis, which was supported at a .05 level of significance, but the scattergram on the Endocrine Diseases tree, which was run to test the "central" hypothesis, had an even better level, .02. The commonly held belief that specific terms are added to a thesaurus when more general ones get too many postings was also tested. The relationship between specificity and dates was supported in MeSH (.015). The corollary--that terms with later dates have fewer postings--was supported at a .001 level of significance. The results for MeSH were much more significant than for other hierarchically structured thesauri, which indicates that thesaurus development at NLM involves interaction with MEDLINE to preclude an excessive number of postings to any one term. PMID:3902130

  14. Ambiguity of Human Gene Symbols in LocusLink and MEDLINE: Creating an Inventory and a Disambiguation Test Collection

    PubMed Central

    Weeber, Marc; Schijvenaars, Bob J. A.; van Mulligen, Erik M.; Mons, Barend; Jelier, Rob; van der Eijk, Christiaan; Kors, Jan A.

    2003-01-01

    Genes are discovered almost on a daily basis and new names have to be found. Although there are guidelines for gene nomenclature, the naming process is highly creative. Human genes are often named with a gene symbol and a longer, more descriptive term; the short form is very often an abbreviation of the long form. Abbreviations in biomedical language are highly ambiguous, i.e., one gene symbol often refers to more than one gene. Using an existing abbreviation expansion algorithm, we explore MEDLINE for the use of human gene symbols derived from LocusLink. It turns out that just over 40% of these symbols occur in MEDLINE, however, many of these occurrences are not related to genes. Along the process of making an inventory, a disambiguation test collection is constructed automatically. PMID:14728264

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

    PubMed Central

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

    1997-01-01

    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

  16. 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

  17. Comparison of two schemes for automatic keyword extraction from MEDLINE for functional gene clustering.

    PubMed

    Liu, Ying; Ciliax, Brian J; Borges, Karin; Dasigi, Venu; Ram, Ashwin; Navathe, Shamkant B; Dingledine, Ray

    2004-01-01

    One of the key challenges of microarray studies is to derive biological insights from the unprecedented quatities of data on gene-expression patterns. Clustering genes by functional keyword association can provide direct information about the nature of the functional links among genes within the derived clusters. However, the quality of the keyword lists extracted from biomedical literature for each gene significantly affects the clustering results. We extracted keywords from MEDLINE that describes the most prominent functions of the genes, and used the resulting weights of the keywords as feature vectors for gene clustering. By analyzing the resulting cluster quality, we compared two keyword weighting schemes: normalized z-score and term frequency-inverse document frequency (TFIDF). The best combination of background comparison set, stop list and stemming algorithm was selected based on precision and recall metrics. In a test set of four known gene groups, a hierarchical algorithm correctly assigned 25 of 26 genes to the appropriate clusters based on keywords extracted by the TDFIDF weighting scheme, but only 23 og 26 with the z-score method. To evaluate the effectiveness of the weighting schemes for keyword extraction for gene clusters from microarray profiles, 44 yeast genes that are differentially expressed during the cell cycle were used as a second test set. Using established measures of cluster quality, the results produced from TFIDF-weighted keywords had higher purity, lower entropy, and higher mutual information than those produced from normalized z-score weighted keywords. The optimized algorithms should be useful for sorting genes from microarray lists into functionally discrete clusters. PMID:16448032

  18. An evaluation of Medline published paediatric audits from 1966 to 1999

    PubMed Central

    O'Gorman, Clodagh Sheila; Ziedan, Yasir; O'Neill, Michael Brendan

    2007-01-01

    Aim To evaluate the quality of paediatric audits from 1966 to 1999. Methods A Medline search was performed using the MeSH terms audit, child, paediatric (and pediatric). Predefined core elements of audit were used as inclusion criteria for entry of an article into this study. These criteria were as follows: (1) an article deals with a healthcare topic; (2) a standard is predefined; (3) actual practice is evaluated; (4) actual practice is compared with the standard. The fifth criterion of audit, dissemination of information and reaudit, was not an inclusion criterion, as it was not used in the early years covered by this study. Empirical grading of standards was used. Results The search yielded 442 articles, of which 303 (100%) were related to paediatric healthcare and were reviewed. Standards were defined in 115 (38%) articles. Audit against the standard was performed in 92 (30.4%) articles, of which 42 (45.6%) were published before, and 50 (54.3%) after, 1990. 18 (5.9%) articles were re?audited: 6 (14.3%) were published before, and 12 (24%) after, 1990. Of the 188 paediatric studies rejected, 119 (63.3%) described practice observations. Conclusion Many articles in paediatrics are published as audits, but they do not contain the core elements of audit. Although audit is a potentially valuable tool in clinical medicine, the publication of poor?quality audits may lead to the decline of the audit concept. Suggestions on ways to improve the quality of published audits are made. PMID:16738000

  19. 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, Andr-M; Osmers, Rdiger; Schnitker, Jrg; 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?

  20. Viscosupplementation for treating knee osteoarthrosis: review of the literature☆

    PubMed Central

    Ammar, Tiago Youssef; Pereira, Tomas Araujo Prado; Mistura, Saulo Luís Lopes; Kuhn, André; Saggin, José Idilio; Lopes Júnior, Osmar Valadão

    2015-01-01

    The aim here was to evaluate the evidence that might support or refute the use of intra-articular viscosupplementation in treating patients with symptomatic knee osteoarthrosis. A review of the literature was conducted using the Medline, PubMed and Cochrane Controlled Trial Register databases and Cochrane database systematic reviews (Cochrane Library). Only studies presenting a high level of evidence were taken into consideration. This study included analysis on randomized clinical trials that included at least 100 patients in each intervention group, meta-analyses and systematic reviews. Two meta-analyses, five systematic reviews and six randomized clinical trials fulfilled the inclusion criteria for this review. In the light of the best evidence available so far, there is no consensus for indicating or even for contraindicating the use of intra-articular viscosupplementation among patients with symptomatic knee osteoarthrosis (level of evidence I and degree of recommendation A). Further studies with appropriate methodology are needed to elucidate this matter. PMID:26535192

  1. Public Library Participation in a MedlinePlus Go Local Project: Perceptions of Georgia Librarians and Staff.

    PubMed

    Smith, Rita B

    2010-01-01

    In an effort to promote public library involvement in Georgia Health - Go Local, a National Library of Medicine initiative to link consumers to health resources in their local areas, staff at a large public library system in south Georgia were trained to enter local records into the Go Local database. Results of two follow-up focus groups indicated that participants were enthusiastic about demonstrating Go Local and MedlinePlus to library users but were not comfortable creating or maintaining Go Local records due to concerns about the relevance of the project, unease with medical terminology, varied levels of computer expertise, and worries about possible liability. PMID:21197119

  2. Public Library Participation in a MedlinePlus Go Local Project: Perceptions of Georgia Librarians and Staff

    PubMed Central

    Smith, Rita B.

    2010-01-01

    In an effort to promote public library involvement in Georgia Health Go Local, a National Library of Medicine initiative to link consumers to health resources in their local areas, staff at a large public library system in south Georgia were trained to enter local records into the Go Local database. Results of two follow-up focus groups indicated that participants were enthusiastic about demonstrating Go Local and MedlinePlus to library users but were not comfortable creating or maintaining Go Local records due to concerns about the relevance of the project, unease with medical terminology, varied levels of computer expertise, and worries about possible liability. PMID:21197119

  3. Using argumentation to retrieve articles with similar citations: an inquiry into improving related articles search in the MEDLINE digital library.

    PubMed

    Tbahriti, Imad; Chichester, Christine; Lisacek, Frdrique; Ruch, Patrick

    2006-06-01

    The aim of this study is to investigate the relationships between citations and the scientific argumentation found abstracts. We design a related article search task and observe how the argumentation can affect the search results. We extracted citation lists from a set of 3200 full-text papers originating from a narrow domain. In parallel, we recovered the corresponding MEDLINE records for analysis of the argumentative moves. Our argumentative model is founded on four classes: PURPOSE, METHODS, RESULTS and CONCLUSION. A Bayesian classifier trained on explicitly structured MEDLINE abstracts generates these argumentative categories. The categories are used to generate four different argumentative indexes. A fifth index contains the complete abstract, together with the title and the list of Medical Subject Headings (MeSH) terms. To appraise the relationship of the moves to the citations, the citation lists were used as the criteria for determining relatedness of articles, establishing a benchmark; it means that two articles are considered as "related" if they share a significant set of co-citations. Our results show that the average precision of queries with the PURPOSE and CONCLUSION features is the highest, while the precision of the RESULTS and METHODS features was relatively low. A linear weighting combination of the moves is proposed, which significantly improves retrieval of related articles. PMID:16165395

  4. Recommendations for the treatment of Sjögren's syndrome.

    PubMed

    Valim, Valéria; Trevisani, Virgínia Fernandes Moça; Pasoto, Sandra Gofinet; Serrano, Erica Vieira; Ribeiro, Sandra Lúcia Euzébio; Fidelix, Tania Sales de Alencar; Vilela, Verônica Silva; Prado, Leandro Lara do; Tanure, Leandro Augusto; Libório-Kimura, Tatiana Nayara; Brito Filho, Odvaldo Honor de; Barros, Liliana Aparecida Pimenta de; Miyamoto, Samira Tatiyama; Lourenço, Silvia Vanessa; Santos, Maria Carmen Lopes Ferreira Silva; Vieira, Luis Antonio; Adán, Consuelo Bueno Diniz; Bernardo, Wanderley Marques

    2015-01-01

    The recommendations proposed by the Sjögren's Syndrome Committee of the Brazilian Society of Rheumatology for the treatment of Sjögren's syndrome were based on a systematic review of literature in Medline (PubMed) and the Cochrane databases until October 2014 and on expert opinion in the absence of studies on the subject. 131 items classified according to Oxford & Grade were included. These recommendations were developed in order to guide the appropriate management and facilitate the access to treatment for those patients with an appropriate indication, considering the Brazilian socioeconomic context and pharmacological agents available in this country. PMID:26360421

  5. 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

  6. The role of the health services in the prevention of alcohol-related facial injury.

    PubMed

    McHugh, E E; Al-Awadhi, E; Stassen, L F A

    2009-10-01

    This paper outlines the preventive health strategic measures that are currently in place and it endeavours to consider how improvements can be made to our national preventive strategy with the goal of reducing alcohol-related facial injuries. It is based on a review of the literature sourced through PubMed, Ovid Medline and the Cochrane database. The main findings are that increased funding, legislative amendment and media involvement are key to improving the work of the health services in their struggle to limit the ever increasing alcohol-related incidents that are experienced by society today. PMID:19848065

  7. 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

  8. Integrating CD-ROM Medline with electronic mail: first step in implementing new strategy for online reference library.

