Database resources of the National Center for Biotechnology Information

PubMed Central

2015-01-01

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

Database resources of the National Center for Biotechnology Information

PubMed Central

2016-01-01

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

[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.

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

PubMed

Chen, Chou-Cheng; Ho, Chung-Liang

2014-01-01

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

Literature searches on Ayurveda: An update.

PubMed

Aggithaya, Madhur G; Narahari, Saravu R

2015-01-01

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

Comparison of PubMed, Scopus, Web of Science, and Google Scholar: strengths and weaknesses.

PubMed

Falagas, Matthew E; Pitsouni, Eleni I; Malietzis, George A; Pappas, Georgios

2008-02-01

The evolution of the electronic age has led to the development of numerous medical databases on the World Wide Web, offering search facilities on a particular subject and the ability to perform citation analysis. We compared the content coverage and practical utility of PubMed, Scopus, Web of Science, and Google Scholar. The official Web pages of the databases were used to extract information on the range of journals covered, search facilities and restrictions, and update frequency. We used the example of a keyword search to evaluate the usefulness of these databases in biomedical information retrieval and a specific published article to evaluate their utility in performing citation analysis. All databases were practical in use and offered numerous search facilities. PubMed and Google Scholar are accessed for free. The keyword search with PubMed offers optimal update frequency and includes online early articles; other databases can rate articles by number of citations, as an index of importance. For citation analysis, Scopus offers about 20% more coverage than Web of Science, whereas Google Scholar offers results of inconsistent accuracy. PubMed remains an optimal tool in biomedical electronic research. Scopus covers a wider journal range, of help both in keyword searching and citation analysis, but it is currently limited to recent articles (published after 1995) compared with Web of Science. Google Scholar, as for the Web in general, can help in the retrieval of even the most obscure information but its use is marred by inadequate, less often updated, citation information.

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.

Using data sources beyond PubMed has a modest impact on the results of systematic reviews of therapeutic interventions.

PubMed

Halladay, Christopher W; Trikalinos, Thomas A; Schmid, Ian T; Schmid, Christopher H; Dahabreh, Issa J

2015-09-01

Searching multiple sources when conducting systematic reviews is considered good practice. We aimed to investigate the impact of using sources beyond PubMed in systematic reviews of therapeutic interventions. We randomly selected 50 Cochrane reviews that searched the PubMed (or MEDLINE) and EMBASE databases and included a meta-analysis of ≥10 studies. We checked whether each eligible record in each review (n = 2,700) was retrievable in PubMed and EMBASE. For the first-listed meta-analysis of ≥10 studies in each review, we examined whether excluding studies not found in PubMed affected results. A median of one record per review was indexed in EMBASE but not in PubMed; a median of four records per review was not indexed in PubMed or EMBASE. Meta-analyses included a median of 13.5 studies; a median of zero studies per meta-analysis was indexed in EMBASE but not in PubMed; a median of one study per meta-analysis was not indexed in PubMed or EMBASE. Meta-analysis using only PubMed-indexed vs. all available studies led to a different conclusion in a single case (on the basis of conventional criteria for statistical significance). In meta-regression analyses, effects in PubMed- vs. non-PubMed-indexed studies were statistically significantly different in a single data set. For systematic reviews of the effects of therapeutic interventions, gains from searching sources beyond PubMed, and from searching EMBASE in particular are modest. Copyright © 2015 Elsevier Inc. All rights reserved.

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

PubMed Central

2014-01-01

Background Currently, most people use NCBI's PubMed to search the MEDLINE database, an important bibliographical information source for life science and biomedical information. However, PubMed has some drawbacks that make it difficult to find relevant publications pertaining to users' individual intentions, especially for non-expert users. To ameliorate the disadvantages of PubMed, we developed G-Bean, a graph based biomedical search engine, to search biomedical articles in MEDLINE database more efficiently. Methods G-Bean addresses PubMed's limitations with three innovations: (1) Parallel document index creation: a multithreaded index creation strategy is employed to generate the document index for G-Bean in parallel; (2) Ontology-graph based query expansion: an ontology graph is constructed by merging four major UMLS (Version 2013AA) vocabularies, MeSH, SNOMEDCT, CSP and AOD, to cover all concepts in National Library of Medicine (NLM) database; a Personalized PageRank algorithm is used to compute concept relevance in this ontology graph and the Term Frequency - Inverse Document Frequency (TF-IDF) weighting scheme is used to re-rank the concepts. The top 500 ranked concepts are selected for expanding the initial query to retrieve more accurate and relevant information; (3) Retrieval and re-ranking of documents based on user's search intention: after the user selects any article from the existing search results, G-Bean analyzes user's selections to determine his/her true search intention and then uses more relevant and more specific terms to retrieve additional related articles. The new articles are presented to the user in the order of their relevance to the already selected articles. Results Performance evaluation with 106 OHSUMED benchmark queries shows that G-Bean returns more relevant results than PubMed does when using these queries to search the MEDLINE database. PubMed could not even return any search result for some OHSUMED queries because it failed to form the appropriate Boolean query statement automatically from the natural language query strings. G-Bean is available at http://bioinformatics.clemson.edu/G-Bean/index.php. Conclusions G-Bean addresses PubMed's limitations with ontology-graph based query expansion, automatic document indexing, and user search intention discovery. It shows significant advantages in finding relevant articles from the MEDLINE database to meet the information need of the user. PMID:25474588

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

PubMed

Bramer, Wichor M; Giustini, Dean; Kramer, Bianca Mr; Anderson, Pf

2013-12-23

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. 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. 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%. 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.

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

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

PubMed

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

2014-01-01

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

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…

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.

Bibliometric assessment of publication output of child and adolescent psychiatric/psychological affiliations between 2005 and 2010 based on the databases PubMed and Scopus.

PubMed

Albayrak, Ozgür; Föcker, Manuel; Wibker, Katrin; Hebebrand, Johannes

2012-06-01

We aimed to determine the quantitative scientific publication output of child and adolescent psychiatric/psychological affiliations during 2005-2010 by country based on both, "PubMed" and "Scopus" and performed a bibliometric qualitative evaluation for 2009 using "PubMed". We performed our search by affiliation related to child and adolescent psychiatric/psychological institutions using "PubMed". For the quantitative analysis for 2005-2010, we counted the number of abstracts. For the qualitative analysis for 2009 we derived the impact factor of each abstract's journal from "Journal Citation Reports". We related total impact factor scores to the gross domestic product (GDP) and population size of each country. Additionally, we used "Scopus" to determine the number of abstracts for each country that was identified via "PubMed" for 2009 and compared the ranking of countries between the two databases. 61 % of the publications between 2005 and 2010 originated from European countries and 26 % from the USA. After adjustment for GDP and population size, the ranking positions changed in favor of smaller European countries with a population size of less than 20 million inhabitants. The ranking of countries for the count of articles in 2009 as derived from "Scopus" was similar to that identified via the "PubMed" search. The performed search revealed only minor differences between "Scopus" and "PubMed" related to the ranking of countries. Our data indicate a sharp difference between countries with a high versus low GDP with regard to scientific publication output in child and adolescent psychiatry/psychology.

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

PubMed

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

2007-06-20

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

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

PubMed Central

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

2007-01-01

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

To Compare PubMed Clinical Queries and UpToDate in Teaching Information Mastery to Clinical Residents: A Crossover Randomized Controlled Trial

PubMed Central

Sayyah Ensan, Ladan; Faghankhani, Masoomeh; Javanbakht, Anna; Ahmadi, Seyed-Foad; Baradaran, Hamid Reza

2011-01-01

Purpose To compare PubMed Clinical Queries and UpToDate regarding the amount and speed of information retrieval and users' satisfaction. Method A cross-over randomized trial was conducted in February 2009 in Tehran University of Medical Sciences that included 44 year-one or two residents who participated in an information mastery workshop. A one-hour lecture on the principles of information mastery was organized followed by self learning slide shows before using each database. Subsequently, participants were randomly assigned to answer 2 clinical scenarios using either UpToDate or PubMed Clinical Queries then crossed to use the other database to answer 2 different clinical scenarios. The proportion of relevantly answered clinical scenarios, time to answer retrieval, and users' satisfaction were measured in each database. Results Based on intention-to-treat analysis, participants retrieved the answer of 67 (76%) questions using UpToDate and 38 (43%) questions using PubMed Clinical Queries (P<0.001). The median time to answer retrieval was 17 min (95% CI: 16 to 18) using UpToDate compared to 29 min (95% CI: 26 to 32) using PubMed Clinical Queries (P<0.001). The satisfaction with the accuracy of retrieved answers, interaction with UpToDate and also overall satisfaction were higher among UpToDate users compared to PubMed Clinical Queries users (P<0.001). Conclusions For first time users, using UpToDate compared to Pubmed Clinical Querries can lead to not only a higher proportion of relevant answer retrieval within a shorter time, but also a higher users' satisfaction. So, addition of tutoring pre-appraised sources such as UpToDate to the information mastery curricula seems to be highly efficient. PMID:21858142

To compare PubMed Clinical Queries and UpToDate in teaching information mastery to clinical residents: a crossover randomized controlled trial.

PubMed

Sayyah Ensan, Ladan; Faghankhani, Masoomeh; Javanbakht, Anna; Ahmadi, Seyed-Foad; Baradaran, Hamid Reza

2011-01-01

To compare PubMed Clinical Queries and UpToDate regarding the amount and speed of information retrieval and users' satisfaction. A cross-over randomized trial was conducted in February 2009 in Tehran University of Medical Sciences that included 44 year-one or two residents who participated in an information mastery workshop. A one-hour lecture on the principles of information mastery was organized followed by self learning slide shows before using each database. Subsequently, participants were randomly assigned to answer 2 clinical scenarios using either UpToDate or PubMed Clinical Queries then crossed to use the other database to answer 2 different clinical scenarios. The proportion of relevantly answered clinical scenarios, time to answer retrieval, and users' satisfaction were measured in each database. Based on intention-to-treat analysis, participants retrieved the answer of 67 (76%) questions using UpToDate and 38 (43%) questions using PubMed Clinical Queries (P<0.001). The median time to answer retrieval was 17 min (95% CI: 16 to 18) using UpToDate compared to 29 min (95% CI: 26 to 32) using PubMed Clinical Queries (P<0.001). The satisfaction with the accuracy of retrieved answers, interaction with UpToDate and also overall satisfaction were higher among UpToDate users compared to PubMed Clinical Queries users (P<0.001). For first time users, using UpToDate compared to Pubmed Clinical Queries can lead to not only a higher proportion of relevant answer retrieval within a shorter time, but also a higher users' satisfaction. So, addition of tutoring pre-appraised sources such as UpToDate to the information mastery curricula seems to be highly efficient.

Literature searches on Ayurveda: An update

PubMed Central

Aggithaya, Madhur G.; Narahari, Saravu R.

2015-01-01

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

Database resources of the National Center for Biotechnology Information.

PubMed

2016-01-04

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

Database resources of the National Center for Biotechnology Information.

PubMed

2015-01-01

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

A literature search tool for intelligent extraction of disease-associated genes.

PubMed

Jung, Jae-Yoon; DeLuca, Todd F; Nelson, Tristan H; Wall, Dennis P

2014-01-01

To extract disorder-associated genes from the scientific literature in PubMed with greater sensitivity for literature-based support than existing methods. We developed a PubMed query to retrieve disorder-related, original research articles. Then we applied a rule-based text-mining algorithm with keyword matching to extract target disorders, genes with significant results, and the type of study described by the article. We compared our resulting candidate disorder genes and supporting references with existing databases. We demonstrated that our candidate gene set covers nearly all genes in manually curated databases, and that the references supporting the disorder-gene link are more extensive and accurate than other general purpose gene-to-disorder association databases. We implemented a novel publication search tool to find target articles, specifically focused on links between disorders and genotypes. Through comparison against gold-standard manually updated gene-disorder databases and comparison with automated databases of similar functionality we show that our tool can search through the entirety of PubMed to extract the main gene findings for human diseases rapidly and accurately.

A search engine to access PubMed monolingual subsets: proof of concept and evaluation in French.

PubMed

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

2014-12-01

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. 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). 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. 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. 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.

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

Time-dependent migration of citations through PubMed and OvidSP subsets: a study on a series of simultaneous PubMed and OvidSP searches.

PubMed

Boeker, Martin; Vach, Werner; Motschall, Edith

2013-01-01

To quantitatively describe (1) differences between search results derived at consecutive time points with the PubMed and OvidSP literature search interfaces over a five day interval, and (2) the migration of citations through different subsets to estimate the timeliness of OvidSP. PubMed-Identifiers (PMIDs) of the following subsets were retrieved from PubMed and OvidSP simultaneously (within 8 h) at 11 days in March and April 2010 including 5 consecutive days: as supplied by publisher, in process, PubMed not MEDLINE, and OLDMEDLINE. Search results were compared for difference and intersection sets. The migration of citations on individual level was determined by comparison of corresponding sets over several days. The "in process" set was stable with about 446,000 - 452,000 citations; a small fraction of up to 3 % of the total subsets were in PubMed only and OvidSP only subsets. About 96 % of the ca. 10,500 citations in the OvidSP only subset migrated within 2 days out of the "in process" subset. The database of OvidSP is updated within a period of two days.

[Limiting a Medline/PubMed query to the "best" articles using the JCR relative impact factor].

PubMed

Avillach, P; Kerdelhué, G; Devos, P; Maisonneuve, H; Darmoni, S J

2014-12-01

Medline/PubMed is the most frequently used medical bibliographic research database. The aim of this study was to propose a new generic method to limit any Medline/PubMed query based on the relative impact factor and the A & B categories of the SIGAPS score. The entire PubMed corpus was used for the feasibility study, then ten frequent diseases in terms of PubMed indexing and the citations of four Nobel prize winners. The relative impact factor (RIF) was calculated by medical specialty defined in Journal Citation Reports. The two queries, which included all the journals in category A (or A OR B), were added to any Medline/PubMed query as a central point of the feasibility study. Limitation using the SIGAPS category A was larger than the when using the Core Clinical Journals (CCJ): 15.65% of PubMed corpus vs 8.64% for CCJ. The response time of this limit applied to the entire PubMed corpus was less than two seconds. For five diseases out of ten, limiting the citations with the RIF was more effective than with the CCJ. For the four Nobel prize winners, limiting the citations with the RIF was more effective than the CCJ. The feasibility study to apply a new filter based on the relative impact factor on any Medline/PubMed query was positive. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

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

PubMed

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

2011-01-01

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

UKPMC: a full text article resource for the life sciences

PubMed Central

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

2011-01-01

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

Generating PubMed Chemical Queries for Consumer Health Literature

PubMed Central

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

2005-01-01

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

OvidSP Medline-to-PubMed search filter translation: a methodology for extending search filter range to include PubMed's unique content.

PubMed

Damarell, Raechel A; Tieman, Jennifer J; Sladek, Ruth M

2013-07-02

PubMed translations of OvidSP Medline search filters offer searchers improved ease of access. They may also facilitate access to PubMed's unique content, including citations for the most recently published biomedical evidence. Retrieving this content requires a search strategy comprising natural language terms ('textwords'), rather than Medical Subject Headings (MeSH). We describe a reproducible methodology that uses a validated PubMed search filter translation to create a textword-only strategy to extend retrieval to PubMed's unique heart failure literature. We translated an OvidSP Medline heart failure search filter for PubMed and established version equivalence in terms of indexed literature retrieval. The PubMed version was then run within PubMed to identify citations retrieved by the filter's MeSH terms (Heart failure, Left ventricular dysfunction, and Cardiomyopathy). It was then rerun with the same MeSH terms restricted to searching on title and abstract fields (i.e. as 'textwords'). Citations retrieved by the MeSH search but not the textword search were isolated. Frequency analysis of their titles/abstracts identified natural language alternatives for those MeSH terms that performed less effectively as textwords. These terms were tested in combination to determine the best performing search string for reclaiming this 'lost set'. This string, restricted to searching on PubMed's unique content, was then combined with the validated PubMed translation to extend the filter's performance in this database. The PubMed heart failure filter retrieved 6829 citations. Of these, 834 (12%) failed to be retrieved when MeSH terms were converted to textwords. Frequency analysis of the 834 citations identified five high frequency natural language alternatives that could improve retrieval of this set (cardiac failure, cardiac resynchronization, left ventricular systolic dysfunction, left ventricular diastolic dysfunction, and LV dysfunction). Together these terms reclaimed 157/834 (18.8%) of lost citations. MeSH terms facilitate precise searching in PubMed's indexed subset. They may, however, work less effectively as search terms prior to subject indexing. A validated PubMed search filter can be used to develop a supplementary textword-only search strategy to extend retrieval to PubMed's unique content. A PubMed heart failure search filter is available on the CareSearch website (http://www.caresearch.com.au) providing access to both indexed and non-indexed heart failure evidence.

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

PubMed

Blümle, A; Lagrèze, W A; Motschall, E

2018-03-01

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

Difficulties and challenges associated with literature searches in operating room management, complete with recommendations.

PubMed

Wachtel, Ruth E; Dexter, Franklin

2013-12-01

The purpose of this article is to teach operating room managers, financial analysts, and those with a limited knowledge of search engines, including PubMed, how to locate articles they need in the areas of operating room and anesthesia group management. Many physicians are unaware of current literature in their field and evidence-based practices. The most common source of information is colleagues. Many people making management decisions do not read published scientific articles. Databases such as PubMed are available to search for such articles. Other databases, such as citation indices and Google Scholar, can be used to uncover additional articles. Nevertheless, most people who do not know how to use these databases are reluctant to utilize help resources when they do not know how to accomplish a task. Most people are especially reluctant to use on-line help files. Help files and search databases are often difficult to use because they have been designed for users already familiar with the field. The help files and databases have specialized vocabularies unique to the application. MeSH terms in PubMed are not useful alternatives for operating room management, an important limitation, because MeSH is the default when search terms are entered in PubMed. Librarians or those trained in informatics can be valuable assets for searching unusual databases, but they must possess the domain knowledge relative to the subject they are searching. The search methods we review are especially important when the subject area (e.g., anesthesia group management) is so specific that only 1 or 2 articles address the topic of interest. The materials are presented broadly enough that the reader can extrapolate the findings to other areas of clinical and management issues in anesthesiology.

PubMedPortable: A Framework for Supporting the Development of Text Mining Applications.

PubMed

Döring, Kersten; Grüning, Björn A; Telukunta, Kiran K; Thomas, Philippe; Günther, Stefan

2016-01-01

Information extraction from biomedical literature is continuously growing in scope and importance. Many tools exist that perform named entity recognition, e.g. of proteins, chemical compounds, and diseases. Furthermore, several approaches deal with the extraction of relations between identified entities. The BioCreative community supports these developments with yearly open challenges, which led to a standardised XML text annotation format called BioC. PubMed provides access to the largest open biomedical literature repository, but there is no unified way of connecting its data to natural language processing tools. Therefore, an appropriate data environment is needed as a basis to combine different software solutions and to develop customised text mining applications. PubMedPortable builds a relational database and a full text index on PubMed citations. It can be applied either to the complete PubMed data set or an arbitrary subset of downloaded PubMed XML files. The software provides the infrastructure to combine stand-alone applications by exporting different data formats, e.g. BioC. The presented workflows show how to use PubMedPortable to retrieve, store, and analyse a disease-specific data set. The provided use cases are well documented in the PubMedPortable wiki. The open-source software library is small, easy to use, and scalable to the user's system requirements. It is freely available for Linux on the web at https://github.com/KerstenDoering/PubMedPortable and for other operating systems as a virtual container. The approach was tested extensively and applied successfully in several projects.

PubMedPortable: A Framework for Supporting the Development of Text Mining Applications

PubMed Central

Döring, Kersten; Grüning, Björn A.; Telukunta, Kiran K.; Thomas, Philippe; Günther, Stefan

2016-01-01

Information extraction from biomedical literature is continuously growing in scope and importance. Many tools exist that perform named entity recognition, e.g. of proteins, chemical compounds, and diseases. Furthermore, several approaches deal with the extraction of relations between identified entities. The BioCreative community supports these developments with yearly open challenges, which led to a standardised XML text annotation format called BioC. PubMed provides access to the largest open biomedical literature repository, but there is no unified way of connecting its data to natural language processing tools. Therefore, an appropriate data environment is needed as a basis to combine different software solutions and to develop customised text mining applications. PubMedPortable builds a relational database and a full text index on PubMed citations. It can be applied either to the complete PubMed data set or an arbitrary subset of downloaded PubMed XML files. The software provides the infrastructure to combine stand-alone applications by exporting different data formats, e.g. BioC. The presented workflows show how to use PubMedPortable to retrieve, store, and analyse a disease-specific data set. The provided use cases are well documented in the PubMedPortable wiki. The open-source software library is small, easy to use, and scalable to the user’s system requirements. It is freely available for Linux on the web at https://github.com/KerstenDoering/PubMedPortable and for other operating systems as a virtual container. The approach was tested extensively and applied successfully in several projects. PMID:27706202

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

PubMed

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

2012-10-01

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

Citation Discovery Tools for Conducting Adaptive Meta-analyses to Update Systematic Reviews.

PubMed

Bae, Jong-Myon; Kim, Eun Hee

2016-03-01

The systematic review (SR) is a research methodology that aims to synthesize related evidence. Updating previously conducted SRs is necessary when new evidence has been produced, but no consensus has yet emerged on the appropriate update methodology. The authors have developed a new SR update method called 'adaptive meta-analysis' (AMA) using the 'cited by', 'similar articles', and 'related articles' citation discovery tools in the PubMed and Scopus databases. This study evaluates the usefulness of these citation discovery tools for updating SRs. Lists were constructed by applying the citation discovery tools in the two databases to the articles analyzed by a published SR. The degree of overlap between the lists and distribution of excluded results were evaluated. The articles ultimately selected for the SR update meta-analysis were found in the lists obtained from the 'cited by' and 'similar' tools in PubMed. Most of the selected articles appeared in both the 'cited by' lists in Scopus and PubMed. The Scopus 'related' tool did not identify the appropriate articles. The AMA, which involves using both citation discovery tools in PubMed, and optionally, the 'related' tool in Scopus, was found to be useful for updating an SR.

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

PubMed

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

2016-02-09

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

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.

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

PubMed

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

2014-04-01

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

Inferring gene and protein interactions using PubMed citations and consensus Bayesian networks.

PubMed

Deeter, Anthony; Dalman, Mark; Haddad, Joseph; Duan, Zhong-Hui

2017-01-01

The PubMed database offers an extensive set of publication data that can be useful, yet inherently complex to use without automated computational techniques. Data repositories such as the Genomic Data Commons (GDC) and the Gene Expression Omnibus (GEO) offer experimental data storage and retrieval as well as curated gene expression profiles. Genetic interaction databases, including Reactome and Ingenuity Pathway Analysis, offer pathway and experiment data analysis using data curated from these publications and data repositories. We have created a method to generate and analyze consensus networks, inferring potential gene interactions, using large numbers of Bayesian networks generated by data mining publications in the PubMed database. Through the concept of network resolution, these consensus networks can be tailored to represent possible genetic interactions. We designed a set of experiments to confirm that our method is stable across variation in both sample and topological input sizes. Using gene product interactions from the KEGG pathway database and data mining PubMed publication abstracts, we verify that regardless of the network resolution or the inferred consensus network, our method is capable of inferring meaningful gene interactions through consensus Bayesian network generation with multiple, randomized topological orderings. Our method can not only confirm the existence of currently accepted interactions, but has the potential to hypothesize new ones as well. We show our method confirms the existence of known gene interactions such as JAK-STAT-PI3K-AKT-mTOR, infers novel gene interactions such as RAS- Bcl-2 and RAS-AKT, and found significant pathway-pathway interactions between the JAK-STAT signaling and Cardiac Muscle Contraction KEGG pathways.

Database resources of the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Barrett, Tanya; Benson, Dennis A.; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Kenton, David L.; Khovayko, Oleg; Lipman, David J.; Madden, Thomas L.; Maglott, Donna R.; Ostell, James; Pruitt, Kim D.; Schuler, Gregory D.; Schriml, Lynn M.; Sequeira, Edwin; Sherry, Stephen T.; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Suzek, Tugba O.; Tatusov, Roman; Tatusova, Tatiana A.; Wagner, Lukas; Yaschenko, Eugene

2006-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Retroviral Genotyping Tools, HIV-1, Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at: . PMID:16381840

Database resources of the National Center for Biotechnology Information.

PubMed

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bolton, Evan; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; Dicuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Krasnov, Sergey; Landsman, David; Lipman, David J; Lu, Zhiyong; Madden, Thomas L; Madej, Tom; Maglott, Donna R; Marchler-Bauer, Aron; Miller, Vadim; Karsch-Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Wang, Yanli; Wilbur, W John; Yaschenko, Eugene; Ye, Jian

2012-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

PubMed Medical publications from Libya

PubMed Central

Bakoush, O; Al-Tubuly, AA; Ashammakhi, N; Elkhammas, EA

2007-01-01

Medical research and publications are the back-bone for advancing the medical field. We identified the Pubmed medical publications that are affiliated with Libya to shed some light on the contribution of this country's medical community to the PubMed database. All publications affiliated with Libya in the PubMed were counted over a five year period ending December 2006. We also used the same method to obtain data on the PubMed medical publications from Tunisia, Morocco and Yemen. Tunisia had the largest number of PubMed publications among the studied countries: 20.4 publications per million population per year and 7.2 publications per year per one billion US$ GDP. Libya had much fewer publications: 2.4 publications per million population per year and 0.4 publications per one billion US$ GDP. The citation frequency for Libyan published research was very low compared to Tunisian and Moroccan related research. Conclusion: This preliminary analysis shows that medical research output in Libya is about twenty times less than in other countries with similar backgrounds, and that it needs to be enhanced. PMID:21503210

Characterization of the mechanism of drug-drug interactions from PubMed using MeSH terms.

PubMed

Lu, Yin; Figler, Bryan; Huang, Hong; Tu, Yi-Cheng; Wang, Ju; Cheng, Feng

2017-01-01

Identifying drug-drug interaction (DDI) is an important topic for the development of safe pharmaceutical drugs and for the optimization of multidrug regimens for complex diseases such as cancer and HIV. There have been about 150,000 publications on DDIs in PubMed, which is a great resource for DDI studies. In this paper, we introduced an automatic computational method for the systematic analysis of the mechanism of DDIs using MeSH (Medical Subject Headings) terms from PubMed literature. MeSH term is a controlled vocabulary thesaurus developed by the National Library of Medicine for indexing and annotating articles. Our method can effectively identify DDI-relevant MeSH terms such as drugs, proteins and phenomena with high accuracy. The connections among these MeSH terms were investigated by using co-occurrence heatmaps and social network analysis. Our approach can be used to visualize relationships of DDI terms, which has the potential to help users better understand DDIs. As the volume of PubMed records increases, our method for automatic analysis of DDIs from the PubMed database will become more accurate.

Risk factors for bladder cancer: challenges of conducting a literature search using PubMed.

PubMed

Joshi, Ashish; Preslan, Elicia

2011-04-01

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

Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts

PubMed Central

Lu, Zhiyong

2012-01-01

Today’s biomedical research has become heavily dependent on access to the biological knowledge encoded in expert curated biological databases. As the volume of biological literature grows rapidly, it becomes increasingly difficult for biocurators to keep up with the literature because manual curation is an expensive and time-consuming endeavour. Past research has suggested that computer-assisted curation can improve efficiency, but few text-mining systems have been formally evaluated in this regard. Through participation in the interactive text-mining track of the BioCreative 2012 workshop, we developed PubTator, a PubMed-like system that assists with two specific human curation tasks: document triage and bioconcept annotation. On the basis of evaluation results from two external user groups, we find that the accuracy of PubTator-assisted curation is comparable with that of manual curation and that PubTator can significantly increase human curatorial speed. These encouraging findings warrant further investigation with a larger number of publications to be annotated. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/ PMID:23160414

Demystifying the Search Button

PubMed Central

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

2015-01-01

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

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.

The Nuclear Protein Database (NPD): sub-nuclear localisation and functional annotation of the nuclear proteome

PubMed Central

Dellaire, G.; Farrall, R.; Bickmore, W.A.

2003-01-01

The Nuclear Protein Database (NPD) is a curated database that contains information on more than 1300 vertebrate proteins that are thought, or are known, to localise to the cell nucleus. Each entry is annotated with information on predicted protein size and isoelectric point, as well as any repeats, motifs or domains within the protein sequence. In addition, information on the sub-nuclear localisation of each protein is provided and the biological and molecular functions are described using Gene Ontology (GO) terms. The database is searchable by keyword, protein name, sub-nuclear compartment and protein domain/motif. Links to other databases are provided (e.g. Entrez, SWISS-PROT, OMIM, PubMed, PubMed Central). Thus, NPD provides a gateway through which the nuclear proteome may be explored. The database can be accessed at http://npd.hgu.mrc.ac.uk and is updated monthly. PMID:12520015

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

PubMed

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

2008-04-22

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

Database resources of the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Barrett, Tanya; Benson, Dennis A.; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Feolo, Michael; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Khovayko, Oleg; Landsman, David; Lipman, David J.; Madden, Thomas L.; Maglott, Donna R.; Miller, Vadim; Ostell, James; Pruitt, Kim D.; Schuler, Gregory D.; Shumway, Martin; Sequeira, Edwin; Sherry, Steven T.; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusov, Roman L.; Tatusova, Tatiana A.; Wagner, Lukas; Yaschenko, Eugene

2008-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace, Assembly, and Short Read Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Database of Genotype and Phenotype, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:18045790

Inferring gene and protein interactions using PubMed citations and consensus Bayesian networks

PubMed Central

Dalman, Mark; Haddad, Joseph; Duan, Zhong-Hui

2017-01-01

The PubMed database offers an extensive set of publication data that can be useful, yet inherently complex to use without automated computational techniques. Data repositories such as the Genomic Data Commons (GDC) and the Gene Expression Omnibus (GEO) offer experimental data storage and retrieval as well as curated gene expression profiles. Genetic interaction databases, including Reactome and Ingenuity Pathway Analysis, offer pathway and experiment data analysis using data curated from these publications and data repositories. We have created a method to generate and analyze consensus networks, inferring potential gene interactions, using large numbers of Bayesian networks generated by data mining publications in the PubMed database. Through the concept of network resolution, these consensus networks can be tailored to represent possible genetic interactions. We designed a set of experiments to confirm that our method is stable across variation in both sample and topological input sizes. Using gene product interactions from the KEGG pathway database and data mining PubMed publication abstracts, we verify that regardless of the network resolution or the inferred consensus network, our method is capable of inferring meaningful gene interactions through consensus Bayesian network generation with multiple, randomized topological orderings. Our method can not only confirm the existence of currently accepted interactions, but has the potential to hypothesize new ones as well. We show our method confirms the existence of known gene interactions such as JAK-STAT-PI3K-AKT-mTOR, infers novel gene interactions such as RAS- Bcl-2 and RAS-AKT, and found significant pathway-pathway interactions between the JAK-STAT signaling and Cardiac Muscle Contraction KEGG pathways. PMID:29049295

The proportion of cancer-related entries in PubMed has increased considerably; is cancer truly "The Emperor of All Maladies"?

PubMed

Reyes-Aldasoro, Constantino Carlos

2017-01-01

In this work, the public database of biomedical literature PubMed was mined using queries with combinations of keywords and year restrictions. It was found that the proportion of Cancer-related entries per year in PubMed has risen from around 6% in 1950 to more than 16% in 2016. This increase is not shared by other conditions such as AIDS, Malaria, Tuberculosis, Diabetes, Cardiovascular, Stroke and Infection some of which have, on the contrary, decreased as a proportion of the total entries per year. Organ-related queries were performed to analyse the variation of some specific cancers. A series of queries related to incidence, funding, and relationship with DNA, Computing and Mathematics, were performed to test correlation between the keywords, with the hope of elucidating the cause behind the rise of Cancer in PubMed. Interestingly, the proportion of Cancer-related entries that contain "DNA", "Computational" or "Mathematical" have increased, which suggests that the impact of these scientific advances on Cancer has been stronger than in other conditions. It is important to highlight that the results obtained with the data mining approach here presented are limited to the presence or absence of the keywords on a single, yet extensive, database. Therefore, results should be observed with caution. All the data used for this work is publicly available through PubMed and the UK's Office for National Statistics. All queries and figures were generated with the software platform Matlab and the files are available as supplementary material.

The proportion of cancer-related entries in PubMed has increased considerably; is cancer truly “The Emperor of All Maladies”?

PubMed Central

2017-01-01

In this work, the public database of biomedical literature PubMed was mined using queries with combinations of keywords and year restrictions. It was found that the proportion of Cancer-related entries per year in PubMed has risen from around 6% in 1950 to more than 16% in 2016. This increase is not shared by other conditions such as AIDS, Malaria, Tuberculosis, Diabetes, Cardiovascular, Stroke and Infection some of which have, on the contrary, decreased as a proportion of the total entries per year. Organ-related queries were performed to analyse the variation of some specific cancers. A series of queries related to incidence, funding, and relationship with DNA, Computing and Mathematics, were performed to test correlation between the keywords, with the hope of elucidating the cause behind the rise of Cancer in PubMed. Interestingly, the proportion of Cancer-related entries that contain “DNA”, “Computational” or “Mathematical” have increased, which suggests that the impact of these scientific advances on Cancer has been stronger than in other conditions. It is important to highlight that the results obtained with the data mining approach here presented are limited to the presence or absence of the keywords on a single, yet extensive, database. Therefore, results should be observed with caution. All the data used for this work is publicly available through PubMed and the UK’s Office for National Statistics. All queries and figures were generated with the software platform Matlab and the files are available as supplementary material. PMID:28282418

OvidSP Medline-to-PubMed search filter translation: a methodology for extending search filter range to include PubMed's unique content

PubMed Central

2013-01-01

Background PubMed translations of OvidSP Medline search filters offer searchers improved ease of access. They may also facilitate access to PubMed’s unique content, including citations for the most recently published biomedical evidence. Retrieving this content requires a search strategy comprising natural language terms (‘textwords’), rather than Medical Subject Headings (MeSH). We describe a reproducible methodology that uses a validated PubMed search filter translation to create a textword-only strategy to extend retrieval to PubMed’s unique heart failure literature. Methods We translated an OvidSP Medline heart failure search filter for PubMed and established version equivalence in terms of indexed literature retrieval. The PubMed version was then run within PubMed to identify citations retrieved by the filter’s MeSH terms (Heart failure, Left ventricular dysfunction, and Cardiomyopathy). It was then rerun with the same MeSH terms restricted to searching on title and abstract fields (i.e. as ‘textwords’). Citations retrieved by the MeSH search but not the textword search were isolated. Frequency analysis of their titles/abstracts identified natural language alternatives for those MeSH terms that performed less effectively as textwords. These terms were tested in combination to determine the best performing search string for reclaiming this ‘lost set’. This string, restricted to searching on PubMed’s unique content, was then combined with the validated PubMed translation to extend the filter’s performance in this database. Results The PubMed heart failure filter retrieved 6829 citations. Of these, 834 (12%) failed to be retrieved when MeSH terms were converted to textwords. Frequency analysis of the 834 citations identified five high frequency natural language alternatives that could improve retrieval of this set (cardiac failure, cardiac resynchronization, left ventricular systolic dysfunction, left ventricular diastolic dysfunction, and LV dysfunction). Together these terms reclaimed 157/834 (18.8%) of lost citations. Conclusions MeSH terms facilitate precise searching in PubMed’s indexed subset. They may, however, work less effectively as search terms prior to subject indexing. A validated PubMed search filter can be used to develop a supplementary textword-only search strategy to extend retrieval to PubMed’s unique content. A PubMed heart failure search filter is available on the CareSearch website (http://www.caresearch.com.au) providing access to both indexed and non-indexed heart failure evidence. PMID:23819658

Chemotext: A Publicly Available Web Server for Mining Drug-Target-Disease Relationships in PubMed.

PubMed

Capuzzi, Stephen J; Thornton, Thomas E; Liu, Kammy; Baker, Nancy; Lam, Wai In; O'Banion, Colin P; Muratov, Eugene N; Pozefsky, Diane; Tropsha, Alexander

2018-02-26

Elucidation of the mechanistic relationships between drugs, their targets, and diseases is at the core of modern drug discovery research. Thousands of studies relevant to the drug-target-disease (DTD) triangle have been published and annotated in the Medline/PubMed database. Mining this database affords rapid identification of all published studies that confirm connections between vertices of this triangle or enable new inferences of such connections. To this end, we describe the development of Chemotext, a publicly available Web server that mines the entire compendium of published literature in PubMed annotated by Medline Subject Heading (MeSH) terms. The goal of Chemotext is to identify all known DTD relationships and infer missing links between vertices of the DTD triangle. As a proof-of-concept, we show that Chemotext could be instrumental in generating new drug repurposing hypotheses or annotating clinical outcomes pathways for known drugs. The Chemotext Web server is freely available at http://chemotext.mml.unc.edu .

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

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 PubMed’s 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

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

PubMed

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

2016-01-01

Metastasis is the dissemination of a cancer/tumor from one organ to another, and it is the most dangerous stage during cancer progression, causing more than 90% of cancer deaths. Improving the understanding of the complicated cellular mechanisms underlying metastasis requires investigations of the signaling pathways. To this end, we developed a METastasis (MET) network visualization and curation tool to assist metastasis researchers retrieve network information of interest while browsing through the large volume of studies in PubMed. MET can recognize relations among genes, cancers, tissues and organs of metastasis mentioned in the literature through text-mining techniques, and then produce a visualization of all mined relations in a metastasis network. To facilitate the curation process, MET is developed as a browser extension that allows curators to review and edit concepts and relations related to metastasis directly in PubMed. PubMed users can also view the metastatic networks integrated from the large collection of research papers directly through MET. For the BioCreative 2015 interactive track (IAT), a curation task was proposed to curate metastatic networks among PubMed abstracts. Six curators participated in the proposed task and a post-IAT task, curating 963 unique metastatic relations from 174 PubMed abstracts using MET.Database URL: http://btm.tmu.edu.tw/metastasisway. © The Author(s) 2016. Published by Oxford University Press.

Database resources of the National Center for Biotechnology Information

PubMed Central

Sayers, Eric W.; Barrett, Tanya; Benson, Dennis A.; Bolton, Evan; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M.; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Krasnov, Sergey; Landsman, David; Lipman, David J.; Lu, Zhiyong; Madden, Thomas L.; Madej, Tom; Maglott, Donna R.; Marchler-Bauer, Aron; Miller, Vadim; Karsch-Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D.; Schuler, Gregory D.; Sequeira, Edwin; Sherry, Stephen T.; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A.; Wagner, Lukas; Wang, Yanli; Wilbur, W. John; Yaschenko, Eugene; Ye, Jian

2012-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:22140104

Database resources of the National Center for Biotechnology Information

PubMed Central

2013-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page. PMID:23193264

Database resources of the National Center for Biotechnology Information.

PubMed

Wheeler, David L; Barrett, Tanya; Benson, Dennis A; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Geer, Lewis Y; Kapustin, Yuri; Khovayko, Oleg; Landsman, David; Lipman, David J; Madden, Thomas L; Maglott, Donna R; Ostell, James; Miller, Vadim; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Steven T; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusov, Roman L; Tatusova, Tatiana A; Wagner, Lukas; Yaschenko, Eugene

2007-01-01

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link(BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace and Assembly Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Viral Genotyping Tools, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Database resources of the National Center for Biotechnology Information.

PubMed

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Feolo, Michael; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Landsman, David; Lipman, David J; Madden, Thomas L; Maglott, Donna R; Miller, Vadim; Mizrachi, Ilene; Ostell, James; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Yaschenko, Eugene; Ye, Jian

2009-01-01

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the web applications is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Chinese literatures of radiation oncology covered by PubMed over the past five years.

PubMed

Niu, Dao-Li; Zhen, Jun-Jie; He, Fen

2010-04-01

PubMed is generally acknowledged for its scientificity in literature coverage and authority of literature retrieval . In recent years, many studies have been published in China about radiation oncology. We aimed to investigate the literatures about radiation oncology in China covered by PubMed over the past five years. We collected primary data by searching the PubMed database using the related subject words. The collected data were analyzed and evaluated by bibliometric methods. In the past five years, 550 articles by Chinese authors related to radiotherapy were indexed in PubMed. These articles were published in 160 journals among 26 Chinese provinces/cities. These articles mainly focused on radiation dose and computer-aided radiation therapy. Sixty-four articles were published by Chinese Journal of Cancer , which ranked the top. Forty-four articles were published by the International Journal of Radiation Oncology Biology Physics (IF=4.29), with the largest number among SCI journals. One hundred and sixteen articles from Guangdong Province were covered, accounting for 21.09%. Over the past five years, the discipline of radiation oncology has been greatly developed. The literatures mainly focus on clinical radiation oncology and their regional distribution is uneven.

Assessment of publication output in the field of general practice and family medicine and by general practitioners and general practice institutions.

PubMed

Jelercic, Stasa; Lingard, Heide; Spiegel, Wolfgang; Pichlhöfer, Otto; Maier, Manfred

2010-10-01

The discipline of family medicine (FM) lacks a comprehensive methodology, which can be applied as a standard for assessing overall research output in both the field of FM and by general practitioners (GPs)/general practice institutions. It was the aim of this study to develop a sensitive search strategy for assessing publication output in the field of FM independent of the author's profession or affiliation and by GPs/general practice institutions independent of their field of scientific interest. Literature searches limited to the year 2005 were conducted in PubMed and ISI Web of Sciences (ISI WoS). In PubMed, all relevant MeSH terms were used. Search terms possibly contained in the author's affiliations have been collected. In ISI WoS, the same entry terms including their abbreviations and plural forms were applied. The final queries were validated by manual review and matching results with selected FM journals. A comprehensive list of combined search terms could be defined. For the field of general practice/FM more publications could be retrieved in PubMed. Almost twice as many publications by GPs/general practice institutions could be retrieved in ISI WoS, where--in contrast to PubMed--the affiliation is documented for all authors. To quantitatively assess publication output in the field of FM, PubMed was identified as the preferable database. To assess publication output by GPs/general practice institutions, the ISI WoS is recommended as the preferable database. Apparently, the ISI WoS is more suitable to compare the research productivity of different countries, authors or institutions.

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

PubMed Central

Masic, Izet

2013-01-01

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

Acta informatica medica is indexed in pubmed and archived in pubmed central.

PubMed

Masic, Izet

2013-03-01

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

Further analysis of the impact factors and submission information for the Journal of Child Neurology.