    PubMed Central

    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

  9. 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 Hamletmostly 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 clichs. Whether they attract readers or citations is unknown, but better ways of gaining attention exist. PMID:16373745

  10. Alignment of systematic reviews published in the Cochrane Database of Systematic Reviews and the Database of Abstracts and Reviews of Effectiveness with global burden-of-disease data: a bibliographic analysis

    PubMed Central

    Yoong, Sze Lin; Hall, Alix; Williams, Christopher M; Skelton, Eliza; Oldmeadow, Christopher; Wiggers, John; Karimkhani, Chante; Boyers, Lindsay N; Dellavalle, Robert P; Hilton, John; Wolfenden, Luke

    2015-01-01

    Background Systematic reviews of high-quality evidence are used to inform policy and practice. To improve community health, the production of such reviews should align with burden of disease. This study aims to assess if the volume of research output from systematic reviews proportionally aligns with burden of disease assessed using percentages of mortality and disability-adjusted life years (DALYs). Methods A cross-sectional audit of reviews published between January 2012 and August 2013 in the Cochrane Database of Systematic Reviews (CDSR) and Database of Abstracts of Reviews of Effects (DARE) was undertaken. Percentages of mortality and DALYs were obtained from the 2010 Global Burden of Disease study. Standardised residual differences (SRD) based on percentages of mortality and DALYs were calculated, where conditions with SRD of more than or less than three were considered overstudied or understudied, respectively. Results 1029 reviews from CDSR and 1928 reviews from DARE were examined. There was a significant correlation between percentage DALYs and systematic reviews published in CDSR and DARE databases (CDSR: r=0.68, p=0.001; DARE: r=0.60, p<0.001). There was no significant correlation between percentage mortality and number of systematic reviews published in either database (CDSR: r=0.34, p=0.14; DARE: r=0.22, p=0.34). Relative to percentage of mortality, mental and behavioural disorders, musculoskeletal conditions and other non-communicable diseases were overstudied. Maternal disorders were overstudied relative to percentages of mortality and DALYs in CDSR. Conclusions The focus of systematic reviews is moderately correlated with DALYs. A number of conditions may be overstudied relative to percentage of mortality particularly in the context of health and medical reviews. PMID:25888595

  11. 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 signed by many different authors (in the same decade, 25.77% of the documents had between 6 and 9 co-authors, and 10.28% had 10 or more). With regard to the network indicators, the average degree gradually increased up to 10.97 in the study period. The percentage of authors pertaining to the largest component also rose to 73.02% of the authors. The clustering coefficient, on the other hand, remained stable throughout the entire 70-year period, with values hovering around 0.9. Finally, the average distance peaked in the decades 1974–1983 (8.29) and 1984–2003 (8.12) then fell over the next two decades, down to 5.25 in 2004–2013. The construction of the co-authorship network (threshold of collaboration ≥ 10 co-authored works) revealed a giant component of 161 researchers, containing 6 highly cohesive sub-components. Conclusions Our study reveals the existence of a growing research community in which collaboration is increasingly important. We can highlight an essential feature associated with scientific collaboration: multi-authored papers, with growing numbers of collaborators contributing to them, are becoming more and more common, therefore the formation of research groups of increasing depth (specialization) and breadth (multidisciplinarity) is now a cornerstone of research success. PMID:26658481

  12. Searching for Controlled Trials of Complementary and Alternative Medicine: A Comparison of 15 Databases

    PubMed Central

    Cogo, Elise; Sampson, Margaret; Ajiferuke, Isola; Manheimer, Eric; Campbell, Kaitryn; Daniel, Raymond; Moher, David

    2011-01-01

    This project aims to assess the utility of bibliographic databases beyond the three major ones (MEDLINE, EMBASE and Cochrane CENTRAL) for finding controlled trials of complementary and alternative medicine (CAM). Fifteen databases were searched to identify controlled clinical trials (CCTs) of CAM not also indexed in MEDLINE. Searches were conducted in May 2006 using the revised Cochrane highly sensitive search strategy (HSSS) and the PubMed CAM Subset. Yield of CAM trials per 100 records was determined, and databases were compared over a standardized period (2005). The Acudoc2 RCT, Acubriefs, Index to Chiropractic Literature (ICL) and Hom-Inform databases had the highest concentrations of non-MEDLINE records, with more than 100 non-MEDLINE records per 500. Other productive databases had ratios between 500 and 1500 records to 100 non-MEDLINE recordsthese were AMED, MANTIS, PsycINFO, CINAHL, Global Health and Alt HealthWatch. Five databases were found to be unproductive: AGRICOLA, CAIRSS, Datadiwan, Herb Research Foundation and IBIDS. Acudoc2 RCT yielded 100 CAM trials in the most recent 100 records screened. Acubriefs, AMED, Hom-Inform, MANTIS, PsycINFO and CINAHL had more than 25 CAM trials per 100 records screened. Global Health, ICL and Alt HealthWatch were below 25 in yield. There were 255 non-MEDLINE trials from eight databases in 2005, with only 10% indexed in more than one database. Yield varied greatly between databases; the most productive databases from both sampling methods were Acubriefs, Acudoc2 RCT, AMED and CINAHL. Low overlap between databases indicates comprehensive CAM literature searches will require multiple databases. PMID:19468052

  13. 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 method allowed them more freedom of action. PMID:25763155

  14. Design and validation of an automated method to detect known adverse drug reactions in MEDLINE: a contribution from the EUADR project

    PubMed Central

    Avillach, Paul; Dufour, Jean-Charles; Diallo, Gayo; Salvo, Francesco; Joubert, Michel; Thiessard, Frantz; Mougin, Fleur; Trifir, Gianluca; Fourrier-Rglat, Annie; Pariente, Antoine; Fieschi, Marius

    2013-01-01

    Objectives The aim of this research was to automate the search of publications concerning adverse drug reactions (ADR) by defining the queries used to search MEDLINE and by determining the required threshold for the number of extracted publications to confirm the drug/event association in the literature. Methods We defined an approach based on the medical subject headings (MeSH) descriptor records and supplementary concept records thesaurus, using the subheadings chemically induced and adverse effects with the pharmacological action knowledge. An expert-built validation set of true positive and true negative drug/adverse event associations (n=61) was used to validate our method. Results Using a threshold of three of more extracted publications, the automated search method presented a sensitivity of 90% and a specificity of 100%. For nine different drug/event pairs selected, the recall of the automated search ranged from 24% to 64% and the precision from 93% to 48%. Conclusions This work presents a method to find previously established relationships between drugs and adverse events in the literature. Using MEDLINE, following a MeSH approach to filter the signals, is a valid option. Our contribution is available as a web service that will be integrated in the final European EUADR project (Exploring and Understanding Adverse Drug Reactions by integrative mining of clinical records and biomedical knowledge) automated system. PMID:23195749

  15. MedlinePlus FAQ: What is MedlinePlus?

    MedlinePLUS

    ... encyclopedia brings health consumers an extensive library of medical images and videos , as well as over 4,000 articles about diseases, tests, symptoms, injuries, and surgeries. The Merriam-Webster medical dictionary allows you to look up definitions and ...

  16. [Systematic review of diagnostic tests accuracy: a narrative review].

    PubMed

    de Oliveira, Glria Maria; Camargo, Fbio Trinca; Gonalves, Eduardo Costa; Duarte, Carlos Vinicius Nascimento; Guimares, 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

  17. Health Videos: MedlinePlus

    MedlinePLUS Videos and Cool Tools

    ... nlm.nih.gov/medlineplus/ency/anatomyvideos.html.htm Health Videos To use the sharing features on this ... first to achieve this important distinction for online health information and services. Learn more about A.D. ...

  18. Surgery Videos: MedlinePlus

    MedlinePLUS Videos and Cool Tools

    ... 3/5/2009) Partial Knee with Personalized Patient Care (New Albany Surgical Hospital, New Albany, OH, 2/ ... Matched Instruments and Total Knee System (Intermountain Health Care Hospital, Park City, UT, 5/10/2011) Personalized ...

  19. Health Topics: MedlinePlus

    MedlinePLUS

    ... Reproductive System Disorders and Conditions Cancers Diabetes Mellitus Genetics/Birth Defects Infections Injuries and Wounds Mental Health and Behavior Metabolic Problems Poisoning, Toxicology, Environmental Health Pregnancy and ...

  20. Medical Dictionary: MedlinePlus

    MedlinePLUS

    ... https://www.nlm.nih.gov/medlineplus/mplusdictionary.html Medical Dictionary To use the sharing features on this ... Search term GO GO Visit the tutorial, Understanding Medical Words You may also be interested in these ...

  1. Medical Encyclopedia: MedlinePlus

    MedlinePLUS

    ... https://www.nlm.nih.gov/medlineplus/encyclopedia.html Medical Encyclopedia To use the sharing features on this ... please enable JavaScript. The A.D.A.M. Medical Encyclopedia includes over 4,000 articles about diseases, ...

  2. Preventive Treatments of Iron Deficiency Anaemia in Pregnancy: A Review of Their Effectiveness and Implications for Health System Strengthening

    PubMed Central

    Osungbade, Kayode O.; Oladunjoye, Adeolu O.

    2012-01-01

    Objectives. We conducted a review of effectiveness of preventive treatments of iron deficiency anaemia in pregnancy in developing countries and highlighted their constraints as well as interventions required to strengthen the health services. Methods. Literature from Pubmed (MEDLINE), AJOL, Google Scholar, and Cochrane database was reviewed. Results. Evidence-based preventive treatment options for iron deficiency anaemia in pregnancy include prophylaxis iron supplements and food fortification with iron. Evidence abounds on their effectiveness in reducing the prevalence of iron deficiency anaemia in pregnancy. However, these prospects are threatened by side effects of iron supplements, low utilization of maternal health service in developing countries, partial implementation of preventive treatments, and weak infrastructure and political commitment to implement mass fortification of local staple foods by national governments. Conclusion. Sustainability of effectiveness of preventive treatments of iron deficiency anaemia in pregnancy could be achieved if the identified threats are adequately addressed. PMID:22848829

  3. Timing of cannulation of arteriovenous grafts: are we too cautious?

    PubMed Central

    Al Shakarchi, Julien; Inston, Nicholas

    2015-01-01

    Background Timing of first cannulation of an arteriovenous graft has been the subject of great debate for clinicians worldwide. In this paper, we reviewed the current literature on the timing of first cannulation of arteriovenous grafts. Methods Searches of PubMed, Medline and the Cochrane Library were performed using specific search terms to identify articles, dealing primarily with the timing of dialysis graft cannulation. Results Following strict inclusion/exclusion criteria by two reviewers, eleven studies were included and divided into subgroups for ePTFE and new generation grafts. Conclusions The current literature does not seem to support the current guidelines as there is no evidence to suggest that a delay in cannulation of grafts will improve graft survival and patency. PMID:26034590

  4. Epidemiological aspects of rheumatoid arthritis patients affected by oral bisphosphonate-related osteonecrosis of the jaws.

    PubMed

    Conte-Neto, Nicolau; Bastos, Alliny Souza; Marcantonio, Rosemary Adriana Chierici; Junior, Elcio Marcantonio

    2012-01-01

    This literature review aims to evaluate the epidemiologic profile of patients with rheumatoid arthritis (RA) that developed a bisphosphonate-related osteonecrosis that affect the jaws (BRONJ), including demographic aspects, as well as clinical and therapeutic issues. A search of PUBMED/MEDLINE, Scopus, and Cochrane databases from January 2003 to September 2011 was conducted with the objective of identifying publications that contained case reports regarding oral BRONJ in RA patients. Patients with RA who develop oral BRONJ are usually women above 60 years taking steroids and long-term alendronate. Most of them have osteoporosis, and lesions, triggered by dental procedures, are usually detected at stage II in the mandible. Although there is no accepted treatment protocol, these patients seem to have better outcomes with conservative approaches that include antibiotic therapy, chlorhexidine, and drug discontinuation. PMID:22376948

  5. Pharmacokinetic drug-drug interaction and their implication in clinical management

    PubMed Central

    Palleria, Caterina; Di Paolo, Antonello; Giofr, Chiara; Caglioti, Chiara; Leuzzi, Giacomo; Siniscalchi, Antonio; De Sarro, Giovambattista; Gallelli, Luca

    2013-01-01

    Drug-drug interactions (DDIs) are one of the commonest causes of medication error in developed countries, particularly in the elderly due to poly-therapy, with a prevalence of 20-40%. In particular, poly-therapy increases the complexity of therapeutic management and thereby the risk of clinically important DDIs, which can both induce the development of adverse drug reactions or reduce the clinical efficacy. DDIs can be classify into two main groups: pharmacokinetic and pharmacodynamic. In this review, using Medline, PubMed, Embase, Cochrane library and Reference lists we searched articles published until June 30 2012, and we described the mechanism of pharmacokinetic DDIs focusing the interest on their clinical implications. PMID:24516494

  6. Laser-assisted treatment of dentinal hypersensitivity: a literature review.

    PubMed

    Biagi, Roberto; Cossellu, Gianguido; Sarcina, Michele; Pizzamiglio, Ilaria Tina; Farronato, Giampietro

    2015-01-01

    The purpose of this literature review was to evaluate the effectiveness of the laser-assisted treatment of dentinal hypersensitivity. A review with inclusion and exclusion criteria was performed from January 2009 to December 2014 with electronic data-bases: MedLine via PubMed, Science Direct and Cochrane Library. Research of paper magazines by hand was not considered. Forty-three articles were selected between literature reviews, in vitro studies, clinical trials, pilot and preliminary studies. The items were divided into laser-used groups for an accurate description, and then the reading of results into various typologies. Laser-assisted treatment reduces dentinal hypersensitivity-related pain, but also a psychosomatic component must be considered, so further studies and more suitable follow-ups are necessary. PMID:26941892

  7. Tranexamic acid for the management of uterine fibroid tumors: A systematic review of the current evidence

    PubMed Central

    Peitsidis, Panagiotis; Koukoulomati, Anna

    2014-01-01

    AIM: To conduct a detailed systematic review of the current evidence on the administration and efficacy of tranexamic acid in patients with menorrhagia due to uterine fibroids. METHODS: We conducted an electronic search on the following databases PubMed and Medline (1950-2013); (1980-2013); Cochrane library (1993-2013). RESULTS: A total of 36 articles were retrieved after the initial electronic search. Careful assessment of the retrieved studies led to the final selection of 5 articles for inclusion in the review. CONCLUSION: Tranexamic acid may reduce blood loss perioperatively in myomectomies. It may reduce the menorrhagia in patients with fibroids, however a stratification of fibroids by size and location is required to define the responses. It is safe in general, with mild adverse effects observed in some cases. More studies with a double-blind randomized design and larger numbers of participants are necessary to reach more precise and safe conclusions. PMID:25516866

  8. Interruptions of nurses' activities and patient safety: an integrative literature review1

    PubMed Central

    Monteiro, Cintia; Avelar, Ariane Ferreira Machado; Pedreira, Mavilde da Luz Gonalves

    2015-01-01

    OBJECTIVES: to identify characteristics related to the interruption of nurses in professional practice, as well as to assess the implications of interruptions for patient safety. METHOD: integrative literature review. The following databases were searched: Pubmed/Medline, LILACS, SciELO and Cochrane Library, using the descriptors interruptions and patient safety. An initial date was not established, but the final date was December 31, 2013. A total of 29 papers met the inclusion criteria. RESULTS: all the papers included describe interruptions as a harmful factor for patient safety. Data analysis revealed three relevant categories: characteristics of interruptions, implications for patient safety, and interventions to minimize interruptions. CONCLUSION: interruptions favor the occurrence of errors in the health field. Therefore, there is a need for further studies to understand such a phenomenon and its effects on clinical practice. PMID:25806646

  9. The application of sonography in shoulder pain evaluation and injection treatment after stroke: a systematic review

    PubMed Central

    Tao, Wu; Fu, Yu; Hai-xin, Song; Yan, Dong; Jian-hua, Li

    2015-01-01

    [Purpose] This review article is designed to expose the application of sonography in shoulder pain after stroke. [Methods] A range of databases was searched to identify articles that address sonography examination, with or without ultrasound guided corticosteroid injection for hemiplegic shoulder pain (HSP). The electronic databases of PubMed, CENTRAL, CINAHL, Cochrane Library, Medline were searched. [Results] According to the articles identified in our databases research, sonographic technique has potential to provide objective measurements in patients with HSP. The main sonography finding of HSP included subacromial subdeltoid (SASD) bursal effusion, tendinosis of the supraspinatus and subscapularis tendon, long head of biceps tendon sheath effusion, and shoulder subluxation. Our analysis also revealed significantly decreased pain score (VAS) and increased passive external rotation degree in the steroid injection group than control group. [Conclusion] The sonography examination is useful for HSP assessment and ultrasound guided technique is recommended for HSP injection treatment. PMID:26504346

  10. The application of sonography in shoulder pain evaluation and injection treatment after stroke: a systematic review.

    PubMed

    Tao, Wu; Fu, Yu; Hai-Xin, Song; Yan, Dong; Jian-Hua, Li

    2015-09-01

    [Purpose] This review article is designed to expose the application of sonography in shoulder pain after stroke. [Methods] A range of databases was searched to identify articles that address sonography examination, with or without ultrasound guided corticosteroid injection for hemiplegic shoulder pain (HSP). The electronic databases of PubMed, CENTRAL, CINAHL, Cochrane Library, Medline were searched. [Results] According to the articles identified in our databases research, sonographic technique has potential to provide objective measurements in patients with HSP. The main sonography finding of HSP included subacromial subdeltoid (SASD) bursal effusion, tendinosis of the supraspinatus and subscapularis tendon, long head of biceps tendon sheath effusion, and shoulder subluxation. Our analysis also revealed significantly decreased pain score (VAS) and increased passive external rotation degree in the steroid injection group than control group. [Conclusion] The sonography examination is useful for HSP assessment and ultrasound guided technique is recommended for HSP injection treatment. PMID:26504346

  11. Nanotechnology and its Application in Dentistry

    PubMed Central

    Abiodun-Solanke, IMF; Ajayi, DM; Arigbede, AO

    2014-01-01

    Nanotechnology influences almost every facet of everyday life from security to medicine. The concept of nanotechnology is that when one goes down to the bottom of things, one can discover unlimited possibilities and potential of the basic particle. In nanotechnology, analysis can be made to the level of manipulating atoms, molecules and chemical bonds between them. The growing interest in the dental applications of nanotechnology is leading to the emergence of a new field called nanodentistry. An electronic database search that included PubMed, MedLine, and Cochrane library was conducted. Key words used in the search are nanotechnology dentistry and applications. Language limitation was set as articles reviewed were only those written and published in English language. We did not search the gray literature. Initially, 52 articles were retrieved from the database, and articles considered were those published from 2008 to 2013. Eight articles that met the selection criteria were eventually selected and reviewed. PMID:25364585

  12. [Ethical problems experienced by nurses in primary health care: integrative literature review].