PubMed

Brumback, Roger A

2004-04-01

Now in its nineteenth volume year, the Journal of Child Neurology continues its preeminence among child neurology journals. The Institute of Scientific Information impact factor value for the year 2002 of 1.338 places the Journal of Child Neurology seventy-first in rank among the 138 clinical neurology journals. Since 1998, the rejection rate for manuscripts has been nearly 25%, with more than half of the accepted manuscripts originating in North America. In its first 18 volumes, the journal published 2144 items as listed in the PubMed database of the National Library of Medicine, and for 2003, the PubMed database indexed 176 published items from the Journal of Child Neurology.

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

PubMed

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

2016-01-01

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

Comparative analysis between scientific and the media communication following facial transplantation.

PubMed

Belanger, M; Harris, P G; Nikolis, A; Danino, A M

2009-03-01

Our aim was to analyze the communications about three outstanding medical reports. Was there any difference in the reports of the three allografts? Was there a correlation between the media and the scientific world? The Internet sites of three major newspapers were used for the media database. Those results were compared with PubMed between 2005 and 2007 using these key words: "facial graft," "facial allograft," "composite tissue allograft," and names of surgeons of the graft. We did a comparative analysis using a word processor and a quality analysis software. We analyzed 51 articles from the media and six from the PubMed database. In PubMed, 100% of the articles were on the first graft and respected the privacy of the patient compared to 67% of the media who unveiled the identity. The communication following a medical premiere depends on the team, which performes the act. We observed a major difference between the three cases. Ethical considerations are different for the media and for scientists. The communication management of a medical premiere takes preparation and evaluation.

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

PubMed Central

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

2008-01-01

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

Database resources of the National Center for Biotechnology Information.

PubMed

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bolton, Evan; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Landsman, David; Lipman, David J; Lu, Zhiyong; Madden, Thomas L; Madej, Tom; Maglott, Donna R; Marchler-Bauer, Aron; Miller, Vadim; Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Wang, Yanli; Wilbur, W John; Yaschenko, Eugene; Ye, Jian

2011-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

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

PubMed Central

Hoeppner, Marilu A.

2013-01-01

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

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

PubMed

Hoeppner, Marilu A

2013-01-01

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

Identifying nurse staffing research in Medline: development and testing of empirically derived search strategies with the PubMed interface

PubMed Central

2010-01-01

Background The identification of health services research in databases such as PubMed/Medline is a cumbersome task. This task becomes even more difficult if the field of interest involves the use of diverse methods and data sources, as is the case with nurse staffing research. This type of research investigates the association between nurse staffing parameters and nursing and patient outcomes. A comprehensively developed search strategy may help identify nurse staffing research in PubMed/Medline. Methods A set of relevant references in PubMed/Medline was identified by means of three systematic reviews. This development set was used to detect candidate free-text and MeSH terms. The frequency of these terms was compared to a random sample from PubMed/Medline in order to identify terms specific to nurse staffing research, which were then used to develop a sensitive, precise and balanced search strategy. To determine their precision, the newly developed search strategies were tested against a) the pool of relevant references extracted from the systematic reviews, b) a reference set identified from an electronic journal screening, and c) a sample from PubMed/Medline. Finally, all newly developed strategies were compared to PubMed's Health Services Research Queries (PubMed's HSR Queries). Results The sensitivities of the newly developed search strategies were almost 100% in all of the three test sets applied; precision ranged from 6.1% to 32.0%. PubMed's HSR queries were less sensitive (83.3% to 88.2%) than the new search strategies. Only minor differences in precision were found (5.0% to 32.0%). Conclusions As with other literature on health services research, nurse staffing studies are difficult to identify in PubMed/Medline. Depending on the purpose of the search, researchers can choose between high sensitivity and retrieval of a large number of references or high precision, i.e. and an increased risk of missing relevant references, respectively. More standardized terminology (e.g. by consistent use of the term "nurse staffing") could improve the precision of future searches in this field. Empirically selected search terms can help to develop effective search strategies. The high consistency between all test sets confirmed the validity of our approach. PMID:20731858

Identifying nurse staffing research in Medline: development and testing of empirically derived search strategies with the PubMed interface.

PubMed

Simon, Michael; Hausner, Elke; Klaus, Susan F; Dunton, Nancy E

2010-08-23

The identification of health services research in databases such as PubMed/Medline is a cumbersome task. This task becomes even more difficult if the field of interest involves the use of diverse methods and data sources, as is the case with nurse staffing research. This type of research investigates the association between nurse staffing parameters and nursing and patient outcomes. A comprehensively developed search strategy may help identify nurse staffing research in PubMed/Medline. A set of relevant references in PubMed/Medline was identified by means of three systematic reviews. This development set was used to detect candidate free-text and MeSH terms. The frequency of these terms was compared to a random sample from PubMed/Medline in order to identify terms specific to nurse staffing research, which were then used to develop a sensitive, precise and balanced search strategy. To determine their precision, the newly developed search strategies were tested against a) the pool of relevant references extracted from the systematic reviews, b) a reference set identified from an electronic journal screening, and c) a sample from PubMed/Medline. Finally, all newly developed strategies were compared to PubMed's Health Services Research Queries (PubMed's HSR Queries). The sensitivities of the newly developed search strategies were almost 100% in all of the three test sets applied; precision ranged from 6.1% to 32.0%. PubMed's HSR queries were less sensitive (83.3% to 88.2%) than the new search strategies. Only minor differences in precision were found (5.0% to 32.0%). As with other literature on health services research, nurse staffing studies are difficult to identify in PubMed/Medline. Depending on the purpose of the search, researchers can choose between high sensitivity and retrieval of a large number of references or high precision, i.e. and an increased risk of missing relevant references, respectively. More standardized terminology (e.g. by consistent use of the term "nurse staffing") could improve the precision of future searches in this field. Empirically selected search terms can help to develop effective search strategies. The high consistency between all test sets confirmed the validity of our approach.

Delay in indexing articles published in major pharmacy practice journals.

PubMed

Rodriguez, Ryan W

2014-02-15

The delay in time from entry in the PubMed database to indexing with medical subject heading (MeSH) terms for articles published in three major pharmacy practice journals was evaluated. In April 2013, MEDLINE data were retrieved for articles published in the American Journal of Health-System Pharmacy (AJHP), the Annals of Pharmacotherapy, and Pharmacotherapy between January 1, 2010, and December 31, 2011. Data collected for each article included the PubMed entry date, MeSH indexing date, and publication type. The PubMed entry date was defined as the Entrez date, the date the citation was added to the PubMed database. Medians and interquartile ranges (IQRs) were calculated for the time to indexing of articles and for the age of unindexed articles. The proportion of unindexed articles was also calculated. A total of 1626 publications were reviewed. Overall, the median time to indexing with MeSH terms was 114 days (IQR, 98-141 days): 107 days (IQR, 94-129 days) for AJHP, 131 days (IQR, 104-157 days) for Annals of Pharmacotherapy, and 114 days (IQR, 99-128 days) for Pharmacotherapy. The median age of unindexed articles was 807 days (IQR, 671-807 days). An analysis of three major pharmacy practice journals showed that the median time to indexing articles published in 2010 and 2011 was 114 days. While all articles from AJHP and Pharmacotherapy were indexed, 40 articles from Annals of Pharmacotherapy remained unindexed.

PubMed-based quantitative analysis of biomedical publications in the SAARC countries: 1985-2009.

PubMed

Azim Majumder, Md Anwarul; Shaban, Sami F; Rahman, Sayeeda; Rahman, Nuzhat; Ahmed, Moslehuddin; Bin Abdulrahman, Khalid A; Islam, Ziauddin

2012-09-01

To conduct a geographical analysis of biomedical publications from the South Asian Association for Regional Cooperation (SAARC) countries over the past 25 years (1985-2009) using the PubMed database. A qualitative study. Web-based search during September 2010. A data extraction program, developed by one of the authors (SFS), was used to extract the raw publication counts from the downloaded PubMed data. A search of PubMed was performed for all journals indexed by selecting the advanced search option and entering the country name in the 'affiliation' field. The publications were normalized by total population, adult illiteracy rate, gross domestic product (GDP), secondary school enrollment ratio and Internet usage rate. The number of PubMed-listed papers published by the SAARC countries over the last 25 years totalled 141,783, which is 1.1% of the total papers indexed by PubMed in the same period. India alone produced 90.5% of total publications generated by SAARC countries. The average number of papers published per year from 1985 to 2009 was 5671 and number of publication increased approximately 242-fold. Normalizing by the population (per million) and GDP (per billion), India (133, 27.6%) and Nepal (323, 37.3%) had the highest publications respectively. There was a marked imbalance among the SAARC countries in terms of biomedical research and publication. Because of huge population and the high disease burden, biomedical research and publication output should receive special attention to formulate health policies, re-orient medical education curricula, and alleviate diseases and poverty.

The Case for Lung Cancer Screening: What Nurses Need to Know.

PubMed

Sorrie, Kerrin; Cates, Lisa; Hill, Alethea

2016-06-01

Lung cancer screening with low-dose helical computed tomography (LDCT) can improve high-risk individuals' chances of being diagnosed at an earlier stage and increase survival. The aims of this article are to present the risk factors associated with the development of lung cancer, identify patients at high risk for lung cancer qualifying for LDCT screening, and understand the importance of early lung cancer detection through the use of LDCT screening. PubMed and CINAHL® databases were searched with key words lung cancer screening to identify full-text academic articles from 2004-2014. This resulted in 529 articles from PubMed and 195 from CINAHL. PubMed offered suggestions for additional relevant journal articles. The National Comprehensive Cancer Network guidelines also provided substantial evidence-based information. Nurses need to provide support, education, and resources for patients undergoing lung cancer screening.

Bibliometric analysis of the Korean Journal of Parasitology: measured from SCI, PubMed, Scopus, and Synapse databases.

PubMed

Lee, Choon Shil

2009-10-01

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

Database resources of the National Center for Biotechnology

PubMed Central

Wheeler, David L.; Church, Deanna M.; Federhen, Scott; Lash, Alex E.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M.; Sequeira, Edwin; Tatusova, Tatiana A.; Wagner, Lukas

2003-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBITaxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGene, ProtEST, Database of Single Nucleotide Polymorphisms (dbSNP), Human/Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker (MM), Evidence Viewer (EV), Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov. PMID:12519941

Information and communication technology in medical education: an experience from a developing country.

PubMed

Houshyari, Asefeh Badiey; Bahadorani, Mahnaz; Tootoonchi, Mina; Gardiner, John Jacob Zucker; Peña, Roberto A; Adibi, Peyman

2012-03-01

This literature review was conducted using PubMed-Medline, PubMed-Central and ERIC databases, 1979- 2010, for research studies and pertinent theoretical publications including journals and texts. Key search words included general terms such as: "medical education," "information and communication technology in medical education," "medical students' computer skills" and "ICT use among medical students". Theoretical approaches were included to place the review within an educational and social context, and selected studies to demonstrate use of ICT in medical education through time and in different countries.

SEER Bibliography

Cancer.gov

Search this database of articles and other publications produced by cancer registry staff and Surveillance Research Program staff. Search by author, title, date, and organization. Provides links to PubMed and abstracts.

CAM on PubMed

MedlinePlus

... citations from the MEDLINE database and additional life science journals. It also includes links to many full-text articles at journal Web sites and other related Web resources. Sample Searches ...

Minimally Invasive Techniques to Accelerate the Orthodontic Tooth Movement: A Systematic Review of Animal Studies

PubMed Central

Qamruddin, Irfan; Alam, Mohammad Khursheed; Khamis, Mohd Fadhli; Husein, Adam

2015-01-01

Objective. To evaluate various noninvasive and minimally invasive procedures for the enhancement of orthodontic tooth movement in animals. Materials and Methods. Literature was searched using NCBI (PubMed, PubMed Central, and PubMed Health), MedPilot (Medline, Catalogue ZB MED, Catalogue Medicine Health, and Excerpta Medica Database (EMBASE)), and Google Scholar from January 2009 till 31 December 2014. We included original articles related to noninvasive and minimally invasive procedures to enhance orthodontic tooth movement in animals. Extraction of data and quality assessments were carried out by two observers independently. Results. The total number of hits was 9195 out of which just 11 fulfilled the inclusion criteria. Nine articles were good and 5 articles were moderate in quality. Low level laser therapy (LLLT) was among the most common noninvasive techniques whereas flapless corticision using various instruments was among the commonest minimally invasive procedures to enhance velocity of tooth movement. Conclusions. LLLT, low intensity pulsed ultrasound (LIPUS), mechanical vibration, and flapless corticision are emerging noninvasive and minimally invasive techniques which need further researches to establish protocols to use them clinically with conviction. PMID:26881201

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

PubMed

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

2017-01-04

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

Comparison of the time-to-indexing in PubMed between biomedical journals according to impact factor, discipline, and focus.

PubMed

Irwin, Adriane N; Rackham, Daniel

Practicing evidence-based medicine requires health care professionals to efficiently retrieve relevant and current literature. The purpose of this study was to compare the time interval between PubMed entry and indexing with Medical Subject Headings (MeSH) between biomedical journals with varying impact factors, focus areas, and health care discipline representation. This was a cross-sectional study of articles entered into PubMed database between January 1 and December 31, 2012. The primary endpoint was the number of days between PubMed entry and indexing with MeSH terms. A total of 7906 articles were reviewed across 18 journals. In the first comparison, the time-to-indexing was 177 ± 100 days, 111 ± 69 days, and 23 ± 40 days for articles published in journals with impact factors of 2.0-2.5, 4.5-6.5, and >25, respectively (P ≤ 0.001). In the second comparison, the time-to-indexing was 111 ± 69 days for general medicine versus 170 ± 74 days for specialty journals (P ≤ 0.001). In the third comparison, the overall time-to-indexing was 177 ± 100 days, 234 ± 107 days, and 163 ± 58 days for medicine, nursing, and pharmacy journals, respectively (P ≤ 0.001). Study results identified a significant delay between entry of articles into the PubMed database and time-to-indexing with MeSH terms across journals of varying impact factor, discipline, and focus. Results suggest that there may be factors that influence the priority by which articles are indexed with MeSH terms. Future research should focus on determining those journal characteristics and any impact of this delay on clinical practice. Copyright © 2016 Elsevier Inc. All rights reserved.

Quantifying publication scholarly activity of psychiatry residency training directors.

PubMed

Johnston, Nathan S; Martinez, Azalia V; Schillerstrom, Jason E; Luber, M Philip; Hamaoka, Derrick A

2015-02-01

The authors quantify the number of PubMed-indexed publications by psychiatry program directors during a 5-year observation period. The authors obtained the names of general adult, child and adolescent, and geriatric psychiatry program directors from the ACGME website and entered them into a PubMed.gov database search. Then, they counted the number of indexed publications from July 2008 to June 2013 and categorized them by academic year. The median number of publications was one for adult psychiatry program directors (n=184), one for child and adolescent directors (n=121), and three for geriatric psychiatry directors (n=58). The number of PubMed-indexed publications for program directors of general adult, child and adolescent, and geriatric psychiatry residencies is relatively low. Further research is needed to identify and examine the challenges facing program directors that may limit their ability to participate in this form of scholarly activity.

Trend in dental research output in Iran over a period of 20 years (1990-2009).

PubMed

Sadeghi, Masoumeh; Shahravan, Arash; Haghdoost, Ali Akbar; Asgary, Saeed; Rad, Maryam

2012-04-01

The number of scientific papers is a conventional metric for the measurement of a country's research performance in a particular area. To evaluate the trend in Iranian publications of dental research results in peer-reviewed international scientific journals over the period 1999-2009, using national and international databases, and to compare the results with other countries. The search process was performed by two independent persons in PubMed and Iranian Medline (IranMedex). Data extraction included the year of publication, total number of dental papers in each year, total number of Iranian dental papers in each year and number of papers with a high level of evidence; these were compared with those in other Asian countries. The total number of dental articles indexed in PubMed during the studied period was 207,689, with 671 being written by researchers who stated their affiliation as Iran. Although the proportion of Iranian dental articles to all published dental articles was 0.01% in 1990, this increased to 1.4% in 2009. Of all clinical trials indexed in PubMed from 1990 to 2009, only 0.62% had an author from Iran. The collaboration rate of authors ranged between 1 and 10. Turkey and Iran had a larger number of dental research publications compared with other Asian countries assessed in this study. During the last two decades, there has been a considerable increase in the number of dental papers by Iranian researchers indexed in the PubMed database. © 2012 FDI World Dental Federation.

An analysis of orthopaedic theses in Turkey: Evidence levels and publication rates.

PubMed

Koca, Kenan; Ekinci, Safak; Akpancar, Serkan; Gemci, Muhammed Hanifi; Erşen, Ömer; Akyıldız, Faruk

2016-10-01

The aim of this study was to present characteristics and publication patterns of studies arise from orthopedic theses obtained from National Thesis Center; database in terms of publication years, study types, topics, level of evidence between 1974 and 2014. Firstly, National Thesis Center database was searched for orthopedics and Traumatology theses. The theses, which their summary or full text were available were included in the study. The topics, study types and quality of study designs were reviewed. Then theses were searched in the PubMed database. Journals of published theses were classified according to category, scope and impact factors of the year 2014. 1508 theses were included into the study. Clinical studies comprised 71,7% of the theses, while 25,6% of the theses were non-clinical experimental and 2,7% of the theses were observational studies. Clinical studies were Level I in 8,6% (n = 93) and Level II in 5,8% of the theses (n = 63). A total of 224 theses (14,9%) were published in the journals indexed in PubMed database from 1974 to 2012. Fifty-two (23,2%) were published in SCI; 136 theses (60,7%) were published in SCI-E journals and 36 theses (16%) were published in other Journals indexed in PubMed. The quantity and quality of published theses need to be improved and effective measures should be taken to promote quality of theses. Theses from universities and Training hospitals which did not allow open access, and; incomplete records of the National Thesis Center database were major limitations of this study. Copyright © 2016 Turkish Association of Orthopaedics and Traumatology. Production and hosting by Elsevier B.V. All rights reserved.

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

PubMed

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

2017-04-01

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

Evidence-Based Practice: Quality Indicator Analysis of Antecedent Exercise in Autism Spectrum Disorders

ERIC Educational Resources Information Center

Kasner, Melanie; Reid, Greg; MacDonald, Cathy

2012-01-01

The purpose of the research was to conduct a quality indicator analysis of studies exploring the effects of antecedent exercise on self-stimulatory behaviors of individuals with autism spectrum disorders (ASD). Educational Resources Information Center (ERIC), Google Scholar, SPORTDiscus, PsychINFO, and PubMed/MedLine databases from 1980 to October…

Identification of risk conditions for the development of adrenal disorders: how optimized PubMed search strategies makes the difference.

PubMed

Guaraldi, Federica; Parasiliti-Caprino, Mirko; Goggi, Riccardo; Beccuti, Guglielmo; Grottoli, Silvia; Arvat, Emanuela; Ghizzoni, Lucia; Ghigo, Ezio; Giordano, Roberta; Gori, Davide

2014-12-01

The exponential growth of scientific literature available through electronic databases (namely PubMed) has increased the chance of finding interesting articles. At the same time, search has become more complicated, time consuming, and at risk of missing important information. Therefore, optimized strategies have to be adopted to maximize searching impact. The aim of this study was to formulate efficient strings to search PubMed for etiologic associations between adrenal disorders (ADs) and other conditions. A comprehensive list of terms identifying endogenous conditions primarily affecting adrenals was compiled. An ad hoc analysis was performed to find the best way to express each term in order to find the highest number of potentially pertinent articles in PubMed. A predefined number of retrieved abstracts were read to assess their association with ADs' etiology. A more sensitive (providing the largest literature coverage) and a more specific (including only those terms retrieving >40 % of potentially pertinent articles) string were formulated. Various researches were performed to assess strings' ability to identify articles of interest in comparison with non-optimized literature searches. We formulated optimized, ready applicable tools for the identification of the literature assessing etiologic associations in the field of ADs using PubMed, and demonstrated the advantages deriving from their application. Detailed description of the methodological process is also provided, so that this work can easily be translated to other fields of practice.

PubMed-EX: a web browser extension to enhance PubMed search with text mining features.

PubMed

Tsai, Richard Tzong-Han; Dai, Hong-Jie; Lai, Po-Ting; Huang, Chi-Hsin

2009-11-15

PubMed-EX is a browser extension that marks up PubMed search results with additional text-mining information. PubMed-EX's page mark-up, which includes section categorization and gene/disease and relation mark-up, can help researchers to quickly focus on key terms and provide additional information on them. All text processing is performed server-side, freeing up user resources. PubMed-EX is freely available at http://bws.iis.sinica.edu.tw/PubMed-EX and http://iisr.cse.yzu.edu.tw:8000/PubMed-EX/.

Sports medicine clinical trial research publications in academic medical journals between 1996 and 2005: an audit of the PubMed MEDLINE database.

PubMed

Nichols, A W

2008-11-01

To identify sports medicine-related clinical trial research articles in the PubMed MEDLINE database published between 1996 and 2005 and conduct a review and analysis of topics of research, experimental designs, journals of publication and the internationality of authorships. Sports medicine research is international in scope with improving study methodology and an evolution of topics. Structured review of articles identified in a search of a large electronic medical database. PubMed MEDLINE database. Sports medicine-related clinical research trials published between 1996 and 2005. Review and analysis of articles that meet inclusion criteria. Articles were examined for study topics, research methods, experimental subject characteristics, journal of publication, lead authors and journal countries of origin and language of publication. The search retrieved 414 articles, of which 379 (345 English language and 34 non-English language) met the inclusion criteria. The number of publications increased steadily during the study period. Randomised clinical trials were the most common study type and the "diagnosis, management and treatment of sports-related injuries and conditions" was the most popular study topic. The knee, ankle/foot and shoulder were the most frequent anatomical sites of study. Soccer players and runners were the favourite study subjects. The American Journal of Sports Medicine had the highest number of publications and shared the greatest international diversity of authorships with the British Journal of Sports Medicine. The USA, Australia, Germany and the UK produced a good number of the lead authorships. In all, 91% of articles and 88% of journals were published in English. Sports medicine-related research is internationally diverse, clinical trial publications are increasing and the sophistication of research design may be improving.

A bibliometric analysis of Australian general practice publications from 1980 to 2007 using PubMed.

PubMed

Mendis, Kumara; Kidd, Michael R; Schattner, Peter; Canalese, Joseph

2010-01-01

We analysed Australian general practice (GP) publications in PubMed from 1980 to 2007 to determine journals, authors, publication types, national health priority areas (NHPA) and compared the results with those from three specialties (public health, cardiology and medical informatics) and two countries (the UK and New Zealand). Australian GP publications were downloaded in MEDLINE format using PubMed queries and were written to a Microsoft Access database using a software application. Search Query Language and online PubMed queries were used for further analysis. There were 4777 publications from 1980 to 2007. Australian Family Physician (38.1%) and the Medical Journal of Australia (17.6%) contributed 55.7% of publications. Reviews (12.7%), letters (6.6%), clinical trials (6.5%) and systematic reviews (5%) were the main PubMed publication types. Thirty five percent of publications addressed National Health Priority Areas with material on mental health (13.7%), neoplasms (6.5%) and cardiovascular conditions (5.9%). The comparable numbers of publications for the three specialties were: public health - 80 911, cardiology - 15 130 and medical informatics - 3338; total country GP comparisons were: UK - 14 658 and New Zealand - 1111. Australian GP publications have shown an impressive growth from 1980 to 2007 with a 15-fold increase. This increase may be due in part to the actions of the Australian government over the past decade to financially support research in primary care, as well as the maturing of academic general practice. This analysis can assist governments, researchers, policy makers and others to target resources so that further developments can be encouraged, supported and monitored.

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

PubMed

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

2013-01-01

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

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

PubMed

Citrome, Leslie

2014-07-01

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

ANTI-VIRAL EFFECTS OF MEDICINAL PLANTS IN THE MANAGEMENT OF DENGUE: A SYSTEMATIC REVIEW.

PubMed

Frederico, Éric Heleno Freira Ferreira; Cardoso, André Luiz Bandeira Dionísio; Moreira-Marconi, Eloá; de Sá-Caputo, Danúbia da Cunha; Guimarães, Carlos Alberto Sampaio; Dionello, Carla da Fontoura; Morel, Danielle Soares; Paineiras-Domingos, Laisa Liane; de Souza, Patricia Lopes; Brandão-Sobrinho-Neto, Samuel; Carvalho-Lima, Rafaelle Pacheco; Guedes-Aguiar, Eliane de Oliveira; Costa-Cavalcanti, Rebeca Graça; Kutter, Cristiane Ribeiro; Bernardo-Filho, Mario

2017-01-01

Dengue is considered as an important arboviral disease. Safe, low-cost, and effective drugs that possess inhibitory activity against dengue virus (DENV) are mostly needed to try to combat the dengue infection worldwide. Medicinal plants have been considered as an important alternative to manage several diseases, such as dengue. As authors have demonstrated the antiviral effect of medicinal plants against DENV, the aim of this study was to review systematically the published research concerning the use of medicinal plants in the management of dengue using the PubMed database. Search and selection of publications were made using the PubMed database following the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA statement). Six publications met the inclusion criteria and were included in the final selection after thorough analysis. It is suggested that medicinal plants' products could be used as potential anti-DENV agents.

PubMedAlertMe - Standalone Windows-based PubMed SDI Software Application

PubMed Central

Ma’ayan, 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

Adjacency and Proximity Searching in the Science Citation Index and Google

DTIC Science & Technology

2005-01-01

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

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

PubMed Central

Aronson, Jeffrey K

2016-01-01

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

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

PubMed

Ferner, Robin E; Aronson, Jeffrey K

2016-12-14

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

Molecular Imaging and Contrast Agent Database (MICAD): evolution and progress.

PubMed

Chopra, Arvind; Shan, Liang; Eckelman, W C; Leung, Kam; Latterner, Martin; Bryant, Stephen H; Menkens, Anne

2012-02-01

The purpose of writing this review is to showcase the Molecular Imaging and Contrast Agent Database (MICAD; www.micad.nlm.nih.gov ) to students, researchers, and clinical investigators interested in the different aspects of molecular imaging. This database provides freely accessible, current, online scientific information regarding molecular imaging (MI) probes and contrast agents (CA) used for positron emission tomography, single-photon emission computed tomography, magnetic resonance imaging, X-ray/computed tomography, optical imaging and ultrasound imaging. Detailed information on >1,000 agents in MICAD is provided in a chapter format and can be accessed through PubMed. Lists containing >4,250 unique MI probes and CAs published in peer-reviewed journals and agents approved by the United States Food and Drug Administration as well as a comma separated values file summarizing all chapters in the database can be downloaded from the MICAD homepage. Users can search for agents in MICAD on the basis of imaging modality, source of signal/contrast, agent or target category, pre-clinical or clinical studies, and text words. Chapters in MICAD describe the chemical characteristics (structures linked to PubChem), the in vitro and in vivo activities, and other relevant information regarding an imaging agent. All references in the chapters have links to PubMed. A Supplemental Information Section in each chapter is available to share unpublished information regarding an agent. A Guest Author Program is available to facilitate rapid expansion of the database. Members of the imaging community registered with MICAD periodically receive an e-mail announcement (eAnnouncement) that lists new chapters uploaded to the database. Users of MICAD are encouraged to provide feedback, comments, or suggestions for further improvement of the database by writing to the editors at micad@nlm.nih.gov.

Molecular Imaging and Contrast Agent Database (MICAD): Evolution and Progress

PubMed Central

Chopra, Arvind; Shan, Liang; Eckelman, W. C.; Leung, Kam; Latterner, Martin; Bryant, Stephen H.; Menkens, Anne

2011-01-01

The purpose of writing this review is to showcase the Molecular Imaging and Contrast Agent Database (MICAD; www.micad.nlm.nih.gov) to students, researchers and clinical investigators interested in the different aspects of molecular imaging. This database provides freely accessible, current, online scientific information regarding molecular imaging (MI) probes and contrast agents (CA) used for positron emission tomography, single-photon emission computed tomography, magnetic resonance imaging, x-ray/computed tomography, optical imaging and ultrasound imaging. Detailed information on >1000 agents in MICAD is provided in a chapter format and can be accessed through PubMed. Lists containing >4250 unique MI probes and CAs published in peer-reviewed journals and agents approved by the United States Food and Drug Administration (FDA) as well as a CSV file summarizing all chapters in the database can be downloaded from the MICAD homepage. Users can search for agents in MICAD on the basis of imaging modality, source of signal/contrast, agent or target category, preclinical or clinical studies, and text words. Chapters in MICAD describe the chemical characteristics (structures linked to PubChem), the in vitro and in vivo activities and other relevant information regarding an imaging agent. All references in the chapters have links to PubMed. A Supplemental Information Section in each chapter is available to share unpublished information regarding an agent. A Guest Author Program is available to facilitate rapid expansion of the database. Members of the imaging community registered with MICAD periodically receive an e-mail announcement (eAnnouncement) that lists new chapters uploaded to the database. Users of MICAD are encouraged to provide feedback, comments or suggestions for further improvement of the database by writing to the editors at: micad@nlm.nih.gov PMID:21989943

PubMed-Indexed Dental Publications from Iran: A Scientometric Study

PubMed Central

Asgary, Saeed; Sabbagh, Sedigheh; Shirazi, Alireza Sarraf; Ahmadyar, Maryam; Shahravan, Arash; Akhoundi, Mohammad Sadegh Ahmad

2016-01-01

Objectives: Scientometric methods and the resulting citations have been applied to investigate the scientific performance of a nation. The present study was designed to collect the statistical information of dental articles by Iranian authors published in PubMed. Materials and Methods: We searched the PubMed database for dental articles of Iranian authors until June 31, 2015. All abstracts were manually reviewed in order to exclude false retrievals. The number of articles per dental subspecialties, distribution of research designs, Scopus/Google Scholar citation of each article, number of authors and affiliation of the first/corresponding author were extracted and transferred to Microsoft Excel. The data were further analyzed to illustrate the related scientometric indicators. Results: A total of 3,835 articles were retrieved according to the selection criteria. The number of PubMed-indexed publications between 2008 and 2015 showed a seven-fold increase. The majority of articles were written by four authors (24.56%). Systematic reviews and clinical trials constituted 9.20% of all publications. The number and percentage of articles with ≥4 citations from Google Scholar (n=2024; 52.78%) were higher than those from Scopus (n=1015; 26.47%). According to affiliated departments of the first authors, the top three dental subspecialties with the highest number of publications belonged to endodontics (19.82%), orthodontics (11.13%) and oral and maxillofacial surgery (10.33%). Moreover, the majority of articles originated from Shahid Beheshti- (14.47%), Tehran- (13.72%) and Mashhad- (12.28%) University of Medical Sciences. Conclusions: Analysis of PubMed-indexed dental publications originating from Iran revealed a growing trend in the recent years. PMID:28392812

Automatically finding relevant citations for clinical guideline development.

PubMed

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

2015-10-01

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

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

PubMed

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

2014-01-01

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

PuReD-MCL: a graph-based PubMed document clustering methodology.

PubMed

Theodosiou, T; Darzentas, N; Angelis, L; Ouzounis, C A

2008-09-01

Biomedical literature is the principal repository of biomedical knowledge, with PubMed being the most complete database collecting, organizing and analyzing such textual knowledge. There are numerous efforts that attempt to exploit this information by using text mining and machine learning techniques. We developed a novel approach, called PuReD-MCL (Pubmed Related Documents-MCL), which is based on the graph clustering algorithm MCL and relevant resources from PubMed. PuReD-MCL avoids using natural language processing (NLP) techniques directly; instead, it takes advantage of existing resources, available from PubMed. PuReD-MCL then clusters documents efficiently using the MCL graph clustering algorithm, which is based on graph flow simulation. This process allows users to analyse the results by highlighting important clues, and finally to visualize the clusters and all relevant information using an interactive graph layout algorithm, for instance BioLayout Express 3D. The methodology was applied to two different datasets, previously used for the validation of the document clustering tool TextQuest. The first dataset involves the organisms Escherichia coli and yeast, whereas the second is related to Drosophila development. PuReD-MCL successfully reproduces the annotated results obtained from TextQuest, while at the same time provides additional insights into the clusters and the corresponding documents. Source code in perl and R are available from http://tartara.csd.auth.gr/~theodos/

GO2PUB: Querying PubMed with semantic expansion of gene ontology terms

PubMed Central

2012-01-01

Background With the development of high throughput methods of gene analyses, there is a growing need for mining tools to retrieve relevant articles in PubMed. As PubMed grows, literature searches become more complex and time-consuming. Automated search tools with good precision and recall are necessary. We developed GO2PUB to automatically enrich PubMed queries with gene names, symbols and synonyms annotated by a GO term of interest or one of its descendants. Results GO2PUB enriches PubMed queries based on selected GO terms and keywords. It processes the result and displays the PMID, title, authors, abstract and bibliographic references of the articles. Gene names, symbols and synonyms that have been generated as extra keywords from the GO terms are also highlighted. GO2PUB is based on a semantic expansion of PubMed queries using the semantic inheritance between terms through the GO graph. Two experts manually assessed the relevance of GO2PUB, GoPubMed and PubMed on three queries about lipid metabolism. Experts’ agreement was high (kappa = 0.88). GO2PUB returned 69% of the relevant articles, GoPubMed: 40% and PubMed: 29%. GO2PUB and GoPubMed have 17% of their results in common, corresponding to 24% of the total number of relevant results. 70% of the articles returned by more than one tool were relevant. 36% of the relevant articles were returned only by GO2PUB, 17% only by GoPubMed and 14% only by PubMed. For determining whether these results can be generalized, we generated twenty queries based on random GO terms with a granularity similar to those of the first three queries and compared the proportions of GO2PUB and GoPubMed results. These were respectively of 77% and 40% for the first queries, and of 70% and 38% for the random queries. The two experts also assessed the relevance of seven of the twenty queries (the three related to lipid metabolism and four related to other domains). Expert agreement was high (0.93 and 0.8). GO2PUB and GoPubMed performances were similar to those of the first queries. Conclusions We demonstrated that the use of genes annotated by either GO terms of interest or a descendant of these GO terms yields some relevant articles ignored by other tools. The comparison of GO2PUB, based on semantic expansion, with GoPubMed, based on text mining techniques, showed that both tools are complementary. The analysis of the randomly-generated queries suggests that the results obtained about lipid metabolism can be generalized to other biological processes. GO2PUB is available at http://go2pub.genouest.org. PMID:22958570

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

PubMed

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

2012-11-21

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

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

Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles.

PubMed

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

2015-01-01

In this study, we present an analysis of data citation practices in full text research articles and their corresponding supplementary data files, made available in the Open Access set of articles from Europe PubMed Central. Our aim is to investigate whether supplementary data files should be considered as a source of information for integrating the literature with biomolecular databases. Using text-mining methods to identify and extract a variety of core biological database accession numbers, we found that the supplemental data files contain many more database citations than the body of the article, and that those citations often take the form of a relatively small number of articles citing large collections of accession numbers in text-based files. Moreover, citation of value-added databases derived from submission databases (such as Pfam, UniProt or Ensembl) is common, demonstrating the reuse of these resources as datasets in themselves. All the database accession numbers extracted from the supplementary data are publicly accessible from http://dx.doi.org/10.5281/zenodo.11771. Our study suggests that supplementary data should be considered when linking articles with data, in curation pipelines, and in information retrieval tasks in order to make full use of the entire research article. These observations highlight the need to improve the management of supplemental data in general, in order to make this information more discoverable and useful.

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

PubMed

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

2015-04-01

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

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

PubMed Central

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

2015-01-01

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

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

Toolbox for Evaluating Residents as Teachers

ERIC Educational Resources Information Center

Coverdale, John H.; Ismail, Nadia; Mian, Ayesha; Dewey, Charlene

2010-01-01

Objective: The authors review existing assessment tools related to evaluating residents' teaching skills and teaching effectiveness. Methods: PubMed and PsycInfo databases were searched using combinations of keywords including "residents," "residents as teachers," "teaching skills," and "assessments" or "rating scales." Results: Eleven evaluation…

Lost in translation? A multilingual Query Builder improves the quality of PubMed queries: a randomised controlled trial.

PubMed

Schuers, Matthieu; Joulakian, Mher; Kerdelhué, Gaetan; Segas, Léa; Grosjean, Julien; Darmoni, Stéfan J; Griffon, Nicolas

2017-07-03

MEDLINE is the most widely used medical bibliographic database in the world. Most of its citations are in English and this can be an obstacle for some researchers to access the information the database contains. We created a multilingual query builder to facilitate access to the PubMed subset using a language other than English. The aim of our study was to assess the impact of this multilingual query builder on the quality of PubMed queries for non-native English speaking physicians and medical researchers. A randomised controlled study was conducted among French speaking general practice residents. We designed a multi-lingual query builder to facilitate information retrieval, based on available MeSH translations and providing users with both an interface and a controlled vocabulary in their own language. Participating residents were randomly allocated either the French or the English version of the query builder. They were asked to translate 12 short medical questions into MeSH queries. The main outcome was the quality of the query. Two librarians blind to the arm independently evaluated each query, using a modified published classification that differentiated eight types of errors. Twenty residents used the French version of the query builder and 22 used the English version. 492 queries were analysed. There were significantly more perfect queries in the French group vs. the English group (respectively 37.9% vs. 17.9%; p < 0.01). It took significantly more time for the members of the English group than the members of the French group to build each query, respectively 194 sec vs. 128 sec; p < 0.01. This multi-lingual query builder is an effective tool to improve the quality of PubMed queries in particular for researchers whose first language is not English.

Nursing identity and patient-centredness in scholarly health services research: a computational text analysis of PubMed abstracts 1986-2013.

PubMed

Bell, Erica; Campbell, Steve; Goldberg, Lynette R

2015-01-22

The most important and contested element of nursing identity may be the patient-centredness of nursing, though this concept is not well-treated in the nursing identity literature. More conceptually-based mapping of nursing identity constructs are needed to help nurses shape their identity. The field of computational text analytics offers new opportunities to scrutinise how growing disciplines such as health services research construct nursing identity. This paper maps the conceptual content of scholarly health services research in PubMed as it relates to the patient-centeredness of nursing. Computational text analytics software was used to analyse all health services abstracts in the database PubMed since 1986. Abstracts were treated as indicative of the content of health services research. The database PubMed was searched for all research papers using the term "service" or "services" in the abstract or keywords for the period 01/01/1986 to 30/06/2013. A total of 234,926 abstracts were obtained. Leximancer software was used in 1) mapping of 4,144,458 instances of 107 concepts; 2) analysis of 106 paired concept co-occurrences for the nursing concept; and 3) sentiment analysis of the nursing concept versus patient, family and community concepts, and clinical concepts. Nursing is constructed within quality assurance or service implementation or workforce development concepts. It is relatively disconnected from patient, family or community care concepts. For those who agree that patient-centredness should be a part of nursing identity in practice, this study suggests that there is a need for development of health services research into both the nature of the caring construct in nursing identity and its expression in practice. More fundamentally, the study raises questions about whether health services research cultures even value the politically popular idea of nurses as patient-centred caregivers and whether they should.

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

PubMed Central

Muin, Michael; Fontelo, Paul; Ackerman, Michael

2005-01-01

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

The Association between Databases for Indexing Studies Intended for an Exercise Meta-Analysis of Arthritis Randomized Controlled Trials

PubMed Central

Kelley, George A.; Kelley, Kristi S.

2012-01-01

Objective. The purpose of this study was to determine the database indexing of randomized controlled trials (RCTs) for a meta-analysis addressing the effects of exercise on pain and physical function in adults with arthritis and other rheumatic diseases (AORD). Methods. The number, percentage, and 95% confidence intervals (CIs) for included articles at initial and follow-up periods were calculated from PubMed, EMBASE, CENTRAL, CINAHL, SPORTDiscus, and DAO databases. The number needed to review (NNR) was also calculated along with the number of articles retrieved by expert review. Cross-referencing from reviews and included articles also occurred. Results. Thirty-four of 36 articles (94.4%, 95% CI, 81.3–99.3) were located by database searching. PubMed and CENTRAL yielded 32 of 36 articles (88.9%, 73.9–96.9). Two articles not identified in any of the other databases were found in either CINAHL or SPORTDicsus. Two other articles were located by scanning the reference lists of review articles. The NNR ranged from 2 (CINAHL) to 118 (SPORTDiscus). More articles were identified in EMBASE at follow-up (36%, 12.1–42.2 versus 86.1%, 70.5–95.3). Conclusions. Searching multiple databases and cross-referencing from reviews was important for identifying RCTs addressing the effects of exercise on pain and physical function in adults with AORD. PMID:22924128

The Association between Databases for Indexing Studies Intended for an Exercise Meta-Analysis of Arthritis Randomized Controlled Trials.

PubMed

Kelley, George A; Kelley, Kristi S

2012-01-01

Objective. The purpose of this study was to determine the database indexing of randomized controlled trials (RCTs) for a meta-analysis addressing the effects of exercise on pain and physical function in adults with arthritis and other rheumatic diseases (AORD). Methods. The number, percentage, and 95% confidence intervals (CIs) for included articles at initial and follow-up periods were calculated from PubMed, EMBASE, CENTRAL, CINAHL, SPORTDiscus, and DAO databases. The number needed to review (NNR) was also calculated along with the number of articles retrieved by expert review. Cross-referencing from reviews and included articles also occurred. Results. Thirty-four of 36 articles (94.4%, 95% CI, 81.3-99.3) were located by database searching. PubMed and CENTRAL yielded 32 of 36 articles (88.9%, 73.9-96.9). Two articles not identified in any of the other databases were found in either CINAHL or SPORTDicsus. Two other articles were located by scanning the reference lists of review articles. The NNR ranged from 2 (CINAHL) to 118 (SPORTDiscus). More articles were identified in EMBASE at follow-up (36%, 12.1-42.2 versus 86.1%, 70.5-95.3). Conclusions. Searching multiple databases and cross-referencing from reviews was important for identifying RCTs addressing the effects of exercise on pain and physical function in adults with AORD.

Library of molecular associations: curating the complex molecular basis of liver diseases.