    PubMed

    Nora, Carlise Rigon Dalla; Zoboli, Elma Lourdes Campos Pavone; Vieira, Margarida

    2015-03-01

    The aim of this study is to identify ethical problems experienced by nurses in primary health care and resources for coping based on publications on the subject. An integrative literature review was performed between the months of October and November 2013, using the databases: BDTD, CINAHL, LILACS, MEDLINE, Biblioteca Cochrane, PubMed, RCAAP and SciELO. Articles, dissertations and theses published in Portuguese, English and Spanish were included, totalling 31 studies published from 1992 to 2013. This analysis resulted in four categories: ethical problems in the relationship between team members, ethical problems in the relationship with the user, ethical problems in health services management and resources for coping with ethical problems. Results showed that nurses need to be prepared to face ethical problems, emphasizing the importance of ethics education during the education process before and during professional practice to enhance the development of ethical sensitivity and competence for problem resolution. PMID:26098811

  13. Laser-assisted treatment of dentinal hypersensitivity: a literature review

    PubMed Central

    Biagi, Roberto; Cossellu, Gianguido; Sarcina, Michele; Pizzamiglio, Ilaria Tina; Farronato, Giampietro

    2015-01-01

    Summary The purpose of this literature review was to evaluate the effectiveness of the laser-assisted treatment of dentinal hypersensitivity. A review with inclusion and exclusion criteria was performed from January 2009 to December 2014 with electronic data-bases: MedLine via PubMed, Science Direct and Cochrane Library. Research of paper magazines by hand was not considered. Forty-three articles were selected between literature reviews, in vitro studies, clinical trials, pilot and preliminary studies. The items were divided into laser-used groups for an accurate description, and then the reading of results into various typologies. Laser-assisted treatment reduces dentinal hypersensitivity-related pain, but also a psychosomatic component must be considered, so further studies and more suitable follow-ups are necessary. PMID:26941892

  14. Pharmaceutical applications and phytochemical profile of Cinnamomum burmannii

    PubMed Central

    Al-Dhubiab, Bandar E.

    2012-01-01

    Extensive studies have been carried out in the last decade to assess the pharmaceutical potential and screen the phytochemical constituents of Cinnamomum burmannii. Databases such as PubMed (MEDLINE), Science Direct (Embase, Biobase, biosis), Scopus, Scifinder, Google Scholar, Google Patent, Cochrane database, and web of science were searched using a defined search strategy. This plant is a member of the genus Cinnamomum and is traditionally used as a spice. Cinnamomum burmannii have been demonstrated to exhibit analgesic, antibacterial, anti-diabetic, anti-fungal, antioxidant, antirheumatic, anti-thrombotic, and anti-tumor activities. The chemical constituents are mostly cinnamyl alcohol, coumarin, cinnamic acid, cinnamaldehyde, anthocynin, and essential oils together with constituents of sugar, protein, crude fats, pectin, and others. This review presents an overview of the current status and knowledge on the traditional usage, the pharmaceutical, biological activities, and phytochemical constituents reported for C. burmannii. PMID:23055638

  15. Squamous cell carcinoma and dental implants: A systematic review of case reports

    PubMed Central

    Jeelani, S.; Rajkumar, E.; Mary, G. Geena; Khan, Parvez Ahmad; Gopal, Harish; Roy, Soumya; Maheswaran, T.; Anand, B.

    2015-01-01

    Cancer is one of the leading causes of death world-wide. Apart from the most common etiopathological factors related to cancer, at times very rare causes such as irritant or foreign body induced carcinogenesis is not to be overlooked. To systematically review case reports concerned with the association between dental implants and oral squamous cell carcinoma. A Medline (PubMed), Cochrane database, and Google Scholar search was conducted of dental article published in English related to case reports concerned with oral squamous cell carcinoma occurring around dental implants from 2000 to 2014. Twenty articles were retrieved, which included 20 rare case reports which were systematically reviewed and the results were obtained pertaining to age, clinical symptoms, habits, previous history of cancer, potentially malignant disorders, systemic illness, and local factors. It is imperative to identify promptly persisting inflammation associated with implants. Since malignancy may disguise as periimplantitis, especially in patients who are at risk with contributing prominent predisposing factors. PMID:26538881

  16. 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

  17. Prevalence of sleep bruxism in children: A systematic review

    PubMed Central

    Machado, Eduardo; Dal-Fabbro, Cibele; Cunali, Paulo Afonso; Kaizer, Osvaldo Bazzan

    2014-01-01

    INTRODUCTION: Prevalence of sleep bruxism (SB) in children is subject to discussions in the literature. OBJECTIVE: This study is a systematic literature review aiming to critically assess the prevalence of SB in children. METHODS: Survey using the following research databases: MEDLINE, Cochrane, EMBASE, PubMed, Lilacs and BBO, from January 2000 to February 2013, focusing on studies specifically assessing the prevalence of SB in children. RESULTS: After applying the inclusion criteria, four studies were retrieved. Among the selected articles, the prevalence rates of SB ranged from 5.9% to 49.6%, and these variations showed possible associations with the diagnostic criteria used for SB. CONCLUSION: There is a small number of studies with the primary objective of assessing SB in children. Additionally, there was a wide variation in the prevalence of SB in children. Thus, further, evidence-based studies with standardized and validated diagnostic criteria are necessary to assess the prevalence of SB in children more accurately. PMID:25628080

  18. An Evidence-Based Review of Fat Modifying Supplemental Weight Loss Products

    PubMed Central

    Egras, Amy M.; Hamilton, William R.; Lenz, Thomas L.; Monaghan, Michael S.

    2011-01-01

    Objective. To review the literature on fat modifying dietary supplements commonly used for weight loss. Methods. Recently published randomized, placebo-controlled trials were identified in PubMed, MEDLINE, International Pharmaceutical Abstracts, Cochrane Database, and Google Scholar using the search terms dietary supplement, herbal, weight loss, obesity, and individual supplement names. Discussion. Data for conjugated linoleic acid (CLA), Garcinia cambogia, chitosan, pyruvate, Irvingia gabonensis, and chia seed for weight loss were identified. CLA, chitosan, pyruvate, and Irvingia gabonensis appeared to be effective in weight loss via fat modifying mechanisms. However, the data on the use of these products is limited. Conclusion. Many obese people use dietary supplements for weight loss. To date, there is little clinical evidence to support their use. More data is necessary to determine the efficacy and safety of these supplements. Healthcare providers should assist patients in weighing the risks and benefits of dietary supplement use for weight loss. PMID:20847896

  19. High Burden of Protein–Energy Malnutrition in Nigeria: Beyond the Health Care Setting

    PubMed Central

    Ubesie, AC; Ibeziakor, NS

    2012-01-01

    There is still a high burden of protein–energy malnutrition in Nigeria. The severe forms of the disease are usually associated with high level of mortality even in the tertiary health facilities. To review the cost-effective health promotional strategies at community levels that could aid prevention, early detection, and prompt treatment of protein–energy malnutrition. The strategy used for locating articles used for this review was to search databases like Google, Google scholar, relevant electronic journals from the universities’ libraries, including PubMed and Scirus, Medline, Cochrane library and WHO's Hinari. We believe that strategies beyond the health care setting have potential of significantly reducing the morbidity and mortality associated with protein–energy malnutrition in Nigeria. PMID:23209994

  20. Disciplinary processes and the management of poor performance among UK nurses: bad apple or systemic failure? A scoping study.

    PubMed

    Traynor, Michael; Stone, Katie; Cook, Hannah; Gould, Dinah; Maben, Jill

    2014-03-01

    The rise of managerialism within healthcare systems has been noted globally. This paper uses the findings of a scoping study to investigate the management of poor performance among nurses and midwives in the United Kingdom within this context. The management of poor performance among clinicians in the NHS has been seen as a significant policy problem. There has been a profound shift in the distribution of power between professional and managerial groups in many health systems globally. We examined literature published between 2000 and 10 to explore aspects of poor performance and its management. We used Web of Science, CINAHL, MEDLINE, British Nursing Index, HMIC, Cochrane Library and PubMed. Empirical data are limited but indicate that nurses and midwives are the clinical groups most likely to be suspended and that poor performance is often represented as an individual deficit. A focus on the individual as a source of trouble can serve as a distraction from more complex systematic problems. PMID:23441729

  1. A systematic review on skin complications of bone-anchored hearing aids in relation to surgical techniques.

    PubMed

    Mohamad, Shwan; Khan, Imran; Hey, S Y; Hussain, S S Musheer

    2016-03-01

    A systematic review to study the skin complications associated with the bone-anchored hearing aid in relation to surgical techniques. The following databases have been searched: MEDLINE, EMBASE, the Cochrane Library , Google scholar and the PubMed. The literature search date was from January 1977 until November 2013. Randomised controlled trials and retrospective studies were included. Initial search identified 420 publications. Thirty articles met the inclusion criteria of this review. The most common surgical techniques identified were full-thickness skin graft, Dermatome and linear incision techniques. The result shows that dermatome technique is associated with higher rate of skin complications when compared to linear incision and skin graft techniques. Based on the available literature, the use of a linear incision technique appears to be associated with lower skin complications; however, there is limited data available supporting this. Higher quality studies would allow a more reliable comparison between the surgical techniques. PMID:25503356

  2. Practice implications and recommendations for managing codeine misuse and dependence.

    PubMed

    Bergin, Michael; Norman, Ian; Foley, Michelle; Harris, Richard; Rapca, Anna; Rich, Eileen; Hout, Marie-Claire Van

    2015-12-01

    Codeine, a weak opiate, requires increased pharmacovigilance relating to availability, heterogeneous nature of misuse, dependence and associated harm. A scoping review of literature on codeine was conducted using Arksey & O'Malley's framework (1). Databases searched included PubMed, EBSCO Host, Science Direct, EMBASE, PsycINFO, Cochrane library and Medline from 1994 to 2014. Follow-up search strategies involved hand searching and searching of pharmaceutical, health, medical and drug related websites. Initial zscreening identified 3,105 articles with 475 meeting the inclusion criteria. Eight broad categories organised the literature, data charting and qualitative synthesis. This paper presents implications for practice and makes recommendations to address these issues. Themes identified relate to raising public and practitioner awareness, risk management, dispensing practices and monitoring and surveillance of codeine. Evidence to inform law enforcement, drug surveillance, public health initiatives, harm reduction approaches, pharmacy, clinical and treatment practices is warranted. PMID:26677894

  3. Eradication of tetanus

    PubMed Central

    Thwaites, C. L.; Loan, H. T.