PubMed

Buchkremer, Stefan; Hendel, Jasmin; Krupp, Markus; Weinmann, Arndt; Schlamp, Kai; Maass, Thorsten; Staib, Frank; Galle, Peter R; Teufel, Andreas

2010-03-20

Systems biology approaches offer novel insights into the development of chronic liver diseases. Current genomic databases supporting systems biology analyses are mostly based on microarray data. Although these data often cover genome wide expression, the validity of single microarray experiments remains questionable. However, for systems biology approaches addressing the interactions of molecular networks comprehensive but also highly validated data are necessary. We have therefore generated the first comprehensive database for published molecular associations in human liver diseases. It is based on PubMed published abstracts and aimed to close the gap between genome wide coverage of low validity from microarray data and individual highly validated data from PubMed. After an initial text mining process, the extracted abstracts were all manually validated to confirm content and potential genetic associations and may therefore be highly trusted. All data were stored in a publicly available database, Library of Molecular Associations http://www.medicalgenomics.org/databases/loma/news, currently holding approximately 1260 confirmed molecular associations for chronic liver diseases such as HCC, CCC, liver fibrosis, NASH/fatty liver disease, AIH, PBC, and PSC. We furthermore transformed these data into a powerful resource for molecular liver research by connecting them to multiple biomedical information resources. Together, this database is the first available database providing a comprehensive view and analysis options for published molecular associations on multiple liver diseases.

Efficient bibliographic searches on allergology using PubMed.

PubMed

Sáez Gómez, J M; Aguinaga Ontoso, E; Negro Alvarez, J M; Guillén-Grima, F; Ivancevich, J C; Bozzola, C M

2007-01-01

PubMed is the most important of the non-specialized databases on biomedical literature. International and quickly updated is elaborated by the American Government and contains only information about papers published in scientific journal/s. Although it can be used as an unique Data Base, as a matter of fact is the addition of several subgroups (among them MEDLINE) that can be searched simultaneously. To present the main characteristics of PubMed, as well as the most important procedures of search, for obtaining efficient results in searches on allergology. PubMed is elaborated by the American Administration, that condition the character of the registered papers, 90 % of them are written in English in American (50 %) or British (20 %) Journals. Because of this, the information for certain specialties or countries must be obtained from other sources. This paper shows how PubMed allows to search in natural language due to the Automatic Term Mapping that links terms from the natural language with the descriptors producing searches with a higher sensitivity although with a low specificity. Nevertheless the MeSH (Medical Subject Headings) thesaurus allows to translate those terms from the natural language to the equivalent descriptor, as well as to make queries in the PubMed's documental language with a high specificity but with lower sensitivity than the natural language. The use of union (OR), intersection (AND) and exclusion (NOT) operators, as well as tags, such as delimiters of the search fields, allows to increase the specificity of the results. Similar results may be obtained with the use of Limits. Searches done using Clinical Queries are very interesting due to their direct clinical application and because allow to find systematic reviews, metaanalysis or clinically oriented papers (treatment, diagnostic, etiology, prognosis or clinical prediction guides) on the area of interest. Other procedures such as the Index, History of searches, and the widening of the selection using Related Articles and the storing of separate results in the Clipboard to be kept by the user, are presented in this paper.

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

ANTI-VIRAL EFFECTS OF MEDICINAL PLANTS IN THE MANAGEMENT OF DENGUE: A SYSTEMATIC REVIEW

PubMed Central

Frederico, Éric Heleno Freira Ferreira; Cardoso, André Luiz Bandeira Dionísio; Moreira-Marconi, Eloá; de Sá-Caputo, Danúbia da Cunha; Guimarães, Carlos Alberto Sampaio; Dionello, Carla da Fontoura; Morel, Danielle Soares; Paineiras-Domingos, Laisa Liane; de Souza, Patricia Lopes; Brandão-Sobrinho-Neto, Samuel; Carvalho-Lima, Rafaelle Pacheco; Guedes-Aguiar, Eliane de Oliveira; Costa-Cavalcanti, Rebeca Graça; Kutter, Cristiane Ribeiro; Bernardo-Filho, Mario

2017-01-01

Background: Dengue is considered as an important arboviral disease. Safe, low-cost, and effective drugs that possess inhibitory activity against dengue virus (DENV) are mostly needed to try to combat the dengue infection worldwide. Medicinal plants have been considered as an important alternative to manage several diseases, such as dengue. As authors have demonstrated the antiviral effect of medicinal plants against DENV, the aim of this study was to review systematically the published research concerning the use of medicinal plants in the management of dengue using the PubMed database. Materials and Methods: Search and selection of publications were made using the PubMed database following the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA statement). Results: Six publications met the inclusion criteria and were included in the final selection after thorough analysis. Conclusion: It is suggested that medicinal plants’ products could be used as potential anti-DENV agents. PMID:28740942

Do we need a Unique Scientist ID for publications in biomedicine?

PubMed

Bohne-Lang, Andreas; Lang, Elke

2005-03-22

BACKGROUND: The PubMed database contains nearly 15 million references from more than 4,800 biomedical journals. In general, authors of scientific articles are addressed by their last name and forename initial. DISCUSSION: In general, names can be too common and not unique enough to be search criteria. Today, Ph.D. students, other researchers and women publish scientific work. A person may not only have one name but several names and publish under each name. A Unique Scientist ID could help to address people in peer-to-peer (P2P) networks. As a starting point, perhaps PubMed could generate and manage such a scientist ID. SUMMARY: A Unique Scientist ID would improve knowledge management in science. Unfortunately in some of the publications, and then within the online databases, only one letter abbreviates the author's forename. A common name with only one initial could retrieve pertinent citations, but include many false drops (retrieval matching searched criteria but indisputably irrelevant).

Online Mendelian Inheritance in Man (OMIM).

PubMed

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

2000-01-01

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

Automatic generation of investigator bibliographies for institutional research networking systems.

PubMed

Johnson, Stephen B; Bales, Michael E; Dine, Daniel; Bakken, Suzanne; Albert, Paul J; Weng, Chunhua

2014-10-01

Publications are a key data source for investigator profiles and research networking systems. We developed ReCiter, an algorithm that automatically extracts bibliographies from PubMed using institutional information about the target investigators. ReCiter executes a broad query against PubMed, groups the results into clusters that appear to constitute distinct author identities and selects the cluster that best matches the target investigator. Using information about investigators from one of our institutions, we compared ReCiter results to queries based on author name and institution and to citations extracted manually from the Scopus database. Five judges created a gold standard using citations of a random sample of 200 investigators. About half of the 10,471 potential investigators had no matching citations in PubMed, and about 45% had fewer than 70 citations. Interrater agreement (Fleiss' kappa) for the gold standard was 0.81. Scopus achieved the best recall (sensitivity) of 0.81, while name-based queries had 0.78 and ReCiter had 0.69. ReCiter attained the best precision (positive predictive value) of 0.93 while Scopus had 0.85 and name-based queries had 0.31. ReCiter accesses the most current citation data, uses limited computational resources and minimizes manual entry by investigators. Generation of bibliographies using named-based queries will not yield high accuracy. Proprietary databases can perform well but requite manual effort. Automated generation with higher recall is possible but requires additional knowledge about investigators. Copyright © 2014 Elsevier Inc. All rights reserved.

Missing data in substance abuse research? Researchers’ reporting practices of sexual orientation and gender identity

PubMed Central

Bacca, Cristina L.; Cochran, Bryan N.

2014-01-01

Background Lesbian, gay, bisexual, and transgender individuals are at higher risk for substance use and substance use disorders than heterosexual individuals and are more likely to seek substance use treatment, yet sexual orientation and gender identity are frequently not reported in the research literature. The purpose of this study was to identify if sexual orientation and gender identity are being reported in the recent substance use literature, and if this has changed over time. Method The PsycINFO and PubMed databases were searched for articles released in 2007 and 2012 using the term “substance abuse” and 200 articles were randomly selected from each time period and database. Articles were coded for the presence or absence of sexual orientation and gender identity information. Results Participants’ sexual orientation was reported in 3.0% and 4.9% of the 2007 and 2.3% and 6.5% of the 2012 sample, in PsycINFO and PubMed sample articles, respectively, while non-binary gender identity was reported in 0% and 1.0% of the 2007 sample and 2.3% and 1.9% of the 2012 PsycINFO and PubMed sample articles. There were no differences in rates of reporting over time. Conclusions Sexual orientation and gender identity are rarely reported in the substance abuse literature, and there has not been a change in reporting practices between 2007 and 2012. Recommendations for future investigators in reporting sexual orientation and gender identity are included. PMID:25496705

Missing data in substance abuse research? Researchers' reporting practices of sexual orientation and gender identity.

PubMed

Flentje, Annesa; Bacca, Cristina L; Cochran, Bryan N

2015-02-01

Lesbian, gay, bisexual, and transgender individuals are at higher risk for substance use and substance use disorders than heterosexual individuals and are more likely to seek substance use treatment, yet sexual orientation and gender identity are frequently not reported in the research literature. The purpose of this study was to identify if sexual orientation and gender identity are being reported in the recent substance use literature, and if this has changed over time. The PsycINFO and PubMed databases were searched for articles released in 2007 and 2012 using the term "substance abuse" and 200 articles were randomly selected from each time period and database. Articles were coded for the presence or absence of sexual orientation and gender identity information. Participants' sexual orientation was reported in 3.0% and 4.9% of the 2007 and 2.3% and 6.5% of the 2012 sample, in PsycINFO and PubMed sample articles, respectively, while non-binary gender identity was reported in 0% and 1.0% of the 2007 sample and 2.3% and 1.9% of the 2012 PsycINFO and PubMed sample articles. There were no differences in rates of reporting over time. Sexual orientation and gender identity are rarely reported in the substance abuse literature, and there has not been a change in reporting practices between 2007 and 2012. Recommendations for future investigators in reporting sexual orientation and gender identity are included. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Automatic generation of investigator bibliographies for institutional research networking systems

PubMed Central

Johnson, Stephen B.; Bales, Michael E.; Dine, Daniel; Bakken, Suzanne; Albert, Paul J.; Weng, Chunhua

2014-01-01

Objective Publications are a key data source for investigator profiles and research networking systems. We developed ReCiter, an algorithm that automatically extracts bibliographies from PubMed using institutional information about the target investigators. Methods ReCiter executes a broad query against PubMed, groups the results into clusters that appear to constitute distinct author identities and selects the cluster that best matches the target investigator. Using information about investigators from one of our institutions, we compared ReCiter results to queries based on author name and institution and to citations extracted manually from the Scopus database. Five judges created a gold standard using citations of a random sample of 200 investigators. Results About half of the 10,471 potential investigators had no matching citations in PubMed, and about 45% had fewer than 70 citations. Interrater agreement (Fleiss’ kappa) for the gold standard was 0.81. Scopus achieved the best recall (sensitivity) of 0.81, while name-based queries had 0.78 and ReCiter had 0.69. ReCiter attained the best precision (positive predictive value) of 0.93 while Scopus had 0.85 and name-based queries had 0.31. Discussion ReCiter accesses the most current citation data, uses limited computational resources and minimizes manual entry by investigators. Generation of bibliographies using named-based queries will not yield high accuracy. Proprietary databases can perform well but requite manual effort. Automated generation with higher recall is possible but requires additional knowledge about investigators. PMID:24694772

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

Genetics Home Reference: ichthyosis with confetti

MedlinePlus

... from the University of Kansas Medical Center: Ichthyosis Scientific Articles on PubMed (1 link) PubMed OMIM (1 link) ... 1;330(6000):94-7. doi: 10.1126/science.1192280. Epub 2010 Aug 26. Citation on PubMed or Free article on PubMed Central Krunic AL, Palcesky D, Busbey S, ...

Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE.

PubMed

Névéol, Aurélie; Wilbur, W John; Lu, Zhiyong

2012-01-01

High-throughput experiments and bioinformatics techniques are creating an exploding volume of data that are becoming overwhelming to keep track of for biologists and researchers who need to access, analyze and process existing data. Much of the available data are being deposited in specialized databases, such as the Gene Expression Omnibus (GEO) for microarrays or the Protein Data Bank (PDB) for protein structures and coordinates. Data sets are also being described by their authors in publications archived in literature databases such as MEDLINE and PubMed Central. Currently, the curation of links between biological databases and the literature mainly relies on manual labour, which makes it a time-consuming and daunting task. Herein, we analysed the current state of link curation between GEO, PDB and MEDLINE. We found that the link curation is heterogeneous depending on the sources and databases involved, and that overlap between sources is low, <50% for PDB and GEO. Furthermore, we showed that text-mining tools can automatically provide valuable evidence to help curators broaden the scope of articles and database entries that they review. As a result, we made recommendations to improve the coverage of curated links, as well as the consistency of information available from different databases while maintaining high-quality curation. Database URLs: http://www.ncbi.nlm.nih.gov/PubMed, http://www.ncbi.nlm.nih.gov/geo/, http://www.rcsb.org/pdb/

Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE

PubMed Central

Névéol, Aurélie; Wilbur, W. John; Lu, Zhiyong

2012-01-01

High-throughput experiments and bioinformatics techniques are creating an exploding volume of data that are becoming overwhelming to keep track of for biologists and researchers who need to access, analyze and process existing data. Much of the available data are being deposited in specialized databases, such as the Gene Expression Omnibus (GEO) for microarrays or the Protein Data Bank (PDB) for protein structures and coordinates. Data sets are also being described by their authors in publications archived in literature databases such as MEDLINE and PubMed Central. Currently, the curation of links between biological databases and the literature mainly relies on manual labour, which makes it a time-consuming and daunting task. Herein, we analysed the current state of link curation between GEO, PDB and MEDLINE. We found that the link curation is heterogeneous depending on the sources and databases involved, and that overlap between sources is low, <50% for PDB and GEO. Furthermore, we showed that text-mining tools can automatically provide valuable evidence to help curators broaden the scope of articles and database entries that they review. As a result, we made recommendations to improve the coverage of curated links, as well as the consistency of information available from different databases while maintaining high-quality curation. Database URLs: http://www.ncbi.nlm.nih.gov/PubMed, http://www.ncbi.nlm.nih.gov/geo/, http://www.rcsb.org/pdb/ PMID:22685160

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.

PubMed

Schomburg, Ida; Chang, Antje; Placzek, Sandra; Söhngen, Carola; Rother, Michael; Lang, Maren; Munaretto, Cornelia; Ulas, Susanne; Stelzer, Michael; Grote, Andreas; Scheer, Maurice; Schomburg, Dietmar

2013-01-01

The BRENDA (BRaunschweig ENzyme DAtabase) enzyme portal (http://www.brenda-enzymes.org) is the main information system of functional biochemical and molecular enzyme data and provides access to seven interconnected databases. BRENDA contains 2.7 million manually annotated data on enzyme occurrence, function, kinetics and molecular properties. Each entry is connected to a reference and the source organism. Enzyme ligands are stored with their structures and can be accessed via their names, synonyms or via a structure search. FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) are based on text mining methods and represent a complete survey of PubMed abstracts with information on enzymes in different organisms, tissues or organelles. The supplemental database DRENDA provides more than 910 000 new EC number-disease relations in more than 510 000 references from automatic search and a classification of enzyme-disease-related information. KENDA (Kinetic ENzyme DAta), a new amendment extracts and displays kinetic values from PubMed abstracts. The integration of the EnzymeDetector offers an automatic comparison, evaluation and prediction of enzyme function annotations for prokaryotic genomes. The biochemical reaction database BKM-react contains non-redundant enzyme-catalysed and spontaneous reactions and was developed to facilitate and accelerate the construction of biochemical models.

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

PubMed

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

2018-05-14

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

Consolidation of proteomics data in the Cancer Proteomics database.

PubMed

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

2015-11-01

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

School-Based Obesity Interventions: A Literature Review

ERIC Educational Resources Information Center

Shaya, Fadia T.; Flores, David; Gbarayor, Confidence M.; Wang, Jingshu

2008-01-01

Background: Childhood obesity is an impending epidemic. This article is an overview of different interventions conducted in school settings so as to guide efforts for an effective management of obesity in children, thus minimizing the risk of adult obesity and related cardiovascular risk. Methods: PubMed and OVID Medline databases were searched…

Adaptive Functioning in Williams Syndrome: A Systematic Review

ERIC Educational Resources Information Center

Brawn, Gabrielle; Porter, Melanie

2018-01-01

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

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

PubMed Central

2016-01-01

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

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

PubMed

Zhen, Yisong

2016-01-01

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

Mapping the literature of nursing: 1996–2000

PubMed Central

Allen, Margaret (Peg); Jacobs, Susan Kaplan; Levy, June R.

2006-01-01

Introduction: This project is a collaborative effort of the Task Force on Mapping the Nursing Literature of the Nursing and Allied Health Resources Section of the Medical Library Association. This overview summarizes eighteen studies covering general nursing and sixteen specialties. Method: Following a common protocol, citations from source journals were analyzed for a three-year period within the years 1996 to 2000. Analysis included cited formats, age, and ranking of the frequency of cited journal titles. Highly cited journals were analyzed for coverage in twelve health sciences and academic databases. Results: Journals were the most frequently cited format, followed by books. More than 60% of the cited resources were published in the previous seven years. Bradford's law was validated, with a small core of cited journals accounting for a third of the citations. Medical and science databases provided the most comprehensive access for biomedical titles, while CINAHL and PubMed provided the best access for nursing journals. Discussion: Beyond a heavily cited core, nursing journal citations are widely dispersed among a variety of sources and disciplines, with corresponding access via a variety of bibliographic tools. Results underscore the interdisciplinary nature of the nursing profession. Conclusion: For comprehensive searches, nurses need to search multiple databases. Libraries need to provide access to databases beyond PubMed, including CINAHL and academic databases. Database vendors should improve their coverage of nursing, biomedical, and psychosocial titles identified in these studies. Additional research is needed to update these studies and analyze nursing specialties not covered. PMID:16636714

Mapping the literature of nursing: 1996-2000.

PubMed

Allen, Margaret Peg; Jacobs, Susan Kaplan; Levy, June R

2006-04-01

This project is a collaborative effort of the Task Force on Mapping the Nursing Literature of the Nursing and Allied Health Resources Section of the Medical Library Association. This overview summarizes eighteen studies covering general nursing and sixteen specialties. Following a common protocol, citations from source journals were analyzed for a three-year period within the years 1996 to 2000. Analysis included cited formats, age, and ranking of the frequency of cited journal titles. Highly cited journals were analyzed for coverage in twelve health sciences and academic databases. Journals were the most frequently cited format, followed by books. More than 60% of the cited resources were published in the previous seven years. Bradford's law was validated, with a small core of cited journals accounting for a third of the citations. Medical and science databases provided the most comprehensive access for biomedical titles, while CINAHL and PubMed provided the best access for nursing journals. Beyond a heavily cited core, nursing journal citations are widely dispersed among a variety of sources and disciplines, with corresponding access via a variety of bibliographic tools. Results underscore the interdisciplinary nature of the nursing profession. For comprehensive searches, nurses need to search multiple databases. Libraries need to provide access to databases beyond PubMed, including CINAHL and academic databases. Database vendors should improve their coverage of nursing, biomedical, and psychosocial titles identified in these studies. Additional research is needed to update these studies and analyze nursing specialties not covered.

Interactive text mining with Pipeline Pilot: a bibliographic web-based tool for PubMed.

PubMed

Vellay, S G P; Latimer, N E Miller; Paillard, G

2009-06-01

Text mining has become an integral part of all research in the medical field. Many text analysis software platforms support particular use cases and only those. We show an example of a bibliographic tool that can be used to support virtually any use case in an agile manner. Here we focus on a Pipeline Pilot web-based application that interactively analyzes and reports on PubMed search results. This will be of interest to any scientist to help identify the most relevant papers in a topical area more quickly and to evaluate the results of query refinement. Links with Entrez databases help both the biologist and the chemist alike. We illustrate this application with Leishmaniasis, a neglected tropical disease, as a case study.

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

PubMed

Eisinger, Daniel; Tsatsaronis, George; Bundschus, Markus; Wieneke, Ulrich; Schroeder, Michael

2013-04-15

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.

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

PubMed

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

2016-02-01

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

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

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

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

PubMed

Huang, Chung-Chi; Lu, Zhiyong

2016-01-01

Identifying relevant papers from the literature is a common task in biocuration. Most current biomedical literature search systems primarily rely on matching user keywords. Semantic search, on the other hand, seeks to improve search accuracy by understanding the entities and contextual relations in user keywords. However, past research has mostly focused on semantically identifying biological entities (e.g. chemicals, diseases and genes) with little effort on discovering semantic relations. In this work, we aim to discover biomedical semantic relations in PubMed queries in an automated and unsupervised fashion. Specifically, we focus on extracting and understanding the contextual information (or context patterns) that is used by PubMed users to represent semantic relations between entities such as 'CHEMICAL-1 compared to CHEMICAL-2' With the advances in automatic named entity recognition, we first tag entities in PubMed queries and then use tagged entities as knowledge to recognize pattern semantics. More specifically, we transform PubMed queries into context patterns involving participating entities, which are subsequently projected to latent topics via latent semantic analysis (LSA) to avoid the data sparseness and specificity issues. Finally, we mine semantically similar contextual patterns or semantic relations based on LSA topic distributions. Our two separate evaluation experiments of chemical-chemical (CC) and chemical-disease (CD) relations show that the proposed approach significantly outperforms a baseline method, which simply measures pattern semantics by similarity in participating entities. The highest performance achieved by our approach is nearly 0.9 and 0.85 respectively for the CC and CD task when compared against the ground truth in terms of normalized discounted cumulative gain (nDCG), a standard measure of ranking quality. These results suggest that our approach can effectively identify and return related semantic patterns in a ranked order 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. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.

Deep learning of mutation-gene-drug relations from the literature.

PubMed

Lee, Kyubum; Kim, Byounggun; Choi, Yonghwa; Kim, Sunkyu; Shin, Wonho; Lee, Sunwon; Park, Sungjoon; Kim, Seongsoon; Tan, Aik Choon; Kang, Jaewoo

2018-01-25

Molecular biomarkers that can predict drug efficacy in cancer patients are crucial components for the advancement of precision medicine. However, identifying these molecular biomarkers remains a laborious and challenging task. Next-generation sequencing of patients and preclinical models have increasingly led to the identification of novel gene-mutation-drug relations, and these results have been reported and published in the scientific literature. Here, we present two new computational methods that utilize all the PubMed articles as domain specific background knowledge to assist in the extraction and curation of gene-mutation-drug relations from the literature. The first method uses the Biomedical Entity Search Tool (BEST) scoring results as some of the features to train the machine learning classifiers. The second method uses not only the BEST scoring results, but also word vectors in a deep convolutional neural network model that are constructed from and trained on numerous documents such as PubMed abstracts and Google News articles. Using the features obtained from both the BEST search engine scores and word vectors, we extract mutation-gene and mutation-drug relations from the literature using machine learning classifiers such as random forest and deep convolutional neural networks. Our methods achieved better results compared with the state-of-the-art methods. We used our proposed features in a simple machine learning model, and obtained F1-scores of 0.96 and 0.82 for mutation-gene and mutation-drug relation classification, respectively. We also developed a deep learning classification model using convolutional neural networks, BEST scores, and the word embeddings that are pre-trained on PubMed or Google News data. Using deep learning, the classification accuracy improved, and F1-scores of 0.96 and 0.86 were obtained for the mutation-gene and mutation-drug relations, respectively. We believe that our computational methods described in this research could be used as an important tool in identifying molecular biomarkers that predict drug responses in cancer patients. We also built a database of these mutation-gene-drug relations that were extracted from all the PubMed abstracts. We believe that our database can prove to be a valuable resource for precision medicine researchers.

Prevalence of purulent vaginal discharge in dairy herds depends on timing but not method of detection

USDA-ARS?s Scientific Manuscript database

A review of existing literature was conducted to determine the prevalence of purulent vaginal discharge (PVD) in dairy herds around the world and detection methodologies that influence prevalence estimates. Four databases (PubMed, Google Scholar, Web of Science, and Scopus) were queried with the sea...

Effect of Active Lessons on Physical Activity, Academic, and Health Outcomes: A Systematic Review

ERIC Educational Resources Information Center

Martin, Rosemarie; Murtagh, Elaine M.

2017-01-01

Purpose: The purpose of this study was to conduct a systematic review of classroom-based physical activity interventions that integrate academic content and assess the effectiveness of the interventions on physical activity, learning, facilitators of learning, and health outcomes. Method: Six electronic databases (ERIC, PubMed, Google Scholar,…

Measuring Person-Centered Care: A Critical Comparative Review of Published Tools

ERIC Educational Resources Information Center

Edvardsson, David; Innes, Anthea

2010-01-01

Purpose of the study: To present a critical comparative review of published tools measuring the person-centeredness of care for older people and people with dementia. Design and Methods: Included tools were identified by searches of PubMed, Cinahl, the Bradford Dementia Group database, and authors' files. The terms "Person-centered,"…

Nutrition and Adults with Intellectual or Developmental Disabilities: Systematic Literature Review Results

ERIC Educational Resources Information Center

Humphries, Kathleen; Traci, Meg Ann; Seekins, Tom

2009-01-01

Approximately 4.5 million Americans have an intellectual or developmental disability. Concern is increasing about these individuals' nutrition-related behavior and its implications for their health. This article reports on a systematic search of the current literature listed in the "PsycINFO" and "PubMed" databases related to nutritional status of…

Waterpipe Smoking among College Students in the United States: A Review of the Literature

ERIC Educational Resources Information Center

Grekin, Emily R.; Ayna, Dinah

2012-01-01

Objective: To review the literature on college student waterpipe use with a focus on undergraduates in the United States. Participants: Undergraduate students. Methods: Studies were accessed using the databases PubMed, MEDLINE, PsycINFO, and Academic Search Premier. Searches included combinations of the following keywords: "waterpipe," "hookah,"…

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…

Sleep Disorders as a Risk to Language Learning and Use. EBP Briefs. Volume 10, Issue 1

ERIC Educational Resources Information Center

McGregor, Karla K.; Alper, Rebecca M.

2015-01-01

Clinical Question: Are people with sleep disorders at higher risk for language learning deficits than healthy sleepers? Method: Scoping Review. Study Sources: PubMed, Google Scholar, Trip Database, ClinicalTrials.gov. Search Terms: sleep disorders AND language AND learning; sleep disorders language learning--deprivation--epilepsy; sleep disorders…

Psychiatric comorbidities in patients with systemic lupus erythematosus: a systematic review of the last 10 years.

PubMed

Asano, Nadja Maria Jorge; Coriolano, Maria das Graças Wanderley de Sales; Asano, Breno Jorge; Lins, Otávio Gomes

2013-01-01

To analyze the frequency of psychiatric comorbidities in patients with systemic lupus erythematosus (SLE) using the systematic review method. A systematic literature search was performed between April and July 2011 in the following databases: BIREME, PubMed and CAPES thesis database. This search prioritized studies published over the last ten years (2001-2011), involving the presence of psychiatric comorbidities in patients with SLE. Out of 314 articles published in scientific journals (PubMed) and 29 (BIREME), previously identified ones, 13 articles on psychiatric disorders and SLE were selected so they could be submitted to the systematic review methodological approach. The articles indicated high frequency of psychiatric comorbidities, especially mood and anxiety disorders. There is no consensus between the disease activity and psychiatric disorders. Patients with active SLE showed a higher risk of developing mood disorders than patients with inactive SLE. Patients with SLE had a higher suicide risk than the general population. More thorough studies to evaluate the psychological and genetic role, specific and non-specific autoimmune inflammatory mechanisms in mood and anxiety disorders are needed.

Towards PubMed 2.0.

PubMed

Fiorini, Nicolas; Lipman, David J; Lu, Zhiyong

2017-10-30

Staff from the National Center for Biotechnology Information in the US describe recent improvements to the PubMed search engine and outline plans for the future, including a new experimental site called PubMed Labs.

Aggression and Violence among Iranian Adolescents and Youth: A 10-year Systematic Review

PubMed Central

Sadeghi, Saeid; Farajzadegan, Ziba; Kelishadi, Roya; Heidari, Kamal

2014-01-01

Background: Although the overwhelming majority of Iranian adolescents are well-adjusted, a substantial group exhibits high levels of maladjustment and deficient functioning. Escalation of criminal violence among the youth population has become a major public policy issue and a serious public health problem. In reviewing a 10-year literature, this article aimed to describe and propose primary assumptions regarding the correlates of aggressive and violent behaviors in Iranian adolescents and youth. Methods: Bibliographic databases such as PubMed and Google Scholar along with Iranian databases including PubMed, IranMedex, Magiran, Irandoc, Psychoinfo, and Emrofor Scientific Information Database, and Magiran constituted the databases which we searched for the relevant literature. Overall 98 articles met the inclusion criteria, allowing us to initiate the discussion. Results: Reportedly, prevalence of violence and aggression among the Iranian adolescents and youth ranged from 30% to 65.5% while males being 2½ times more affected than females. The role of gender, family environment, family size, socioeconomic status, and victimization in perpetuating the circumstances was apparent. Conclusions: Relatively high prevalence of violence and aggression among Iranian youth and adolescents is a warning sign and a great challenge to the social system. Reviewed studies suffer from certain methodological and conceptual limitations. Undertaking community-based studies to estimate the actual extent of the problem is warranted. PMID:26157572

Genetics Home Reference: lymphedema-distichiasis syndrome

MedlinePlus

... on PubMed or Free article on PubMed Central Erickson RP, Dagenais SL, Caulder MS, Downs CA, Herman ... article on PubMed Central Fang J, Dagenais SL, Erickson RP, Arlt MF, Glynn MW, Gorski JL, Seaver ...

Genetics Home Reference: VACTERL association

MedlinePlus

... PubMed Raam MS, Pineda-Alvarez DE, Hadley DW, Solomon BD. Long-term outcomes of adults with features ... on PubMed or Free article on PubMed Central Solomon BD, Pineda-Alvarez DE, Raam MS, Bous SM, ...

Towards PubMed 2.0

PubMed Central

Fiorini, Nicolas; Lipman, David J; Lu, Zhiyong

2017-01-01

Staff from the National Center for Biotechnology Information in the US describe recent improvements to the PubMed search engine and outline plans for the future, including a new experimental site called PubMed Labs. PMID:29083299

Genetics Home Reference: congenital myasthenic syndrome

MedlinePlus

... 1196/annals.1405.049. Citation on PubMed Engel AG, Shen XM, Selcen D, Sine SM. What have ... PubMed or Free article on PubMed Central Engel AG. Current status of the congenital myasthenic syndromes. Neuromuscul ...

Genetics Home Reference: Robinow syndrome

MedlinePlus

... PubMed or Free article on PubMed Central White JJ, Mazzeu JF, Coban-Akdemir Z, Bayram Y, Bahrambeigi ... Epub ahead of print] Citation on PubMed White JJ, Mazzeu JF, Hoischen A, Bayram Y, Withers M, ...

Supplementary searches of PubMed to improve currency of MEDLINE and MEDLINE In-Process searches via Ovid.

PubMed

Duffy, Steven; de Kock, Shelley; Misso, Kate; Noake, Caro; Ross, Janine; Stirk, Lisa

2016-10-01

The research investigated whether conducting a supplementary search of PubMed in addition to the main MEDLINE (Ovid) search for a systematic review is worthwhile and to ascertain whether this PubMed search can be conducted quickly and if it retrieves unique, recently published, and ahead-of-print studies that are subsequently considered for inclusion in the final systematic review. Searches of PubMed were conducted after MEDLINE (Ovid) and MEDLINE In-Process (Ovid) searches had been completed for seven recent reviews. The searches were limited to records not in MEDLINE or MEDLINE In-Process (Ovid). Additional unique records were identified for all of the investigated reviews. Search strategies were adapted quickly to run in PubMed, and reviewer screening of the results was not time consuming. For each of the investigated reviews, studies were ordered for full screening; in six cases, studies retrieved from the supplementary PubMed searches were included in the final systematic review. Supplementary searching of PubMed for studies unavailable elsewhere is worthwhile and improves the currency of the systematic reviews.

Supplementary searches of PubMed to improve currency of MEDLINE and MEDLINE In-Process searches via Ovid

PubMed Central

Duffy, Steven; de Kock, Shelley; Misso, Kate; Noake, Caro; Ross, Janine; Stirk, Lisa

2016-01-01

Objective The research investigated whether conducting a supplementary search of PubMed in addition to the main MEDLINE (Ovid) search for a systematic review is worthwhile and to ascertain whether this PubMed search can be conducted quickly and if it retrieves unique, recently published, and ahead-of-print studies that are subsequently considered for inclusion in the final systematic review. Methods Searches of PubMed were conducted after MEDLINE (Ovid) and MEDLINE In-Process (Ovid) searches had been completed for seven recent reviews. The searches were limited to records not in MEDLINE or MEDLINE In-Process (Ovid). Results Additional unique records were identified for all of the investigated reviews. Search strategies were adapted quickly to run in PubMed, and reviewer screening of the results was not time consuming. For each of the investigated reviews, studies were ordered for full screening; in six cases, studies retrieved from the supplementary PubMed searches were included in the final systematic review. Conclusion Supplementary searching of PubMed for studies unavailable elsewhere is worthwhile and improves the currency of the systematic reviews. PMID:27822154

Rule-based deduplication of article records from bibliographic databases.

PubMed

Jiang, Yu; Lin, Can; Meng, Weiyi; Yu, Clement; Cohen, Aaron M; Smalheiser, Neil R

2014-01-01

We recently designed and deployed a metasearch engine, Metta, that sends queries and retrieves search results from five leading biomedical databases: PubMed, EMBASE, CINAHL, PsycINFO and the Cochrane Central Register of Controlled Trials. Because many articles are indexed in more than one of these databases, it is desirable to deduplicate the retrieved article records. This is not a trivial problem because data fields contain a lot of missing and erroneous entries, and because certain types of information are recorded differently (and inconsistently) in the different databases. The present report describes our rule-based method for deduplicating article records across databases and includes an open-source script module that can be deployed freely. Metta was designed to satisfy the particular needs of people who are writing systematic reviews in evidence-based medicine. These users want the highest possible recall in retrieval, so it is important to err on the side of not deduplicating any records that refer to distinct articles, and it is important to perform deduplication online in real time. Our deduplication module is designed with these constraints in mind. Articles that share the same publication year are compared sequentially on parameters including PubMed ID number, digital object identifier, journal name, article title and author list, using text approximation techniques. In a review of Metta searches carried out by public users, we found that the deduplication module was more effective at identifying duplicates than EndNote without making any erroneous assignments.

Rule-based deduplication of article records from bibliographic databases

PubMed Central

Jiang, Yu; Lin, Can; Meng, Weiyi; Yu, Clement; Cohen, Aaron M.; Smalheiser, Neil R.

2014-01-01

We recently designed and deployed a metasearch engine, Metta, that sends queries and retrieves search results from five leading biomedical databases: PubMed, EMBASE, CINAHL, PsycINFO and the Cochrane Central Register of Controlled Trials. Because many articles are indexed in more than one of these databases, it is desirable to deduplicate the retrieved article records. This is not a trivial problem because data fields contain a lot of missing and erroneous entries, and because certain types of information are recorded differently (and inconsistently) in the different databases. The present report describes our rule-based method for deduplicating article records across databases and includes an open-source script module that can be deployed freely. Metta was designed to satisfy the particular needs of people who are writing systematic reviews in evidence-based medicine. These users want the highest possible recall in retrieval, so it is important to err on the side of not deduplicating any records that refer to distinct articles, and it is important to perform deduplication online in real time. Our deduplication module is designed with these constraints in mind. Articles that share the same publication year are compared sequentially on parameters including PubMed ID number, digital object identifier, journal name, article title and author list, using text approximation techniques. In a review of Metta searches carried out by public users, we found that the deduplication module was more effective at identifying duplicates than EndNote without making any erroneous assignments. PMID:24434031

Genetics Home Reference: nonsyndromic holoprosencephaly

MedlinePlus

... on PubMed or Free article on PubMed Central Solomon BD, Gropman A, Muenke M. Holoprosencephaly Overview. 2000 ... nlm.nih.gov/books/NBK1530/ Citation on PubMed Solomon BD, Mercier S, Vélez JI, Pineda-Alvarez DE, Wyllie ...

Genetics Home Reference: giant axonal neuropathy

MedlinePlus

... 002. Epub 2014 Dec 19. Citation on PubMed Johnson-Kerner BL, Garcia Diaz A, Ekins S, Wichterle H. ... on PubMed or Free article on PubMed Central Johnson-Kerner BL, Roth L, Greene JP, Wichterle H, ...

Genetics Home Reference: dentinogenesis imperfecta

MedlinePlus

... Epub 2004 Feb 3. Citation on PubMed McKnight DA, Simmer JP, Hart PS, Hart TC, Fisher LW. ... PubMed or Free article on PubMed Central McKnight DA, Suzanne Hart P, Hart TC, Hartsfield JK, Wilson ...

Correction to: The minimally invasive flexor carpi radialis approach: a new perspective for distal radius fractures.

PubMed

Igeta, Yuka; Vernet, Paul; Facca, Sybille; Naroura, Ismaël; Hidalgo Diaz, Juan José; Liverneaux, Philippe A

2018-03-03

With regards to Juan José Hidalgo Diaz, fifth author. The author's name is incorrectly listed on Pub-Med. The first and last name has been mixed up.Correct first name is: JJ (on PubMed: JJH.).Correct last name is: Hidalgo Diaz (on PubMed: Diaz).On SpringerLink the name is listed correctly, but on PubMed he is listed as Diaz JJH.

Analysis of vascular endothelial dysfunction genes and related pathways in obesity through systematic bioinformatics.

PubMed

Zhang, Hui; Wang, Jing; Sun, Ling; Xu, Qiuqin; Hou, Miao; Ding, Yueyue; Huang, Jie; Chen, Ye; Cao, Lei; Zhang, Jianmin; Qian, Weiguo; Lv, Haitao

2015-01-01

Obesity has become an increasingly serious health problem and popular research topic. It is associated with many diseases, especially cardiovascular disease (CVD)-related endothelial dysfunction. This study analyzed genes related to endothelial dysfunction and obesity and then summarized their most significant signaling pathways. Genes related to vascular endothelial dysfunction and obesity were extracted from a PubMed database, and analyzed by STRING, DAVID, and Gene-Go Meta-Core software. 142 genes associated with obesity were found to play a role in endothelial dysfunction in PubMed. A significant pathway (Angiotensin system maturation in protein folding and maturation) associated with obesity and endothelial dysfunction was explored. The genes and the pathway explored may play an important role in obesity. Further studies about preventing vascular endothelial dysfunction obesity should be conducted through targeting these loci and pathways.

Use of scientific social networking to improve the research strategies of PubMed readers.

PubMed

Evdokimov, Pavel; Kudryavtsev, Alexey; Ilgisonis, Ekaterina; Ponomarenko, Elena; Lisitsa, Andrey

2016-02-18

Keeping up with journal articles on a daily basis is an important activity of scientists engaged in biomedical research. Usually, journal articles and papers in the field of biomedicine are accessed through the Medline/PubMed electronic library. In the process of navigating PubMed, researchers unknowingly generate user-specific reading profiles that can be shared within a social networking environment. This paper examines the structure of the social networking environment generated by PubMed users. A web browser plugin was developed to map [in Medical Subject Headings (MeSH) terms] the reading patterns of individual PubMed users. We developed a scientific social network based on the personal research profiles of readers of biomedical articles. A browser plugin is used to record the digital object identifier or PubMed ID of web pages. Recorded items are posted on the activity feed and automatically mapped to PubMed abstract. Within the activity feed a user can trace back previously browsed articles and insert comments. By calculating the frequency with which specific MeSH occur, the research interests of PubMed users can be visually represented with a tag cloud. Finally, research profiles can be searched for matches between network users. A social networking environment was created using MeSH terms to map articles accessed through the Medline/PubMed online library system. In-network social communication is supported by the recommendation of articles and by matching users with similar scientific interests. The system is available at http://bioknol.org/en/.

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

PubMed

Muin, Michael; Fontelo, Paul

2006-11-03

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

Genetics Home Reference: Carpenter syndrome

MedlinePlus

... doi: 10.1097/SCS.0b013e318184357a. Citation on PubMed Jenkins D, Baynam G, De Catte L, Elcioglu N, ... on PubMed or Free article on PubMed Central Jenkins D, Seelow D, Jehee FS, Perlyn CA, Alonso ...

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.

Quantity and quality assessment of randomized controlled trials on orthodontic practice in PubMed.

PubMed

Shimada, Tatsuo; Takayama, Hisako; Nakamura, Yoshiki

2010-07-01

To find current high-quality evidence for orthodontic practice within a reasonable time, we tested the performance of a PubMed search. PubMed was searched using publication type randomized controlled trial and medical subject heading term "orthodontics" for articles published between 2003 and 2007. The PubMed search results were compared with those from a hand search of four orthodontic journals to determine the sensitivity of PubMed search. We evaluated the precision of the PubMed search result and assessed the quality of individual randomized controlled trials using the Jadad scale. Sensitivity and precision were 97.46% and 58.12%, respectively. In PubMed, of the 277 articles retrieved, 161 (58.12%) were randomized controlled trials on orthodontic practice, and 115 of the 161 articles (71.42%) were published in four orthodontic journals: American Journal of Orthodontics and Dentofacial Orthopedics, The Angle Orthodontist, the European Journal of Orthodontics, and the Journal of Orthodontics. Assessment by the Jadad scale revealed 60 high-quality randomized controlled trials on orthodontic practice, of which 45 (75%) were published in these four journals. PubMed is a highly desirable search engine for evidence-based orthodontic practice. To stay current and get high-quality evidence, it is reasonable to look through four orthodontic journals: American Journal of Orthodontics and Dentofacial Orthopedics, The Angle Orthodontist, the European Journal of Orthodontics, and the Journal of Orthodontics.

A study on PubMed search tag usage pattern: association rule mining of a full-day PubMed query log.