    2015-01-01

    Introduction The causative agent of tetanus, Clostridium tetani is widespread in the environment throughout the world and cannot be eradicated. To reduce the number of cases of tetanus efforts are focussed on prevention using vaccination and post-exposure wound care. Sources of data Medline, Pubmed and Cochrane databases; World Health Organization and United Nations Children's Fund publications. Areas of agreement The maternal and neonatal tetanus elimination initiative has resulted in significant reductions in mortality from neonatal tetanus throughout the world. Areas of controversy Although there are few data available it is likely that large numbers of children and adults, particularly men, remain unprotected due to lack of booster immunization. Areas timely for developing research It remains unclear how HIV and malaria affect both responses to vaccination and transplacental transfer of antibodies or how this might affect timing of vaccination doses. PMID:26598719

  4. Fenestrated and Chimney Technique for Juxtarenal Aortic Aneurysm: A Systematic Review and Pooled Data Analysis.

    PubMed

    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

  5. 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

  6. The tadpole of Dendropsophus branneri (Cochran, 1948) (Amphibia, Anura, Hylidae).

    PubMed

    De Abreu, Rafael Oliveira; Junc, Flora Acua; Souza, Isana Carla Amorim; Napoli, Marcelo Felgueiras

    2015-01-01

    Dendropsophus branneri is a small treefrog largely distributed throughout the Tropical Atlantic and Caatinga morphoclimatic domains (see Ab'Sber 1977 for morphoclimatic domains), from northeastern to southeastern Brazil [Lutz 1973, Frost 2014; see Zina et al. 2014 for taxonomic comments on D. minusculus (Rivero, 1971) and D. branneri]. This species is currently placed in the D. microcephalus species group according to Bastos & Pombal (1996) and Faivovich et al. (2005). The D. microcephalus group comprises 36 species (Frost 2014), 14 of which have known tadpoles. Here, we describe the external morphology and color patterns of the previously unknown tadpole of D. branneri. PMID:25947693

  7. 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…

  8. Is fibrin sealant effective and safe in total knee arthroplasty? A meta-analysis of randomized trials

    PubMed Central

    2014-01-01

    The objective of this study was to evaluate the efficacy and safety of fibrin sealant in patients following total knee arthroplasty (TKA). A comprehensive literature search of the electronic databases PubMed, MEDLINE, Web of Science, and Cochrane Library for published randomized controlled trials (RCTs) was undertaken. The evidence base was critically appraised using a tool from the Cochrane Bone, Joint and Muscle Trauma Group. Eight RCTs involving 641 patients were included. The use of fibrin sealant significantly reduced postoperative drainage (weighted mean difference (WMD) −346, 95% confidence interval (CI) −496.29 to −197.54, P < 0.00001) and blood transfusions (risk ratio (RR) 0.47, 95% CI 0.35 to 0.63, P < 0.00001) and led to a significant improvement in the range of motion (WMD 16.59, 95% CI 6.92 to 26.25, P = 0.0008). However, using fibrin sealant did not significantly reduced total blood loss (WMD −305.25, 95% CI −679.44 to 68.95, P = 0.11). Regarding complications, there were no significant differences in any adverse events, fever, infection, or hematoma among the study groups. In conclusion, the present meta-analysis indicates that the use of fibrin sealant was effective and safe as a hemostatic therapy for patients with TKA. PMID:24884626

  9. Isolated patellofemoral osteoarthritis

    PubMed Central

    Poolman, Rudolf W; van Kampen, Albert

    2010-01-01

    Background and purpose The optimal treatment for isolated patellofemoral osteoarthritis is unclear at present. We systematically reviewed the highest level of available evidence on the nonoperative and operative treatment of isolated patellofemoral osteoarthritis to develop an evidenced-based discussion of treatment options. Methods A systematic computerized database search (Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, MEDLINE (PubMed), and EMBASE) was performed in March 2009. The quality of the studies was assessed independently by two authors using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach. Results We extracted data from 44 articles. The best available evidence for treatment of isolated patellofemoral osteoarthritis is sparse and of generally low methodological quality. Nonoperative treatment using physiotherapy (GRADE: high quality, weak recommendation for use), taping (GRADE: moderate quality, weak recommendation for use), or injection therapy (GRADE: very low quality, weak recommendation for use) may result in short-term relief. Joint-preserving surgical treatment may result in insufficient, unpredictable, or only short-term improvement (GRADE: low quality, weak recommendation against use). Total knee replacement with patellar resurfacing results in predictable and good, durable results (GRADE: low quality, weak recommendation for use). Outcome after patellofemoral arthroplasty in selected patients is good to excellent (GRADE: low quality, weak recommendation for use). Interpretation Methodologically good quality comparative studies, preferably using a patient-relevant outcome instrument, are needed to establish the optimal treatment strategy for patients with isolated patellofemoral osteoarthritis. PMID:20175647

  10. Comparative Effectiveness of Dental Anatomy Carving Pedagogy: A Systematic Review.

    PubMed

    de Azevedo, Renato de A; da Rosa, Wellington Luiz de O; da Silva, Adriana F; Correa, Marcos B; Torriani, Marcos A; Lund, Rafael G

    2015-08-01

    The aim of this study was to review the effectiveness of methods used for teaching dental anatomy carving to dental students in operative dentistry as evaluated in published studies. This systematic review is described in accordance with the PRISMA statement. Two independent reviewers performed a systematic literature search of research published from January 1945 until May 2014. Seven databases were screened: MedLine (PubMed), Lilacs, IBECS, Web of Science, Scopus, SciELO, and The Cochrane Library. After removing duplicates, only studies using dental carving to assess the practical knowledge of anatomy were selected. The tabulated data were organized by title of article, names of authors, number of students assessed, assessment method, material used, groups tested, main results, and conclusions. The methodology quality was assessed according to the Cochrane Handbook for Systematic Reviews of Interventions. Initially, 2,258 studies were identified in all databases. Five articles met the eligibility criteria and were included in this review. According to these studies, the geometric method, teaching step-by-step along with the teacher, and adjuvant methods such as the use of tutors and teaching through digital media with DVDs proved to be effective in improving learning. There is no standard technique that is widely accepted for the teaching of dental carving, nor is there an appropriately validated method of evaluation to verify whether the teaching methods used are effective for the acquisition of skills and expertise in dental anatomy by students. PMID:26246529

  11. Malignant transformation of hepatocellular adenomas into hepatocellular carcinomas: a systematic review including more than 1600 adenoma cases

    PubMed Central

    Stoot, Jan HMB; Coelen, Robert JS; de Jong, Mechteld C; Dejong, Cornelis HC

    2010-01-01

    Background Malignant transformation of hepatocellular adenomas (HCAs) into hepatocellular carcinomas (HCCs) has been reported repeatedly and is considered to be one of the main reasons for surgical treatment. However, its actual risk is currently unknown. Objective To provide an estimation of the frequency of malignant transformation of HCAs and to discuss its clinical implications. Methods A systematic literature search was conducted using the following databases: The Cochrane Hepatobiliary Group Controlled Trials Register, The Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, MEDLINE and EMBASE. Results One hundred and fifty-seven relevant series and 17 case reports (a total of 1635 HCAs) were retrieved, reporting an overall frequency of malignant transformation of 4.2%. Only three cases (4.4%) of malignant alteration were reported in a tumour smaller than 5 cm in diameter. Discussion Malignant transformation of HCAs into HCCs remains a rare phenomenon with a reported frequency of 4.2%. A better selection of exactly those patients presenting with an HCA with an amplified risk of malignant degeneration is advocated in order to reduce the number of liver resections and thus reducing the operative risk for these predominantly young patients. The Bordeaux adenoma tumour markers are a promising method of identifying these high-risk adenomas. PMID:20887318

  12. Biphasic Regulation of Lipid Metabolism: A Meta-Analysis of Icodextrin in Peritoneal Dialysis

    PubMed Central

    Huang, Yan-Feng; Zhu, Da-Jian; Chen, Xiao-Wu; Ouyang, Man-Zhao; Zhang, Wei-Jie

    2015-01-01

    Objectives. The objective of this systematic meta-analysis was to study the impact of icodextrin (ICO) on lipid profiles. Methods. MEDLINE, PubMed, Embase, Chinese Biomedical Literature, and the Cochrane Library and Reference lists were searched (last search September 2014) in accordance with the Cochrane Handbook for Systematic Reviews of Interventions. Results. Searches identified 13 eligible trials with a total of 850 patients. The differentials of total cholesterol (TC) and free fatty acid (FFA) in the ICO group were greater than those in the GLU group. Metaregression analysis showed that TC levels positively correlated with its baseline levels. In the subgroup of patients with dialysis duration more than 6 months, TC and TG in the ICO group were less. In pooled data from cross-sectional studies, differential of TG in the ICO group was less. In the subgroup of patients with diabetes (Martikainen et al., 2005, Sniderman et al., 2014, and Takatori et al., 2011), differential of high-density lipoprotein cholesterol (HDL-C) in the ICO group was less. There was no significant effect on low-density lipoprotein cholesterol (LDL-C), very low-density lipoprotein cholesterol (VLDL-C), or lipoprotein(a). Conclusions. ICO may be beneficial to lipid metabolism, especially for its biphasic regulation of plasma TC levels. PMID:26788499

  13. Diagnostic Accuracy of Xpert Test in Tuberculosis Detection: A Systematic Review and Meta-analysis

    PubMed Central

    Kaur, Ravdeep; Kachroo, Kavita; Sharma, Jitendar Kumar; Vatturi, Satyanarayana Murthy; Dang, Amit