PubMed

Mosa, Abu Saleh Mohammad; Yoo, Illhoi

2013-01-09

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

Net Improvement of Correct Answers to Therapy Questions After PubMed Searches: Pre/Post Comparison

PubMed Central

Keepanasseril, Arun

2013-01-01

Background Clinicians search PubMed for answers to clinical questions although it is time consuming and not always successful. Objective To determine if PubMed used with its Clinical Queries feature to filter results based on study quality would improve search success (more correct answers to clinical questions related to therapy). Methods We invited 528 primary care physicians to participate, 143 (27.1%) consented, and 111 (21.0% of the total and 77.6% of those who consented) completed the study. Participants answered 14 yes/no therapy questions and were given 4 of these (2 originally answered correctly and 2 originally answered incorrectly) to search using either the PubMed main screen or PubMed Clinical Queries narrow therapy filter via a purpose-built system with identical search screens. Participants also picked 3 of the first 20 retrieved citations that best addressed each question. They were then asked to re-answer the original 14 questions. Results We found no statistically significant differences in the rates of correct or incorrect answers using the PubMed main screen or PubMed Clinical Queries. The rate of correct answers increased from 50.0% to 61.4% (95% CI 55.0%-67.8%) for the PubMed main screen searches and from 50.0% to 59.1% (95% CI 52.6%-65.6%) for Clinical Queries searches. These net absolute increases of 11.4% and 9.1%, respectively, included previously correct answers changing to incorrect at a rate of 9.5% (95% CI 5.6%-13.4%) for PubMed main screen searches and 9.1% (95% CI 5.3%-12.9%) for Clinical Queries searches, combined with increases in the rate of being correct of 20.5% (95% CI 15.2%-25.8%) for PubMed main screen searches and 17.7% (95% CI 12.7%-22.7%) for Clinical Queries searches. Conclusions PubMed can assist clinicians answering clinical questions with an approximately 10% absolute rate of improvement in correct answers. This small increase includes more correct answers partially offset by a decrease in previously correct answers. PMID:24217329

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/.

Mapping the literature of home health nursing.

PubMed

Friedman, Yelena

2006-04-01

The purpose of this study was to identify core journals in home health nursing and to determine how well these journals were covered by indexing and abstracting services. The study was part of the project for mapping the nursing literature of the Medical Library Association's Nursing and Allied Health Resource Section. A citation analysis of two core journals was done to determine distribution of references by format types and age of citations and dispersion of the literature, according to Bradford's Law of Scattering. The analysis of indexing coverage for Zone 1 and 2 was also provided. The study showed that 64.2% of citations came from journals, versus 22.9% from books and 12.9% from other publications. PubMed/ MEDLINE rated highest in average indexing coverage of Zone 1 and 2 journals, followed by CINAHL. PsycINFO, SocioAbstracts, and EBSCO Health Business FullTEXT showed practically no coverage for the home health nursing literature. As expected, journal articles were found to be the primary source for referencing and books, the secondary source. In regard to bibliographic control, no databases provided full coverage of the journals in the field of home health nursing. PubMed/MEDLINE and CINAHL gave better results in combination, because CINAHL tended to cover more nursing journals, while PubMed/MEDLINE did better with medical titles.

The Clinical Aspects of Mirror Therapy in Rehabilitation: A Systematic Review of the Literature

ERIC Educational Resources Information Center

Rothgangel, Andreas Stefan; Braun, Susy M.; Beurskens, Anna J.; Seitz, Rudiger J.; Wade, Derick T.

2011-01-01

The objective of this study was to evaluate the clinical aspects of mirror therapy (MT) interventions after stroke, phantom limb pain and complex regional pain syndrome. A systematic literature search of the Cochrane Database of controlled trials, PubMed/MEDLINE, CINAHL, EMBASE, PsycINFO, PEDro, RehabTrials and Rehadat, was made by two…

Incorporating a New Bioinformatics Component into Genetics at a Historically Black College: Outcomes and Lessons

ERIC Educational Resources Information Center

Holtzclaw, J. David; Eisen, Arri; Whitney, Erika M.; Penumetcha, Meera; Hoey, J. Joseph; Kimbro, K. Sean

2006-01-01

Many students at minority-serving institutions are underexposed to Internet resources such as the human genome project, PubMed, NCBI databases, and other Web-based technologies because of a lack of financial resources. To change this, we designed and implemented a new bioinformatics component to supplement the undergraduate Genetics course at…

The Relationship between Sleep and Epilepsy: The Effect on Cognitive Functioning in Children

ERIC Educational Resources Information Center

Parisi, Pasquale; Bruni, Oliviero; Pia Villa, Maria; Verrotti, Alberto; Miano, Silvia; Luchetti, Anna; Curatolo, Paolo

2010-01-01

Aim: The purpose of this review was to examine the possible pathophysiological links between epilepsy, cognition, sleep macro- and microstructure, and sleep disorders to highlight the contributions and interactions of sleep and epilepsy on cognitive functioning in children with epilepsy. Method: PubMed was used as the medical database source. No…

Uterine transplantation: Review in human research.

PubMed

Favre-Inhofer, A; Rafii, A; Carbonnel, M; Revaux, A; Ayoubi, J M

2018-06-01

Uterine transplantation is the solution to treat absolute uterine fertility. In this review, we present the historical, medical, technical, psychological and ethical perspectives in human uterine transplantation research. We reviewed the PubMed database following PRISMA guidelines and added data presented by several research teams during the first international congress on uterine transplantation. Copyright © 2018. Published by Elsevier Masson SAS.

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…

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…

Nutrition Education and Body Mass Index in Grades K-12: A Systematic Review

ERIC Educational Resources Information Center

Price, Cayla; Cohen, Deborah; Pribis, Peter; Cerami, Jean

2017-01-01

Background: Overweight and obese body mass index (BMI) status affects an increasing number of children in the United States. The school setting has been identified as a focus area to implement obesity prevention programs. Methods: A database search of PubMed, Education Search Complete, and Cumulative Index to Nursing and Allied Health Literature…

Using Active Video Games for Physical Activity Promotion: A Systematic Review of the Current State of Research

ERIC Educational Resources Information Center

Peng, Wei; Crouse, Julia C.; Lin, Jih-Hsuan

2013-01-01

This systematic review evaluates interventions using active video games (AVGs) to increase physical activity and summarizes laboratory studies quantifying intensity of AVG play among children and adults. Databases (Cochrane Library, PsychInfo, PubMed, SPORTDiscus, Web of Science) and forward citation and reference list searches were used to…

Examining the Impact of the National Institutes of Health Public Access Policy on the Citation Rates of Journal Articles

PubMed Central

De Groote, Sandra L.; Shultz, Mary; Smalheiser, Neil R.

2015-01-01

Purpose To examine whether National Institutes of Health (NIH) funded articles that were archived in PubMed Central (PMC) after the release of the 2008 NIH Public Access Policy show greater scholarly impact than comparable articles not archived in PMC. Methods A list of journals across several subject areas was developed from which to collect article citation data. Citation information and cited reference counts of the articles published in 2006 and 2009 from 122 journals were obtained from the Scopus database. The articles were separated into categories of NIH funded, non-NIH funded and whether they were deposited in PubMed Central. An analysis of citation data across a five-year timespan was performed on this set of articles. Results A total of 45,716 articles were examined, including 7,960 with NIH-funding. An analysis of the number of times these articles were cited found that NIH-funded 2006 articles in PMC were not cited significantly more than NIH-funded non-PMC articles. However, 2009 NIH funded articles in PMC were cited 26% more than 2009 NIH funded articles not in PMC, 5 years after publication. This result is highly significant even after controlling for journal (as a proxy of article quality and topic). Conclusion Our analysis suggests that factors occurring between 2006 and 2009 produced a subsequent boost in scholarly impact of PubMed Central. The 2008 Public Access Policy is likely to be one such factor, but others may have contributed as well (e.g., growing size and visibility of PMC, increasing availability of full-text linkouts from PubMed, and indexing of PMC articles by Google Scholar). PMID:26448551

Research Trend Visualization by MeSH Terms from PubMed.

PubMed

Yang, Heyoung; Lee, Hyuck Jai

2018-05-30

Motivation : PubMed is a primary source of biomedical information comprising search tool function and the biomedical literature from MEDLINE which is the US National Library of Medicine premier bibliographic database, life science journals and online books. Complimentary tools to PubMed have been developed to help the users search for literature and acquire knowledge. However, these tools are insufficient to overcome the difficulties of the users due to the proliferation of biomedical literature. A new method is needed for searching the knowledge in biomedical field. Methods : A new method is proposed in this study for visualizing the recent research trends based on the retrieved documents corresponding to a search query given by the user. The Medical Subject Headings (MeSH) are used as the primary analytical element. MeSH terms are extracted from the literature and the correlations between them are calculated. A MeSH network, called MeSH Net, is generated as the final result based on the Pathfinder Network algorithm. Results : A case study for the verification of proposed method was carried out on a research area defined by the search query (immunotherapy and cancer and "tumor microenvironment"). The MeSH Net generated by the method is in good agreement with the actual research activities in the research area (immunotherapy). Conclusion : A prototype application generating MeSH Net was developed. The application, which could be used as a "guide map for travelers", allows the users to quickly and easily acquire the knowledge of research trends. Combination of PubMed and MeSH Net is expected to be an effective complementary system for the researchers in biomedical field experiencing difficulties with search and information analysis.

Finding abbreviations in biomedical literature: three BioC-compatible modules and four BioC-formatted corpora.

PubMed

Islamaj Doğan, Rezarta; Comeau, Donald C; Yeganova, Lana; Wilbur, W John

2014-01-01

BioC is a recently created XML format to share text data and annotations, and an accompanying input/output library to promote interoperability of data and tools for natural language processing of biomedical text. This article reports the use of BioC to address a common challenge in processing biomedical text information-that of frequent entity name abbreviation. We selected three different abbreviation definition identification modules, and used the publicly available BioC code to convert these independent modules into BioC-compatible components that interact seamlessly with BioC-formatted data, and other BioC-compatible modules. In addition, we consider four manually annotated corpora of abbreviations in biomedical text: the Ab3P corpus of 1250 PubMed abstracts, the BIOADI corpus of 1201 PubMed abstracts, the old MEDSTRACT corpus of 199 PubMed(®) citations and the Schwartz and Hearst corpus of 1000 PubMed abstracts. Annotations in these corpora have been re-evaluated by four annotators and their consistency and quality levels have been improved. We converted them to BioC-format and described the representation of the annotations. These corpora are used to measure the three abbreviation-finding algorithms and the results are given. The BioC-compatible modules, when compared with their original form, have no difference in their efficiency, running time or any other comparable aspects. They can be conveniently used as a common pre-processing step for larger multi-layered text-mining endeavors. Database URL: Code and data are available for download at the BioC site: http://bioc.sourceforge.net. Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

Reporting characteristics and risk of bias in randomised controlled trials of acupuncture analgesia published in PubMed-listed journals.

PubMed

Li, Xiuxia; Wang, Rong; Shi, Xiue; Chen, Zehao; Pan, Yuanqing; Li, Xusheng; Yang, Kehu

2017-08-01

Acupuncture analgesia has been evaluated by a number of randomised controlled trials (RCTs); however, a systematic summary of reporting quality of RCTs in this specific field is lacking. To examine the reporting characteristics and risk of bias of RCTs of acupuncture analgesia indexed in the PubMed database. A PubMed search of RCTs of acupuncture analgesia was conducted through November 2015. The Cochrane Collaboration Risk of Bias Tool was used to assess the risk of bias of each trial. 206 articles were identified across 59 journals (impact factor 0.4-20), of which 56% of articles and 86% of journals were Science Citation Index (SCI)-indexed. Nearly half of the articles were published in China. The next most represented countries of origin were the UK (22%) and USA (21%). Of the included trials, postoperative pain was the most prevalent phenotype, and manual acupuncture was the most frequently applied type of stimulation (46%). A total of 12% of articles reported on analgesic mechanisms. The most frequently used acupuncture points were LI4, ST36, PC6, SP6 and Shenmen . The overwhelming majority of trials were considered to be at high risk of bias (84%). Furthermore, 79% of trials enrolled <50 participants per treatment arm. RCTs of acupuncture analgesia indexed in PubMed journals generally exhibited poor reporting of methodological and treatment details. Future studies should provide more information regarding clinical trial registration, blinding of participants (including sham procedures where applicable) and outcome assessors, as well as the training and qualification of acupuncturists. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Genetics Home Reference: X-linked adrenoleukodystrophy

MedlinePlus

... Orphanet J Rare Dis. 2012 Aug 13;7:51. doi: 10.1186/1750-1172-7-51. Citation on PubMed or Free article on PubMed ... Clin Pract Neurol. 2007 Mar;3(3):140-51. Review. Citation on PubMed Moser HW, Raymond GV, ...

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

PubMed Central

Muin, Michael; Fontelo, Paul

2006-01-01

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

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

PubMed Central

2013-01-01

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

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

PubMed

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

2013-06-03

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

Current biomedical scientific impact (2013) of institutions, academic journals and researchers in the Republic of Macedonia.

PubMed

Spiroski, Mirko

2014-01-01

To analyse current ranking (2013) of institutions, journals and researchers in the Republic of Macedonia. the country rankings of R. Macedonia were analyzed with SCImago Country & Journal Rank (SJR) for subject area Medicine in the years 1996-2013, and ordered by H-index. SCImago Institutions Rankings for 2013 was used for the scientific impact of biomedical institutions in the Republic of Macedonia. Journal metrics from Elsevier for the Macedonian scholarly journals for the period 2009-2013 were performed. Source Normalized Impact per Paper (SNIP), the Impact per Publication (IPP), and SCImago Journal Rank (SJR) were analysed. Macedonian scholarly biomedical journals included in Google Scholar metrics (2013, 2012) were analysed with h5-index and h5-median (June 2014). A semantic analysis of the PubMed database was performed with GoPubMed on November 2, 2014 in order to identify published papers from the field of biomedical sciences affiliated with the country of Macedonia. Harzing's Publish or Perish software was used for author impact analysis and the calculation of the Hirsh-index based on Google Scholar query. The rank of subject area Medicine of R. Macedonia according to the SCImago Journal & Country Rank (SJR) is 110th in the world and 17th in Eastern Europe. Of 20 universities in Macedonia, only Ss Cyril and Methodius University, Skopje, and the University St Clement of Ohrid, Bitola, are listed in the SCImago Institutions Rankings (SIR) for 2013. A very small number of Macedonian scholarly journals is included in Web of Sciences (2), PubMed (1), PubMed Central (1), SCOPUS (6), SCImago (6), and Google Scholar metrics (6). The rank of Hirsh index (h-index) was different from the rank of number of abstracts indexed in PubMed for the top 20 authors from R. Macedonia. The current biomedical scientific impact (2013) of institutions, academic journals and researchers in R. Macedonia is very low. There is an urgent need for organized measures to improve the quality and output of institutions, scholarly journals, and researchers in R. Macedonia in order to achieve higher international standards.

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

PubMed

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

2015-02-01

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

[Colciencias and disdain for Colombian scientists: from the Stone Age to the impact factor].

PubMed

Leon-Sarmiento, Fidias E; Bayona-Prieto, Jaime; Bayona, Edgardo; Leon, Martha E

2005-01-01

Writing has dramatically evolved in the world; however, qualification of scientific production in Colombia has not, including the improper use of decree 1444/93 and 1279/02. The last of these decrees authorized Colciencias, the Colombian government institute created to support scientific research in Colombia, to establish rules for its implementation. Colciencias decided to evaluate scientific papers produced in Colombia based on the non-scientific method of the "impact factor", and considered that citations in MEDLINE/PubMed and PsylNFO were second line publications thus violating Colombian law. This affects not only the progress of scientific research in Colombia but also researchers' income and puts Colombia's scientific journals and publications at great disadvantage. Scientific papers indexed in qualified databases such as MEDLINE/PubMed must be judged according to law in order to prevent further injuries to the developing Colombian scientific production.

Effect of biomaterials on angiogenesis during vital pulp therapy

PubMed Central

SAGHIRI, Mohammad Ali; ASATOURIAN, Armen; GARCIA-GODOY, Franklin; SHEIBANI, Nader

2016-01-01

This review intended to provide an overview of the effects of dental materials, used in dentin-pulp complex and dental pulp regeneration, on angiogenesis processes during regenerative endodontic procedures. An electronic search was performed in PubMed and MEDLINE databases via OVID using the keywords mentioned in the PubMed and MeSH headings for English language published articles from January 2005–April 2014 that evaluated the angiogenic properties of different dental materials used in regenerative endodontic procedures. Of the articles identified in an initial search, only 40 articles met the inclusion criteria set for this review. Vital pulp therapy materials might have positive effects on angiogenesis events, while most of the canal irrigating solutions and antibiotic pastes have anti-angiogenic activity except for EDTA. Future clinical studies will be helpful in defining the mechanisms of action for dental materials that promote or inhibit angiogenesis events at applied areas. PMID:27546854

HIM-herbal ingredients in-vivo metabolism database.

PubMed

Kang, Hong; Tang, Kailin; Liu, Qi; Sun, Yi; Huang, Qi; Zhu, Ruixin; Gao, Jun; Zhang, Duanfeng; Huang, Chenggang; Cao, Zhiwei

2013-05-31

Herbal medicine has long been viewed as a valuable asset for potential new drug discovery and herbal ingredients' metabolites, especially the in vivo metabolites were often found to gain better pharmacological, pharmacokinetic and even better safety profiles compared to their parent compounds. However, these herbal metabolite information is still scattered and waiting to be collected. HIM database manually collected so far the most comprehensive available in-vivo metabolism information for herbal active ingredients, as well as their corresponding bioactivity, organs and/or tissues distribution, toxicity, ADME and the clinical research profile. Currently HIM contains 361 ingredients and 1104 corresponding in-vivo metabolites from 673 reputable herbs. Tools of structural similarity, substructure search and Lipinski's Rule of Five are also provided. Various links were made to PubChem, PubMed, TCM-ID (Traditional Chinese Medicine Information database) and HIT (Herbal ingredients' targets databases). A curated database HIM is set up for the in vivo metabolites information of the active ingredients for Chinese herbs, together with their corresponding bioactivity, toxicity and ADME profile. HIM is freely accessible to academic researchers at http://www.bioinformatics.org.cn/.

Radiolucent rim as a possible diagnostic aid for differentiating jaw lesions

PubMed Central

Mortazavi, Hamed; Rahmani, Somayeh; Jafari, Soudeh; Parvaei, Parvin

2015-01-01

In this study, we formulate a new proposal that complements previous classifications in order to assist dental practitioners in performing a differential diagnosis based on patients' radiographs. We used general search engines and specialized databases such as Google Scholar, PubMed, PubMed Central, MedLine Plus, Science Direct, Scopus, and well-recognized textbooks to find relevant studies by using keywords such as "jaw disease," "jaw lesions," "radiolucent rim," "radiolucent border," and "radiolucent halo." More than 200 articles were found, of which 70 were broadly relevant to the topic. We ultimately included 50 articles that were closely related to the topic of interest. When the relevant data were compiled, the following eight lesions were identified as having a radiolucent rim: periapical cemento-osseous dysplasia, focal cemento-osseous dysplasia, florid cemento-osseous dysplasia, cemento-ossifying fibroma, osteoid osteoma, osteoblastoma, odontoma, and cementoblastoma. We propose a novel subcategory, jaw lesions with a radiolucent rim, which includes eight entities. The implementation of this new category can help improve the diagnoses that dental practitioners make based on patients' radiographs. PMID:26730374

Chemotherapeutic Targeting of Fibulin-5 to Suppress Breast Cancer Invasion and Metastasis Stimulated by Transforming Growth Factor-Beta

DTIC Science & Technology

2012-10-22

Res. Commun 2004;316:997–1001. [PubMed: 15044083] 178. Karin M. NF-κB in cancer development and progression. Nature 2006;441:431. [PubMed: 16724054...of TWIST gene expression. Cancer Res 2007;67:9066–9076. [PubMed: 17909010] 199. Ali S, Coombes RC. Endocrine-responsive breast cancer and strategies...for combating resistance. Nat. Rev. Cancer 2002;2:101–112. [PubMed: 12635173] 200. Coombes RC, Gibson L, Hall E, Emson M, Bliss J. Aromatase

Evidence-Based Systematic Review: Effects of Intensity of Treatment and Constraint-Induced Language Therapy for Individuals with Stroke-Induced Aphasia

ERIC Educational Resources Information Center

Cherney, Leora R.; Patterson, Janet P.; Raymer, Anastasia; Frymark, Tobi; Schooling, Tracy

2008-01-01

Purpose: This systematic review summarizes evidence for intensity of treatment and constraint-induced language therapy (CILT) on measures of language impairment and communication activity/participation in individuals with stroke-induced aphasia. Method: A systematic search of the aphasia literature using 15 electronic databases (e.g., PubMed,…

Comparative Recall and Precision of Simple and Expert Searches in Google Scholar and Eight Other Databases

ERIC Educational Resources Information Center

Walters, William H.

2011-01-01

This study evaluates the effectiveness of simple and expert searches in Google Scholar (GS), EconLit, GEOBASE, PAIS, POPLINE, PubMed, Social Sciences Citation Index, Social Sciences Full Text, and Sociological Abstracts. It assesses the recall and precision of 32 searches in the field of later-life migration: nine simple keyword searches and 23…

Functioning and Participation of Students with ADHD in Higher Education According to the ICF-Framework

ERIC Educational Resources Information Center

Emmers, Elke; Jansen, Dorien; Petry, Katja; van der Oord, Saskia; Baeyens, Dieter

2017-01-01

Due to an increasing number of students with ADHD in higher education and the difficult course of their academic career, a comprehensive overview of participation and functioning of this group is needed. A comprehensive search was performed in MEDLINE (PubMed), EMBASE, CINAHL and ERIC electronic databases in June 2014. This systematic literature…

A meta-analysis of efficacy of Morus alba Linn. to improve blood glucose and lipid profile.

PubMed

Phimarn, Wiraphol; Wichaiyo, Kittisak; Silpsavikul, Khuntawan; Sungthong, Bunleu; Saramunee, Kritsanee

2017-06-01

The previous studies have reported the Morus alba may improve blood glucose and lipid profile. The evidence from these studies is not consistent. This meta-analysis was to evaluate efficacy of products derived from M. alba on blood glucose and lipid levels. Literature was reviewed via international database (PubMed, PubMed Central, ScienceDirect, and SciSearch) and Thai databases. Thirteen RCTs with high quality, assessed by Jadad score, were included. M. alba expressed a significant reduction in postprandial glucose (PPG) at 30 min (MD -1.04, 95 % CI -1.36, -0.73), 60 min (MD -0.87, 95 % CI -1.27, -0.48) and 90 min (MD -0.55, 95 % CI -0.87, -0.22). The difference was not found in the levels of other glycaemic (FBS, HbA1C, or HOMA-IR) and lipidaemic (TC, TG, LDL, or HDL) markers. Serious adverse effects were found neither in the control nor in the group received M. alba. Products derived from M. alba can effectively contribute to the reduction in PPG levels, but large-scale RCTs would be informative.

TwiMed: Twitter and PubMed Comparable Corpus of Drugs, Diseases, Symptoms, and Their Relations

PubMed Central

Miyao, Yusuke; Collier, Nigel

2017-01-01

Background Work on pharmacovigilance systems using texts from PubMed and Twitter typically target at different elements and use different annotation guidelines resulting in a scenario where there is no comparable set of documents from both Twitter and PubMed annotated in the same manner. Objective This study aimed to provide a comparable corpus of texts from PubMed and Twitter that can be used to study drug reports from these two sources of information, allowing researchers in the area of pharmacovigilance using natural language processing (NLP) to perform experiments to better understand the similarities and differences between drug reports in Twitter and PubMed. Methods We produced a corpus comprising 1000 tweets and 1000 PubMed sentences selected using the same strategy and annotated at entity level by the same experts (pharmacists) using the same set of guidelines. Results The resulting corpus, annotated by two pharmacists, comprises semantically correct annotations for a set of drugs, diseases, and symptoms. This corpus contains the annotations for 3144 entities, 2749 relations, and 5003 attributes. Conclusions We present a corpus that is unique in its characteristics as this is the first corpus for pharmacovigilance curated from Twitter messages and PubMed sentences using the same data selection and annotation strategies. We believe this corpus will be of particular interest for researchers willing to compare results from pharmacovigilance systems (eg, classifiers and named entity recognition systems) when using data from Twitter and from PubMed. We hope that given the comprehensive set of drug names and the annotated entities and relations, this corpus becomes a standard resource to compare results from different pharmacovigilance studies in the area of NLP. PMID:28468748

TwiMed: Twitter and PubMed Comparable Corpus of Drugs, Diseases, Symptoms, and Their Relations.

PubMed

Alvaro, Nestor; Miyao, Yusuke; Collier, Nigel

2017-05-03

Work on pharmacovigilance systems using texts from PubMed and Twitter typically target at different elements and use different annotation guidelines resulting in a scenario where there is no comparable set of documents from both Twitter and PubMed annotated in the same manner. This study aimed to provide a comparable corpus of texts from PubMed and Twitter that can be used to study drug reports from these two sources of information, allowing researchers in the area of pharmacovigilance using natural language processing (NLP) to perform experiments to better understand the similarities and differences between drug reports in Twitter and PubMed. We produced a corpus comprising 1000 tweets and 1000 PubMed sentences selected using the same strategy and annotated at entity level by the same experts (pharmacists) using the same set of guidelines. The resulting corpus, annotated by two pharmacists, comprises semantically correct annotations for a set of drugs, diseases, and symptoms. This corpus contains the annotations for 3144 entities, 2749 relations, and 5003 attributes. We present a corpus that is unique in its characteristics as this is the first corpus for pharmacovigilance curated from Twitter messages and PubMed sentences using the same data selection and annotation strategies. We believe this corpus will be of particular interest for researchers willing to compare results from pharmacovigilance systems (eg, classifiers and named entity recognition systems) when using data from Twitter and from PubMed. We hope that given the comprehensive set of drug names and the annotated entities and relations, this corpus becomes a standard resource to compare results from different pharmacovigilance studies in the area of NLP. ©Nestor Alvaro, Yusuke Miyao, Nigel Collier. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 03.05.2017.

Net improvement of correct answers to therapy questions after pubmed searches: pre/post comparison.

PubMed

McKibbon, Kathleen Ann; Lokker, Cynthia; Keepanasseril, Arun; Wilczynski, Nancy L; Haynes, R Brian

2013-11-08

Clinicians search PubMed for answers to clinical questions although it is time consuming and not always successful. To determine if PubMed used with its Clinical Queries feature to filter results based on study quality would improve search success (more correct answers to clinical questions related to therapy). We invited 528 primary care physicians to participate, 143 (27.1%) consented, and 111 (21.0% of the total and 77.6% of those who consented) completed the study. Participants answered 14 yes/no therapy questions and were given 4 of these (2 originally answered correctly and 2 originally answered incorrectly) to search using either the PubMed main screen or PubMed Clinical Queries narrow therapy filter via a purpose-built system with identical search screens. Participants also picked 3 of the first 20 retrieved citations that best addressed each question. They were then asked to re-answer the original 14 questions. We found no statistically significant differences in the rates of correct or incorrect answers using the PubMed main screen or PubMed Clinical Queries. The rate of correct answers increased from 50.0% to 61.4% (95% CI 55.0%-67.8%) for the PubMed main screen searches and from 50.0% to 59.1% (95% CI 52.6%-65.6%) for Clinical Queries searches. These net absolute increases of 11.4% and 9.1%, respectively, included previously correct answers changing to incorrect at a rate of 9.5% (95% CI 5.6%-13.4%) for PubMed main screen searches and 9.1% (95% CI 5.3%-12.9%) for Clinical Queries searches, combined with increases in the rate of being correct of 20.5% (95% CI 15.2%-25.8%) for PubMed main screen searches and 17.7% (95% CI 12.7%-22.7%) for Clinical Queries searches. PubMed can assist clinicians answering clinical questions with an approximately 10% absolute rate of improvement in correct answers. This small increase includes more correct answers partially offset by a decrease in previously correct answers.

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.

Comparison of PubMed and Google Scholar literature searches.

PubMed

Anders, Michael E; Evans, Dennis P

2010-05-01

Literature searches are essential to evidence-based respiratory care. To conduct literature searches, respiratory therapists rely on search engines to retrieve information, but there is a dearth of literature on the comparative efficiencies of search engines for researching clinical questions in respiratory care. To compare PubMed and Google Scholar search results for clinical topics in respiratory care to that of a benchmark. We performed literature searches with PubMed and Google Scholar, on 3 clinical topics. In PubMed we used the Clinical Queries search filter. In Google Scholar we used the search filters in the Advanced Scholar Search option. We used the reference list of a related Cochrane Collaboration evidence-based systematic review as the benchmark for each of the search results. We calculated recall (sensitivity) and precision (positive predictive value) with 2 x 2 contingency tables. We compared the results with the chi-square test of independence and Fisher's exact test. PubMed and Google Scholar had similar recall for both overall search results (71% vs 69%) and full-text results (43% vs 51%). PubMed had better precision than Google Scholar for both overall search results (13% vs 0.07%, P < .001) and full-text results (8% vs 0.05%, P < .001). Our results suggest that PubMed searches with the Clinical Queries filter are more precise than with the Advanced Scholar Search in Google Scholar for respiratory care topics. PubMed appears to be more practical to conduct efficient, valid searches for informing evidence-based patient-care protocols, for guiding the care of individual patients, and for educational purposes.

Improving accuracy for identifying related PubMed queries by an integrated approach

PubMed Central

Lu, Zhiyong; Wilbur, W. John

2009-01-01

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 1,539 pairs of consecutive user queries in 351 user sessions. The prediction results of 1,396 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

PubMed Phrases, an open set of coherent phrases for searching biomedical literature

PubMed Central

Kim, Sun; Yeganova, Lana; Comeau, Donald C.; Wilbur, W. John; Lu, Zhiyong

2018-01-01

In biomedicine, key concepts are often expressed by multiple words (e.g., ‘zinc finger protein’). Previous work has shown treating a sequence of words as a meaningful unit, where applicable, is not only important for human understanding but also beneficial for automatic information seeking. Here we present a collection of PubMed® Phrases that are beneficial for information retrieval and human comprehension. We define these phrases as coherent chunks that are logically connected. To collect the phrase set, we apply the hypergeometric test to detect segments of consecutive terms that are likely to appear together in PubMed. These text segments are then filtered using the BM25 ranking function to ensure that they are beneficial from an information retrieval perspective. Thus, we obtain a set of 705,915 PubMed Phrases. We evaluate the quality of the set by investigating PubMed user click data and manually annotating a sample of 500 randomly selected noun phrases. We also analyze and discuss the usage of these PubMed Phrases in literature search. PMID:29893755

Publication rates of public health theses in international and national peer-review journals in Turkey.

PubMed

Sipahi, H; Durusoy, R; Ergin, I; Hassoy, H; Davas, A; Karababa, Ao

2012-01-01

Thesis is an important part of specialisation and doctorate education and requires intense work. The aim of this study was to investigate the publication rates of Turkish Public Health Doctorate Theses (PHDT) and Public Health Specialization (PHST) theses in international and Turkish national peer-review journals and to analyze the distribution of research areas. List of all theses upto 30 September 2009 were retrieved from theses database of the Council of Higher Education of the Republic of Turkey. The publication rates of these theses were found by searching PubMed, Science Citation Index-Expanded, Turkish Academic Network and Information Center (ULAKBIM) Turkish Medical Database, and Turkish Medline databases for the names of thesis author and mentor. The theses which were published in journals indexed either in PubMed or SCI-E were considered as international publications. Our search yielded a total of 538 theses (243 PHDT, 295 PHST). It was found that the overall publication rate in Turkish national journals was 18%. The overall publication rate in international journals was 11.9%. Overall the most common research area was occupational health. Publication rates of Turkish PHDT and PHST are low. A better understanding of factors affecting this publication rate is important for public health issues where national data is vital for better intervention programs and develop better public health policies.

Publication Rates of Public Health Theses in International and National Peer-Review Journals in Turkey

PubMed Central

Sipahi, H; Durusoy, R; Ergin, I; Hassoy, H; Davas, A; Karababa, AO

2012-01-01

Background: Thesis is an important part of specialisation and doctorate education and requires intense work. The aim of this study was to investigate the publication rates of Turkish Public Health Doctorate Theses (PHDT) and Public Health Specialization (PHST) theses in international and Turkish national peer-review journals and to analyze the distribution of research areas. Methods: List of all theses upto 30 September 2009 were retrieved from theses database of the Council of Higher Education of the Republic of Turkey. The publication rates of these theses were found by searching PubMed, Science Citation Index-Expanded, Turkish Academic Network and Information Center (ULAKBIM) Turkish Medical Database, and Turkish Medline databases for the names of thesis author and mentor. The theses which were published in journals indexed either in PubMed or SCI-E were considered as international publications. Results: Our search yielded a total of 538 theses (243 PHDT, 295 PHST). It was found that the overall publication rate in Turkish national journals was 18%. The overall publication rate in international journals was 11.9%. Overall the most common research area was occupational health. Conclusion: Publication rates of Turkish PHDT and PHST are low. A better understanding of factors affecting this publication rate is important for public health issues where national data is vital for better intervention programs and develop better public health policies. PMID:23193503

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

PubMed

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

2015-01-01

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

Analysis of queries sent to PubMed at the point of care: Observation of search behaviour in a medical teaching hospital

PubMed Central

Hoogendam, Arjen; Stalenhoef, Anton FH; Robbé, Pieter F de Vries; Overbeke, A John PM

2008-01-01

Background The use of PubMed to answer daily medical care questions is limited because it is challenging to retrieve a small set of relevant articles and time is restricted. Knowing what aspects of queries are likely to retrieve relevant articles can increase the effectiveness of PubMed searches. The objectives of our study were to identify queries that are likely to retrieve relevant articles by relating PubMed search techniques and tools to the number of articles retrieved and the selection of articles for further reading. Methods This was a prospective observational study of queries regarding patient-related problems sent to PubMed by residents and internists in internal medicine working in an Academic Medical Centre. We analyzed queries, search results, query tools (Mesh, Limits, wildcards, operators), selection of abstract and full-text for further reading, using a portal that mimics PubMed. Results PubMed was used to solve 1121 patient-related problems, resulting in 3205 distinct queries. Abstracts were viewed in 999 (31%) of these queries, and in 126 (39%) of 321 queries using query tools. The average term count per query was 2.5. Abstracts were selected in more than 40% of queries using four or five terms, increasing to 63% if the use of four or five terms yielded 2–161 articles. Conclusion Queries sent to PubMed by physicians at our hospital during daily medical care contain fewer than three terms. Queries using four to five terms, retrieving less than 161 article titles, are most likely to result in abstract viewing. PubMed search tools are used infrequently by our population and are less effective than the use of four or five terms. Methods to facilitate the formulation of precise queries, using more relevant terms, should be the focus of education and research. PMID:18816391

Mapping the literature of home health nursing

PubMed Central

Friedman, Yelena

2006-01-01

Objectives: The purpose of this study was to identify core journals in home health nursing and to determine how well these journals were covered by indexing and abstracting services. The study was part of the project for mapping the nursing literature of the Medical Library Association's Nursing and Allied Health Resource Section. Methods: A citation analysis of two core journals was done to determine distribution of references by format types and age of citations and dispersion of the literature, according to Bradford's Law of Scattering. The analysis of indexing coverage for Zone 1 and 2 was also provided. Results: The study showed that 64.2% of citations came from journals, versus 22.9% from books and 12.9% from other publications. PubMed/ MEDLINE rated highest in average indexing coverage of Zone 1 and 2 journals, followed by CINAHL. PsycINFO, SocioAbstracts, and EBSCO Health Business FullTEXT showed practically no coverage for the home health nursing literature. Conclusion: As expected, journal articles were found to be the primary source for referencing and books, the secondary source. In regard to bibliographic control, no databases provided full coverage of the journals in the field of home health nursing. PubMed/MEDLINE and CINAHL gave better results in combination, because CINAHL tended to cover more nursing journals, while PubMed/MEDLINE did better with medical titles. PMID:16710463

Tracking Australian health and medical research expenditure with a PubMed bibliometric method.

PubMed

Mendis, Kumara; Bailey, Jannine; McLean, Rick

2015-06-01

To assess Australian health and medical research (HMR) investment returns by measuring the trends in HMR expenditure and PubMed publications by Australian authors. Bibliometric analysis collating Australian HMR expenditure reported by the Australian Institute of Health and Welfare and Australian HMR publications indexed in PubMed. Similar methods were applied to data from the United Kingdom and New Zealand. From financial year 2000/01 through 2011/12, HMR investment increased by 232% from $1.49 to $4.94 billion (current prices adjusted for inflation), while PubMed publications increased by 123% from 10,696 to 23,818. The average HMR investment required for a single PubMed publication rose by 49% from $139,304 in 2000/01 to $207,364 in 2011/12. Quality analyses showed an increase in systematic reviews, cohort studies and clinical trials, and a decrease in publications in PubMed's core clinical journal collection. Comparisons with New Zealand and the United Kingdom showed that Australia has had the greatest overall percentage increase in gross publication numbers and publications per capita. Our analyses confirm that increased HMR expenditure is associated with an increase in HMR publications in PubMed. Tracking HMR investment outcomes using this method could be useful for future policy and funding decisions at a federal and specific institution level. © 2015 Public Health Association of Australia.

Impact of Orthodontic Treatment on Periodontal Tissues: A Narrative Review of Multidisciplinary Literature

PubMed Central

Gorbunkova, Angelina; Pagni, Giorgio; Brizhak, Anna; Farronato, Giampietro; Rasperini, Giulio

2016-01-01

The aim of this review is to describe the most commonly observed changes in periodontium caused by orthodontic treatment in order to facilitate specialists' collaboration and communication. An electronic database search was carried out using PubMed abstract and citation database and bibliographic material was then used in order to find other appropriate sources. Soft and hard periodontal tissues changes during orthodontic treatment and maintenance of the patients are discussed in order to provide an exhaustive picture of the possible interactions between these two interwoven disciplines. PMID:26904120

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

PubMed

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

2014-01-01

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

Review of the health effects of wildland fire smoke on wildland firefighters and the public

Treesearch

Olorunfemi Adetona; Timothy E. Reinhardt; Joe Domitrovich; George Broyles; Anna M. Adetona; Michael T. Kleinman; Roger D. Ottmar; Luke P. Naeher

2016-01-01

Each year, the general public and wildland firefighters in the US are exposed to smoke from wildland fires. As part of an effort to characterize health risks of breathing this smoke, a review of the literature was conducted using five major databases, including PubMed and MEDLINE Web of Knowledge, to identify smoke components that present the highest hazard potential,...

Brain Development of Very Preterm and Very Low-Birthweight Children in Childhood and Adolescence: A Meta-Analysis

ERIC Educational Resources Information Center

de Kieviet, Jorrit F.; Zoetebier, Lydia; van Elburg, Ruurd M.; Vermeulen, R. Jeroen; Oosterlaan, Jaap

2012-01-01

Aim: The aim of this article was to clarify the impact and consequences of very preterm birth (born less than 32wks of gestation) and/or very low birthweight ([VLBW], weighing less than 1500g) on brain volume development throughout childhood and adolescence. Method: The computerized databases PubMed, Web of Knowledge, and EMBASE were searched for…

MScanner: a classifier for retrieving Medline citations

PubMed Central

Poulter, Graham L; Rubin, Daniel L; Altman, Russ B; Seoighe, Cathal

2008-01-01

Background Keyword searching through PubMed and other systems is the standard means of retrieving information from Medline. However, ad-hoc retrieval systems do not meet all of the needs of databases that curate information from literature, or of text miners developing a corpus on a topic that has many terms indicative of relevance. Several databases have developed supervised learning methods that operate on a filtered subset of Medline, to classify Medline records so that fewer articles have to be manually reviewed for relevance. A few studies have considered generalisation of Medline classification to operate on the entire Medline database in a non-domain-specific manner, but existing applications lack speed, available implementations, or a means to measure performance in new domains. Results MScanner is an implementation of a Bayesian classifier that provides a simple web interface for submitting a corpus of relevant training examples in the form of PubMed IDs and returning results ranked by decreasing probability of relevance. For maximum speed it uses the Medical Subject Headings (MeSH) and journal of publication as a concise document representation, and takes roughly 90 seconds to return results against the 16 million records in Medline. The web interface provides interactive exploration of the results, and cross validated performance evaluation on the relevant input against a random subset of Medline. We describe the classifier implementation, cross validate it on three domain-specific topics, and compare its performance to that of an expert PubMed query for a complex topic. In cross validation on the three sample topics against 100,000 random articles, the classifier achieved excellent separation of relevant and irrelevant article score distributions, ROC areas between 0.97 and 0.99, and averaged precision between 0.69 and 0.92. Conclusion MScanner is an effective non-domain-specific classifier that operates on the entire Medline database, and is suited to retrieving topics for which many features may indicate relevance. Its web interface simplifies the task of classifying Medline citations, compared to building a pre-filter and classifier specific to the topic. The data sets and open source code used to obtain the results in this paper are available on-line and as supplementary material, and the web interface may be accessed at . PMID:18284683

[Health system research in the Republic of Croatia 1990-2010].

PubMed

Kovacević, Jasmina; Sogorić, Selma; Dzakula, Aleksandar

2010-12-01

The aim of this study was to determine the scope and contents of peer-reviewed scientific publications that bring the results of the Health System Research (HSR) in the Republic of Croatia during the 1990-2010 period. The basic guidelines are in line with the research project, Health Services Research into European Policy and Practice (HSREPP). This project is being implemented with the aim of identifying, evaluating and improving the contribution of Health System Research to the development of Health Policy in Europe. This study included scientific publications indexed in the PubMed database and master theses and doctoral dissertations published at Schools of Medicine in Zagreb, Osijek, Rijeka and Split during the 1990-2010 period. In accordance with the project methodology, scientific publications indexed in PubMed (http://www.ncbi.nlm.nih.gov/pubmed) were searched for by the key words "Croatia AND (Health Care System OR Health System OR Healthcare System)". Then, the database of scientific publications indexed in PubMed was narrowed by key words divided into 4 groups according to HSREPP instructions. The search for master theses and doctoral dissertations was carried out by direct inspection of the completed works in the library of Andrija Stampar School of Public Health, School of Medicine, University of Zagreb. Access to master theses and doctoral dissertations at the other three medical schools was done by the Internet. We analyzed the collected summaries of all publications, master theses and doctoral dissertations and excluded all those that did not correspond to our research. Using this method, we found a total of 536 publications indexed in PubMed-in, 70 master theses and 22 doctoral dissertations meeting the study criteria. For further analysis, we separately considered master theses and doctoral dissertations on the one side, and scientific publications indexed in PubMed on the other side. All papers were listed by the year of publication, the author and the means of publication. Upon inclusion of the key words, 277 papers met the required criteria. After abstract analysis, 158 PubMed indexed papers were found to meet all the criteria and addressed the Health System Research in Croatia. There was a significant increase in the number of published papers during the 5-year study period. Upon analysis of the summary contents of master theses and doctoral dissertations, we separated 6 doctoral dissertations and 35 master theses that met the criteria of the research. They were divided into four groups: research of macro-, mezzo- and micro-level of Health System and assessment of Health Care System results. The group investigating the organization and delivery of health services (meso-level) and the group investigating health technology assessment (micro/meso-level) predominated. There were only a small number of high quality researches dealing with HSR in Croatia. Descriptive approach to the analysis predominated. Reform interventions require research, but are not part of the designed strategy. Funding of HSR is an important issue. The research in Croatia is financed by the Croatian Ministry of Science, Education and Sports. In the UK and the USA, HSR is funded by the National Health Services. In all publications, we could not find a systematic research of the Health System; however, we recognized a growing trend in the number of articles dealing with HSR in Croatia over the past 20 years. Comparison of the number of papers on the Health Care System in Croatia indicated a significant lag in comparison to Western Europe, and similarity with the countries of Eastern Europe.

Leaving the Lecture Behind: Putting PubMed Instruction into the Hands of the Students.

PubMed

Turner, Rose L; M Ketchum, Andrea; Ratajeski, Melissa A; Wessel, Charles B

2017-01-01

This column describes the development of a one-shot PubMed instruction class for medical students at a health sciences library. Background information on the objective is presented and discussed in the context of educational practice literature. The new course design centers on a guided group method of instruction in order to integrate more active learning. Surveyed students reported that the method was an effective way to learn how to search PubMed and that they preferred it to a traditional lecture. Pros and cons of the method are offered for other health sciences libraries interested in presenting PubMed instruction in a similar manner.

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.

Predicting clicks of PubMed articles.

PubMed

Mao, Yuqing; Lu, Zhiyong

2013-01-01

Predicting the popularity or access usage of an article has the potential to improve the quality of PubMed searches. We can model the click trend of each article as its access changes over time by mining the PubMed query logs, which contain the previous access history for all articles. In this article, we examine the access patterns produced by PubMed users in two years (July 2009 to July 2011). We explore the time series of accesses for each article in the query logs, model the trends with regression approaches, and subsequently use the models for prediction. We show that the click trends of PubMed articles are best fitted with a log-normal regression model. This model allows the number of accesses an article receives and the time since it first becomes available in PubMed to be related via quadratic and logistic functions, with the model parameters to be estimated via maximum likelihood. Our experiments predicting the number of accesses for an article based on its past usage demonstrate that the mean absolute error and mean absolute percentage error of our model are 4.0% and 8.1% lower than the power-law regression model, respectively. The log-normal distribution is also shown to perform significantly better than a previous prediction method based on a human memory theory in cognitive science. This work warrants further investigation on the utility of such a log-normal regression approach towards improving information access in PubMed.

Predicting clicks of PubMed articles

PubMed Central

Mao, Yuqing; Lu, Zhiyong

2013-01-01

Predicting the popularity or access usage of an article has the potential to improve the quality of PubMed searches. We can model the click trend of each article as its access changes over time by mining the PubMed query logs, which contain the previous access history for all articles. In this article, we examine the access patterns produced by PubMed users in two years (July 2009 to July 2011). We explore the time series of accesses for each article in the query logs, model the trends with regression approaches, and subsequently use the models for prediction. We show that the click trends of PubMed articles are best fitted with a log-normal regression model. This model allows the number of accesses an article receives and the time since it first becomes available in PubMed to be related via quadratic and logistic functions, with the model parameters to be estimated via maximum likelihood. Our experiments predicting the number of accesses for an article based on its past usage demonstrate that the mean absolute error and mean absolute percentage error of our model are 4.0% and 8.1% lower than the power-law regression model, respectively. The log-normal distribution is also shown to perform significantly better than a previous prediction method based on a human memory theory in cognitive science. This work warrants further investigation on the utility of such a log-normal regression approach towards improving information access in PubMed. PMID:24551386

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

PubMed

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

2016-01-01

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

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

PubMed

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

2012-06-01

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

How Artificial Intelligence Can Improve Our Understanding of the Genes Associated with Endometriosis: Natural Language Processing of the PubMed Database

PubMed Central

Mashiach, R.; Cohen, S.; Kedem, A.; Baron, A.; Zajicek, M.; Feldman, I.; Seidman, D.; Soriano, D.

2018-01-01

Endometriosis is a disease characterized by the development of endometrial tissue outside the uterus, but its cause remains largely unknown. Numerous genes have been studied and proposed to help explain its pathogenesis. However, the large number of these candidate genes has made functional validation through experimental methodologies nearly impossible. Computational methods could provide a useful alternative for prioritizing those most likely to be susceptibility genes. Using artificial intelligence applied to text mining, this study analyzed the genes involved in the pathogenesis, development, and progression of endometriosis. The data extraction by text mining of the endometriosis-related genes in the PubMed database was based on natural language processing, and the data were filtered to remove false positives. Using data from the text mining and gene network information as input for the web-based tool, 15,207 endometriosis-related genes were ranked according to their score in the database. Characterization of the filtered gene set through gene ontology, pathway, and network analysis provided information about the numerous mechanisms hypothesized to be responsible for the establishment of ectopic endometrial tissue, as well as the migration, implantation, survival, and proliferation of ectopic endometrial cells. Finally, the human genome was scanned through various databases using filtered genes as a seed to determine novel genes that might also be involved in the pathogenesis of endometriosis but which have not yet been characterized. These genes could be promising candidates to serve as useful diagnostic biomarkers and therapeutic targets in the management of endometriosis. PMID:29750165

How Artificial Intelligence Can Improve Our Understanding of the Genes Associated with Endometriosis: Natural Language Processing of the PubMed Database.

PubMed

Bouaziz, J; Mashiach, R; Cohen, S; Kedem, A; Baron, A; Zajicek, M; Feldman, I; Seidman, D; Soriano, D

2018-01-01

Endometriosis is a disease characterized by the development of endometrial tissue outside the uterus, but its cause remains largely unknown. Numerous genes have been studied and proposed to help explain its pathogenesis. However, the large number of these candidate genes has made functional validation through experimental methodologies nearly impossible. Computational methods could provide a useful alternative for prioritizing those most likely to be susceptibility genes. Using artificial intelligence applied to text mining, this study analyzed the genes involved in the pathogenesis, development, and progression of endometriosis. The data extraction by text mining of the endometriosis-related genes in the PubMed database was based on natural language processing, and the data were filtered to remove false positives. Using data from the text mining and gene network information as input for the web-based tool, 15,207 endometriosis-related genes were ranked according to their score in the database. Characterization of the filtered gene set through gene ontology, pathway, and network analysis provided information about the numerous mechanisms hypothesized to be responsible for the establishment of ectopic endometrial tissue, as well as the migration, implantation, survival, and proliferation of ectopic endometrial cells. Finally, the human genome was scanned through various databases using filtered genes as a seed to determine novel genes that might also be involved in the pathogenesis of endometriosis but which have not yet been characterized. These genes could be promising candidates to serve as useful diagnostic biomarkers and therapeutic targets in the management of endometriosis.

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

PubMed Central

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

2015-01-01

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

The identification of clinically important elements within medical journal abstracts: Patient-Population-Problem, Exposure-Intervention, Comparison, Outcome, Duration and Results (PECODR).

PubMed

Dawes, Martin; Pluye, Pierre; Shea, Laura; Grad, Roland; Greenberg, Arlene; Nie, Jian-Yun

2007-01-01

Information retrieval in primary care is becoming more difficult as the volume of medical information held in electronic databases expands. The lexical structure of this information might permit automatic indexing and improved retrieval. To determine the possibility of identifying the key elements of clinical studies, namely Patient-Population-Problem, Exposure-Intervention, Comparison, Outcome, Duration and Results (PECODR), from abstracts of medical journals. We used a convenience sample of 20 synopses from the journal Evidence-Based Medicine (EBM) and their matching original journal article abstracts obtained from PubMed. Three independent primary care professionals identified PECODR-related extracts of text. Rules were developed to define each PECODR element and the selection process of characters, words, phrases and sentences. From the extracts of text related to PECODR elements, potential lexical patterns that might help identify those elements were proposed and assessed using NVivo software. A total of 835 PECODR-related text extracts containing 41,263 individual text characters were identified from 20 EBM journal synopses. There were 759 extracts in the corresponding PubMed abstracts containing 31,947 characters. PECODR elements were found in nearly all abstracts and synopses with the exception of duration. There was agreement on 86.6% of the extracts from the 20 EBM synopses and 85.0% on the corresponding PubMed abstracts. After consensus this rose to 98.4% and 96.9% respectively. We found potential text patterns in the Comparison, Outcome and Results elements of both EBM synopses and PubMed abstracts. Some phrases and words are used frequently and are specific for these elements in both synopses and abstracts. Results suggest a PECODR-related structure exists in medical abstracts and that there might be lexical patterns specific to these elements. More sophisticated computer-assisted lexical-semantic analysis might refine these results, and pave the way to automating PECODR indexing, and improve information retrieval in primary care.

[Scientific output of orthopaedic hospitals in the Netherlands: not all hospitals meet the requirements of the Dutch orthopaedic residency programme].

PubMed

Eshuis, Rienk; Verheyen, Cees C P M; de Gast, Arthur

2011-01-01

To evaluate the feasibility of the requirements for scientific participation in the Dutch orthopaedic residency programme by assessing the numbers of articles published by orthopaedic teaching hospitals. Descriptive. All 29 orthopaedic teaching hospitals in the Netherlands were asked to draw up a list of articles published from 2004 to 2009. The publications were subdivided into papers indexed in PubMed and papers published in the Nederlands Tijdschrift voor Orthopedie (NTvO, Netherlands Journal of Orthopaedics) and the Nederlands Tijdschrift voor Traumatologie (NTvT, Netherlands Journal of Traumatology). There was an overall response rate of 72% (21/29). For the 8 non-responders a search of PubMed and the NTvO-NTvT journal databases was used to compile a list of their publications. The university teaching hospitals (n = 8) published 1150 articles, 1118 of which were indexed in PubMed, 19 published in the NTvO and 13 in the NTvT. Peripheral teaching hospitals (n = 21) published 689 articles: 590 indexed in PubMed, 77 published in the NTvO and 22 in the NTvT. In the peripheral teaching hospitals there was a positive correlation between the number of orthopaedic surgeons and PhD students and the number of published articles. Of the 29 teaching hospitals, 9 (31%) did not meet the requirements for publication specified in the Dutch orthopaedic residency programme guidelines. The number of published articles is related to the numbers of orthopaedic surgeons and PhD students in peripheral teaching hospitals. The requirements for the minimum number of publications could therefore be revised to reflect the proportion of orthopaedic surgeons in each teaching hospital. The introduction of a weighting factor that accounts for the quality of the publications would also result in a more balanced assessment.

Genetics Home Reference: hand-foot-genital syndrome

MedlinePlus

... article on PubMed Central Goodman FR, Scambler PJ. Human HOX gene mutations. Clin Genet. 2001 Jan;59(1):1- ... on PubMed Goodman FR. Limb malformations and the human HOX genes. Am J Med Genet. 2002 Oct 15;112( ...

Genetics Home Reference: lactose intolerance

MedlinePlus

... or Free article on PubMed Central Järvelä IE. Molecular genetics of adult-type hypolactasia. Ann Med. 2005;37( ... Citation on PubMed Robayo-Torres CC, Nichols BL. Molecular differentiation of congenital lactase ... Bulletins Genetics Home Reference Celebrates Its ...

Enriching PubMed Related Article Search with Sentence Level Co-citations

PubMed Central

Tran, Nam; Alves, Pedro; Ma, Shuangge

2009-01-01

PubMed related article links identify closely related articles and enhance our ability to navigate the biomedical literature. They are derived by calculating the word similarity between two articles, relating articles with overlapping word content. In this paper, we propose to enrich PubMed with a new type of related article link based on citations within a single sentence (i.e. sentence level co-citations or SLCs). Using different similarity metrics, we demonstrated that articles linked by SLCs are highly related. We also showed that only half of SLCs are found among PubMed related article links. Additionally, we discuss how the citing sentence of an SLC explains the connection between two articles. PMID:20351935

LAMDA at TREC CDS track 2015: Clinical Decision Support Track

DTIC Science & Technology

2015-11-20

outperforms all the other vector space models supported by Elasticsearch. MetaMap is the online tool that maps biomedical text to the Metathesaurus, and...cases. The medical knowledge consists of 700,000 biomedical documents supported by the PubMed Central [3] which is online digital database freely...Science Research Program through the National Research Foundation (NRF) of Korea funded by the Ministry of Science, ICT , and Future Planning (MSIP

Tuberculosis treatment outcome monitoring in European Union countries: systematic review

PubMed Central

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

2013-01-01

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

When can a woman resume or initiate contraception after taking emergency contraceptive pills? A systematic review.

PubMed

Salcedo, Jennifer; Rodriguez, Maria I; Curtis, Kathryn M; Kapp, Nathalie

2013-05-01

Hormonal emergency contraception can postpone ovulation, making a woman vulnerable to pregnancy later in the same cycle. However, concern exists as to whether concurrently administered emergency contraception pills (ECP) and other hormonal methods of contraception may affect the effectiveness of both medications. A systematic review of the literature using PubMed and the Cochrane databases was performed to identify articles concerning the resumption or initiation of regular contraception within the same cycle as ECP use. We searched for articles in any language, published between 1980 and April 2012 and included all methods of emergency contraception pills available in the USA. The search strategy identified 184 articles in the PubMed and Cochrane databases, of which none met inclusion criteria. The drug manufacturer advises continuation or initiation of routine contraception as soon as possible after use of ulipristal acetate, with concomitant use of a reliable barrier method until next menses. However, a theoretical concern exists that given ulipristal acetate's function as a selective progesterone receptor modulator, coadministration of a progestin could decrease its effectiveness as an emergency contraceptive. Initiation of hormonal contraception following levonorgestrel or the Yuzpe regimen for emergency contraception carries no similar concern for decreased method effectiveness. Copyright © 2013 Elsevier Inc. All rights reserved.

EcoGene 3.0

PubMed Central

Zhou, Jindan; Rudd, Kenneth E.

2013-01-01

EcoGene (http://ecogene.org) is a database and website devoted to continuously improving the structural and functional annotation of Escherichia coli K-12, one of the most well understood model organisms, represented by the MG1655(Seq) genome sequence and annotations. Major improvements to EcoGene in the past decade include (i) graphic presentations of genome map features; (ii) ability to design Boolean queries and Venn diagrams from EcoArray, EcoTopics or user-provided GeneSets; (iii) the genome-wide clone and deletion primer design tool, PrimerPairs; (iv) sequence searches using a customized EcoBLAST; (v) a Cross Reference table of synonymous gene and protein identifiers; (vi) proteome-wide indexing with GO terms; (vii) EcoTools access to >2000 complete bacterial genomes in EcoGene-RefSeq; (viii) establishment of a MySql relational database; and (ix) use of web content management systems. The biomedical literature is surveyed daily to provide citation and gene function updates. As of September 2012, the review of 37 397 abstracts and articles led to creation of 98 425 PubMed-Gene links and 5415 PubMed-Topic links. Annotation updates to Genbank U00096 are transmitted from EcoGene to NCBI. Experimental verifications include confirmation of a CTG start codon, pseudogene restoration and quality assurance of the Keio strain collection. PMID:23197660

EcoGene 3.0.

PubMed

Zhou, Jindan; Rudd, Kenneth E

2013-01-01

EcoGene (http://ecogene.org) is a database and website devoted to continuously improving the structural and functional annotation of Escherichia coli K-12, one of the most well understood model organisms, represented by the MG1655(Seq) genome sequence and annotations. Major improvements to EcoGene in the past decade include (i) graphic presentations of genome map features; (ii) ability to design Boolean queries and Venn diagrams from EcoArray, EcoTopics or user-provided GeneSets; (iii) the genome-wide clone and deletion primer design tool, PrimerPairs; (iv) sequence searches using a customized EcoBLAST; (v) a Cross Reference table of synonymous gene and protein identifiers; (vi) proteome-wide indexing with GO terms; (vii) EcoTools access to >2000 complete bacterial genomes in EcoGene-RefSeq; (viii) establishment of a MySql relational database; and (ix) use of web content management systems. The biomedical literature is surveyed daily to provide citation and gene function updates. As of September 2012, the review of 37 397 abstracts and articles led to creation of 98 425 PubMed-Gene links and 5415 PubMed-Topic links. Annotation updates to Genbank U00096 are transmitted from EcoGene to NCBI. Experimental verifications include confirmation of a CTG start codon, pseudogene restoration and quality assurance of the Keio strain collection.

The influence of morphological awareness on reading and writing: a systematic review.

PubMed

Silva, Ainoã Athaide Macedo; Martins-Reis, Vanessa de Oliveira

2017-02-16

this study aimed to perform a systematic review of national and international studies about the relationship between morphological awareness, reading/writing, reading comprehension, and spelling. a search for national and international literature was carried out using databases Medline (via PubMed) and Portal de Periódicos da Capes (Eric, PsycINFO, LILACS, SciELO) from August to September 2015. the inclusion criteria were: studies that answered the guiding question and addressed the subject matter established by the descriptors and keywords. Studies with animals, laboratories, opinion/expert pieces, case series, case reports and review studies were excluded. the following markers were considered: type and objective of the study, the skills related to morphological awareness (reading, writing, reading comprehension and spelling), tests performed, and their main results. the search carried out in the pre-established databases with descriptors and free terms resulted in 203 articles. The search in PubMed resulted in 81 studies, and in Portal de Periódicos Capes, 122. Of the total, 154 were excluded according to the title and abstract, whereas 39 were excluded upon reading the full text. This allowed for the analysis of 10 articles. children with better scores in the morphological awareness test show better results in reading and writing across all school grades.

Need for more research on and health interventions for transgender people.

PubMed

Ortiz-Martínez, Yeimer; Ríos-González, Carlos Miguel

2017-04-01

Background Recently, lesbian, gay, bisexual, and transgender (LGBT) scientific production is growing, but transgender (TG) people is less considered in the LGBT-related research, highlighting the lack of representative data on this neglected population. To assess the current status of scientific production on TG population, a bibliometric study was performed using the articles on TG people deposited in five databases, including PubMed/Medline, Scopus, Science Citation Index (SCI), Scientific Electronic Library Online (SciELO) and Latin American and Caribbean Health Sciences Literature (LILACS). The PubMed/Medline search retrieved 2370 documents, which represented 0.008% of all articles recorded in Medline. The Scopus search identified 4974 articles. At SCI, 2863 articles were identified. A search of the SciELO database identified 39 articles, whereas the LILACS search identified 44 articles. Most papers were from the US (57.59%), followed by Canada (5.15%), the UK (4.42%), Australia (3.19%), The Netherlands (2.46%) and Peru (1.83%). These six countries accounted for 74.6% of all scientific output. The findings indicate that the TG-related research is low, especially in low-income developing countries, where stigma and discrimination are common. More awareness, knowledge, and sensitivity in healthcare communities are needed to eliminate barriers in health attention and research in this population.

Worldwide access to evidence-based mental health literature: how useful is PubMed in Anglo-Saxon and non-Anglo-Saxon countries?

PubMed

Morlino, Massimo; Polese, Daniela; Bruni, Andrea; Renato, Bellinello

2005-10-01

The aim of this study was to verify the presence of cultural variety among the psychiatric journals available on PubMed, the major online tool for accessing literature. Data for analysis were taken from a survey of the world psychiatric journals indexed in Index Medicus 1999 (IM), the alphabetical list used by PubMed, and from the mean impact factor (IF) values of the journals. Approximately 80% of international psychiatric literature available on PubMed is published in Anglo-Saxon countries, especially in the USA (59.8% of the total). The widespread use of the English language (94.9% of all the journals) further stresses the dominance of the Anglo-Saxon cultural model, as do the mean IF values of Anglo-Saxon journals compared to non-Anglo-Saxon publications (3.252 vs. 1.693; P=0.0079). The under-representation of non-Anglo-Saxon cultural models on PubMed plays a negative role for bringing about a truly multicultural literature in psychiatry.

Genetics Home Reference: sitosterolemia

MedlinePlus

... Sitosterolemia ClinicalTrials.gov (1 link) ClinicalTrials.gov Scientific Articles on PubMed (1 link) PubMed OMIM (1 link) SITOSTEROLEMIA Sources for This Page Berge KE. Sitosterolemia: a gateway to new knowledge about cholesterol metabolism. Ann Med. 2003;35(7):502-11. Review. ...

Review of common conditions associated with periodontal ligament widening

PubMed Central

Mortazavi, Hamed

2016-01-01

Purpose The aim of this article is to review a group of lesions associated with periodontal ligament (PDL) widening. Materials and Methods An electronic search was performed using specialized databases such as Google Scholar, PubMed, PubMed Central, Science Direct, and Scopus to find relevant studies by using keywords such as “periodontium”, “periodontal ligament”, “periodontal ligament space”, “widened periodontal ligament”, and “periodontal ligament widening”. Results Out of nearly 200 articles, about 60 were broadly relevant to the topic. Ultimately, 47 articles closely related to the topic of interest were reviewed. When the relevant data were compiled, the following 10 entities were identified: occlusal/orthodontic trauma, periodontal disease/periodontitis, pulpo-periapical lesions, osteosarcoma, chondrosarcoma, non-Hodgkin lymphoma, progressive systemic sclerosis, radiation-induced bone defect, bisphosphonate-related osteonecrosis, and osteomyelitis. Conclusion Although PDL widening may be encountered by many dentists during their routine daily procedures, the clinician should consider some serious related conditions as well. PMID:28035300

Implant Supported Fixed Restorations versus Implant Supported Removable Overdentures: A Systematic Review

PubMed Central

Selim, Khaled; Ali, Sherif; Reda, Ahmed

2016-01-01

AIM: The aim of this study is to systematically evaluate and compare implant retained fixed restoration versus implant retained over denture. MATERIAL AND METHODS: Search was made in 2 databases including PubMed and PubMed Central. Title and abstract were screened to select studies comparing implant retained fixed restorations versus implant retained removable overdentures. Articles which did not follow the inclusion criteria were excluded. Included papers were then read carefully for a second stage filter, this was followed by manual searching of bibliography of selected articles. RESULTS: The search resulted in 5 included papers. One study evaluated the masticatory function, while the other 4 evaluated the patient satisfaction. Two of them used Visual Analogue Scale (VAS) as a measurement tool, while the other two used VAS and Categorical Scales (CAT). Stability, ability to chew, ability to clean, ability to speak and esthetics were the main outcomes of the 4 included papers. CONCLUSION: Conflicting results was observed between the fixed and removable restorations. PMID:28028423

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

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

PubMed

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

2010-07-01

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.

Clostridium difficile contamination of health care workers' hands and its potential contribution to the spread of infection: Review of the literature.

PubMed

Jullian-Desayes, Ingrid; Landelle, Caroline; Mallaret, Marie-Reine; Brun-Buisson, Christian; Barbut, Frédéric

2017-01-01

Clostridium difficile infection (CDI) can be transmitted from patient to patient by the hands of health care workers (HCWs); however, the relative importance of this route in the spread of C difficile in the hospital is currently unknown. Our aim was to review studies examining HCWs' hand carriage and its potential role in CDI transmission. First, English-speaking references addressing HCWs' hand sampling obtained from the PubMed database were reviewed. Second, C difficile outbreaks definitely or probably implicating HCWs were retrieved from the Outbreak Database Web site (www.outbreak-database.com). Finally, cases of C difficile occurring in HCWs after contact with an infected patient were retrieved from PubMed. A total of 11 studies dealing with HCWs' hand carriage were selected and reviewed. Between 0% and 59% of HCWs' hands were found contaminated with C difficile after caring for a patient with CDI. There were several differences between studies regarding site of hands sampling, timing after contact, and bacteriologic methods. Only 2 C difficile outbreaks implicating HCWs and 6 series of cases of transmission from patients to HCWs have been reported. This review shows that HCWs' hands could play an important role in the transmission of C difficile. Hand hygiene and reduction of environmental contamination are essential to control C difficile transmission. Copyright © 2017 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

[The use of bibliographic information resources and Web 2.0 by neuropaediatricians].

PubMed

González de Dios, Javier; Camino-León, Rafael; Ramos-Lizana, Julio

2011-06-16

To determine the state of knowledge and use of the main sources of bibliographic information and Web 2.0 resources in a sample of pediatricians linked professionally to child neurology. Anonymous opinion survey to 44 pediatricians (36 neuropediatric staffs and 8 residents) with two sections: sources of bibliographic information: (25 questions) and Web 2.0 resources (14 questions). The most consulted journals are Revista de Neurología and Anales de Pediatría. All use PubMed database and less frequently Índice Médico Español (40%) and Embase (27%); less than 20% use of other international and national databases. 81% of respondents used the Cochrane Library, and less frequently other sources of evidence-based medicine: Tripdatabase (39%), National Guideline Clearinghouse (37%), Excelencia Clínica (12%) and Sumsearch (3%). 45% regularly receive some e-TOC (electronic table of contents) of biomedical journals, but only 7% reported having used the RSS (really system syndication). The places to start searching for information are PubMed (55%) and Google (23%). The four resources most used of Web 2.0 are YouTube (73%), Facebook (43%), Picasa (27%) and blogs (25%). We don't found differences in response between the group of minus or equal to 34 and major or equal to 35 years. Knowledge of the patterns of use of information databases and Web 2.0 resources can identify the limitations and opportunities for improvement in the field of pediatric neurology training and information.

Do Language Fluency and Other Socioeconomic Factors Influence the Use of PubMed and MedlinePlus?

PubMed Central

Sheets, L.; Gavino, A.; Callaghan, F.; Fontelo, P.

2013-01-01

Background Increased usage of MedlinePlus by Spanish-speakers was observed after introduction of MedlinePlus in Spanish. This probably reflects increased usage of MEDLINE and PubMed by those with greater fluency in the language in which it is presented; but this has never been demonstrated in English speakers. Evidence that lack of English fluency deters international healthcare personnel from using PubMed could support the use of multi-language search tools like Babel-MeSH. Objectives This study aims to measure the effects of language fluency and other socioeconomic factors on PubMed MEDLINE and MedlinePlus access by international users. Methods We retrospectively reviewed server pageviews of PubMed and MedlinePlus from various periods of time, and analyzed them against country statistics on language fluency, GDP, literacy rate, Internet usage, medical schools, and physicians per capita, to determine whether they were associated. Results We found fluency in English to be positively associated with pageviews of PubMed and MedlinePlus in countries with high literacy rates. Spanish was generally found to be positively associated with pageviews of MedlinePlus en Español. The other parameters also showed varying degrees of association with pageviews. Conclusions After adjusting for the other factors investigated in this study, language fluency was a consistently significant predictor of the use of PubMed, MedlinePlus English and MedlinePlus en Español. This study may support the need for multi-language search tools and may increase access of health information resources from non-English speaking countries. PMID:23874356

Do language fluency and other socioeconomic factors influence the use of PubMed and MedlinePlus?

PubMed

Sheets, L; Gavino, A; Callaghan, F; Fontelo, P

2013-01-01

Increased usage of MedlinePlus by Spanish-speakers was observed after introduction of MedlinePlus in Spanish. This probably reflects increased usage of MEDLINE and PubMed by those with greater fluency in the language in which it is presented; but this has never been demonstrated in English speakers. Evidence that lack of English fluency deters international healthcare personnel from using PubMed could support the use of multi-language search tools like Babel-MeSH. This study aims to measure the effects of language fluency and other socioeconomic factors on PubMed MEDLINE and MedlinePlus access by international users. We retrospectively reviewed server pageviews of PubMed and MedlinePlus from various periods of time, and analyzed them against country statistics on language fluency, GDP, literacy rate, Internet usage, medical schools, and physicians per capita, to determine whether they were associated. We found fluency in English to be positively associated with pageviews of PubMed and MedlinePlus in countries with high literacy rates. Spanish was generally found to be positively associated with pageviews of MedlinePlus en Español. The other parameters also showed varying degrees of association with pageviews. After adjusting for the other factors investigated in this study, language fluency was a consistently significant predictor of the use of PubMed, MedlinePlus English and MedlinePlus en Español. This study may support the need for multi-language search tools and may increase access of health information resources from non-English speaking countries.

For 481 biomedical open access journals, articles are not searchable in the Directory of Open Access Journals nor in conventional biomedical databases.

PubMed

Liljekvist, Mads Svane; Andresen, Kristoffer; Pommergaard, Hans-Christian; Rosenberg, Jacob

2015-01-01

Background. Open access (OA) journals allows access to research papers free of charge to the reader. Traditionally, biomedical researchers use databases like MEDLINE and EMBASE to discover new advances. However, biomedical OA journals might not fulfill such databases' criteria, hindering dissemination. The Directory of Open Access Journals (DOAJ) is a database exclusively listing OA journals. The aim of this study was to investigate DOAJ's coverage of biomedical OA journals compared with the conventional biomedical databases. Methods. Information on all journals listed in four conventional biomedical databases (MEDLINE, PubMed Central, EMBASE and SCOPUS) and DOAJ were gathered. Journals were included if they were (1) actively publishing, (2) full OA, (3) prospectively indexed in one or more database, and (4) of biomedical subject. Impact factor and journal language were also collected. DOAJ was compared with conventional databases regarding the proportion of journals covered, along with their impact factor and publishing language. The proportion of journals with articles indexed by DOAJ was determined. Results. In total, 3,236 biomedical OA journals were included in the study. Of the included journals, 86.7% were listed in DOAJ. Combined, the conventional biomedical databases listed 75.0% of the journals; 18.7% in MEDLINE; 36.5% in PubMed Central; 51.5% in SCOPUS and 50.6% in EMBASE. Of the journals in DOAJ, 88.7% published in English and 20.6% had received impact factor for 2012 compared with 93.5% and 26.0%, respectively, for journals in the conventional biomedical databases. A subset of 51.1% and 48.5% of the journals in DOAJ had articles indexed from 2012 and 2013, respectively. Of journals exclusively listed in DOAJ, one journal had received an impact factor for 2012, and 59.6% of the journals had no content from 2013 indexed in DOAJ. Conclusions. DOAJ is the most complete registry of biomedical OA journals compared with five conventional biomedical databases. However, DOAJ only indexes articles for half of the biomedical journals listed, making it an incomplete source for biomedical research papers in general.

Searching for randomized controlled trials and systematic reviews on exercise. A descriptive study.

PubMed

Grande, Antonio José; Hoffmann, Tammy; Glasziou, Paul

2015-01-01

The current paradigm of science is to accumulate as much research data as possible, with less thought given to navigation or synthesis of the resulting mass, which hampers locating and using the research. The aim here was to describe the number of randomized controlled trials (RCTs) and systematic reviews (SRs) focusing on exercise, and their journal sources, that have been indexed in PubMed over time. Descriptive study conducted at Bond University, Australia. To find RCTs, a search was conducted in PubMed Clinical Queries, using the category "Therapy" and the Medical Subject Headings (MeSH) term "Exercise". To find SRs, a search was conducted in PubMed Clinical Queries, using the category "Therapy", the MeSH term "Exercise" and various methodological filters. Up until 2011, 9,354 RCTs about exercise were published in 1,250 journals and 1,262 SRs in 513 journals. Journals in the area of Sports Science published the greatest number of RCTs and journals categorized as belonging to "Other health professions" area (for example nursing or psychology) published the greatest number of SRs. The Cochrane Database of Systematic Reviews was the principal source for SRs, with 9.8% of the total, while the Journal of Strength and Conditioning Research and Medicine & Science in Sports & Exercise published 4.4% and 5.0% of the RCTs, respectively. The rapid growth and resulting scatter of RCTs and SRs on exercise presents challenges for locating and using this research. Solutions for this issue need to be considered.

Pediatric cancer risk in association with birth defects: A systematic review

PubMed Central

Padda, Hannah; Feng, Qianxi; Partap, Sonia; Fowler, Susan A.; Druley, Todd E.

2017-01-01

Background Many epidemiological studies have examined associations between birth defects (BDs) and pediatric malignancy over the past several decades. Our objective was to conduct a systematic literature review of studies reporting on this association. Methods We used librarian-designed searches of the PubMed Medline and Embase databases to identify primary research articles on pediatric neoplasms and BDs. English language articles from PubMed and Embase up to 10/12/2015, and in PubMed up to 5/12/2017 following an updated search, were eligible for inclusion if they reported primary epidemiological research results on associations between BDs and pediatric malignancies. Two reviewers coded each article based on the title and abstract to identify eligible articles that were abstracted using a structured form. Additional articles were identified through reference lists and other sources. Results were synthesized for pediatric cancers overall and for nine major pediatric cancer subtypes. Results A total of 14,778 article citations were identified, of which 80 met inclusion criteria. Pediatric cancer risk was increased in most studies in association with BDs overall with some notable specific findings, including increased risks for CNS tumors in association with CNS abnormalities and positive associations between rib anomalies and several pediatric cancer types. Conclusions Some children born with BDs may be at increased risk for specific pediatric malignancy types. This work provides a foundation for future investigations that are needed to clarify specific BD types predisposing toward malignancy and possible underlying causes of both BDs and malignancy. PMID:28749971

Dataset of breath research manuscripts curated using PubMed search strings from 1995-2016.

PubMed

Geer Wallace, M Ariel; Pleil, Joachim D

2018-06-01

The data contained in this article are PubMed search strings and search string builders used to curate breath research manuscripts published from 1995-2016 and the respective number of articles found that satisfied the search requirements for selected categories. Breath sampling represents a non-invasive technique that has gained usefulness for public health, clinical, diagnostic, and environmental exposure assessment applications over the years. This data article includes search strings that were utilized to retrieve publications through the PubMed database for different breath research-related topics that were related to the analysis of exhaled breath, exhaled breath condensate (EBC), and exhaled breath aerosol (EBA) as well as the analysis of cellular headspace. Manuscripts were curated for topics including EBC, EBA, Direct MS, GC-MS, LC-MS, alcohol, and sensors. A summary of the number of papers published per year for the data retrieved using each of the search strings is also included. These data can be utilized to discern trends in the number of breath research publications in each of the different topics over time. A supplementary Appendix A containing the titles, author lists, journal names, publication dates, PMID numbers, and EntrezUID numbers for each of the journal articles curated using the finalized search strings for the seven breath research-related topics can also be found within this article. The selected manuscripts can be used to explore the impact that breath research has had on expanding the scientific knowledge in each of the investigated topics.

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

PubMed Interact: an Interactive Search Application for MEDLINE/PubMed

PubMed Central

Muin, Michael; Fontelo, Paul; Ackerman, Michael

2006-01-01

Online search and retrieval systems are important resources for medical literature research. Progressive Web 2.0 technologies provide opportunities to improve search strategies and user experience. Using PHP, Document Object Model (DOM) manipulation and Asynchronous JavaScript and XML (Ajax), PubMed Interact allows greater functionality so users can refine search parameters with ease and interact with the search results to retrieve and display relevant information and related articles. PMID:17238658

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

PubMed Central

2013-01-01

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

Scoliosis in patients with Prader Willi Syndrome - comparisons of conservative and surgical treatment.

PubMed

Weiss, Hans-Rudolf; Goodall, Deborah

2009-05-06

In children with Prader Willi syndrome (PWS), besides growth hormone (GH) therapy, control of the food environment and regular exercise, surgical treatment of scoliosis deformities seems the treatment of choice, even though the risks of spinal surgery in this specific population is very high. Therefore the question arises as to whether the risks of spinal surgery outweigh the benefits in a condition, which bears significant risks per se. The purpose of this systematic review of the Pub Med literature was to find mid or long-term results of spinal fusion surgery in patients with PWS, and to present the conservative treatment in a case study of nine patients with this condition. Types of studies included; all kinds of studies; retrospective and prospective ones, which reported upon the outcome of scoliosis surgery in patients with PWS.Types of participants included: patients with scoliosis and PWS.Type of intervention: surgery.Search strategy for identification of the studies; Pub Med; limited to English language and bibliographies of all reviewed articles.Nine patients with PWS from our data-base treated conservatively have been found, being 19 years or over at the time this study has been performed. The results of conservative management are described and related to the natural history and treatment results found in the Pub Med review. From 2210 titles displayed in the Pub Med database with the key word being "Prader Willi syndrome", 5 different papers were displayed at the date of the search containing some information on the outcome of surgery and none appeared to contain a mid or long-term follow-up. The PWS patients treated conservatively from our series all stayed below 70 degrees and some of which improved. If the curve of scoliosis patients with PWS can be kept within certain limits (usually below 70 degrees) conservatively, this treatment seems to have fewer complications than surgical treatments. The results of our retrospective study of nine patients demonstrate that scoliosis in this entity plays only a minor role and surgery is unnecessary when high quality conservative management exists. There is lack of the long follow-up studies in post-surgical cases in patients with PWS and scoliosis. The rate of complications of spinal fusion in patients with PWS and scoliosis is very high and the death rates have been found to be higher than in patients with Adolescent Idiopathic Scoliosis (AIS). The long-term side-effects of the intervention are detrimental, so that the risk-benefit ratio favours the conservative approaches over spinal fusion surgery.

Scoliosis in patients with Prader Willi Syndrome – comparisons of conservative and surgical treatment

PubMed Central

Weiss, Hans-Rudolf; Goodall, Deborah

2009-01-01

In children with Prader Willi syndrome (PWS), besides growth hormone (GH) therapy, control of the food environment and regular exercise, surgical treatment of scoliosis deformities seems the treatment of choice, even though the risks of spinal surgery in this specific population is very high. Therefore the question arises as to whether the risks of spinal surgery outweigh the benefits in a condition, which bears significant risks per se. The purpose of this systematic review of the Pub Med literature was to find mid or long-term results of spinal fusion surgery in patients with PWS, and to present the conservative treatment in a case study of nine patients with this condition. Types of studies included; all kinds of studies; retrospective and prospective ones, which reported upon the outcome of scoliosis surgery in patients with PWS. Types of participants included: patients with scoliosis and PWS. Type of intervention: surgery. Search strategy for identification of the studies; Pub Med; limited to English language and bibliographies of all reviewed articles. Nine patients with PWS from our data-base treated conservatively have been found, being 19 years or over at the time this study has been performed. The results of conservative management are described and related to the natural history and treatment results found in the Pub Med review. From 2210 titles displayed in the Pub Med database with the key word being "Prader Willi syndrome", 5 different papers were displayed at the date of the search containing some information on the outcome of surgery and none appeared to contain a mid or long-term follow-up. The PWS patients treated conservatively from our series all stayed below 70° and some of which improved. If the curve of scoliosis patients with PWS can be kept within certain limits (usually below 70 degrees) conservatively, this treatment seems to have fewer complications than surgical treatments. The results of our retrospective study of nine patients demonstrate that scoliosis in this entity plays only a minor role and surgery is unnecessary when high quality conservative management exists. There is lack of the long follow-up studies in post-surgical cases in patients with PWS and scoliosis. The rate of complications of spinal fusion in patients with PWS and scoliosis is very high and the death rates have been found to be higher than in patients with Adolescent Idiopathic Scoliosis (AIS). The long-term side-effects of the intervention are detrimental, so that the risk-benefit ratio favours the conservative approaches over spinal fusion surgery. PMID:19419581

For 481 biomedical open access journals, articles are not searchable in the Directory of Open Access Journals nor in conventional biomedical databases

PubMed Central

Andresen, Kristoffer; Pommergaard, Hans-Christian; Rosenberg, Jacob

2015-01-01

Background. Open access (OA) journals allows access to research papers free of charge to the reader. Traditionally, biomedical researchers use databases like MEDLINE and EMBASE to discover new advances. However, biomedical OA journals might not fulfill such databases’ criteria, hindering dissemination. The Directory of Open Access Journals (DOAJ) is a database exclusively listing OA journals. The aim of this study was to investigate DOAJ’s coverage of biomedical OA journals compared with the conventional biomedical databases. Methods. Information on all journals listed in four conventional biomedical databases (MEDLINE, PubMed Central, EMBASE and SCOPUS) and DOAJ were gathered. Journals were included if they were (1) actively publishing, (2) full OA, (3) prospectively indexed in one or more database, and (4) of biomedical subject. Impact factor and journal language were also collected. DOAJ was compared with conventional databases regarding the proportion of journals covered, along with their impact factor and publishing language. The proportion of journals with articles indexed by DOAJ was determined. Results. In total, 3,236 biomedical OA journals were included in the study. Of the included journals, 86.7% were listed in DOAJ. Combined, the conventional biomedical databases listed 75.0% of the journals; 18.7% in MEDLINE; 36.5% in PubMed Central; 51.5% in SCOPUS and 50.6% in EMBASE. Of the journals in DOAJ, 88.7% published in English and 20.6% had received impact factor for 2012 compared with 93.5% and 26.0%, respectively, for journals in the conventional biomedical databases. A subset of 51.1% and 48.5% of the journals in DOAJ had articles indexed from 2012 and 2013, respectively. Of journals exclusively listed in DOAJ, one journal had received an impact factor for 2012, and 59.6% of the journals had no content from 2013 indexed in DOAJ. Conclusions. DOAJ is the most complete registry of biomedical OA journals compared with five conventional biomedical databases. However, DOAJ only indexes articles for half of the biomedical journals listed, making it an incomplete source for biomedical research papers in general. PMID:26038727

OReFiL: an online resource finder for life sciences.

PubMed

Yamamoto, Yasunori; Takagi, Toshihisa

2007-08-06

Many online resources for the life sciences have been developed and introduced in peer-reviewed papers recently, ranging from databases and web applications to data-analysis software. Some have been introduced in special journal issues or websites with a search function, but others remain scattered throughout the Internet and in the published literature. The searchable resources on these sites are collected and maintained manually and are therefore of higher quality than automatically updated sites, but also require more time and effort. We developed an online resource search system called OReFiL to address these issues. We developed a crawler to gather all of the web pages whose URLs appear in MEDLINE abstracts and full-text papers on the BioMed Central open-access journals. The URLs were extracted using regular expressions and rules based on our heuristic knowledge. We then indexed the online resources to facilitate their retrieval and comparison by researchers. Because every online resource has at least one PubMed ID, we can easily acquire its summary with Medical Subject Headings (MeSH) terms and confirm its credibility through reference to the corresponding PubMed entry. In addition, because OReFiL automatically extracts URLs and updates the index, minimal time and effort is needed to maintain the system. We developed OReFiL, a search system for online life science resources, which is freely available. The system's distinctive features include the ability to return up-to-date query-relevant online resources introduced in peer-reviewed papers; the ability to search using free words, MeSH terms, or author names; easy verification of each hit following links to the corresponding PubMed entry or to papers citing the URL through the search systems of BioMed Central, Scirus, HighWire Press, or Google Scholar; and quick confirmation of the existence of an online resource web page.