    2016-01-01

    Background: World Health Organization (WHO) recommends the use of Xpert MTB/RIF assay for rapid diagnosis of tuberculosis (TB) and detection of rifampicin resistance. This systematic review was done to know about the diagnostic accuracy and cost-effectiveness of the Xpert MTB/RIF assay. Methods: A systematic literature search was conducted in following databases: Cochrane Central Register of Controlled Trials and Cochrane Database of Systematic Reviews, MEDLINE, PUBMED, Scopus, Science Direct and Google Scholar for relevant studies for studies published between 2010 and December 2014. Studies given in the systematic reviews were accessed separately and used for analysis. Selection of studies, data extraction and assessment of quality of included studies was performed independently by two reviewers. Studies evaluating the diagnostic accuracy of Xpert MTB/RIF assay among adult or predominantly adult patients (≥14 years), presumed to have pulmonary TB with or without HIV infection were included in the review. Also, studies that had assessed the diagnostic accuracy of Xpert MTB/RIF assay using sputum and other respiratory specimens were included. Results: The included studies had a low risk of any form of bias, showing that findings are of high scientific validity and credibility. Quantitative analysis of 37 included studies shows that Xpert MTB/RIF is an accurate diagnostic test for TB and detection of rifampicin resistance. Conclusion: Xpert MTB/RIF assay is a robust, sensitive and specific test for accurate diagnosis of tuberculosis as compared to conventional tests like culture and microscopic examination. PMID:27013842

  14. Hybrid surgery versus anterior cervical discectomy and fusion for multilevel cervical degenerative disc diseases: a meta-analysis

    PubMed Central

    Tian, Peng; Fu, Xin; Li, Zhi-Jun; Sun, Xiao-Lei; Ma, Xin-Long

    2015-01-01

    The objective of this meta-analysis is to compare hybrid surgery (HS) and cervical discectomy and fusion (ACDF) for multilevel cervical degenerative disc diseases (DDD). Systematic searches of all published studies through March 2015 were identified from Cochrane Library, Medline, PubMed, Embase, ScienceDirect, CNKI, WANFANG DATA and CQVIP. Randomized controlled trials (RCTs) and non-RCTs involving HS and ACDF for multilevel DDD were included. All literature was searched and assessed by two independent reviewers according to the standard of Cochrane systematic review. Data of functional and radiological outcomes in two groups were pooled, which was then analyzed by RevMan 5.2 software. One RCT and four non-RCTs encompassing 160 patients met the inclusion criteria. Meta-analysis revealed significant differences in blood loss (p?=?0.005), postoperative C2C7 ROM (p?=?0.002), ROM of superior adjacent segment (p?

  15. Evidence-based treatment of maisonneuve fractures.

    PubMed

    Stufkens, Sjoerd A; van den Bekerom, Michel P J; Doornberg, Job N; van Dijk, C Niek; Kloen, Peter

    2011-01-01

    The objective of the current study was to review the published clinical evidence available for the treatment of Maisonneuve fractures. Medline via PubMed, Orthopaedic Trauma Association (OTA) annual meetings' abstracts archives Web site, Embase, the Cochrane Database of Systematic Reviews, and the Cochrane Clinical Trial register were searched for the period extending from January 1970 to May 2009 in order to identify studies relating to the treatment of Maisonneuve ankle fractures. Six level 4 (case series, N ≥ 5) studies, describing a total of 83 patients with a Maisonneuve fracture, were included in the review. Although the authors did not compare the different treatment strategies described in the reports, the overall outcomes were generally good, and included 74 (89%) patients in which the outcome was considered good or excellent, and 9 (11%) patients in which the outcome was considered fair or poor. Based on this review, some grade B and C recommendations for the treatment of Maisonneuve fractures were formulated, including: 1) the medial malleolus should be fixated, 2) the torn deltoid ligament need not be directly repaired, 3) syndesmotic instability can be treated with one or two 3- or 4-cortical screws and these can be placed percutaneously, and 4) the proximal fibular fracture does not require direct internal fixation. Recommendations for future research were also formulated and described in this report. PMID:21172642

  16. New approach to managing genital warts

    PubMed Central

    Lopaschuk, Catharine C.

    2013-01-01

    Abstract Objective To summarize and determine the appropriate use for the new and old management tools for genital warts. Sources of information The following databases were searched: MEDLINE, PubMed, EMBASE, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, ACP Journal Club, and Trip. The bibliographies of retrieved papers were also reviewed. Clinical trials, qualitative review articles, consensus reports, and clinical practice guidelines were retrieved. Main message Symptomatic warts are prevalent in at least 1% of the population between the ages of 15 and 49, with estimates of up to 50% of the population being infected with human papillomavirus at some point in their lifetime. Imiquimod and podophyllotoxin are 2 new treatments for external genital warts that are less painful and can be applied by patients at home. In addition, the quadrivalent human papillomavirus vaccine has been shown to be efficacious in preventing genital warts and cervical cancer. There is still a role for the older treatment methods in certain situations, such as intravaginal, urethral, anal, or recalcitrant warts; or for pregnant patients. Conclusion The new treatments of external genital warts can reduce the pain of treatment and the number of office visits. Other treatment methods are still useful in certain situations. PMID:23851535

  17. Laparoscopic colorectal resection versus open colorectal resection in octogenarians: a systematic review and meta-analysis of safety and efficacy.

    PubMed

    Li, Y; Wang, S; Gao, S; Yang, C; Yang, W; Guo, S

    2016-03-01

    Octogenarians are more often viewed as high-risk surgical candidates. This increased risk is attributed to an age-related decline in physical function and reserve capacity coupled with the presence of various underlying diseases. There are no current guidelines or consensus on the optimal treatment strategy for this cohort of complex patients. The aim of this systematic review and meta-analysis was to compare the efficacy and safety of laparoscopic colorectal resection versus open colorectal resection in octogenarians. The meta-analysis was conducted following all aspects of the Cochrane Handbook for Systematic Reviews and Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. A systematic literature review was carried out using the following databases: MEDLINE, Embase, PubMed, the Cochrane Library, Google Scholar and OVID. Only studies comparing outcome of laparoscopic and open colorectal resections in the elderly population (?80years) were selected. The data collected included the patient demographics, interventions, observed outcome and sources of bias. When performing the statistical analysis, we used the odds ratio for categorical variables and the weighted mean difference for continuous variables. The results of this systematic review and pooled analysis demonstrated the safety and potential benefits of laparoscopic colorectal resection in octogenarians. LC can reduce the length of hospital stay, intraoperative blood loss, time to return of normal bowel function, and incidence of postoperative pneumonia, wound infection, and postoperative ileus. PMID:26783029

  18. The Physiological and Biochemical Outcomes Associated with a Reflexology Treatment: A Systematic Review

    PubMed Central

    McCullough, J. E. M.; Liddle, S. D.; Sinclair, M.; Close, C.; Hughes, C. M.

    2014-01-01

    Background. Reflexology is one of the top forms of complementary and alternative medicine in the UK and is used for healthcare by a diverse range of people. However, it is offered by few healthcare providers as little scientific evidence is available explaining how it works or any health benefits it may confer. The aim of this review was to assess the current evidence available from reflexology randomised controlled trials (RCTs) that have investigated changes in physiological or biochemical outcomes. Methods. Guidelines from the Cochrane Handbook of Systematic Reviews of Interventions were followed: the following databases were searched from inception to December 2013: AMED, CAM Quest, CINAHL Plus, Cochrane Central Register of Controlled Trials, Embase, Medline Ovid, Proquest, and Pubmed. Risk of bias was assessed independently by two members of the review team and overall strength of the evidence was assessed using the Grading of Recommendations, Assessment, Development, and Evaluation guidelines. Results. Seventeen eligible RCTs met all inclusion criteria. A total of 34 objective outcome measures were analysed. Although twelve studies showed significant changes within the reflexology group, only three studies investigating blood pressure, cardiac index, and salivary amylase resulted in significant between group changes in favour of reflexology. The overall quality of the studies was low. PMID:24883067

  19. Definitions and outcome measures of clinical trials regarding opioid-induced constipation: a systematic review.

    PubMed

    Gaertner, Jan; Siemens, Waldemar; Camilleri, Michael; Davies, Andrew; Drossman, Douglas A; Webster, Lynn R; Becker, Gerhild

    2015-01-01

    Opioid-induced constipation (OIC) is a frequent symptom in patients treated with opioids and impacts the patients' quality of life. However, there is no generally accepted definition for OIC. The aims of this study were to identify definitions for OIC in clinical trials and Cochrane Reviews and to compile assessment tools and outcome measures that were used in clinical trials. In a systematic review, 5 databases (MEDLINE, PubMed, The Cochrane Library, Web of Science, and EMBASE) were searched to identify clinical trials assessing OIC in adult patients or healthy volunteers. Studies published between 1993 and August 2013 were included. A total of 1488 studies were retrieved and 47 publications were included in the analysis. A minority of the publications (n=16, 34%) provided a clear definition for OIC. The definitions were highly variable and the present or recent history of opioid therapy was frequently (n=6, 38%) not included in these definitions. Of 46 clinical trials, 17 (37%) relied exclusively on objective measures such as bowel movement frequency, whereas another 17 studies additionally included patient-reported outcome measures such as, "feeling of incomplete bowel evacuation." Few trials (n=7, 15%) assessed the patient-reported global burden of OIC. Standard definitions and outcome measures are necessary (i) for consistency in OIC diagnosis in clinical practice and clinical trials; and (ii) to assure comparability of trial findings (eg, in meta-analyses). An OIC definition and outcome measures are proposed. PMID:25356996

  20. Sexual and gender-based violence in areas of armed conflict: a systematic review of mental health and psychosocial support interventions

    PubMed Central

    2013-01-01

    Background Sexual and other forms of gender-based violence are common in conflict settings and are known risk factors for mental health and psychosocial wellbeing. We present findings from a systematic review of the academic and grey literature focused on the effectiveness of mental health and psychosocial support interventions for populations exposed to sexual and other forms of gender-based violence in the context of armed conflicts. Methods We searched the Cochrane Database of Systematic Reviews, Cochrane Controlled Trials Register, PubMed/ Medline, psycINFO, and PILOTS, as well as grey literature to search for evaluations of interventions, without date limitations. Results Out of 5,684 returned records 189 full text papers were assessed for eligibility. Seven studies met inclusion criteria: 1 non-randomized controlled study; 3 non-controlled pre- post-test designs; 1 retrospective cohort with a matched comparison group; and 2 case studies. Studies were conducted in West and Central Africa; Albania; UK and USA, included female participants, and focused on individual and group counseling; combined psychological, medical, social and economic interventions; and cognitive behavioral therapy (two single case studies). Conclusions The seven studies, while very limited, tentatively suggest beneficial effects of mental health and psychosocial interventions for this population, and show feasibility of evaluation and implementation of such interventions in real-life settings through partnerships with humanitarian organizations. Robust conclusions on the effectiveness of particular approaches are not possible on the basis of current evidence. More rigorous research is urgently needed. PMID:23915821

  1. Describing methods and interventions: a protocol for the systematic analysis of the perioperative quality improvement literature

    PubMed Central

    2014-01-01

    Background Quality improvement (QI) methods are widely used in surgery in an effort to improve care, often using techniques such as Plan-Do-Study-Act cycles to implement specific interventions. Explicit definition of both the QI method and quality intervention is necessary to enable the accurate replication of effective interventions in practice, facilitate cumulative learning, reduce research waste and optimise benefits to patients. This systematic review aims to assess quality of reporting of QI methods and quality interventions in perioperative care. Methods Studies reporting on quality interventions implemented in perioperative care settings will be identified. Searches will be conducted in the Ovid SP version of Medline, Scopus, the Cochrane Central Register of Controlled Trials, the Cochrane Effective Practice and Organisation of Care database and the related articles function of PubMed. The journal BMJ Quality will be searched separately. Search strategy terms will relate to (i) surgery, (ii) QI and (iii) evaluation methods. Explicit exclusion and inclusion criteria will be applied. Data from studies will be extracted using a data extraction form. The Template for Intervention Description and Replication (TIDieR) checklist will be used to evaluate quality of reporting, together with additional items aimed at assessing QI methods specifically. Systematic review registration PROSPERO http://CRD42014012845 PMID:25193066

  2. The effectiveness of opioid substitution treatments for patients with opioid dependence: a systematic review and multiple treatment comparison protocol

    PubMed Central

    2014-01-01

    Background Opioids are psychoactive analgesic drugs prescribed for pain relief and palliative care. Due to their addictive potential, effort and vigilance in controlling prescriptions is needed to avoid misuse and dependence. Despite the effort, the prevalence of opioid use disorder continues to rise. Opioid substitution therapies are commonly used to treat opioid dependence; however, there is minimal consensus as to which therapy is most effective. Available treatments include methadone, heroin, buprenorphine, as well as naltrexone. This systematic review aims to assess and compare the effect of all available opioid substitution therapies on the treatment of opioid dependence. Methods/Design The authors will search Medline, EMBASE, PubMed, PsycINFO, Web of Science, Cochrane Library, Cochrane Clinical Trials Registry, World Health Organization International Clinical Trials Registry Platform Search Portal, and the National Institutes for Health Clinical Trials Registry. The title, abstract, and full-text screening will be completed in duplicate. When appropriate, multiple treatment comparison Bayesian meta-analytic methods will be performed to deduce summary statistics estimating the effectiveness of all opioid substitution therapies in terms of retention and response to treatment (as measured through continued opioid abuse). Discussion Using evidence gained from this systematic review, we anticipate disseminating an objective review of the current available literature on the effectiveness of all opioid substitution therapies for the treatment of opioid use disorder. The results of this systematic review are imperative to the further enhancement of clinical practice in addiction medicine. Systematic review registration PROSPERO CRD42013006507. PMID:25239213

  3. Molecular Genetic Testing in Reward Deficiency Syndrome (RDS): Facts and Fiction

    PubMed Central

    Blum, Kenneth; Badgaiyan, Rajendra D.; Agan, Gozde; Fratantonio, James; Simpatico, Thomas; Febo, Marcelo; Haberstick, Brett C.; Smolen, Andrew; Gold, Mark S.

    2015-01-01

    Background The Brain Reward Cascade (BRC) is an interaction of neurotransmitters and their respective genes to control the amount of dopamine released within the brain. Any variations within this pathway, whether genetic or environmental (epigenetic), may result in addictive behaviors or RDS, which was coined to define addictive behaviors and their genetic components. Methods To carry out this review we searched a number of important databases including: Filtered: Cochrane Systematic reviews; DARE; Pubmed Central Clinical Quaries; National Guideline Clearinghouse and unfiltered resources: PsychINFO; ACP PIER; PsychSage; Pubmed/Medline. The major search terms included: dopamine agonist therapy for Addiction; dopamine agonist therapy for Reward dependence; dopamine antagonistic therapy for addiction; dopamine antagonistic therapy for reward dependence and neurogenetics of RDS. Results While there are many studies claiming a genetic association with RDS behavior, not all are scientifically accurate. Conclusion Albeit our bias, this Clinical Pearl discusses the facts and fictions behind molecular genetic testing in RDS and the significance behind the development of the Genetic Addiction Risk Score (GARSPREDX™), the first test to accurately predict one’s genetic risk for RDS. PMID:26052557

  4. Online Medical Literature Consultation Habits of Academic Teaching Physicians in the EU and CIS Countries: A Cross-Sectional Study

    PubMed Central

    van der Voort, Chiel T. M.; Swenne, Cees A.; van der Hoorn-van Velthoven, Catharina A. M.; Belt, Johannes H. J.

    2012-01-01

    Background Both in the Commonwealth of Independent States (CIS) and in the European Union (EU2004), ample availability of up to date medical scientific literature is important for progress in medical science and for the education of the next generation of healthcare workers. The aim of this research is to assess if the use of online medical literature among academic teaching (AT) physicians is at the same level in the CIS as in the EU2004. Methodology/Principal Findings In the capital cities of the CIS and the EU2004 member states, AT physicians holding an academic position at least equivalent to an associate professor and performing the three classical tasks in academic medicine (teaching, research and patient care) were interviewed about their use of and familiarity with the Internet and 9 online literature services, including journals and bibliographical databases such as PubMed (Medline), The Cochrane Library and Web of Science. Library staff members were interviewed about the availability of these online literature services at their libraries. About 750 physicians and 40 library staff members were invited for participation. Eventually 124 AT physicians and 22 library staff members participated. Internet was everywhere available, but used daily by more AT physicians in the EU2004 (71% versus 48% in the CIS, P?=?.005). AT physicians in the EU2004 accessed a higher percentage of all articles online (74% versus 43% in the CIS, P<.001). PubMed (P<.001), The Cochrane Library (P<.001) and Web of Science (P<.003) were used more frequently in the EU2004. In the EU2004 more AT physicians were familiar with Open Access journals (89% versus 51% in the CIS, P<.001). Conclusions/Significance AT physicians in the CIS use online medical literature less than in the EU2004. It is recommended that the awareness of freely available online literature services such as Open Access journals is enhanced among AT physicians and library staff members, especially in the CIS. PMID:23133588

  5. Local Oestrogen for Pelvic Floor Disorders: A Systematic Review

    PubMed Central

    Weber, M. A.; Kleijn, M. H.; Langendam, M.; Limpens, J.; Heineman, M. J.; Roovers, J. P.

    2015-01-01

    Objective The decline in available oestrogen after menopause is a possible etiological factor in pelvic floor disorders like vaginal atrophy (VA), urinary incontinence (UI), overactive bladder (OAB) and pelvic organ prolapse (POP). This systematic review will examine the evidence for local oestrogen therapy in the treatment of these pelvic floor disorders. Evidence Acquisition We performed a systematic search in MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials and the non-MEDLINE subset of PubMed from inception to May 2014. We searched for local oestrogens and VA (I), UI/OAB (II) and POP (III). Part I was combined with broad methodological filters for randomized controlled trials (RCTs) and secondary evidence. For part I and II two reviewers independently selected RCTs evaluating the effect of topical oestrogens on symptoms and signs of VA and UI/OAB. In part III all studies of topical oestrogen therapy in the treatment of POP were selected. Data extraction and the assessment of risk of bias using the Cochrane Risk of Bias Tool was undertaken independently by two reviewers. Evidence Synthesis The included studies varied in ways of topical application, types of oestrogen, dosage and treatment durations. Objective and subjective outcomes were assessed by a variety of measures. Overall, subjective and urodynamic outcomes, vaginal maturation and vaginal pH changed in favor of vaginal oestrogens compared to placebo. No obvious differences between different application methods were revealed. Low doses already seemed to have a beneficial effect. Studies evaluating the effect of topical oestrogen in women with POP are scarce and mainly assessed symptoms and signs associated with VA instead of POP symptoms. Conclusion Topical oestrogen administration is effective for the treatment of VA and seems to decrease complaints of OAB and UI. The potential for local oestrogens in the prevention as well as treatment of POP needs further research. PMID:26383760

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

    PubMed Central

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

    2013-01-01

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

  7. Protocol for an overview of systematic reviews of interventions to reduce unscheduled hospital admissions among adults

    PubMed Central

    Bobrovitz, Niklas; Onakpoya, Igho; Roberts, Nia; Heneghan, Carl; Mahtani, Kamal R

    2015-01-01

    Introduction Unscheduled hospital admissions are an increasing burden on health systems worldwide. To date, initiatives to reduce admissions have had limited success as it is unclear which strategies effectively reduce admissions and are supported by a strong evidence-base. Therefore, we will conduct an overview to find, assess and summarise all published peer-reviewed systematic reviews of randomised controlled trials that examine the effect of an intervention on unplanned admissions among adults. Methods and analysis This is a protocol for a systematic overview of reviews. We will search four databases: Ovid MEDLINE, PubMed, Cochrane Database of Systematic Reviews and the Cochrane Database of Abstracts of Reviews of Effects. We will consider systematic reviews and meta-analyses of randomised controlled trials in adults (?16?years old) evaluating the effect of any intervention on unscheduled hospital admissions including those to treat, monitor, diagnose or prevent a health problem. We will only include reviews that identified unscheduled hospitalisations as a prespecified outcome. Two authors will independently screen articles for inclusion using a priori criteria. We will assess the quality of included reviews and extract ratings of the quality of evidence from within each review. We will create a hierarchical list of interventions based on estimates of absolute admission reductions and the quality of the evidence. Presentation of results will align with guidelines in the Cochrane Handbook of Systematic Reviews of Interventions and the Preferred Reporting Items for Systematic Reviews and Meta-Analysis statement. Ethics and dissemination Ethics approval is not required. We will submit the results of this study for peer-review publication. The results will inform future research and could be used by healthcare managers, administrators and policymakers to guide resource allocation decisions and inform local implementation and optimisation of interventions to reduce unscheduled hospital admissions. PMID:26297366

  8. Malignant pleural effusions and the role of talc poudrage and talc slurry: a systematic review and meta-analysis

    PubMed Central

    Mummadi, Srinivas; Kumbam, Anusha; Hahn, Peter Y.