OReFiL: an online resource finder for life sciences

PubMed Central

Yamamoto, Yasunori; Takagi, Toshihisa

2007-01-01

Background Many online resources for the life sciences have been developed and introduced in peer-reviewed papers recently, ranging from databases and web applications to data-analysis software. Some have been introduced in special journal issues or websites with a search function, but others remain scattered throughout the Internet and in the published literature. The searchable resources on these sites are collected and maintained manually and are therefore of higher quality than automatically updated sites, but also require more time and effort. Description We developed an online resource search system called OReFiL to address these issues. We developed a crawler to gather all of the web pages whose URLs appear in MEDLINE abstracts and full-text papers on the BioMed Central open-access journals. The URLs were extracted using regular expressions and rules based on our heuristic knowledge. We then indexed the online resources to facilitate their retrieval and comparison by researchers. Because every online resource has at least one PubMed ID, we can easily acquire its summary with Medical Subject Headings (MeSH) terms and confirm its credibility through reference to the corresponding PubMed entry. In addition, because OReFiL automatically extracts URLs and updates the index, minimal time and effort is needed to maintain the system. Conclusion We developed OReFiL, a search system for online life science resources, which is freely available. The system's distinctive features include the ability to return up-to-date query-relevant online resources introduced in peer-reviewed papers; the ability to search using free words, MeSH terms, or author names; easy verification of each hit following links to the corresponding PubMed entry or to papers citing the URL through the search systems of BioMed Central, Scirus, HighWire Press, or Google Scholar; and quick confirmation of the existence of an online resource web page. PMID:17683589

Genetics Home Reference: lipoid proteinosis

MedlinePlus

... Problems National Alliance on Mental Illness Pediatric Dermatology Research Alliance GeneReviews (1 link) Lipoid Proteinosis Scientific Articles on PubMed (1 link) PubMed OMIM (1 link) LIPOID PROTEINOSIS OF URBACH AND WIETHE MedGen (1 link) Lipid proteinosis Sources for This Page Callizo M, Ibáñez- ...

Enabling multi-level relevance feedback on PubMed by integrating rank learning into DBMS.

PubMed

Yu, Hwanjo; Kim, Taehoon; Oh, Jinoh; Ko, Ilhwan; Kim, Sungchul; Han, Wook-Shin

2010-04-16

Finding relevant articles from PubMed is challenging because it is hard to express the user's specific intention in the given query interface, and a keyword query typically retrieves a large number of results. Researchers have applied machine learning techniques to find relevant articles by ranking the articles according to the learned relevance function. However, the process of learning and ranking is usually done offline without integrated with the keyword queries, and the users have to provide a large amount of training documents to get a reasonable learning accuracy. This paper proposes a novel multi-level relevance feedback system for PubMed, called RefMed, which supports both ad-hoc keyword queries and a multi-level relevance feedback in real time on PubMed. RefMed supports a multi-level relevance feedback by using the RankSVM as the learning method, and thus it achieves higher accuracy with less feedback. RefMed "tightly" integrates the RankSVM into RDBMS to support both keyword queries and the multi-level relevance feedback in real time; the tight coupling of the RankSVM and DBMS substantially improves the processing time. An efficient parameter selection method for the RankSVM is also proposed, which tunes the RankSVM parameter without performing validation. Thereby, RefMed achieves a high learning accuracy in real time without performing a validation process. RefMed is accessible at http://dm.postech.ac.kr/refmed. RefMed is the first multi-level relevance feedback system for PubMed, which achieves a high accuracy with less feedback. It effectively learns an accurate relevance function from the user's feedback and efficiently processes the function to return relevant articles in real time.

Enabling multi-level relevance feedback on PubMed by integrating rank learning into DBMS

PubMed Central

2010-01-01

Background Finding relevant articles from PubMed is challenging because it is hard to express the user's specific intention in the given query interface, and a keyword query typically retrieves a large number of results. Researchers have applied machine learning techniques to find relevant articles by ranking the articles according to the learned relevance function. However, the process of learning and ranking is usually done offline without integrated with the keyword queries, and the users have to provide a large amount of training documents to get a reasonable learning accuracy. This paper proposes a novel multi-level relevance feedback system for PubMed, called RefMed, which supports both ad-hoc keyword queries and a multi-level relevance feedback in real time on PubMed. Results RefMed supports a multi-level relevance feedback by using the RankSVM as the learning method, and thus it achieves higher accuracy with less feedback. RefMed "tightly" integrates the RankSVM into RDBMS to support both keyword queries and the multi-level relevance feedback in real time; the tight coupling of the RankSVM and DBMS substantially improves the processing time. An efficient parameter selection method for the RankSVM is also proposed, which tunes the RankSVM parameter without performing validation. Thereby, RefMed achieves a high learning accuracy in real time without performing a validation process. RefMed is accessible at http://dm.postech.ac.kr/refmed. Conclusions RefMed is the first multi-level relevance feedback system for PubMed, which achieves a high accuracy with less feedback. It effectively learns an accurate relevance function from the user’s feedback and efficiently processes the function to return relevant articles in real time. PMID:20406504

Searching PubMed for a broad subject area: how effective are palliative care clinicians in finding the evidence in their field?

PubMed

Damarell, Raechel A; Tieman, Jennifer J

2016-03-01

Health professionals must be able to search competently for evidence to support practice. We sought to understand how palliative care clinicians construct searches for palliative care literature in PubMed, to quantify search efficacy in retrieving a set of relevant articles and to compare performance against a Palliative CareSearch Filter (PCSF). Included studies from palliative care systematic reviews formed a test set. Palliative care clinicians (n = 37) completed a search task using PubMed. Individual clinician searches were reconstructed in PubMed and combined with the test set to calculate retrieval sensitivity. PCSF performance in the test set was also determined. Many clinicians struggled to create useful searches. Twelve used a single search term, 17 narrowed the search inappropriately and 8 confused Boolean operators. The mean number of test set citations (n = 663) retrieved was 166 (SD = 188), or 25% although 76% of clinicians believed they would find more than 50% of the articles. Only 8 participants (22%) achieved this. Correlations between retrieval and PubMed confidence (r = 0.13) or frequency of use (r = -0.18) were weak. Many palliative care clinicians search PubMed ineffectively. Targeted skills training and PCSF promotion may improve evidence retrieval. © 2015 Health Libraries Group.

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.

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

PubMed

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

2018-02-10

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

Growth of Global Publishing Output of Health Economics in the Twenty-First Century: A Bibliographic Insight.

PubMed

Jakovljevic, Mihajlo Michael; Pejcic, Ana V

2017-01-01

Strong growth of interdisciplinary sciences might find exceptional example in academic health economics. We decided to observe the quantitative output in this science since the beginning of the twenty-first century. Electronic search of the published literature was conducted in four different databases: one medical database-MEDLINE/PubMed, two general databases-Scopus/Elsevier and Web of Science (WoS), and one specialized health economic database-NHS Economic Evaluation Database (EED). The applied combination of key words was carefully chosen to cover the most commonly used terms in titles of publications dealing with conceptual areas of health economics. All bibliographic units were taken into account. Within the time horizon from January 1, 2000 to December 31, 2016, without language or limitations on bibliographic unit types, we identified an output ranging approximately from 60,345 to 88,246 records with applied search strategy in MEDLINE/PubMed, Scopus/Elsevier, and WoS. In NHS EED, we detected 14,761 records of economic evaluations of health interventions during the period in which database was maintained and regularly updated. With slightly more than one-third of the identified records, USA clearly dominates in this field. United Kingdom takes a strong second place with about 12% of identified records. Consistently, USA and UK universities are the most frequent among the top 15 affiliations/organizations of the authors of the identified records. Authors from Harvard University contributed to the largest number of the identified records. There is a clear evidence of both the upward stream of blossoming in health economics publications and its acceleration. Based on this bibliographic data set, it is difficult to distinguish the actual impact growth of this output provided dominantly by academia with modest contribution by pharmaceutical/medicinal device industry and diverse national government-based agencies. Further insight into the citation track record of these individual publications could provide helpful upgrade and a perspective on ongoing development.

Efficacy of Noninvasive Stellate Ganglion Blockade Performed Using Physical Agent Modalities in Patients with Sympathetic Hyperactivity-Associated Disorders: A Systematic Review and Meta-Analysis.

PubMed

Liao, Chun-De; Tsauo, Jau-Yih; Liou, Tsan-Hon; Chen, Hung-Chou; Rau, Chi-Lun

2016-01-01

Stellate ganglion blockade (SGB) is mainly used to relieve symptoms of neuropathic pain in conditions such as complex regional pain syndrome and has several potential complications. Noninvasive SGB performed using physical agent modalities (PAMs), such as light irradiation and electrical stimulation, can be clinically used as an alternative to conventional invasive SGB. However, its application protocols vary and its clinical efficacy remains controversial. This study investigated the use of noninvasive SGB for managing neuropathic pain or other disorders associated with sympathetic hyperactivity. We performed a comprehensive search of the following online databases: Medline, PubMed, Excerpta Medica Database, Cochrane Library Database, Ovid MEDLINE, Europe PubMed Central, EBSCOhost Research Databases, CINAHL, ProQuest Research Library, Physiotherapy Evidence Database, WorldWideScience, BIOSIS, and Google Scholar. We identified and included quasi-randomized or randomized controlled trials reporting the efficacy of SGB performed using therapeutic ultrasound, transcutaneous electrical nerve stimulation, light irradiation using low-level laser therapy, or xenon light or linearly polarized near-infrared light irradiation near or over the stellate ganglion region in treating complex regional pain syndrome or disorders requiring sympatholytic management. The included articles were subjected to a meta-analysis and risk of bias assessment. Nine randomized and four quasi-randomized controlled trials were included. Eleven trials had good methodological quality with a Physiotherapy Evidence Database (PEDro) score of ≥6, whereas the remaining two trials had a PEDro score of <6. The meta-analysis results revealed that the efficacy of noninvasive SGB on 100-mm visual analog pain score is higher than that of a placebo or active control (weighted mean difference, -21.59 mm; 95% CI, -34.25, -8.94; p = 0.0008). Noninvasive SGB performed using PAMs effectively relieves pain of various etiologies, making it a valuable addition to the contemporary pain management armamentarium. However, this evidence is limited by the potential risk of bias.

Genetics Home Reference: Rotor syndrome

MedlinePlus

... syndrome). Best Pract Res Clin Gastroenterol. 2010 Oct;24(5):555-71. doi: 10.1016/j.bpg.2010.07.007. Review. Citation on PubMed Wolkoff AW, Wolpert E, Pascasio FN, Arias IM. Rotor's syndrome. A distinct inheritable pathophysiologic entity. Am J Med. 1976 Feb;60(2):173-9. Citation on PubMed ...

Genetics Home Reference: surfactant dysfunction

MedlinePlus

... Infant ClinicalTrials.gov (1 link) ClinicalTrials.gov Scientific Articles on PubMed (1 link) PubMed OMIM (4 links) SURFACTANT METABOLISM DYSFUNCTION, PULMONARY, 1 SURFACTANT METABOLISM DYSFUNCTION, PULMONARY, 2 ...

Gaps in affiliation indexing in Scopus and PubMed.

PubMed

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

2016-04-01

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

Genetics Home Reference: biotin-thiamine-responsive basal ganglia disease

MedlinePlus

... link) Biotin-Thiamine-Responsive Basal Ganglia Disease Scientific Articles on PubMed (1 link) PubMed OMIM (1 link) THIAMINE METABOLISM DYSFUNCTION SYNDROME 2 (BIOTIN- OR THIAMINE-RESPONSIVE TYPE) ...

A guide to writing case reports for the Journal of Medical Case Reports and BioMed Central Research Notes

PubMed Central

2013-01-01

Case reports are a time-honored, important, integral, and accepted part of the medical literature. Both the Journal of Medical Case Reports and the Case Report section of BioMed Central Research Notes are committed to case report publication, and each have different criteria. Journal of Medical Case Reports was the world’s first international, PubMed-listed medical journal devoted to publishing case reports from all clinical disciplines and was launched in 2007. The Case Report section of BioMed Central Research Notes was created and began publishing case reports in 2012. Between the two of them, thousands of peer-reviewed case reports have now been published with a worldwide audience. Authors now also have Cases Database, a continually updated, freely accessible database of thousands of medical case reports from multiple publishers. This informal editorial outlines the process and mechanics of how and when to write a case report, and provides a brief look into the editorial process behind each of these complementary journals along with the author’s anecdotes in the hope of inspiring all authors (both novice and experienced) to write and continue writing case reports of all specialties. Useful hyperlinks are embedded throughout for easy and quick reference to style guidelines for both journals. PMID:24283456

Genetics Home Reference: Brody myopathy

MedlinePlus

... Citation on PubMed Odermatt A, Barton K, Khanna VK, Mathieu J, Escolar D, Kuntzer T, Karpati G, ... Citation on PubMed Odermatt A, Taschner PE, Khanna VK, Busch HF, Karpati G, Jablecki CK, Breuning MH, ...

HIV Infection and Cancer Risk

MedlinePlus

... patients in the United States. Journal of Clinical Oncology 2015; 33(21):2376-2383. [PubMed Abstract] Coghill ... for cancer risk and prevention. Current Opinion in Oncology 2012; 24(5):506-16 [PubMed Abstract] Goncalves ...

Genetics Home Reference: Aicardi syndrome

MedlinePlus

... 1080/13816810802320209. Citation on PubMed Eble TN, Sutton VR, Sangi-Haghpeykar H, Wang X, Jin W, Lewis ... Free article on PubMed Central Glasmacher MA, Sutton VR, Hopkins B, Eble T, Lewis RA, Park Parsons ...

Antioxidants and Cancer Prevention

MedlinePlus

... 95. [PubMed Abstract] Patterson RE, White E, Kristal AR, et al. Vitamin supplements and cancer risk: the ... 1750. [PubMed Abstract] Neuhouser ML, Barnett MJ, Kristal AR, et al. Dietary supplement use and prostate cancer ...

Human Papillomavirus (HPV) Vaccines

MedlinePlus

... 2162. [PubMed Abstract] Huh WK, Joura EA, Giuliano AR, et al. Final efficacy, immunogenicity, and safety analyses ... 2017; 390(10108):2143-2159. [PubMed Abstract] Giuliano AR, Palefsky JM, Goldstone S, et al. Efficacy of quadrivalent ...

Genetics Home Reference: aceruloplasminemia

MedlinePlus

... PubMed Harris ZL. Aceruloplasminemia. J Neurol Sci. 2003 Mar 15;207(1-2):108-9. Review. Citation ... nervous system. Ann N Y Acad Sci. 2004 Mar;1012:267-81. Review. Citation on PubMed Vassiliev ...

Genetics Home Reference: encephalocraniocutaneous lipomatosis

MedlinePlus

... PubMed or Free article on PubMed Central Hunter AG. Oculocerebrocutaneous and encephalocraniocutaneous lipomatosis syndromes: blind men and ... qualified healthcare professional . About Selection Criteria for Links Data Files & API Site Map Subscribe Customer Support USA. ...

Genetics Home Reference: vitiligo

MedlinePlus

... PubMed or Free article on PubMed Central Smith AG, Sturm RA. Multiple genes and locus interactions in ... qualified healthcare professional . About Selection Criteria for Links Data Files & API Site Map Subscribe Customer Support USA. ...

Genetics Home Reference: spina bifida

MedlinePlus

... PubMed or Free article on PubMed Central Bassuk AG, Kibar Z. Genetic basis of neural tube defects. ... qualified healthcare professional . About Selection Criteria for Links Data Files & API Site Map Subscribe Customer Support USA. ...

Genetics Home Reference: anencephaly

MedlinePlus

... PubMed or Free article on PubMed Central Bassuk AG, Kibar Z. Genetic basis of neural tube defects. ... qualified healthcare professional . About Selection Criteria for Links Data Files & API Site Map Subscribe Customer Support USA. ...

Physical Activity and Cancer

MedlinePlus

... 4003. [PubMed Abstract] Wolin KY, Yan Y, Colditz GA, Lee IM. Physical activity and colon cancer prevention: ... 505. [PubMed Abstract] Wolin KY, Yan Y, Colditz GA. Physical activity and risk of colon adenoma: a ...

Genetics Home Reference: GRACILE syndrome

MedlinePlus

... University of Utah Eccles Health Sciences Library: Iron Metabolism Patient Support and Advocacy Resources (1 link) Climb: National Information Centre for Metabolic Diseases Scientific Articles on PubMed (1 link) PubMed OMIM (1 link) ...

Oral Microbial Shift: Factors affecting the Microbiome and Prevention of Oral Disease.

PubMed

Dagli, Namrata; Dagli, Rushabh; Darwish, Shrouq; Baroudi, Kusai

2016-01-01

Recently, oral microbiome has gained popularity among scientists. Microorganisms are no longer considered as disease-producing pathogens, rather they are now considered as partners of human in maintaining health. Since ancient times, changes in our lifestyle have affected our microbiome and the balance with their human host has been perturbed. The present review includes the description about factors affecting oral microbiome and establishing symbiosis with the human host so that they contribute in maintaining health rather than eliciting diseases. A comprehensive literature search was performed on databases such as Google Scholar, PubMed and Medline until April 2015. First, articles were selected on the basis of their titles and then abstracts were screened and unwanted articles were excluded. Articles obtained from all the databases were checked and duplicate articles were removed. Articles obtained from various databases: PubMed = 35, Google Scholar=8. Out of these 43 articles, total 29 articles were finally selected for this review. The published literature suggests that the modern oral microbiome is less biodiverse, and possess more pathogenic bacterial species and lesser beneficial bacteria. The possible factors mainly responsible for this shift in microbiome were found to be change in diet, industrial revolution and indiscriminate use of antibiotics. Various changes in lifestyles have affected oral microbiome adversely and perturb the symbiosis between the microbiome and their hosts. The present oral microbiome is found to be less diverse and more pathogenic. The present review may be helpful in understanding the relationship between the microbiome and their human hosts so that microbiome contributes in maintaining healthy state of the body.

Gaps in affiliation indexing in Scopus and PubMed

PubMed Central

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

2016-01-01

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

Query Refinement: Negation Detection and Proximity Learning Georgetown at TREC 2014 Clinical Decision Support Track

DTIC Science & Technology

2014-11-01

created to serve as idealized representations of actual medical records, and include information such as medical history , current symptoms, diagnosis...NLM Medical Text Indexer (MTI).3 MeSH, or Medical Subject Headings, are terminology used by the NLM to index articles, catalog books, and searching...MeSH- indexed databases such as PubMed. However, since many medical conditions may be expressed in varying terminology , a single representation of a

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

PubMed

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

2017-04-13

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

Efficacy of botulinum toxins on bruxism: an evidence-based review.

PubMed

Long, Hu; Liao, Zhengyu; Wang, Yan; Liao, Lina; Lai, Wenli

2012-02-01

The objective of this study was to assess the efficacy of botulinum toxins on bruxism. Electronic databases (PubMed, Embase and Science Citation Index), websites (Cochrane Central Register of Controlled Trials and ClinicalTrials.gov) and the literature database of SIGLE (System for Information on Grey Literature in Europe) were searched from January 1990 to April 2011 for randomised controlled trials or nonrandomised studies assessing the efficacy of botulinum toxins on bruxism. There was no language restriction. Through a predefined search strategy, we retrieved 28 studies from PubMed, 94 from Embase, 60 from the Science Citation Index, two ongoing clinical trials and two from the Cochrane Central Register of Controlled Trials. Of these, only four studies met our inclusion criteria and were finally included. Of the four included studies, two were randomised controlled trials and two were controlled before-and-after studies. These studies showed that botulinum toxin injections can reduce the frequency of bruxism events, decrease bruxism-induced pain levels and satisfy patients' self-assessment with regard to the effectiveness of botulinum toxins on bruxism. In comparison with oral splint, botulinum toxins are equally effective on bruxism. Furthermore, botulinum toxin injections at a dosage of <100 U are safe for otherwise healthy patients. Botulinum toxin injections are effective on bruxism and are safe to use. Therefore, they can be used clinically for otherwise healthy patients with bruxism. © 2012 FDI World Dental Federation.

References that anyone can edit: review of Wikipedia citations in peer reviewed health science literature.

PubMed

Bould, M Dylan; Hladkowicz, Emily S; Pigford, Ashlee-Ann E; Ufholz, Lee-Anne; Postonogova, Tatyana; Shin, Eunkyung; Boet, Sylvain

2014-03-06

To examine indexed health science journals to evaluate the prevalence of Wikipedia citations, identify the journals that publish articles with Wikipedia citations, and determine how Wikipedia is being cited. Bibliometric analysis. Publications in the English language that included citations to Wikipedia were retrieved using the online databases Scopus and Web of Science. To identify health science journals, results were refined using Ulrich's database, selecting for citations from journals indexed in Medline, PubMed, or Embase. Using Thomson Reuters Journal Citation Reports, 2011 impact factors were collected for all journals included in the search. Resulting citations were thematically coded, and descriptive statistics were calculated. 1433 full text articles from 1008 journals indexed in Medline, PubMed, or Embase with 2049 Wikipedia citations were accessed. The frequency of Wikipedia citations has increased over time; most citations occurred after December 2010. More than half of the citations were coded as definitions (n = 648; 31.6%) or descriptions (n=482; 23.5%). Citations were not limited to journals with a low or no impact factor; the search found Wikipedia citations in many journals with high impact factors. Many publications are citing information from a tertiary source that can be edited by anyone, although permanent, evidence based sources are available. We encourage journal editors and reviewers to use caution when publishing articles that cite Wikipedia.

Assessment of quality of life in patients with laryngeal cancer: A review of articles.

PubMed

Kolator, Mateusz; Kolator, Patrycja; Zatoński, Tomasz

2018-04-19

This article presents a review of the medical literature published between 1994 and 2014 with the use of the PubMed database concerning quality-of-life instruments for head and neck cancer patients used to assess general well-being of patients with laryngeal cancer. The PubMed database was searched for articles containing the keywords "quality of life", "laryngeal neoplasm" and "questionnaires". The resulting articles were reviewed and analyzed. After the identification of questionnaires, an additional search was performed. The articles and questionnaires were described and analyzed. In 43 articles, the authors used questionnaires specific to the head and neck regions in order to assess the quality of life in patients with laryngeal cancer. Four different questionnaires were identified. The European Organization for Research and Treatment of Cancer (EORTC) questionnaire is most commonly used to assess the quality of life in patients with laryngeal cancer. Questionnaires are generally used in order to select from a range of different treatment methods. There are a few head and neck cancer-related quality-of-life instruments which are widely used to assess the quality of life in patients with laryngeal cancer, but they are not dedicated to that region of the body. Today, there is much more attention paid to the quality of life; therefore, there is a real need to develop specific scales for different types of cancer.

Evaluation of Role of Myofibroblasts in Oral Cancer: A Systematic Review.

PubMed

Sekhon, Harjeet K; Sircar, Keya; Kaur, Gurbani; Marwah, Muneet

2016-01-01

To conduct a systematic review on the role of myofibroblasts in progression of oral cancer. The myofibroblast is essential for the integrity of the mammalian body by virtue of its role in wound healing, but it also plays a negative role due to their role in promoting tumor development. Systematic review. Bibliographic searches were conducted in several electronic databases using all publications in PubMed, PubMed central, EMBASE, CancerLit, Google scholar, and Cochrane CCTR between 1990 and June 2015. The search of all publications from various electronic databases revealed 1,371 citations. The total number of studies considered for systematic review was 43. The total number of patients included in the studies was 990. Myofibroblasts are a significant component in stroma of oral cancer cases, though not identified in all cases. This systematic review shows that clinical, pathological, and immunohistochemistry tests have correlated the presence of high myofibroblast count in oral cancer cell stroma. Myofibroblasts play a significant role in oral cancer invasion and progression. Various studies have demonstrated their association with oral cancer. This review tends to highlight their role in the pathogenesis of oral cancer over the decade. Sekhon HK, Sircar K, Kaur G, Marwah M. Evaluation of Role of Myofibroblasts in Oral Cancer: A Systematic Review. Int J Clin Pediatr Dent 2016;9(3):233-239.

Obstructive sleep apnea and oral language disorders.

PubMed

Corrêa, Camila de Castro; Cavalheiro, Maria Gabriela; Maximino, Luciana Paula; Weber, Silke Anna Theresa

Children and adolescents with obstructive sleep apnea (OSA) may have consequences, such as daytime sleepiness and learning, memory, and attention disorders, that may interfere in oral language. To verify, based on the literature, whether OSA in children was correlated to oral language disorders. A literature review was carried out in the Lilacs, PubMed, Scopus, and Web of Science databases using the descriptors "Child Language" AND "Obstructive Sleep Apnea". Articles that did not discuss the topic and included children with other comorbidities rather than OSA were excluded. In total, no articles were found at Lilacs, 37 at PubMed, 47 at Scopus, and 38 at Web of Science databases. Based on the inclusion and exclusion criteria, six studies were selected, all published from 2004 to 2014. Four articles demonstrated an association between primary snoring/OSA and receptive language and four articles showed an association with expressive language. It is noteworthy that the articles used different tools and considered different levels of language. The late diagnosis and treatment of obstructive sleep apnea is associated with a delay in verbal skill acquisition. The professionals who work with children should be alert, as most of the phonetic sounds are acquired during ages 3-7 years, which is also the peak age for hypertrophy of the tonsils and childhood OSA. Copyright © 2016 Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial. Published by Elsevier Editora Ltda. All rights reserved.

Update on the treatment of narcolepsy: clinical efficacy of pitolisant

PubMed Central

Calik, Michael W

2017-01-01

Narcolepsy is a neurological disease that affects 1 in 2,000 individuals and is characterized by excessive daytime sleepiness (EDS). In 60–70% of individuals with narcolepsy, it is also characterized by cataplexy or a sudden loss of muscle tone that is triggered by positive or negative emotions. Narcolepsy decreases the quality of life of the afflicted individuals. Currently used drugs treat EDS alone (modafinil/armodafinil, methylphenidate, and amphetamine), cataplexy alone (“off-label” use of antidepressants), or both EDS and cataplexy (sodium oxybate). These drugs have abuse, tolerability, and adherence issues. A greater diversity of drug options is needed to treat narcolepsy. The small molecule drug, pitolisant, acts as an inverse agonist/antagonist at the H3 receptor, thus increasing histaminergic tone in the wake promoting system of the brain. Pitolisant has been studied in animal models of narcolepsy and used in clinical trials as a treatment for narcolepsy. A comprehensive search of online databases (eg, Medline, PubMed, EMBASE, the Cochrane Library Database, Ovid MEDLINE, Europe PubMed Central, EBSCOhost CINAHL, ProQuest Research Library, Google Scholar, and ClinicalTrials.gov) was performed. Nonrandomized and randomized studies were included. This review focuses on the outcomes of four clinical trials of pitolisant to treat narcolepsy. These four trials show that pitolisant is an effective drug to treat EDS and cataplexy in narcolepsy. PMID:28490912

Testing search strategies for systematic reviews in the Medline literature database through PubMed.

PubMed

Volpato, Enilze S N; Betini, Marluci; El Dib, Regina

2014-04-01

A high-quality electronic search is essential in ensuring accuracy and completeness in retrieved records for the conducting of a systematic review. We analysed the available sample of search strategies to identify the best method for searching in Medline through PubMed, considering the use or not of parenthesis, double quotation marks, truncation and use of a simple search or search history. In our cross-sectional study of search strategies, we selected and analysed the available searches performed during evidence-based medicine classes and in systematic reviews conducted in the Botucatu Medical School, UNESP, Brazil. We analysed 120 search strategies. With regard to the use of phrase searches with parenthesis, there was no difference between the results with and without parenthesis and simple searches or search history tools in 100% of the sample analysed (P = 1.0). The number of results retrieved by the searches analysed was smaller using double quotations marks and using truncation compared with the standard strategy (P = 0.04 and P = 0.08, respectively). There is no need to use phrase-searching parenthesis to retrieve studies; however, we recommend the use of double quotation marks when an investigator attempts to retrieve articles in which a term appears to be exactly the same as what was proposed in the search form. Furthermore, we do not recommend the use of truncation in search strategies in the Medline via PubMed. Although the results of simple searches or search history tools were the same, we recommend using the latter.

PubMed search strategies for the identification of etiologic associations between hypothalamic-pituitary disorders and other medical conditions.

PubMed

Guaraldi, Federica; Grottoli, Silvia; Arvat, Emanuela; Mattioli, Stefano; Ghigo, Ezio; Gori, Davide

2013-12-01

Biomedical literature has enormously grown in the last decades and become broadly available through online databases. Ad-hoc search methods, created on the basis of research field and goals, are required to enhance the quality of searching. Aim of this study was to formulate efficient, evidence-based PubMed search strategies to retrieve articles assessing etiologic associations between a condition of interest and hypothalamic-pituitary disorders (HPD). Based on expert knowledge, 17 MeSH (Medical Subjects Headings) and 79 free terms related to HPD were identified to search PubMed. Using random samples of abstracts retrieved by each term, we estimated the proportion of articles containing pertinent information and formulated two strings (one more specific, one more sensitive) for the detection of articles focusing on the etiology of HPD, that were then applied to retrieve articles identifying possible etiologic associations between HPD and three diseases (malaria, LHON and celiac disease) considered not associated to HPD, and define the number of abstracts needed to read (NNR) to find one potentially pertinent article. We propose two strings: one sensitive string derived from the combination of articles providing the largest literature coverage in the field and one specific including combined terms retrieving ≥40% of potentially pertinent articles. NNR were 2.1 and 1.6 for malaria, 3.36 and 2.29 for celiac disease, 2.8 and 2.2 for LHON, respectively. For the first time, two reliable, readily applicable strings are proposed for the retrieval of medical literature assessing putative etiologic associations between HPD and other medical conditions of interest.

Genetics Home Reference: chylomicron retention disease

MedlinePlus

... PubMed Charcosset M, Sassolas A, Peretti N, Roy CC, Deslandres C, Sinnett D, Levy E, Lachaux A. ... Epub 2007 Oct 22. Citation on PubMed Shoulders CC, Naoumova RP. The genes and proteins of atherogenic ...

Radon and Cancer

MedlinePlus

... in the Danish study: another source of dose. Health Physics 2009; 97(4):343–347. [PubMed Abstract] Krewski ... radiation and leukemia risk among German uranium miners. Health Physics 2010; 99(3):314–321. [PubMed Abstract] National ...

Genetics Home Reference: Kleefstra syndrome

MedlinePlus

... PubMed Kleefstra T, Brunner HG, Amiel J, Oudakker AR, Nillesen WM, Magee A, Geneviève D, Cormier-Daire ... PubMed Kleefstra T, Smidt M, Banning MJ, Oudakker AR, Van Esch H, de Brouwer AP, Nillesen W, ...

Genetics Home Reference: adenylosuccinate lyase deficiency

MedlinePlus

... its chemical cousin RNA, and molecules such as ATP that serve as energy sources in the cell. ... For People With Intellectual and Developmental Disabilities Scientific Articles on PubMed (1 link) PubMed OMIM (1 link) ...

Genetics Home Reference: histiocytosis-lymphadenopathy plus syndrome

MedlinePlus

... its chemical cousin RNA, and molecules such as ATP and GTP, which serve as energy sources in ... Skin Association Histiocytosis Association: Rosai-Dorfman Disease Scientific Articles on PubMed (1 link) PubMed OMIM (1 link) ...

Genetics Home Reference: Arts syndrome

MedlinePlus

... its chemical cousin RNA, and molecules such as ATP and GTP that serve as energy sources in ... Syndrome ClinicalTrials.gov (1 link) ClinicalTrials.gov Scientific Articles on PubMed (1 link) PubMed OMIM (1 link) ...

Genetics Home Reference: Liebenberg syndrome

MedlinePlus

... changes affect regions of DNA known as regulatory elements, which help turn on or turn off genes ( ... Citation on PubMed or Free article on PubMed Central Seoighe DM, Gadancheva V, Regan R, McDaid J, ...

Genetics Home Reference: familial atrial fibrillation

MedlinePlus

... genes provide instructions for making parts of structural elements of cardiac muscle, such as sarcomeres. These structures ... Citation on PubMed or Free article on PubMed Central Hucker WJ, Saini H, Lubitz SA, Ellinor PT. ...

Genetics Home Reference: molybdenum cofactor deficiency

MedlinePlus

... called molybdenum cofactor. Molybdenum cofactor, which contains the element molybdenum, is essential to the function of several ... Citation on PubMed or Free article on PubMed Central Reiss J, Gross-Hardt S, Christensen E, Schmidt P, ...

Genetics Home Reference: motion sickness

MedlinePlus

... motion, particularly traveling in a car, bus, train, airplane, or boat. Amusement park rides, skiing, and virtual ... Association ClinicalTrials.gov (1 link) ClinicalTrials.gov Scientific Articles on PubMed (1 link) PubMed OMIM (1 link) ...

Genetics Home Reference: Chediak-Higashi syndrome

MedlinePlus

... 68(2):283-303. Review. Citation on PubMed Kaplan J, De Domenico I, Ward DM. Chediak-Higashi ... 22. Citation on PubMed Ward DM, Shiflett SL, Kaplan J. Chediak-Higashi syndrome: a clinical and molecular ...

Genetics Home Reference: craniofacial microsomia

MedlinePlus

... nlm.nih.gov/books/NBK5199/ Citation on PubMed Johnson JM, Moonis G, Green GE, Carmody R, Burbank ... Epub 2010 Mar 18. Review. Citation on PubMed Johnson JM, Moonis G, Green GE, Carmody R, Burbank ...

Genetics Home Reference: multiple familial trichoepithelioma

MedlinePlus

... 13. Citation on PubMed Bowen S, Gill M, Lee DA, Fisher G, Geronemus RG, Vazquez ME, Celebi JT. ... Fernandez-Figueras, Maria Tereza]. Citation on PubMed Lee DA, Grossman ME, Schneiderman P, Celebi JT. Genetics of ...

Genetics Home Reference: Brooke-Spiegler syndrome

MedlinePlus

... article on PubMed Central Bowen S, Gill M, Lee DA, Fisher G, Geronemus RG, Vazquez ME, Celebi JT. ... 124(5):919-20. Citation on PubMed Lee DA, Grossman ME, Schneiderman P, Celebi JT. Genetics of ...

Genetics Home Reference: Pelizaeus-Merzbacher disease

MedlinePlus

... 2004 Dec 31. Review. Citation on PubMed Laukka JJ, Kamholz J, Bessert D, Skoff RP. Novel pathologic ... 59-65. Citation on PubMed Sarret C, Lemaire JJ, Tonduti D, Sontheimer A, Coste J, Pereira B, ...

Genetics Home Reference: Hermansky-Pudlak syndrome

MedlinePlus

... PUDLAK SYNDROME 1 Sources for This Page Bultema JJ, Ambrosio AL, Burek CL, Di Pietro SM. BLOC- ... PubMed or Free article on PubMed Central Bultema JJ, Di Pietro SM. Cell type-specific Rab32 and ...

Genetics Home Reference: lissencephaly with cerebellar hypoplasia

MedlinePlus

... on PubMed or Free article on PubMed Central Ross ME, Swanson K, Dobyns WB. Lissencephaly with cerebellar ... AA, Abdel-Salam G, Koeller HB, Ilkin Y, Ross ME, Dobyns WB, Gleeson JG. Identification of a ...

Information-seeking behavior changes in community-based teaching practices.

PubMed

Byrnes, Jennifer A; Kulick, Tracy A; Schwartz, Diane G

2004-07-01

A National Library of Medicine information access grant allowed for a collaborative project to provide computer resources in fourteen clinical practice sites that enabled health care professionals to access medical information via PubMed and the Internet. Health care professionals were taught how to access quality, cost-effective information that was user friendly and would result in improved patient care. Selected sites were located in medically underserved areas and received a computer, a printer, and, during year one, a fax machine. Participants were provided dial-up Internet service or were connected to the affiliated hospital's network. Clinicians were trained in how to search PubMed as a tool for practicing evidence-based medicine and to support clinical decision making. Health care providers were also taught how to find patient-education materials and continuing education programs and how to network with other professionals. Prior to the training, participants completed a questionnaire to assess their computer skills and familiarity with searching the Internet, MEDLINE, and other health-related databases. Responses indicated favorable changes in information-seeking behavior, including an increased frequency in conducting MEDLINE searches and Internet searches for work-related information.

Diagnostic Features of Common Oral Ulcerative Lesions: An Updated Decision Tree

PubMed Central

Safi, Yaser

2016-01-01

Diagnosis of oral ulcerative lesions might be quite challenging. This narrative review article aims to introduce an updated decision tree for diagnosing oral ulcerative lesions on the basis of their diagnostic features. Various general search engines and specialized databases including PubMed, PubMed Central, Medline Plus, EBSCO, Science Direct, Scopus, Embase, and authenticated textbooks were used to find relevant topics by means of MeSH keywords such as “oral ulcer,” “stomatitis,” and “mouth diseases.” Thereafter, English-language articles published since 1983 to 2015 in both medical and dental journals including reviews, meta-analyses, original papers, and case reports were appraised. Upon compilation of the relevant data, oral ulcerative lesions were categorized into three major groups: acute, chronic, and recurrent ulcers and into five subgroups: solitary acute, multiple acute, solitary chronic, multiple chronic, and solitary/multiple recurrent, based on the number and duration of lesions. In total, 29 entities were organized in the form of a decision tree in order to help clinicians establish a logical diagnosis by stepwise progression. PMID:27781066

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

PubMed

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

2015-10-01

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

Biomedical research platforms and their influence on article submissions and journal rankings: An update.

PubMed Central

Lippi, Giuseppe; Favaloro, Emmanuel J; Simundic, Ana-Maria

2012-01-01

After being indexed in 2006 in EMBASE/Excerpta Medica and Scopus, and later in Science Citation Index Expanded and Journal Citation Reports/Science Edition citation databases, Biochemia Medica launched a new web page and online manuscript submission system in 2010, and celebrated its first Impact Factor in the same year. Now, starting from the end of the 2011, the journal will also be indexed in PubMed/Medline, and this will contribute to increase the journal’s exposure and accessibility worldwide. This is an important breakthrough, which is expected to further increase the popularity of the journal, as well as the submission rate and citations. Although several tools are currently available as Web resources to retrieve scientific articles, whose functioning and basic criteria are thought to be rather similar, the functionality, coverage, notoriety and prominence may differ widely. The recent indexing of Biochemia Medica in PubMed/Medline has thereby given us the opportunity to provide a timely update on biomedical research platforms, their relationship with article submissions and journal rankings. PMID:22384515

Sensitivity and predictive value of 15 PubMed search strategies to answer clinical questions rated against full systematic reviews.

PubMed

Agoritsas, Thomas; Merglen, Arnaud; Courvoisier, Delphine S; Combescure, Christophe; Garin, Nicolas; Perrier, Arnaud; Perneger, Thomas V

2012-06-12

Clinicians perform searches in PubMed daily, but retrieving relevant studies is challenging due to the rapid expansion of medical knowledge. Little is known about the performance of search strategies when they are applied to answer specific clinical questions. To compare the performance of 15 PubMed search strategies in retrieving relevant clinical trials on therapeutic interventions. We used Cochrane systematic reviews to identify relevant trials for 30 clinical questions. Search terms were extracted from the abstract using a predefined procedure based on the population, interventions, comparison, outcomes (PICO) framework and combined into queries. We tested 15 search strategies that varied in their query (PIC or PICO), use of PubMed's Clinical Queries therapeutic filters (broad or narrow), search limits, and PubMed links to related articles. We assessed sensitivity (recall) and positive predictive value (precision) of each strategy on the first 2 PubMed pages (40 articles) and on the complete search output. The performance of the search strategies varied widely according to the clinical question. Unfiltered searches and those using the broad filter of Clinical Queries produced large outputs and retrieved few relevant articles within the first 2 pages, resulting in a median sensitivity of only 10%-25%. In contrast, all searches using the narrow filter performed significantly better, with a median sensitivity of about 50% (all P < .001 compared with unfiltered queries) and positive predictive values of 20%-30% (P < .001 compared with unfiltered queries). This benefit was consistent for most clinical questions. Searches based on related articles retrieved about a third of the relevant studies. The Clinical Queries narrow filter, along with well-formulated queries based on the PICO framework, provided the greatest aid in retrieving relevant clinical trials within the 2 first PubMed pages. These results can help clinicians apply effective strategies to answer their questions at the point of care.

Health Technology Assessment in nursing: a literature review.

PubMed

Ramacciati, N

2013-03-01

The Health Technology Assessment (HTA) approach, which provides scientific support for the decisions taken within the health field, is of increasing importance worldwide. In a context of limited resources, HTA has the potential of being an efficient tool for addressing the sustainability problems and the allocation choices arising from the constant increase in demand. This study aims to investigate HTA use in nursing, both in terms of quantifying HTA evaluations of nursing phenomena which have been conducted and in terms of the extent to which nursing has used the HTA approach. The Italian context has been analysed because of the growing diffusion of the HTA in Italy along with the recent developments in the nursing profession. A narrative review of international literature was undertaken using the following databases: HTA, PubMed, CINAHL, ILISI. Seventy evaluation studies on nursing were identified from the HTA database (1.12% of all studies in the database). The areas of nursing intervention and the country of origin of the studies were identified. Two nursing studies on the HTA approach were found in the PubMed, CINAHL and HTA databases. The first focused on the evaluation of nursing technology process and analysed 126 studies in six main thematic areas; the second was a systematic review on HTA in nursing and analysed 192 studies (46 meta-analyses, 31 Finnish primary studies, 117 international primary studies). Three Italian studies were identified from the ILISI database and Italian grey literature. In the international literature, although analyses regarding the efficacy of nursing interventions have been conducted, there are to date very few research projects that focus exclusively on the HTA process as applied to nursing. The recent development of a standardized nursing language coupled with the open debate as to which research method (qualitative vs. quantitative) best serves to 'read' nursing phenomena may explain the scarce diffusion of HTA in the field of nursing. © 2012 The Author. International Nursing Review © 2012 International Council of Nurses.

Genetics Home Reference: atelosteogenesis type 2

MedlinePlus

... 49-53. Review. Citation on PubMed or Free article on PubMed Central Rossi A, Superti-Furga A. Mutations in the diastrophic dysplasia sulfate transporter (DTDST) gene (SLC26A2): 22 novel mutations, mutation review, associated skeletal ...

Genetics Home Reference: CLN1 disease

MedlinePlus

... 10.1172/JCI33482. Citation on PubMed or Free article on PubMed Central Kollmann K, Uusi-Rauva K, Scifo E, Tyynelä J, Jalanko A, Braulke T. Cell biology and function of neuronal ceroid lipofuscinosis-related proteins. ...

Genetics Home Reference: SATB2-associated syndrome

MedlinePlus

... factor Satb2 interacts with matrix attachment region DNA elements in a tissue-specific manner and demonstrates cell- ... Citation on PubMed or Free article on PubMed Central Britanova O, de Juan Romero C, Cheung A, ...

Genetics Home Reference: isolated Pierre Robin sequence

MedlinePlus

... PG, Fitzpatrick DR, Lyonnet S. Highly conserved non-coding elements on either side of SOX9 associated with Pierre ... Citation on PubMed or Free article on PubMed Central Jakobsen LP, Ullmann R, Christensen SB, Jensen KE, ...

Genetics Home Reference: neuroblastoma

MedlinePlus

... 2008 Oct 16;455(7215):967-70. doi: 10.1038/nature07398. Citation on PubMed Maris JM. Recent advances ... 2008 Oct 16;455(7215):930-5. doi: 10.1038/nature07261. Epub 2008 Aug 24. Citation on PubMed ...

Genetics Home Reference: gestational diabetes

MedlinePlus

... 2012 Jan 10. Citation on PubMed or Free article on PubMed Central Lowe WL Jr, Scholtens DM, Sandler V, Hayes MG. Genetics of Gestational Diabetes Mellitus and Maternal Metabolism. Curr Diab Rep. 2016 Feb;16(2):15. ...

Genetics Home Reference: glutathione synthetase deficiency

MedlinePlus

... Ristoff E, Larsson A. Inborn errors in the metabolism of glutathione. Orphanet J Rare Dis. 2007 Mar 30;2:16. Review. Citation on PubMed or Free article on PubMed Central Wu G, Fang YZ, Yang S, ...

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

Retrieval of diagnostic and treatment studies for clinical use through PubMed and PubMed's Clinical Queries filters.

PubMed

Lokker, Cynthia; Haynes, R Brian; Wilczynski, Nancy L; McKibbon, K Ann; Walter, Stephen D

2011-01-01

Clinical Queries filters were developed to improve the retrieval of high-quality studies in searches on clinical matters. The study objective was to determine the yield of relevant citations and physician satisfaction while searching for diagnostic and treatment studies using the Clinical Queries page of PubMed compared with searching PubMed without these filters. Forty practicing physicians, presented with standardized treatment and diagnosis questions and one question of their choosing, entered search terms which were processed in a random, blinded fashion through PubMed alone and PubMed Clinical Queries. Participants rated search retrievals for applicability to the question at hand and satisfaction. For treatment, the primary outcome of retrieval of relevant articles was not significantly different between the groups, but a higher proportion of articles from the Clinical Queries searches met methodologic criteria (p=0.049), and more articles were published in core internal medicine journals (p=0.056). For diagnosis, the filtered results returned more relevant articles (p=0.031) and fewer irrelevant articles (overall retrieval less, p=0.023); participants needed to screen fewer articles before arriving at the first relevant citation (p<0.05). Relevance was also influenced by content terms used by participants in searching. Participants varied greatly in their search performance. Clinical Queries filtered searches returned more high-quality studies, though the retrieval of relevant articles was only statistically different between the groups for diagnosis questions. Retrieving clinically important research studies from Medline is a challenging task for physicians. Methodological search filters can improve search retrieval.

Kefir and Cancer: A Systematic Review of Literatures.

PubMed

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

2015-12-01

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

Genetics Home Reference: spastic paraplegia type 3A

MedlinePlus

... on PubMed or Free article on PubMed Central Blackstone C. Cellular pathways of hereditary spastic paraplegia. Annu ... PP, Soderblom C, Tao-Cheng JH, Stadler J, Blackstone C. SPG3A protein atlastin-1 is enriched in ...

Genetics Home Reference: microphthalmia with linear skin defects syndrome

MedlinePlus

... oxidative phosphorylation , by which mitochondria generate adenosine triphosphate (ATP), the cell's main energy source. It also plays ... Syndrome ClinicalTrials.gov (1 link) ClinicalTrials.gov Scientific Articles on PubMed (1 link) PubMed OMIM (1 link) ...

Genetics Home Reference: cytogenetically normal acute myeloid leukemia

MedlinePlus

... on PubMed Marcucci G, Haferlach T, Döhner H. Molecular genetics of adult acute myeloid leukemia: prognostic and therapeutic ... on PubMed Sanders MA, Valk PJ. The evolving molecular genetic landscape in acute myeloid leukaemia. Curr Opin Hematol. ...

Genetics Home Reference: Holt-Oram syndrome

MedlinePlus

... PubMed OMIM: HOLT-ORAM SYNDROME Hatcher CJ, McDermott DA. Using the TBX5 transcription factor to grow and ... 2002;67:115-20. Citation on PubMed McDermott DA, Bressan MC, He J, Lee JS, Aftimos S, Brueckner ...

Genetics Home Reference: alpha-1 antitrypsin deficiency

MedlinePlus

... 27(3):274-81. Review. Citation on PubMed de Serres FJ, Blanco I, Fernández-Bustillo E. Estimated ... 9. Epub 2006 Sep 27. Citation on PubMed de Serres FJ, Blanco I, Fernández-Bustillo E. Estimating ...

Genetics Home Reference: Imerslund-Gräsbeck syndrome

MedlinePlus

... 1172-7-56. Citation on PubMed or Free article on PubMed Central Watkins D, Rosenblatt DS. Lessons in biology from patients with inborn errors of vitamin B12 metabolism. Biochimie. 2013 May;95(5):1019-22. doi: ...

A systematic review of pseudophakic monovision for presbyopia correction

PubMed Central

Labiris, Georgios; Toli, Aspa; Perente, Aslin; Ntonti, Panagiota; Kozobolis, Vassilios P.

2017-01-01

A systematic review of the recent literature regarding pseudophakic monovision as a reliable methods for presbyopia correction was performed based on the PubMed, MEDLINE, Nature and the American Academy of Ophthalmology databases in July 2015 and data from 18 descriptive and 12 comparative studies were included in this narrative review. Pseudophakic monosvision seems to be an effective method for presbyopia with high rates of spectacles independence and minimal dysphotopsia side-effects, that should be considered by the modern cataract surgeons. PMID:28730093

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

PubMed Central

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

2017-01-01

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

Causal Reasoning on Biological Networks: Interpreting Transcriptional Changes

NASA Astrophysics Data System (ADS)

Chindelevitch, Leonid; Ziemek, Daniel; Enayetallah, Ahmed; Randhawa, Ranjit; Sidders, Ben; Brockel, Christoph; Huang, Enoch

Over the past decade gene expression data sets have been generated at an increasing pace. In addition to ever increasing data generation, the biomedical literature is growing exponentially. The PubMed database (Sayers et al., 2010) comprises more than 20 million citations as of October 2010. The goal of our method is the prediction of putative upstream regulators of observed expression changes based on a set of over 400,000 causal relationships. The resulting putative regulators constitute directly testable hypotheses for follow-up.

A systematic review of teleophthalmological studies in Europe

PubMed Central

Labiris, Georgios; Panagiotopoulou, Eirini-Kanella; Kozobolis, Vassilios P.

2018-01-01

A systematic review of the recent literature regarding a series of ocular diseases involved in European telemedicine projects was performed based on the PubMed, Google Scholar and Springer databases in June 2017. Literature review returned 44 eligible studies; among them, emergency ophthalmology, diabetic retinopathy, glaucoma, age-related macular disease, cataract and retinopathy of prematurity. The majority of studies indicate teleophthalmology as a valid, reliable and cost-efficient method for care-provision in ophthalmology patients which delivers comparable outcomes to the traditional examination methods. PMID:29487825

Genetics Home Reference: isolated sulfite oxidase deficiency

MedlinePlus

... Metabolic Disorders (CLIMB) March of Dimes: Amino Acid Metabolism Disorders The Compassionate Friends GeneReviews (1 link) Isolated Sulfite Oxidase Deficiency ClinicalTrials.gov (1 link) ClinicalTrials.gov Scientific Articles on PubMed (1 link) PubMed OMIM (1 link) ...

Genetics Home Reference: arginine:glycine amidinotransferase deficiency

MedlinePlus

... amidinotransferase deficiency: the third inborn error of creatine metabolism in humans. Am J Hum Genet. 2001 Nov;69(5):1127-33. Epub 2001 Sep 10. Citation on PubMed or Free article on PubMed Central Nasrallah F, Feki M, Kaabachi ...

Genetics Home Reference: neuroferritinopathy

MedlinePlus

... J. Neuroferritinopathy: a new inborn error of iron metabolism. Neurogenetics. 2012 Feb;13(1):93-6. doi: 10.1007/s10048-011-0310-9. Epub 2012 Jan 26. Citation on PubMed or Free article on PubMed Central Keogh MJ, Morris CM, Chinnery ...

[Taehan Kan Hakhoe Chi (The Korean Journal of Hepatology) and Index Medicus (Medline/PubMed)].

PubMed

Lee, Dong Hoo

2003-03-01

It is our great pleasure to announce that the Taehan Kan Hakhoe Chi (The Korean Journal of Hepatology) was approved for listing, from 2002, in the Index Medicus, Medline/PubMed of the National Library of Medicine, NIH of USA. Herein, I review the searching tools employing a Medical Subject Heading (MeSH) such as liver disease and liver neoplasm or an author index for this Journal in the PubMed at a website. Of course, The Korean Journal of Hepatology should be continually striving to be upgraded. Dream comes true.

Data regarding articles retracted from PubMed indexed dental journals from India.

PubMed

Shamim, Thorakkal

2018-06-01

This data aimed to audit the articles retracted from PubMed indexed dental journals from India. The PubMed indexed journals considered are Indian Journal of Dental research, Journal of Indian Society of Periodontology, Contemporary Clinical Dentistry, Journal of Indian Society of Pedodontics and Preventive Dentistry, Journal of Oral and Maxillofacial Pathology and Journal of Indian Prosthodontic Society for type of article, name of dental specialty, topic of individual dental specialties, causes for retraction of article and authorship trend of retracted articles using web-based search. Among PubMed indexed Indian dental journals,the number of retracted articles were as follows: Indian Journal of Dental research (4) followed by Journal of Indian Society of Periodontology (3), Contemporary Clinical Dentistry (3), Journal of Indian Society of Pedodontics and Preventive Dentistry (2), Journal of Oral and Maxillofacial Pathology (2) and Journal of Indian Prosthodontic Society (1). Out of 15 retracted articles from PubMed indexed Indian dental journals, case reports (7) form a major share followed by original articles(6) and review articles (2). Among the dental specialties of retracted articles, oral pathology and microbiology (5) constitute the major share followed by periodontics (4), pedodontics (4), oral medicine and radiology (1) and prosthodontics (1). Duplicate publication (7), plagiarism (5) and authorship dispute (3) are the causes for the retraction of article.

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.

Combining PubMed knowledge and EHR data to develop a weighted bayesian network for pancreatic cancer prediction.

PubMed

Zhao, Di; Weng, Chunhua

2011-10-01

In this paper, we propose a novel method that combines PubMed knowledge and Electronic Health Records to develop a weighted Bayesian Network Inference (BNI) model for pancreatic cancer prediction. We selected 20 common risk factors associated with pancreatic cancer and used PubMed knowledge to weigh the risk factors. A keyword-based algorithm was developed to extract and classify PubMed abstracts into three categories that represented positive, negative, or neutral associations between each risk factor and pancreatic cancer. Then we designed a weighted BNI model by adding the normalized weights into a conventional BNI model. We used this model to extract the EHR values for patients with or without pancreatic cancer, which then enabled us to calculate the prior probabilities for the 20 risk factors in the BNI. The software iDiagnosis was designed to use this weighted BNI model for predicting pancreatic cancer. In an evaluation using a case-control dataset, the weighted BNI model significantly outperformed the conventional BNI and two other classifiers (k-Nearest Neighbor and Support Vector Machine). We conclude that the weighted BNI using PubMed knowledge and EHR data shows remarkable accuracy improvement over existing representative methods for pancreatic cancer prediction. Copyright © 2011 Elsevier Inc. All rights reserved.

Combining PubMed Knowledge and EHR Data to Develop a Weighted Bayesian Network for Pancreatic Cancer Prediction

PubMed Central

Zhao, Di; Weng, Chunhua

2011-01-01

In this paper, we propose a novel method that combines PubMed knowledge and Electronic Health Records to develop a weighted Bayesian Network Inference (BNI) model for pancreatic cancer prediction. We selected 20 common risk factors associated with pancreatic cancer and used PubMed knowledge to weigh the risk factors. A keyword-based algorithm was developed to extract and classify PubMed abstracts into three categories that represented positive, negative, or neutral associations between each risk factor and pancreatic cancer. Then we designed a weighted BNI model by adding the normalized weights into a conventional BNI model. We used this model to extract the EHR values for patients with or without pancreatic cancer, which then enabled us to calculate the prior probabilities for the 20 risk factors in the BNI. The software iDiagnosis was designed to use this weighted BNI model for predicting pancreatic cancer. In an evaluation using a case-control dataset, the weighted BNI model significantly outperformed the conventional BNI and two other classifiers (k-Nearest Neighbor and Support Vector Machine). We conclude that the weighted BNI using PubMed knowledge and EHR data shows remarkable accuracy improvement over existing representative methods for pancreatic cancer prediction. PMID:21642013

Agreement between Medline searches using the Medline-CD-Rom and Internet Pubmed, BioMedNet, Medscape and Gateway search-engines.

PubMed

Caro-Rojas, Rosa Angela; Eslava-Schmalbach, Javier H

2005-01-01

To compare the information obtained from the Medline database using Internet commercial search engines with that obtained from a compact disc (Medline-CD). An agreement study was carried out based on 101 clinical scenarios provided by specialists in internal medicine, pharmacy, gynaecology-obstetrics, surgery and paediatrics. 175 search strategies were employed using the connector AND plus text within quotation marks. The search was limited to 1991-1999. Internet search-engines were selected by common criteria. Identical search strategies were independently applied to and masked from Internet search engines, as well as the Medline-CD. 3,488 articles were obtained using 129 search strategies. Agreement with the Medline-CD was 54% for PubMed, 57% for Gateway, 54% for Medscape and 65% for BioMedNet. The highest agreement rate for a given speciality (paediatrics) was 78.1% for BioMedNet, having greater -/- than +/+ agreement. Even though free access to Medline has encouraged the boom and growth of evidence-based medicine, these results must be considered within the context of which search engine was selected for doing the searches. The Internet search engines studied showed a poor agreement with the Medline-CD, the rate of agreement differing according to speciality, thus significantly affecting searches and their reproducibility. Software designed for conducting Medline database searches, including the Medline-CD, must be standardised and validated.

Genetics Home Reference: Cohen syndrome

MedlinePlus

... complex and directs neurite outgrowth. J Biol Chem. 2015 Feb 6;290(6):3349-58. doi: 10.1074/jbc.M114.608174. Epub 2014 Dec 9. Citation on PubMed or Free article on PubMed Central Wang H, Falk MJ, Wensel C, Traboulsi EI. Cohen ...

Genetics Home Reference: congenital hemidysplasia with ichthyosiform erythroderma and limb defects

MedlinePlus

... lesions. Arch Dermatol. 2006 Mar;142(3):348-51. Citation on PubMed Herman GE. Disorders of cholesterol ... Genet A. 2003 Oct 15;122A(3):246-51. Citation on PubMed Kaminska-Winciorek G, Brzezinska-Wcisło ...

Genetics Home Reference: Ohdo syndrome, Say-Barber-Biesecker-Young-Simpson variant

MedlinePlus

... Bean LJH, Bird TD, Ledbetter N, Mefford HC, Smith RJH, Stephens K, editors. GeneReviews® [Internet]. Seattle (WA): ... PubMed or Free article on PubMed Central Clayton-Smith J, O'Sullivan J, Daly S, Bhaskar S, Day R, ...

Genetics Home Reference: cerebral folate transport deficiency

MedlinePlus

... a treatable neurodegenerative disorder associated with disturbed myelin metabolism. Am J Hum Genet. 2009 Sep;85(3):354-63. doi: 10.1016/j.ajhg.2009.08.005. Citation on PubMed or Free article on PubMed Central Toelle SP, Wille D, Schmitt ...

Definition of the Mediterranean Diet; a Literature Review.

PubMed

Davis, Courtney; Bryan, Janet; Hodgson, Jonathan; Murphy, Karen

2015-11-05

Numerous studies over several decades suggest that following the Mediterranean diet (MedDiet) can reduce the risk of cardiovascular disease and cancer, and improve cognitive health. However, there are inconsistencies among methods used for evaluating and defining the MedDiet. Through a review of the literature, we aimed to quantitatively define the MedDiet by food groups and nutrients. Databases PubMed, MEDLINE, Science Direct, Academic Search Premier and the University of South Australia Library Catalogue were searched. Articles were included if they defined the MedDiet in at least two of the following ways: (1) general descriptive definitions; (2) diet pyramids/numbers of servings of key foods; (3) grams of key foods/food groups; and (4) nutrient and flavonoid content. Quantity of key foods and nutrient content was recorded and the mean was calculated. The MedDiet contained three to nine serves of vegetables, half to two serves of fruit, one to 13 serves of cereals and up to eight serves of olive oil daily. It contained approximately 9300 kJ, 37% as total fat, 18% as monounsaturated and 9% as saturated, and 33 g of fibre per day. Our results provide a defined nutrient content and range of servings for the MedDiet based on past and current literature. More detailed reporting amongst studies could refine the definition further.

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

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

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

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 themore » 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.« less

MeSHy: Mining unanticipated PubMed information using frequencies of occurrences and concurrences of MeSH terms.

PubMed

Theodosiou, T; Vizirianakis, I S; Angelis, L; Tsaftaris, A; Darzentas, N

2011-12-01

PubMed is the most widely used database of biomedical literature. To the detriment of the user though, the ranking of the documents retrieved for a query is not content-based, and important semantic information in the form of assigned Medical Subject Headings (MeSH) terms is not readily presented or productively utilized. The motivation behind this work was the discovery of unanticipated information through the appropriate ranking of MeSH term pairs and, indirectly, documents. Such information can be useful in guiding novel research and following promising trends. A web-based tool, called MeSHy, was developed implementing a mainly statistical algorithm. The algorithm takes into account the frequencies of occurrences, concurrences, and the semantic similarities of MeSH terms in retrieved PubMed documents to create MeSH term pairs. These are then scored and ranked, focusing on their unexpectedly frequent or infrequent occurrences. MeSHy presents results through an online interactive interface facilitating further manipulation through filtering and sorting. The results themselves include the MeSH term pairs, along with MeSH categories, the score, and document IDs, all of which are hyperlinked for convenience. To highlight the applicability of the tool, we report the findings of an expert in the pharmacology field on querying the molecularly-targeted drug imatinib and nutrition-related flavonoids. To the best of our knowledge, MeSHy is the first publicly available tool able to directly provide such a different perspective on the complex nature of published work. Implemented in Perl and served by Apache2 at http://bat.ina.certh.gr/tools/meshy/ with all major browsers supported. Copyright © 2011 Elsevier Inc. All rights reserved.

Methodological quality evaluation of systematic reviews or meta-analyses on ERCC1 in non-small cell lung cancer: a systematic review.

PubMed

Tao, Huan; Zhang, Yueyuan; Li, Qian; Chen, Jin

2017-11-01

To assess the methodological quality of systematic reviews (SRs) or meta-analysis concerning the predictive value of ERCC1 in platinum chemotherapy of non-small cell lung cancer. We searched the PubMed, EMbase, Cochrane library, international prospective register of systematic reviews, Chinese BioMedical Literature Database, China National Knowledge Infrastructure, Wan Fang and VIP database for SRs or meta-analysis. The methodological quality of included literatures was evaluated by risk of bias in systematic review (ROBIS) scale. Nineteen eligible SRs/meta-analysis were included. The most frequently searched databases were EMbase (74%), PubMed, Medline and CNKI. Fifteen SRs did additional retrieval manually, but none of them retrieved the registration platform. 47% described the two-reviewers model in the screening for eligible original articles, and seven SRs described the two reviewers to extract data. In methodological quality assessment, inter-rater reliability Kappa was 0.87 between two reviewers. Research question were well related to all SRs in phase 1 and the eligibility criteria was suitable for each SR, and rated as 'low' risk bias. But the 'high' risk bias existed in all the SRs regarding methods used to identify and/or select studies, and data collection and study appraisal. More than two-third of SRs or meta-analysis were finished with high risk of bias in the synthesis, findings and the final phase. The study demonstrated poor methodological quality of SRs/meta-analysis assessing the predictive value of ERCC1 in chemotherapy among the NSCLC patients, especially the high performance bias. Registration or publishing the protocol is recommended in future research.

A systematic review on the prevalence of metabolic syndrome in Iranian children and adolescents.

PubMed

Kelishadi, Roya; Hovsepian, Silva; Djalalinia, Shirin; Jamshidi, Fahimeh; Qorbani, Mostafa

2016-01-01

Metabolic syndrome (MetS), a cluster of cardiovascular risk factors, is one of the most common metabolic disorders, which lead to many chronic diseases. The link between childhood MetS and occurrence of atherosclerosis and its sequels in adulthood is well documented. This study aims to systematically review the prevalence of MetS among Iranian children and adolescents. An electronic search was conducted on studies published from January 1990 to January 2015. The main international electronic data sources were PubMed and the NLM Gateway (for MEDLINE), Institute of Scientific Information (ISI), and SCOPUS. For Persian databases, we used domestic databases. We included all available population-based studies and national surveys conducted in the pediatric age group aged 3-21-year-old. In this review, 2138 articles were identified (PubMed: 265; SCOPUS: 368; ISI: 465; Scientific Information Database: 189; IranMedex: 851; Irandoc: 46). After quality assessment, 13 qualified articles were evaluated. The number of total population and points of data were 24,772 and 125, respectively. Regarding the geographical distribution, we found 2 national, 6 provincial, and 5 district level points of data. The prevalence range of MetS among children was 1-22% using different definitions. Reported range of pediatric MetS defined by different criteria was as follows: National Cholesterol Education Program-Adult Treatment Panel III; 3-16%, International Diabetes Federation; 0-8%, American Heart Association; 4-9.5%, The National Health and Nutrition Examination Survey III; 1-18%, de Ferranti; 0-22%. MetS is a common metabolic disorder among Iranian children and adolescents, with increasing trends during the last decades. This finding provides baseline useful information for health policy makers to implement evidence based-health promotion for appropriate controlling of this growing health problem for the pediatric population.

Prevalence of dyslipidemia in Iranian children and adolescents: A systematic review.

PubMed

Hovsepian, Silva; Kelishadi, Roya; Djalalinia, Shirin; Farzadfar, Farshad; Naderimagham, Shohreh; Qorbani, Mostafa

2015-05-01

Dyslipidemia is considered as an important modifiable risk factor for cardiovascular disease (CVD). The link between childhood dyslipidemia and occurrence of atherosclerosis and its sequels in adulthood are well-documented. This study aimed to systematically review the prevalence of dyslipidemia among Iranian children and adolescents. An electronic search was conducted on studies published from January 1990 to January 2014. The main international electronic data sources were PubMed and the NLM Gateway (for MEDLINE), Institute of Scientific Information (ISI), and SCOPUS. For Persian databases, we used domestic databases with systematic search capability including IranMedex, Irandoc, and Scientific Information Database (SID). We included all available population-based studies and national surveys conducted in the pediatric age group (aged <21 years). In this review, 1772 articles were identified (PubMed: 1464; Scopus: 11; ISI: 58; SID: 90; IranMedex: 149; Irandoc: 57). During three refine steps and after removing of duplicates, 182 articles related to the study domain were selected. After quality assessment, 46 studies were selected for text appraisal, of which 26 qualified articles were evaluated at the final step. The prevalence range of hypercholesterolemia, hypertriglyceridemia, elevated low-density lipoprotein cholesterol, and low high-density lipoprotein cholesterol (HDL-C) were 3-48%, 3-50%, 5-20% and 5-88%, respectively. Low HDL-C and hypertriglyceridemia were the most prevalent lipid disorders in this group of population. Dyslipidemia is a common health problem among Iranian children and adolescents. Few data were available in preschool children. This finding provides useful information for health policy makers to implement action-oriented interventions for prevention and early control of this important CVD risk factor.

Evaluation of generic medical information accessed via mobile phones at the point of care in resource-limited settings

PubMed Central

Goldbach, Hayley; Chang, Aileen Y; Kyer, Andrea; Ketshogileng, Dineo; Taylor, Lynne; Chandra, Amit; Dacso, Matthew; Kung, Shiang-Ju; Rijken, Taatske; Fontelo, Paul; Littman-Quinn, Ryan; Seymour, Anne K; Kovarik, Carrie L

2014-01-01

Objective Many mobile phone resources have been developed to increase access to health education in the developing world, yet few studies have compared these resources or quantified their performance in a resource-limited setting. This study aims to compare the performance of resident physicians in answering clinical scenarios using PubMed abstracts accessed via the PubMed for Handhelds (PubMed4Hh) website versus medical/drug reference applications (Medical Apps) accessed via software on the mobile phone. Methods A two-arm comparative study with crossover design was conducted. Subjects, who were resident physicians at the University of Botswana, completed eight scenarios, each with multi-part questions. The primary outcome was a grade for each question. The primary independent variable was the intervention arm and other independent variables included residency and question. Results Within each question type there were significant differences in ‘percentage correct’ between Medical Apps and PubMed4Hh for three of the six types of questions: drug-related, diagnosis/definitions, and treatment/management. Within each of these question types, Medical Apps had a higher percentage of fully correct responses than PubMed4Hh (63% vs 13%, 33% vs 12%, and 41% vs 13%, respectively). PubMed4Hh performed better for epidemiologic questions. Conclusions While mobile access to primary literature remains important and serves an information niche, mobile applications with condensed content may be more appropriate for point-of-care information needs. Further research is required to examine the specific information needs of clinicians in resource-limited settings and to evaluate the appropriateness of current resources in bridging location- and context-specific information gaps. PMID:23535665

Impact of PubMed search filters on the retrieval of evidence by physicians.

PubMed

Shariff, Salimah Z; Sontrop, Jessica M; Haynes, R Brian; Iansavichus, Arthur V; McKibbon, K Ann; Wilczynski, Nancy L; Weir, Matthew A; Speechley, Mark R; Thind, Amardeep; Garg, Amit X

2012-02-21

Physicians face challenges when searching PubMed for research evidence, and they may miss relevant articles while retrieving too many nonrelevant articles. We investigated whether the use of search filters in PubMed improves searching by physicians. We asked a random sample of Canadian nephrologists to answer unique clinical questions derived from 100 systematic reviews of renal therapy. Physicians provided the search terms that they would type into PubMed to locate articles to answer these questions. We entered the physician-provided search terms into PubMed and applied two types of search filters alone or in combination: a methods-based filter designed to identify high-quality studies about treatment (clinical queries "therapy") and a topic-based filter designed to identify studies with renal content. We evaluated the comprehensiveness (proportion of relevant articles found) and efficiency (ratio of relevant to nonrelevant articles) of the filtered and nonfiltered searches. Primary studies included in the systematic reviews served as the reference standard for relevant articles. The average physician-provided search terms retrieved 46% of the relevant articles, while 6% of the retrieved articles were relevant (corrected) (the ratio of relevant to nonrelevant articles was 1:16). The use of both filters together produced a marked improvement in efficiency, resulting in a ratio of relevant to nonrelevant articles of 1:5 (16 percentage point improvement; 99% confidence interval 9% to 22%; p < 0.003) with no substantive change in comprehensiveness (44% of relevant articles found; p = 0.55). The use of PubMed search filters improves the efficiency of physician searches. Improved search performance may enhance the transfer of research into practice and improve patient care.

Validation of search filters for identifying pediatric studies in PubMed.

PubMed

Leclercq, Edith; Leeflang, Mariska M G; van Dalen, Elvira C; Kremer, Leontien C M

2013-03-01

To identify and validate PubMed search filters for retrieving studies including children and to develop a new pediatric search filter for PubMed. We developed 2 different datasets of studies to evaluate the performance of the identified pediatric search filters, expressed in terms of sensitivity, precision, specificity, accuracy, and number needed to read (NNR). An optimal search filter will have a high sensitivity and high precision with a low NNR. In addition to the PubMed Limits: All Child: 0-18 years filter (in May 2012 renamed to PubMed Filter Child: 0-18 years), 6 search filters for identifying studies including children were identified: 3 developed by Kastner et al, 1 developed by BestBets, one by the Child Health Field, and 1 by the Cochrane Childhood Cancer Group. Three search filters (Cochrane Childhood Cancer Group, Child Health Field, and BestBets) had the highest sensitivity (99.3%, 99.5%, and 99.3%, respectively) but a lower precision (64.5%, 68.4%, and 66.6% respectively) compared with the other search filters. Two Kastner search filters had a high precision (93.0% and 93.7%, respectively) but a low sensitivity (58.5% and 44.8%, respectively). They failed to identify many pediatric studies in our datasets. The search terms responsible for false-positive results in the reference dataset were determined. With these data, we developed a new search filter for identifying studies with children in PubMed with an optimal sensitivity (99.5%) and precision (69.0%). Search filters to identify studies including children either have a low sensitivity or a low precision with a high NNR. A new pediatric search filter with a high sensitivity and a low NNR has been developed. Copyright © 2013 Mosby, Inc. All rights reserved.

Role of Statin Drugs for Polycystic Ovary Syndrome.

PubMed

Cassidy-Vu, Lisa; Joe, Edwina; Kirk, Julienne K

2016-12-01

Objective: To review the potential role and specific impact of statin drugs in women with PCOS. The evidence for this use of statins in PCOS is limited and still under further investigation. Materials and methods: A search was conducted using PubMed, DynaMed and PubMedHealth databases through October 16, 2016 using the terms polycystic ovary syndrome, PCOS, hydroxymethylglutaryl-CoA reductase inhibitors, hydroxymethylglutaryl-CoA, statin, atorvastatin, fluvastatin, lovastatin, pitavastatin, pravastatin, rosuvastatin and simvastatin . English-language trials evaluating statins in PCOS were obtained and incorporated if they provided relevant data for providers. Results: We summarize twelve trials involving statins in PCOS. The trials were predominantly 12 weeks to 3 months in length (8 of the 12 trials) and low to moderate dose of statin drugs were used. The majority (10 of 12) of the trials show that statins reduce testosterone levels or other androgen hormones (DHEA-S and androstenedione), half of the trials evaluating LH/FSH ratio show an improvement, and all had positive effects on lipid profiles. Conclusion: Statins show promising improvements in serum levels of androgens and LH/FSH ratios translating to improved cardiovascular risk factors above and beyond simply lowering LDL levels. More investigation is needed to determine if statins can clinically impact women with PCOS long term, particularly those who are young and are not yet candidates for traditional preventative treatment with a statin medication.

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.

Genetics Home Reference: Chanarin-Dorfman syndrome

MedlinePlus

... abnormalities in the ichthyoses: inherited disorders of lipid metabolism. J Lipid Res. 2008 Apr;49(4):697-714. doi: 10.1194/jlr.R800002-JLR200. Epub 2008 Feb 2. Review. Citation on PubMed or Free article on PubMed Central Lass A, Zimmermann R, Haemmerle ...

Genetics Home Reference: ethylmalonic encephalopathy

MedlinePlus

... Tiranti V, Zeviani M. Altered sulfide (H(2)S) metabolism in ethylmalonic encephalopathy. Cold Spring Harb Perspect Biol. 2013 Jan 1;5(1):a011437. doi: 10.1101/cshperspect.a011437. Review. Citation on PubMed or Free article on PubMed Central More from Genetics Home Reference ...

Genetics Home Reference: Weyers acrofacial dysostosis

MedlinePlus

... Ellis-van Creveld Syndrome Resource list from the University of Kansas Medical Center: Dwarfism / Short Stature Scientific Articles on PubMed (1 link) PubMed OMIM (1 link) WEYERS ACROFACIAL DYSOSTOSIS Sources for This Page Howard TD, Guttmacher AE, McKinnon W, Sharma M, McKusick ...

How to improve your PubMed/MEDLINE searches: 2. display settings, complex search queries and topic searching.

PubMed

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

2014-01-01

The way that PubMed results are displayed can be changed using the Display Settings drop-down menu in the result screen. There are three groups of options: Format, Items per page and Sort by, which allow a good deal of control. The results from several searches can be temporarily stored on the Clipboard. Records of interest can be selected on the results page using check boxes and can then be combined, for example to form a reference list. The Related Citations is a valuable feature of PubMed that can provide a set of similar articles when you have identified a record of interest among the results. You can easily search for RCTs or reviews using the appropriate filters or field tags. If you are interested in clinical articles, rather than basic science or health service research, then the Clinical Queries tool on the PubMed home page can be used to retrieve them.

[Sarcoidosis related pleural effusion: 6 case reports and literatures review].

PubMed

Wang, Feng; Tong, Zhaohui; Wang, Zhen; Wang, Xiaojuan; Xu, Lili

2015-02-01

To summarize the clinical features and the diagnosis-treatment points of sarcoidosis related pleural effusion. Six typical sarcoidosis related pleural effusion cases with pathological evidence were reviewed, and the clinical data of these cases were retrospectively analyzed and the related literatures were reviewed. The literature review was carried out respectively with "sarcoidosis", "pleural disease" and "pleural effusion" as the keywords in CNKI and PubMed database by January 2014. Six cases, including 1 male and 5 females, with sarcoidosis related pleural effusions were reported. 3 cases had bilateral effusions, 2 cases had left effusion and 1 case had right effusion. The pleural effusion routine test had a low specificity, which demonstrated that the fluid was exudate and consisted with large number of lymphocytes. 3 of these cases were diagnosed by medical thoracoscopy. Medical thoracoscopy revealed that pleural involvement was variable with multiple nodulespresent in some cases and subtle change in others. A total of 28 literatures and 92 cases with pleural involvement in sarcoidosis were retrieved from CNKI and PubMed database (time range: 2004.1-2014.1), including 59 cases of pleural effusion, 29 cases of pleural thickening, 3 cases of pneumothorax and 1 case of nodules in pleura. Pleural involvement in sarcoidosis was often misdiagnosed or mistreated as tuberculous pleurisy because the routine tests regarding pleural effusion usually had a low specificity. Medical thoracoscopy could provide clinicians with important clues to assist differentiation of the cause for non-conclusive pleural effusion in this situation.

Systematic review: Eosinophilic esophagitis in Asian countries

PubMed Central

Kinoshita, Yoshikazu; Ishimura, Norihisa; Oshima, Naoki; Ishihara, Shunji

2015-01-01

AIM: To investigate the prevalence and the clinical characteristics of Asian patients with eosinophilic esophagitis. METHODS: We conducted a systematic search of the PubMed and Web of Science databases for original studies, case series, and individual case reports of eosinophilic esophagitis in Asian countries published from January 1980 to January 2015. We found 66 and 80 articles in the PubMed and Web of Science databases, respectively; 24 duplicate articles were removed. After excluding animal studies, articles not written in English, and meeting abstracts, 25 articles containing 217 patients were selected for analysis. RESULTS: Sample size-weighted mean values were determined for all pooled prevalence data and clinical characteristics. The mean age of the adult patients with eosinophilic esophagitis was approximately 50 years, and 73% of these patients were male. They frequently presented with allergic diseases including bronchial asthma, allergic rhinitis, food allergy, and atopic dermatitis. Bronchial asthma was the most frequent comorbid allergic disease, occurring in 24% of patients with eosinophilic esophagitis. Dysphagia was the primary symptom reported; 44% of the patients complained of dysphagia. Although laboratory blood tests are not adequately sensitive for an accurate diagnosis of eosinophilic esophagitis, endoscopic examinations revealed abnormal findings typical of this disease, including longitudinal furrows and concentric rings, in 82% of the cases. One-third of the cases responded to proton pump inhibitor administration. CONCLUSION: The characteristics of eosinophilic esophagitis in Asian patients were similar to those reported in Western patients, indicating that this disease displays a similar pathogenesis between Western and Asian patients. PMID:26217096

Bibliography of clinical research in malaysia: methods and brief results.

PubMed

Teng, C L; Zuhanariah, M N; Ng, C S; Goh, C C

2014-08-01

This article describes the methodology of this bibliography. A search was conducted on the following: (1) bibliographic databases (PubMed, Scopus, and other databases) using search terms that maximize the retrieval of Malaysian publications; (2) Individual journal search of Malaysian healthrelated journals; (3) A targeted search of Google and Google Scholar; (4) Searching of Malaysian institutional repositories; (5) Searching of Ministry of Health and Clinical Research Centre website. The publication years were limited to 2000- 2013. The citations were imported or manually entered into bibliographic software Refworks. After removing duplicates, and correcting data entry errors, PubMed's Medical Subject Headings (MeSH terms) were added. Clinical research is coded using the definition "patient-oriented-research or research conducted with human subjects (or on material of human origin) for which the investigator directly interacts with the human subjects at some point during the study." A bibliography of citations [n=2056] that fit the criteria of clinical research in Malaysia in selected topics within five domains was generated: Cancers [589], Cardiovascular diseases [432], Infections [795], Injuries [142], and Mental Health [582]. This is done by retrieving citations with the appropriate MESH terms, as follow: For cancers (Breast Neoplasms; Colorectal Neoplasms; Uterine Cervical Neoplasms), for cardiovascular diseases (Coronary Disease; Hypertension; Stroke), for infections (Dengue; Enterovirus Infections, HIV Infections; Malaria; Nipah Virus; Tuberculosis), for injuries (Accidents, Occupational; Accidents, Traffic; Child Abuse; Occupational Injuries), for mental health (Depression; Depressive Disorder; Depressive Disorder, Major; Drug Users; Psychotic Disorders; Suicide; Suicide, Attempted; Suicidal Ideation; Substance- Related Disorders).

References that anyone can edit: review of Wikipedia citations in peer reviewed health science literature

PubMed Central

Hladkowicz, Emily S; Pigford, Ashlee-Ann E; Ufholz, Lee-Anne; Postonogova, Tatyana; Shin, Eunkyung; Boet, Sylvain

2014-01-01

Objectives To examine indexed health science journals to evaluate the prevalence of Wikipedia citations, identify the journals that publish articles with Wikipedia citations, and determine how Wikipedia is being cited. Design Bibliometric analysis. Study selection Publications in the English language that included citations to Wikipedia were retrieved using the online databases Scopus and Web of Science. Data sources To identify health science journals, results were refined using Ulrich’s database, selecting for citations from journals indexed in Medline, PubMed, or Embase. Using Thomson Reuters Journal Citation Reports, 2011 impact factors were collected for all journals included in the search. Data extraction Resulting citations were thematically coded, and descriptive statistics were calculated. Results 1433 full text articles from 1008 journals indexed in Medline, PubMed, or Embase with 2049 Wikipedia citations were accessed. The frequency of Wikipedia citations has increased over time; most citations occurred after December 2010. More than half of the citations were coded as definitions (n=648; 31.6%) or descriptions (n=482; 23.5%). Citations were not limited to journals with a low or no impact factor; the search found Wikipedia citations in many journals with high impact factors. Conclusions Many publications are citing information from a tertiary source that can be edited by anyone, although permanent, evidence based sources are available. We encourage journal editors and reviewers to use caution when publishing articles that cite Wikipedia. PMID:24603564

Systematic review: Eosinophilic esophagitis in Asian countries.

PubMed

Kinoshita, Yoshikazu; Ishimura, Norihisa; Oshima, Naoki; Ishihara, Shunji

2015-07-21

To investigate the prevalence and the clinical characteristics of Asian patients with eosinophilic esophagitis. We conducted a systematic search of the PubMed and Web of Science databases for original studies, case series, and individual case reports of eosinophilic esophagitis in Asian countries published from January 1980 to January 2015. We found 66 and 80 articles in the PubMed and Web of Science databases, respectively; 24 duplicate articles were removed. After excluding animal studies, articles not written in English, and meeting abstracts, 25 articles containing 217 patients were selected for analysis. Sample size-weighted mean values were determined for all pooled prevalence data and clinical characteristics. The mean age of the adult patients with eosinophilic esophagitis was approximately 50 years, and 73% of these patients were male. They frequently presented with allergic diseases including bronchial asthma, allergic rhinitis, food allergy, and atopic dermatitis. Bronchial asthma was the most frequent comorbid allergic disease, occurring in 24% of patients with eosinophilic esophagitis. Dysphagia was the primary symptom reported; 44% of the patients complained of dysphagia. Although laboratory blood tests are not adequately sensitive for an accurate diagnosis of eosinophilic esophagitis, endoscopic examinations revealed abnormal findings typical of this disease, including longitudinal furrows and concentric rings, in 82% of the cases. One-third of the cases responded to proton pump inhibitor administration. The characteristics of eosinophilic esophagitis in Asian patients were similar to those reported in Western patients, indicating that this disease displays a similar pathogenesis between Western and Asian patients.