    2015-01-01

    Background: Malignant Pleural Effusion (MPE) is common with advanced malignancy. Palliative care with minimal adverse events is the cornerstone of management. Although talc pleurodesis plays an important role in treatment, the best modality of talc application remains controversial.   Objective: To compare rates of successful pleurodesis, rates of respiratory and non-respiratory complications between thoracoscopic talc insufflation/poudrage (TTI) and talc slurry (TS).  Data sources and study selection: MEDLINE (PubMed, OVID),  EBM Reviews (Cochrane database of Systematic Reviews, ACP Journal Club, DARE, Cochrane Central Register of Controlled Trials, Cochrane Methodology Register, Health Technology Assessment and NHS Economic Evaluation Database), EMBASE and Scopus. Randomized controlled trials published between 01/01/1980 - 10/1/2014 and comparing the two strategies were selected.  Results: Twenty-eight potential studies were identified of which 24 studies were further excluded, leaving four studies. No statistically significant difference in the probability of successful pleurodesis was observed between TS and TTI groups (RR 1.06; 95 % CI 0.99-1.14; Q statistic, 4.84). There was a higher risk of post procedural respiratory complications in the TTI group compared to the TS group (RR 1.91, 95% CI= 1.24-2.93, Q statistic 3.15). No statistically significant difference in the incidence of non-respiratory complications between the TTI group and the TS group was observed (RR 0.88, 95% CI= 0.72-1.07, Q statistic 4.61). Conclusions: There is no difference in success rates of pleurodesis based on patient centered outcomes between talc poudrage and talc slurry treatments.  Respiratory complications are more common with talc poudrage via thoracoscopy. PMID:25878773

  9. Knowledge Retrieval from PubMed Abstracts and Electronic Medical Records with the Multiple Sclerosis Ontology

    PubMed Central

    Malhotra, Ashutosh; Gndel, Michaela; Rajput, Abdul Mateen; Mevissen, Heinz-Theodor; Saiz, Albert; Pastor, Xavier; Lozano-Rubi, Raimundo; Martinez-Lapsicina, Elena H.; Zubizarreta, Irati; Mueller, Bernd; Kotelnikova, Ekaterina; Toldo, Luca; Hofmann-Apitius, Martin; Villoslada, Pablo

    2015-01-01

    Background In order to retrieve useful information from scientific literature and electronic medical records (EMR) we developed an ontology specific for Multiple Sclerosis (MS). Methods The MS Ontology was created using scientific literature and expert review under the Protg OWL environment. We developed a dictionary with semantic synonyms and translations to different languages for mining EMR. The MS Ontology was integrated with other ontologies and dictionaries (diseases/comorbidities, gene/protein, pathways, drug) into the text-mining tool SCAIView. We analyzed the EMRs from 624 patients with MS using the MS ontology dictionary in order to identify drug usage and comorbidities in MS. Testing competency questions and functional evaluation using F statistics further validated the usefulness of MS ontology. Results Validation of the lexicalized ontology by means of named entity recognition-based methods showed an adequate performance (F score = 0.73). The MS Ontology retrieved 80% of the genes associated with MS from scientific abstracts and identified additional pathways targeted by approved disease-modifying drugs (e.g. apoptosis pathways associated with mitoxantrone, rituximab and fingolimod). The analysis of the EMR from patients with MS identified current usage of disease modifying drugs and symptomatic therapy as well as comorbidities, which are in agreement with recent reports. Conclusion The MS Ontology provides a semantic framework that is able to automatically extract information from both scientific literature and EMR from patients with MS, revealing new pathogenesis insights as well as new clinical information. PMID:25665127

  10. Finding Complex Biological Relationships in Recent PubMed Articles Using Bio-LDA

    PubMed Central

    Wang, Huijun; Ding, Ying; Tang, Jie; Dong, Xiao; He, Bing; Qiu, Judy; Wild, David J.

    2011-01-01

    The overwhelming amount of available scholarly literature in the life sciences poses significant challenges to scientists wishing to keep up with important developments related to their research, but also provides a useful resource for the discovery of recent information concerning genes, diseases, compounds and the interactions between them. In this paper, we describe an algorithm called Bio-LDA that uses extracted biological terminology to automatically identify latent topics, and provides a variety of measures to uncover putative relations among topics and bio-terms. Relationships identified using those approaches are combined with existing data in life science datasets to provide additional insight. Three case studies demonstrate the utility of the Bio-LDA model, including association predication, association search and connectivity map generation. This combined approach offers new opportunities for knowledge discovery in many areas of biology including target identification, lead hopping and drug repurposing. PMID:21448266

  11. Publications in PubMed on Ebola and the 2014 outbreak

    PubMed Central

    Ballabeni, Andrea; Boggio, Andrea

    2015-01-01

    In this research note we examine the biomedical publication output about Ebola in 2014. We show that the volume of publications has dramatically increased in the past year. In 2014 there have been over 888 publications with ‘ebola’ or ‘ebolavirus’ in the title, approximately 13 times the volume of publication of 2013. The rise reflects an impressive growth starting in the month of August, concomitant with or following the surge in infections, deaths and coverage in news and social media. Though non-research articles have been the major contributors to this growth, there has been a substantial increase in original research articles too, including many papers of basic science. The United States has been the country with the highest number of research articles, followed by Canada and the United Kingdom. We present a comprehensive set of charts and facts that, by describing the volumes and nature of publications in 2014, show how the scientific community has responded to the Ebola outbreak and how it might respond to future similar global threats and media events. This information will assist scholars and policymakers in their efforts to improve scientific research policies with the goal of maximizing both public health and knowledge advancement. PMID:26539291

  12. PubMed on Tap: discovering design principles for online information delivery to handheld computers.

    PubMed

    Hauser, Susan E; Demner-Fushman, Dina; Ford, Glenn; Thoma, George R

    2004-01-01

    Online access to biomedical information from handheld computers will be a valuable adjunct to other popular medical applications if information delivery systems are designed with handheld computers in mind. The goal of this project is to discover design principles to facilitate practitioners' access to online medical information at the point-of-care. A prototype system was developed to serve as a testbed for this research. Using the testbed, an initial evaluation has yielded several user interface design principles. Continued research is expected to discover additional user interface design principles as well as guidelines for results organization and system performance PMID:15361051

  13. Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information

    PubMed Central

    Wilbur, W. John

    2012-01-01

    The Comparative Toxicogenomics Database (CTD) contains manually curated literature that describes chemicalgene interactions, chemicaldisease relationships and genedisease relationships. Finding articles containing this information is the first and an important step to assist manual curation efficiency. However, the complex nature of named entities and their relationships make it challenging to choose relevant articles. In this article, we introduce a machine learning framework for prioritizing CTD-relevant articles based on our prior system for the proteinprotein interaction article classification task in BioCreative III. To address new challenges in the CTD task, we explore a new entity identification method for genes, chemicals and diseases. In addition, latent topics are analyzed and used as a feature type to overcome the small size of the training set. Applied to the BioCreative 2012 Triage dataset, our method achieved 0.8030 mean average precision (MAP) in the official runs, resulting in the top MAP system among participants. Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team. PMID:23160415

  14. Use of autologous fat grafting for reconstruction postmastectomy and breast conserving surgery: a systematic review protocol

    PubMed Central

    Agha, Riaz A; Goodacre, Tim; Orgill, Dennis P

    2013-01-01

    Introduction There is growing interest in the potential use of autologous fat grafting (AFG) for the purposes of breast reconstruction. However, concerns have been raised regarding the technique's clinical effectiveness, safety and interference with screening mammography. The objective of this systematic review was to determine the oncological, clinical, aesthetic and functional, patient reported, process and radiological outcomes for AFG. Methods and analysis All original studies, including randomised controlled trials, cohorts studies, casecontrol studies, case series and case reports involving women undergoing breast reconstruction. All AFG techniques performed for the purposes of reconstruction in the postmastectomy or breast conserving surgery setting will be considered. Outcomes are defined within this protocol along; oncological, clinical, aesthetic and functional, patient reported, process and radiological domains. The search strategy has been devised to find papers about fat grafting and breast reconstruction and is outlined within the body of this protocol. The full search strategy is outlined within the body of the protocol. The following electronic databases will be searched from 1 January 1986 to 6 June 2013: PubMed, MEDLINE, EMBASE, SCOPUS, CINAHL, PsycINFO, SciELO, The Cochrane Library, including the Cochrane Database of Systematic Reviews (CDSR), Cochrane Central Register of Controlled Trials (CENTRAL), Database of Abstracts of Reviews of Effect (DARE), the Cochrane Methodology Register, Health Technology Assessment Database, the NHS Economic Evaluation Databases and Cochrane Groups, ClinicalTrials.gov, Current Controlled Trials Database, the World Health Organisation (WHO) International Clinical Trials Registry Platform, UpToDate.com, NHS Evidence and the York Centre for Reviews and Dissemination. Grey literature searches will also be conducted as detailed in our review protocol. Eligibility assessment occurred in two stages, title and abstract screening and then full text assessment. Data were extracted and stored in a database with standardised extraction fields to facilitate easy and consistent data entry. Ethics and dissemination This systematic review will be published in a peer-reviewed journal. It will also be presented at national and international conferences in the fields of plastic, reconstructive and aesthetic surgery and at more general surgical and methodological conferences. It will be disseminated electronically and in print. Brief reports of the review findings will be disseminated directly to the appropriate audiences of surgeons and societies through email and other modes of communication. Updates of the review will be conducted to inform and guide healthcare practice and policy. Protocol Registration PROSPERONational Institute of Health Research (NIHR) Prospective Register of Systematic Reviews (CRD42013005254) PMID:24154518

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