Sensitivity and Predictive Value of 15 PubMed Search Strategies to Answer Clinical Questions Rated Against Full Systematic Reviews

PubMed Central

Merglen, Arnaud; Courvoisier, Delphine S; Combescure, Christophe; Garin, Nicolas; Perrier, Arnaud; Perneger, Thomas V

2012-01-01

Background Clinicians perform searches in PubMed daily, but retrieving relevant studies is challenging due to the rapid expansion of medical knowledge. Little is known about the performance of search strategies when they are applied to answer specific clinical questions. Objective To compare the performance of 15 PubMed search strategies in retrieving relevant clinical trials on therapeutic interventions. Methods We used Cochrane systematic reviews to identify relevant trials for 30 clinical questions. Search terms were extracted from the abstract using a predefined procedure based on the population, interventions, comparison, outcomes (PICO) framework and combined into queries. We tested 15 search strategies that varied in their query (PIC or PICO), use of PubMed’s Clinical Queries therapeutic filters (broad or narrow), search limits, and PubMed links to related articles. We assessed sensitivity (recall) and positive predictive value (precision) of each strategy on the first 2 PubMed pages (40 articles) and on the complete search output. Results The performance of the search strategies varied widely according to the clinical question. Unfiltered searches and those using the broad filter of Clinical Queries produced large outputs and retrieved few relevant articles within the first 2 pages, resulting in a median sensitivity of only 10%–25%. In contrast, all searches using the narrow filter performed significantly better, with a median sensitivity of about 50% (all P < .001 compared with unfiltered queries) and positive predictive values of 20%–30% (P < .001 compared with unfiltered queries). This benefit was consistent for most clinical questions. Searches based on related articles retrieved about a third of the relevant studies. Conclusions The Clinical Queries narrow filter, along with well-formulated queries based on the PICO framework, provided the greatest aid in retrieving relevant clinical trials within the 2 first PubMed pages. These results can help clinicians apply effective strategies to answer their questions at the point of care. PMID:22693047

MMpI: A WideRange of Available Compounds of Matrix Metalloproteinase Inhibitors

PubMed Central

Muvva, Charuvaka; Patra, Sanjukta; Venkatesan, Subramanian

2016-01-01

Matrix metalloproteinases (MMPs) are a family of zinc-dependent proteinases involved in the regulation of the extracellular signaling and structural matrix environment of cells and tissues. MMPs are considered as promising targets for the treatment of many diseases. Therefore, creation of database on the inhibitors of MMP would definitely accelerate the research activities in this area due to its implication in above-mentioned diseases and associated limitations in the first and second generation inhibitors. In this communication, we report the development of a new MMpI database which provides resourceful information for all researchers working in this field. It is a web-accessible, unique resource that contains detailed information on the inhibitors of MMP including small molecules, peptides and MMP Drug Leads. The database contains entries of ~3000 inhibitors including ~72 MMP Drug Leads and ~73 peptide based inhibitors. This database provides the detailed molecular and structural details which are necessary for the drug discovery and development. The MMpI database contains physical properties, 2D and 3D structures (mol2 and pdb format files) of inhibitors of MMP. Other data fields are hyperlinked to PubChem, ChEMBL, BindingDB, DrugBank, PDB, MEROPS and PubMed. The database has extensive searching facility with MMpI ID, IUPAC name, chemical structure and with the title of research article. The MMP inhibitors provided in MMpI database are optimized using Python-based Hierarchical Environment for Integrated Xtallography (Phenix) software. MMpI Database is unique and it is the only public database that contains and provides the complete information on the inhibitors of MMP. Database URL: http://clri.res.in/subramanian/databases/mmpi/index.php. PMID:27509041

Application of traditional Chinese medicine injection in treatment of primary liver cancer: a review.

PubMed

Li, Mouduo; Qiao, Cuixia; Qin, Liping; Zhang, Junyong; Ling, Changquan

2012-09-01

To investigate the application of Traditional Chinese Medicine Injections (TCMIs) for treatment of primary liver cancer (PLC). A literature review was conducted using PubMed/Medline, Cochrane Library Controlled Clinical Trials Database, China National Knowledge Infrastructure (CNKI), China Scientific Journal Database (CSJD) and China Biology Medicine (CBM). Online websites including journal websites and databases of ongoing trials, as well as some Traditional Chinese Medicine journals that are not indexed in the electronic databases were also searched. as adjunctive medication for the treatment of PLC could regulate patient immunity, reduce bone marrow suppression, relieve clinical symptoms, and improve quality of life, as well as control disease progression and prolong survival time. Within the limitations of this review, we conclude that application of TCMIs as adjunctive medication may provide benefits for patients with PLC. Further large, high-quality trials are warranted.

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

PubMed

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

2017-01-01

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

GenBank

PubMed Central

Benson, Dennis A.; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Wheeler, David L.

2007-01-01

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 240 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage (). PMID:17202161

Efficacy of Noninvasive Stellate Ganglion Blockade Performed Using Physical Agent Modalities in Patients with Sympathetic Hyperactivity-Associated Disorders: A Systematic Review and Meta-Analysis

PubMed Central

Liao, Chun-De; Tsauo, Jau-Yih; Liou, Tsan-Hon

2016-01-01

Background Stellate ganglion blockade (SGB) is mainly used to relieve symptoms of neuropathic pain in conditions such as complex regional pain syndrome and has several potential complications. Noninvasive SGB performed using physical agent modalities (PAMs), such as light irradiation and electrical stimulation, can be clinically used as an alternative to conventional invasive SGB. However, its application protocols vary and its clinical efficacy remains controversial. This study investigated the use of noninvasive SGB for managing neuropathic pain or other disorders associated with sympathetic hyperactivity. Materials and Methods We performed a comprehensive search of the following online databases: Medline, PubMed, Excerpta Medica Database, Cochrane Library Database, Ovid MEDLINE, Europe PubMed Central, EBSCOhost Research Databases, CINAHL, ProQuest Research Library, Physiotherapy Evidence Database, WorldWideScience, BIOSIS, and Google Scholar. We identified and included quasi-randomized or randomized controlled trials reporting the efficacy of SGB performed using therapeutic ultrasound, transcutaneous electrical nerve stimulation, light irradiation using low-level laser therapy, or xenon light or linearly polarized near-infrared light irradiation near or over the stellate ganglion region in treating complex regional pain syndrome or disorders requiring sympatholytic management. The included articles were subjected to a meta-analysis and risk of bias assessment. Results Nine randomized and four quasi-randomized controlled trials were included. Eleven trials had good methodological quality with a Physiotherapy Evidence Database (PEDro) score of ≥6, whereas the remaining two trials had a PEDro score of <6. The meta-analysis results revealed that the efficacy of noninvasive SGB on 100-mm visual analog pain score is higher than that of a placebo or active control (weighted mean difference, −21.59 mm; 95% CI, −34.25, −8.94; p = 0.0008). Conclusions Noninvasive SGB performed using PAMs effectively relieves pain of various etiologies, making it a valuable addition to the contemporary pain management armamentarium. However, this evidence is limited by the potential risk of bias. PMID:27911934

Kalium: a database of potassium channel toxins from scorpion venom.

PubMed

Kuzmenkov, Alexey I; Krylov, Nikolay A; Chugunov, Anton O; Grishin, Eugene V; Vassilevski, Alexander A

2016-01-01

Kalium (http://kaliumdb.org/) is a manually curated database that accumulates data on potassium channel toxins purified from scorpion venom (KTx). This database is an open-access resource, and provides easy access to pages of other databases of interest, such as UniProt, PDB, NCBI Taxonomy Browser, and PubMed. General achievements of Kalium are a strict and easy regulation of KTx classification based on the unified nomenclature supported by researchers in the field, removal of peptides with partial sequence and entries supported by transcriptomic information only, classification of β-family toxins, and addition of a novel λ-family. Molecules presented in the database can be processed by the Clustal Omega server using a one-click option. Molecular masses of mature peptides are calculated and available activity data are compiled for all KTx. We believe that Kalium is not only of high interest to professional toxinologists, but also of general utility to the scientific community.Database URL:http://kaliumdb.org/. © The Author(s) 2016. Published by Oxford University Press.

Database resources of the National Center for Biotechnology Information: 2002 update

PubMed Central

Wheeler, David L.; Church, Deanna M.; Lash, Alex E.; Leipe, Detlef D.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M.; Tatusova, Tatiana A.; Wagner, Lukas; Rapp, Barbara A.

2002-01-01

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI’s web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, Human¡VMouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov. PMID:11752242

Genetics Home Reference: ataxia neuropathy spectrum

MedlinePlus

... 48(3):492-501. Citation on PubMed or Free article on PubMed Central Rocher C, Taanman JW, Pierron D, Faustin B, Benard G, Rossignol R, Malgat M, Pedespan L, Letellier T. Influence of mitochondrial DNA level on cellular energy metabolism: implications for mitochondrial diseases. J Bioenerg Biomembr. ...

Genetics Home Reference: aromatic l-amino acid decarboxylase deficiency

MedlinePlus

... Nov 18. Review. Citation on PubMed Pearl PL, Taylor JL, Trzcinski S, Sokohl A. The pediatric neurotransmitter disorders. J Child Neurol. 2007 May;22(5):606-16. Review. Citation on PubMed Pons R, Ford B, Chiriboga CA, Clayton PT, Hinton V, Hyland K, ...

Genetics Home Reference: congenital sucrase-isomaltase deficiency

MedlinePlus

... Leeb T, Naim HY. Novel mutations in the human sucrase-isomaltase gene (SI) that cause congenital carbohydrate malabsorption. Hum Mutat. 2006 Jan;27(1):119. Citation on PubMed Sibley E. Carbohydrate intolerance. Curr Opin Gastroenterol. 2004 Mar;20(2):162-7. Citation on PubMed More ...

Genetics Home Reference: phosphoglycerate mutase deficiency

MedlinePlus

... PubMed Tsujino S, Shanske S, Sakoda S, Fenichel G, DiMauro S. The molecular genetic basis of muscle phosphoglycerate mutase (PGAM) deficiency. Am ... PubMed Central Tsujino S, Shanske S, Sakoda S, Toscano A, DiMauro S. Molecular genetic studies in muscle phosphoglycerate mutase (PGAM-M) deficiency. ...

Genetics Home Reference: carbonic anhydrase VA deficiency

MedlinePlus

... implicates both enzymes in ammonia detoxification and glucose metabolism. Proc Natl Acad Sci U S A. 2013 Apr 30;110(18):7423-8. doi: 10.1073/pnas.1305805110. Epub 2013 Apr 15. Citation on PubMed or Free article on PubMed Central Sly WS, Hu PY. Human ...

Effectiveness of massage therapy on the range of motion of the shoulder: a systematic review and meta-analysis.

PubMed

Yeun, Young-Ran

2017-02-01

[Purpose] This study was conducted to identify and analyze the degree of effect of massage therapy on the range of motion of the shoulder. [Subjects and Methods] The database search was conducted using PubMed, CINAHL, Embase, PsycINFO, RISS, NDSL, NANET, DBpia, and KoreaMed. The meta-analysis was based on 7 studies, covered a total of 237 participants, and used a random-effects model. [Results] The effect size estimate showed that massage therapy significantly improved the shoulder range of motion, especially the flexion (SMD: 18.21, 95% CI 1.57-34.85) and abduction (SMD: 22.07, 95% CI 5.84-38.30). [Conclusion] The review findings suggest that massage therapy is effective in improving the shoulder flexion and abduction.

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

PubMed

Spiroski, Mirko

2016-06-15

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

The Moroccan Genetic Disease Database (MGDD): a database for DNA variations related to inherited disorders and disease susceptibility.

PubMed

Charoute, Hicham; Nahili, Halima; Abidi, Omar; Gabi, Khalid; Rouba, Hassan; Fakiri, Malika; Barakat, Abdelhamid

2014-03-01

National and ethnic mutation databases provide comprehensive information about genetic variations reported in a population or an ethnic group. In this paper, we present the Moroccan Genetic Disease Database (MGDD), a catalogue of genetic data related to diseases identified in the Moroccan population. We used the PubMed, Web of Science and Google Scholar databases to identify available articles published until April 2013. The Database is designed and implemented on a three-tier model using Mysql relational database and the PHP programming language. To date, the database contains 425 mutations and 208 polymorphisms found in 301 genes and 259 diseases. Most Mendelian diseases in the Moroccan population follow autosomal recessive mode of inheritance (74.17%) and affect endocrine, nutritional and metabolic physiology. The MGDD database provides reference information for researchers, clinicians and health professionals through a user-friendly Web interface. Its content should be useful to improve researches in human molecular genetics, disease diagnoses and design of association studies. MGDD can be publicly accessed at http://mgdd.pasteur.ma.

Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization

PubMed Central

Wei, Chih-Hsuan; Hakala, Kai; Pyysalo, Sampo; Ananiadou, Sophia; Kao, Hung-Yu; Lu, Zhiyong; Salakoski, Tapio; Van de Peer, Yves; Ginter, Filip

2013-01-01

Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (http://www.evexdb.org/api/v001/). Finally, to allow for large-scale bioinformatic analyses, the entire resource is available for bulk download from http://evexdb.org/download/, under the Creative Commons – Attribution – Share Alike (CC BY-SA) license. PMID:23613707

Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification.

PubMed

Mehryary, Farrokh; Kaewphan, Suwisa; Hakala, Kai; Ginter, Filip

2016-01-01

Biomedical event extraction is one of the key tasks in biomedical text mining, supporting various applications such as database curation and hypothesis generation. Several systems, some of which have been applied at a large scale, have been introduced to solve this task. Past studies have shown that the identification of the phrases describing biological processes, also known as trigger detection, is a crucial part of event extraction, and notable overall performance gains can be obtained by solely focusing on this sub-task. In this paper we propose a novel approach for filtering falsely identified triggers from large-scale event databases, thus improving the quality of knowledge extraction. Our method relies on state-of-the-art word embeddings, event statistics gathered from the whole biomedical literature, and both supervised and unsupervised machine learning techniques. We focus on EVEX, an event database covering the whole PubMed and PubMed Central Open Access literature containing more than 40 million extracted events. The top most frequent EVEX trigger words are hierarchically clustered, and the resulting cluster tree is pruned to identify words that can never act as triggers regardless of their context. For rarely occurring trigger words we introduce a supervised approach trained on the combination of trigger word classification produced by the unsupervised clustering method and manual annotation. The method is evaluated on the official test set of BioNLP Shared Task on Event Extraction. The evaluation shows that the method can be used to improve the performance of the state-of-the-art event extraction systems. This successful effort also translates into removing 1,338,075 of potentially incorrect events from EVEX, thus greatly improving the quality of the data. The method is not solely bound to the EVEX resource and can be thus used to improve the quality of any event extraction system or database. The data and source code for this work are available at: http://bionlp-www.utu.fi/trigger-clustering/.

Mediterranean Diet and Cardiodiabesity: A Review

PubMed Central

García-Fernández, Elena; Rico-Cabanas, Laura; Rosgaard, Nanna; Estruch, Ramón; Bach-Faig, Anna

2014-01-01

Cardiodiabesity has been used to define and describe the well-known relationship between type 2 Diabetes Mellitus (T2DM), obesity, the metabolic syndrome (MetS) and cardiovascular disease (CVD). The objective of this study was to perform a scientific literature review with a systematic search to examine all the cardiovascular risk factors combined and their relationship with adherence to the Mediterranean Diet (MedDiet) pattern as primary prevention against cardiodiabesity in a holistic approach. Research was conducted using the PubMed database including clinical trials, cross-sectional and prospective cohort studies. Thirty-seven studies were reviewed: fourteen related to obesity, ten to CVD, nine to MetS, and four to T2DM. Indeed 33 provided strong evidence on the association between adherence to a MedDiet and a reduced incidence of collective cardiodiabesity risk in epidemiological studies. This scientific evidence makes the MedDiet pattern very useful for preventive strategies directed at the general population and also highlights the need to consider all these diet-related risk factors and health outcomes together in daily primary care. PMID:25192027

Genetics Home Reference: myoclonic epilepsy myopathy sensory ataxia

MedlinePlus

... 48(3):492-501. Citation on PubMed or Free article on PubMed Central Rocher C, Taanman JW, Pierron D, Faustin B, Benard G, Rossignol R, Malgat M, Pedespan L, Letellier T. Influence of mitochondrial DNA level on cellular energy metabolism: implications for mitochondrial diseases. J Bioenerg Biomembr. ...

Gestational Age, Infant Birth Weight, and Subsequent Risk of Type 2 Diabetes in Mothers: Nurses' Health Study II

MedlinePlus

... 401. CrossRef PubMed Metzger BE, Lowe LP, Dyer AR, Trimble ER, Chaovarindr U, Coustan DR, et al. ... 805. CrossRef PubMed Schmidt MI, Duncan BB, Sharrett AR, Lindberg G, Savage PJ, Offenbacher S, et al. Markers ...

Genetics Home Reference: distal hereditary motor neuropathy, type V

MedlinePlus

... PubMed Irobi J, De Jonghe P, Timmerman V. Molecular genetics of distal hereditary motor neuropathies. Hum Mol Genet. 2004 Oct 1;13 Spec No 2:R195-202. Review. Citation on PubMed Ito D, Suzuki N. Molecular pathogenesis of seipin/BSCL2-related motor neuron diseases. ...

Genetics Home Reference: 17q12 duplication

MedlinePlus

... books/NBK344340/ Citation on PubMed Mefford HC, Clauin S, Sharp AJ, Moller RS, Ullmann R, Kapur R, Pinkel D, Cooper GM, ... 10.1002/ajmg.a.37848. Citation on PubMed Sharp AJ, Hansen S, Selzer RR, Cheng Z, Regan R, Hurst JA, Stewart H, Price SM, Blair E, ...

Genetics Home Reference: ocular albinism

MedlinePlus

... Available from http://www.ncbi.nlm.nih.gov/books/NBK1343/ Citation on PubMed Oetting WS. New insights into ocular albinism type 1 (OA1): Mutations and polymorphisms of the OA1 gene. Hum Mutat. 2002 Feb;19(2):85-92. Review. Citation on PubMed Tak WJ, Kim MN, Hong ...

Implant-abutment gap versus microbial colonization: Clinical significance based on a literature review.

PubMed

Passos, Sheila Pestana; Gressler May, Liliana; Faria, Renata; Özcan, Mutlu; Bottino, Marco Antonio

2013-10-01

Microorganisms from the oral cavity may settle at the implant-abutment interface (IAI). As a result, tissue inflammation could occur around these structures. The databases MEDLINE/PubMed and PubMed Central were used to identify articles published from 1981 through 2012 related to the microbial colonization in the implant-abutment gap and its consequence in terms of crest bone loss and osseointegration. The following considerations could be put forward, with respect to the clinical importance of IAI: (a) the space present at the IAI seems to allow bacterial leakage to occur, in spite of the size of this space; (b) bacterial leakage seems to occur at the IAI, irrespective of the type of connection. More studies are necessary to clarify the relationship between leakage at IAI and abutment connection designs; (c) losses at the peri-implant bone crests cannot be related to the IAI size, since few studies have shown no relationship. Also, the microbial leakage at the IAI cannot be related to the bone crest loss, since there are no articles reporting this relationship; remains controversial the influence of the IAI position on the bone crest losses. Copyright © 2013 Wiley Periodicals, Inc.

Information-seeking behavior changes in community-based teaching practices*†

PubMed Central

Byrnes, Jennifer A.; Kulick, Tracy A.; Schwartz, Diane G.

2004-01-01

A National Library of Medicine information access grant allowed for a collaborative project to provide computer resources in fourteen clinical practice sites that enabled health care professionals to access medical information via PubMed and the Internet. Health care professionals were taught how to access quality, cost-effective information that was user friendly and would result in improved patient care. Selected sites were located in medically underserved areas and received a computer, a printer, and, during year one, a fax machine. Participants were provided dial-up Internet service or were connected to the affiliated hospital's network. Clinicians were trained in how to search PubMed as a tool for practicing evidence-based medicine and to support clinical decision making. Health care providers were also taught how to find patient-education materials and continuing education programs and how to network with other professionals. Prior to the training, participants completed a questionnaire to assess their computer skills and familiarity with searching the Internet, MEDLINE, and other health-related databases. Responses indicated favorable changes in information-seeking behavior, including an increased frequency in conducting MEDLINE searches and Internet searches for work-related information. PMID:15243639

Essential oils, their therapeutic properties, and implication in dentistry: A review.

PubMed

Dagli, Namrata; Dagli, Rushabh; Mahmoud, Rasha Said; Baroudi, Kusai

2015-01-01

Antibacterial treatments currently used for treatment cause several side effects, and bacterial resistance to the antibiotics is also increasing. Therefore, there is need to find better alternatives. Essential oils (EOs) have been used for treatment of various ailments since ancient times and have gained popularity over the years. Safety and efficacy of EOs have been proved by several clinical trials. This review gives an overview on the EOs, their uses, and adverse effects. A literature search was performed in the PubMed for clinical trial studies and review articles on EOs published up to February 2015. The search was performed during March 2015. The following keywords were used: "Lavender essential oil," "cinnamon oil," "clove oil," "eucalyptus oil," "peppermint oil," "lemon EOs," and "tea tree oil." Total 70 relevant articles were found in PubMed database. After screening of abstracts, 52 articles were selected to be included in the present review. On the basis of the available information, it can be concluded that EOs have the potential to be developed as preventive or therapeutic agents for various oral diseases, but further clinical trials are required to establish their safety and efficacy.

Peripheral Exophytic Oral Lesions: A Clinical Decision Tree

PubMed Central

Safi, Yaser; Jafari, Soudeh

2017-01-01

Diagnosis of peripheral oral exophytic lesions might be quite challenging. This review article aimed to introduce a decision tree for oral exophytic lesions according to their clinical features. General search engines and specialized databases including PubMed, PubMed Central, Medline Plus, EBSCO, Science Direct, Scopus, Embase, and authenticated textbooks were used to find relevant topics by means of keywords such as “oral soft tissue lesion,” “oral tumor like lesion,” “oral mucosal enlargement,” and “oral exophytic lesion.” Related English-language articles published since 1988 to 2016 in both medical and dental journals were appraised. Upon compilation of data, peripheral oral exophytic lesions were categorized into two major groups according to their surface texture: smooth (mesenchymal or nonsquamous epithelium-originated) and rough (squamous epithelium-originated). Lesions with smooth surface were also categorized into three subgroups according to their general frequency: reactive hyperplastic lesions/inflammatory hyperplasia, salivary gland lesions (nonneoplastic and neoplastic), and mesenchymal lesions (benign and malignant neoplasms). In addition, lesions with rough surface were summarized in six more common lesions. In total, 29 entities were organized in the form of a decision tree in order to help clinicians establish a logical diagnosis by a stepwise progression method. PMID:28757870

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.

Primary mucinous cystadenocarcinoma of the breast with endocervical-like mucinous epithelium.

PubMed

Lin, Dong-Liang; Hu, Ji-Lin; Shao, Shi-Hong; Sun, Dong-Mei; Wang, Ji-Gang

2013-12-01

Primary mucinous cystadenocarcinoma of the breast is an extremely rare entity. To the best of our knowledge, only 17 patients have been described in the PubMed database. Here, we report a primary breast mucinous cystadenocarcinoma with endocervical-like mucinous epithelium in a 62-year-old woman. The patient was followed for 5 months without any adjuvant treatment and she continues to be disease free. Primary breast mucinous cystadenocarcinoma usually displays unique pathologic and immunohistochemical characteristics simulating its ovarian counterparts; it seems to have a good prognosis after complete resection.

Current Understanding of Antiobesity Property of Capsaicin

PubMed Central

Narang, Nithida; Jiraungkoorskul, Wannee; Jamrus, Parinda

2017-01-01

The capsaicin is an ingredient that we normally mix in food in many cultural cuisines even in fresh and dried production. Because of its anticancer, anticholesterolemic, antidiabetic, antihypertensive, anti-inflammatory, antimicrobial, and antioxidant properties, capsaicin is used worldwide. Moreover, capsaicin is also used for the protection of cardiovascular and hepatic diseases. The electronic databases PubMed, Scopus, Web of Science, Google Scholar, and ScienceDirect were searched since 2000 to present for antiobesity term. This review article is provided the update information about the antiobesity property and mechanism of capsaicin for further researches. PMID:28503049

Genetic polymorphisms associated with heart failure: A literature review.

PubMed

Guo, Mengqi; Guo, Guanlun; Ji, Xiaoping

2016-02-01

To review possible associations reported between genetic variants and the risk, therapeutic response and prognosis of heart failure. Electronic databases (PubMed, Web of Science and CNKI) were systematically searched for relevant papers, published between January 1995 and February 2015. Eighty-two articles covering 29 genes and 39 polymorphisms were identified. Genetic association studies of heart failure have been highly controversial. There may be interaction or synergism of several genetic variants that together result in the ultimate pathological phenotype for heart failure. © The Author(s) 2016.

The Impact of Library Resources and Services on the Scholarly Activity of Medical Faculty and Residents.

PubMed

Quesenberry, Alexandria C; Oelschlegel, Sandy; Earl, Martha; Leonard, Kelsey; Vaughn, Cynthia J

2016-01-01

Librarians at an academic medical center library gathered data to determine if library services and resources impacted scholarly activity. A survey was developed and sent out to faculty and residents asking how they used the library during scholarly activity. Sixty-five faculty members and residents responded to the survey. The majority of respondents involved with scholarly activity use the library's services and resources. PubMed is the most frequently used database. The positive results show the library impacts the scholarly activity of medical faculty and residents.

[Controlling wound odor with metronidazole: a systematic review].

PubMed

Castro, Diana Lima Villela de; Santos, Vera Lúcia Conceição de Gouveia

2015-10-01

Verifying the evidence of therapeutic efficacy in the topical application of metronidazole for controlling wound odor. A systematic literature review, according to the Cochrane Collaboration recommendations. 329 articles were identified in the Cochrane, LILACS, SciELO, CINAHL and PubMed databases, with 14 of them being included in the final sample. Two of the studies were double-blind randomized clinical trial studies. The actual effectiveness of metronidazole in controlling wound odor cannot yet be evidenced due to the absence of strong evidence from studies on the subject, despite clinical practice recommending its benefits.

The importance of civilian nursing organizations: integrative literature review.

PubMed

Santos, James Farley Estevam Dos; Santos, Regina Maria Dos; Costa, Laís de Miranda Crispim; Almeida, Lenira Maria Wanderley Santos de; Macêdo, Amanda Cavalcante de; Santos, Tânia Cristina Franco

2016-06-01

to identify and analyze evidence from studies about the importance of civilian nursing organizations. an integrative literature review, for which searches were conducted in the databases LILACS, PubMed/MEDLINE, SciELO, BDENF, and Scopus. sixteen articles published between the years 2004-2013 were selected, 68.75% of which were sourced from Brazilian journals and 31.25% from American journals. civilian nursing organizations are important and necessary, because they have collaborated decisively in nursing struggles in favor of the working class and society in general, and these contributions influence different axes of professional performance.

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 chemical–gene interactions, chemical–disease relationships and gene–disease 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 protein–protein 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

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

PubMed

Kim, Sun; Kim, Won; Wei, Chih-Hsuan; Lu, Zhiyong; Wilbur, W John

2012-01-01

The Comparative Toxicogenomics Database (CTD) contains manually curated literature that describes chemical-gene interactions, chemical-disease relationships and gene-disease 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 protein-protein 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.

DATS, the data tag suite to enable discoverability of datasets.

PubMed

Sansone, Susanna-Assunta; Gonzalez-Beltran, Alejandra; Rocca-Serra, Philippe; Alter, George; Grethe, Jeffrey S; Xu, Hua; Fore, Ian M; Lyle, Jared; Gururaj, Anupama E; Chen, Xiaoling; Kim, Hyeon-Eui; Zong, Nansu; Li, Yueling; Liu, Ruiling; Ozyurt, I Burak; Ohno-Machado, Lucila

2017-06-06

Today's science increasingly requires effective ways to find and access existing datasets that are distributed across a range of repositories. For researchers in the life sciences, discoverability of datasets may soon become as essential as identifying the latest publications via PubMed. Through an international collaborative effort funded by the National Institutes of Health (NIH)'s Big Data to Knowledge (BD2K) initiative, we have designed and implemented the DAta Tag Suite (DATS) model to support the DataMed data discovery index. DataMed's goal is to be for data what PubMed has been for the scientific literature. Akin to the Journal Article Tag Suite (JATS) used in PubMed, the DATS model enables submission of metadata on datasets to DataMed. DATS has a core set of elements, which are generic and applicable to any type of dataset, and an extended set that can accommodate more specialized data types. DATS is a platform-independent model also available as an annotated serialization in schema.org, which in turn is widely used by major search engines like Google, Microsoft, Yahoo and Yandex.

Extracting and connecting chemical structures from text sources using chemicalize.org.

PubMed

Southan, Christopher; Stracz, Andras

2013-04-23

Exploring bioactive chemistry requires navigating between structures and data from a variety of text-based sources. While PubChem currently includes approximately 16 million document-extracted structures (15 million from patents) the extent of public inter-document and document-to-database links is still well below any estimated total, especially for journal articles. A major expansion in access to text-entombed chemistry is enabled by chemicalize.org. This on-line resource can process IUPAC names, SMILES, InChI strings, CAS numbers and drug names from pasted text, PDFs or URLs to generate structures, calculate properties and launch searches. Here, we explore its utility for answering questions related to chemical structures in documents and where these overlap with database records. These aspects are illustrated using a common theme of Dipeptidyl Peptidase 4 (DPPIV) inhibitors. Full-text open URL sources facilitated the download of over 1400 structures from a DPPIV patent and the alignment of specific examples with IC50 data. Uploading the SMILES to PubChem revealed extensive linking to patents and papers, including prior submissions from chemicalize.org as submitting source. A DPPIV medicinal chemistry paper was completely extracted and structures were aligned to the activity results table, as well as linked to other documents via PubChem. In both cases, key structures with data were partitioned from common chemistry by dividing them into individual new PDFs for conversion. Over 500 structures were also extracted from a batch of PubMed abstracts related to DPPIV inhibition. The drug structures could be stepped through each text occurrence and included some converted MeSH-only IUPAC names not linked in PubChem. Performing set intersections proved effective for detecting compounds-in-common between documents and merged extractions. This work demonstrates the utility of chemicalize.org for the exploration of chemical structure connectivity between documents and databases, including structure searches in PubChem, InChIKey searches in Google and the chemicalize.org archive. It has the flexibility to extract text from any internal, external or Web source. It synergizes with other open tools and the application is undergoing continued development. It should thus facilitate progress in medicinal chemistry, chemical biology and other bioactive chemistry domains.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

2008-01-01

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.

GenBank

PubMed Central

Benson, Dennis A.; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Wheeler, David L.

2008-01-01

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov PMID:18073190

Building and evaluating an informatics tool to facilitate analysis of a biomedical literature search service in an academic medical center library.

PubMed

Hinton, Elizabeth G; Oelschlegel, Sandra; Vaughn, Cynthia J; Lindsay, J Michael; Hurst, Sachiko M; Earl, Martha

2013-01-01

This study utilizes an informatics tool to analyze a robust literature search service in an academic medical center library. Structured interviews with librarians were conducted focusing on the benefits of such a tool, expectations for performance, and visual layout preferences. The resulting application utilizes Microsoft SQL Server and .Net Framework 3.5 technologies, allowing for the use of a web interface. Customer tables and MeSH terms are included. The National Library of Medicine MeSH database and entry terms for each heading are incorporated, resulting in functionality similar to searching the MeSH database through PubMed. Data reports will facilitate analysis of the search service.

Long-Term Neurodevelopmental Outcomes After Preterm Birth

PubMed Central

Soleimani, Farin; Zaheri, Farzaneh; Abdi, Fatemeh

2014-01-01

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

Genetics Home Reference: primary coenzyme Q10 deficiency

MedlinePlus

... q10 deficiency. Mol Syndromol. 2014 Jul;5(3-4):156-62. doi: 10.1159/000362826. Citation on PubMed or Free article on PubMed Central Emmanuele V, López LC, Berardo A, Naini A, Tadesse S, Wen B, D'Agostino E, Solomon M, DiMauro S, Quinzii C, Hirano M. Heterogeneity of ...

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…

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

PubMed Central

Spiroski, Mirko

2016-01-01

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

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

PubMed Central

Schimming, Laura M.

2008-01-01

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

Gender indexing in publications of clinical trials: 1991-2008.

PubMed

Drye, Lea T; Meinert, Jill L; Meinert, Curtis L

2010-12-01

In 1993 Congress passed the NIH Revitalization Act, which instructed the Director of the NIH to ensure that phase III clinical trials are 'designed and carried out in a manner sufficient to provide for a valid analysis of whether the variables being studied in the trial affect females or members of minority groups, as the case may be, differently than other subjects in the trial.' The purpose of this article is to track the PubMed indexing of gender in clinical trial publications since 1991 with a view toward assessing the impact of the legislation on the number of gender specific trials. We searched PubMed for full-length publications from years 1991 to 2008 of research on humans indexed as publication type 'clinical trial', 'randomized clinical trial' and multicenter randomized trial ('multicenter study' AND 'randomized clinical trial'), and counted the number of trials indexed as male-only, female-only, male and female, and gender unknown in PubMed. The majority of trial publications were indexed in PubMed as including both genders. The proportion of publications indexed as including both genders has increased while the number of publications not indexed with respect to gender and the number of publications indexed as male-only have decreased. In 2005, approximately 13% of NIH expenditures were for female specific or related research compared to 6% for male specific or related research. The proportion of clinical trial publications that were indexed in PubMed as including females began to increase before the legislation so it is difficult to conclude that changes in the number of female-only or male-only trials are due to the legislation. PubMed listings do not include gender enrollment, so female and male enrollment totals could not be compared. The NIH policy should be rewritten to be made gender neutral to bring it in line with the principle of justice as embodied in the Belmont Report.

GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains

PubMed Central

Lu, Zhiyong

2015-01-01

The automatic recognition of gene names and their associated database identifiers from biomedical text has been widely studied in recent years, as these tasks play an important role in many downstream text-mining applications. Despite significant previous research, only a small number of tools are publicly available and these tools are typically restricted to detecting only mention level gene names or only document level gene identifiers. In this work, we report GNormPlus: an end-to-end and open source system that handles both gene mention and identifier detection. We created a new corpus of 694 PubMed articles to support our development of GNormPlus, containing manual annotations for not only gene names and their identifiers, but also closely related concepts useful for gene name disambiguation, such as gene families and protein domains. GNormPlus integrates several advanced text-mining techniques, including SimConcept for resolving composite gene names. As a result, GNormPlus compares favorably to other state-of-the-art methods when evaluated on two widely used public benchmarking datasets, achieving 86.7% F1-score on the BioCreative II Gene Normalization task dataset and 50.1% F1-score on the BioCreative III Gene Normalization task dataset. The GNormPlus source code and its annotated corpus are freely available, and the results of applying GNormPlus to the entire PubMed are freely accessible through our web-based tool PubTator. PMID:26380306

Specialist Bibliographic Databases

PubMed Central

2016-01-01

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

Specialist Bibliographic Databases.

PubMed

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

2016-05-01

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

Xerostomia Due to Systemic Disease: A Review of 20 Conditions and Mechanisms

PubMed Central

Mortazavi, H; Baharvand, M; Movahhedian, A; Mohammadi, M; Khodadoustan, A

2014-01-01

Xerostomia is a common complaint of nearly half of the elderly population and about one-fifth of younger adults. It causes several signs and symptoms, and compromise oral functions and health-related quality-of-life. Multiple reasons are proposed to describe the etiology of xerostomia such as local factors, psychogenic factors, and systemic diseases. In order to manage xerostomia effectively, identification of the main causality is mandatory. The aim of this review was to present systemic diseases leading to xerostomia with their mechanisms of action. We used various general search engines and specialized databases such as Google, Google Scholar, Yahoo, PubMed, PubMed Central, MedLine Plus, Medknow, EBSCO, ScienceDirect, Scopus, WebMD, EMBASE, and authorized textbooks to find relevant topics by means of Medical Subject Headings keywords such as “xerostomia,” “hyposalivations,” “mouth dryness,” “disease,” and “systemic.” We appraised 97 English-language articles published over the last 40 years in both medical and dental journals including reviews, meta-analysis, original papers, and case reports. Upon compilation of relevant data, it was concluded that autoimmune diseases most frequently involve salivary glands and cause xerostomia followed by diabetes mellitus, renal failure, and graft-versus-host disease. Moreover, the underlying mechanisms of systemic disease-related xerostomia are: autoimmunity, infiltration of immunocompetent cells, granuloma formation, fibrosis and dehydration, deposition of proteinaceous substances, bacterial infection, and side-effects of medications. PMID:25221694

Weight loss in combat sports: physiological, psychological and performance effects.

PubMed

Franchini, Emerson; Brito, Ciro José; Artioli, Guilherme Giannini

2012-12-13

The present article briefly reviews the weight loss processes in combat sports. We aimed to discuss the most relevant aspects of rapid weight loss (RWL) in combat sports. This review was performed in the databases MedLine, Lilacs, PubMed and SciELO, and organized into sub-topics: (1) prevalence, magnitude and procedures, (2) psychological, physiological and performance effects, (3) possible strategies to avoid decreased performance (4) organizational strategies to avoid such practices. There was a high prevalence (50%) of RWL, regardless the specific combat discipline. Methods used are harmful to performance and health, such as laxatives, diuretics, use of plastic or rubber suits, and sauna. RWL affects physical and cognitive capacities, and may increase the risk of death. Recommendations during different training phases, educational and organizational approaches are presented to deal with or to avoid RWL.

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. Copyright © 2012 Lippincott Williams & Wilkins.

Herbal extracts in oral health care - A review of the current scenario and its future needs.

PubMed

Chandra Shekar, Byalakere Rudraiah; Nagarajappa, Ramesh; Suma, Shankarappa; Thakur, Rupesh

2015-01-01

Oral diseases are among the major public health problems and the commonest of chronic diseases that affect mankind. The application of natural products for the control of oral diseases is considered as an interesting alternative to synthetic antimicrobials due to their lower negative impact, and for the effort to overcome primary or secondary resistance to the drug during therapy. To review the current evidence on the antimicrobial efficacy of 10 plant extracts on dental caries and plaque microorganisms. A comprehensive literature search was made by one of the authors for 2 months in PubMed, PubMed Central, MEDLINE, LILACS/BBO, Cochrane database of systematic reviews, SCIENCE DIRECT, and Google scholar databases. The results from the relevant published literatures are discussed. The extracts of Azadirachta Indica, Ocimum sanctum, Murraya koenigii L., Acacia nilotica, Eucalyptus camaldulensis, Hibiscus sabdariffa, Mangifera indica, Psidium guajava, Rosa indica, and Aloe barbadensis Miller have all been found to inhibit certain dental caries and periodontal pathogens. The current evidence is on individual plant extracts against bacteria involved in either caries or periodontitis. "Herbal shotgun" or "synergistic multitarget effects" are the terms used for the strategy of combining different extracts. The research assessing the antimicrobial efficacy of a combination of these plant extracts against dental caries and periodontal pathogens is the need of the hour, and such research will aid in the development of a novel, innovative method that can simultaneously inhibit two of the most common dental diseases of mankind, besides slowing the development of drug resistance.

Toward a formalization of the process to select IMIA Yearbook best papers.

PubMed

Lamy, J-B; Séroussi, B; Griffon, N; Kerdelhué, G; Jaulent, M-C; Bouaud, J

2015-01-01

Each year, the International Medical Informatics Association Yearbook recognizes significant scientific papers, labelled as "best papers", published the previous year in the subfields of biomedical informatics that correspond to the different section topics of the journal. For each section, about fifteen pre-selected "candidate" best papers are externally peer-reviewed to select the actual best papers. Although based on the available literature, little is known about the pre-selection process. To move toward an explicit formalization of the candidate best papers selection process to reduce variability in the literature search across sections and over years. A methodological framework is proposed to build for each section topic specific queries tailored to PubMed and Web of Science citation databases. The two sets of returned papers are merged and reviewed by two independent section editors and citations are tagged as "discarded", "pending", and "kept". A protocolized consolidation step is then jointly conducted to resolve conflicts. A bibliographic software tool, BibReview, was developed to support the whole process. The proposed search strategy was fully applied to the Decision Support section of the 2013 edition of the Yearbook. For this section, 1124 references were returned (689 PubMed-specific, 254 WoS-specific, 181 common to both databases) among which the 15 candidate best papers were selected. The search strategy for determining candidate best papers for an IMIA Yearbook's section is now explicitly specified and allows for reproducibility. However, some aspects of the whole process remain reviewer-dependent, mostly because there is no characterization of a "best paper".

Behavioural and emotional disorders in childhood: A brief overview for paediatricians

PubMed Central

Ogundele, Michael O

2018-01-01

Mental health problems in children and adolescents include several types of emotional and behavioural disorders, including disruptive, depression, anxiety and pervasive developmental (autism) disorders, characterized as either internalizing or externalizing problems. Disruptive behavioural problems such as temper tantrums, attention deficit hyperactivity disorder, oppositional, defiant or conduct disorders are the commonest behavioural problems in preschool and school age children. The routine Paediatric clinic or Family Medicine/General Practitioner surgery presents with several desirable characteristics that make them ideal for providing effective mental health services to children and adolescents. DSM-5 and ICD-10 are the universally accepted standard criteria for the classification of mental and behaviour disorders in childhood and adults. The age and gender prevalence estimation of various childhood behavioural disorders are variable and difficult to compare worldwide. A review of relevant published literature was conducted, including published meta-analyses and national guidelines. We searched for articles indexed by Ovid, PubMed, PubMed Medical Central, CINAHL, EMBASE, Database of Abstracts and Reviews, and the Cochrane Database of Systematic reviews and other online sources. The searches were conducted using a combination of search expressions including “childhood”, “behaviour”, “disorders” or “problems”. Childhood behaviour and emotional problems with their related disorders have significant negative impacts on the individual, the family and the society. They are commonly associated with poor academic, occupational, and psychosocial functioning. It is important for all healthcare professionals, especially the Paediatricians to be aware of the range of presentation, prevention and management of the common mental health problems in children and adolescents. PMID:29456928

Endovascular Therapy Research in Lower Limb Peripheral Arterial Disease Published Over a 5-Year Period: Who is Publishing and Where?

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

Asadi, H.; Lee, R. J.; Sheehan, M.

IntroductionPeripheral arterial disease (PAD) is being increasingly managed by endovascular therapies. In this study, we identified the clinical services publishing research as well as the journals of publication over a 5-year period.MethodsTwenty keywords and phrases related to endovascular intervention were identified, and a literature search was performed through the PubMed database from January 2009 to January 2014. Inclusion criteria were English language, study population more than five patients, and matching the keyword search. Eligible studies were collated into a database and classified by journal of publication, PubMed number, article title, publishing clinical service, type of publication, country of origin, andmore » authors.Results825 studies from 114 different journals were identified. 297 papers were excluded. Of the 528 included papers, 204 (39%) were published by Vascular Surgery (VS), 157 (30%) by Interventional Radiology (IR), 101 (19%) by Cardiology, 43 (8%) by Angiology, 6 (1%) by Vascular Medicine, and 17 (3%) from miscellaneous services. 283 (54%) studies originated from Europe, 157 (30%) from North America, 76 (14%) from Asia, 6 from Australia, 3 each from South America and Africa. IR published the most papers on PAD endovascular intervention in Europe with VS second while this trend was reversed in the USA. The 528 papers were published in 98 different journals with retrospective case series (72%), the majority.ConclusionIR continues to play a significant research role in endovascular intervention in PAD, particularly in Europe, and specifically in below the knee intervention, pedal intervention, and drug-eluting technologies.« less

Diabetes research in Middle East countries; a scientometrics study from 1990 to 2012.

PubMed

Peykari, Niloofar; Djalalinia, Shirin; Kasaeian, Amir; Naderimagham, Shohreh; Hasannia, Tahereh; Larijani, Bagher; Farzadfar, Farshad

2015-03-01

Diabetes burden is a serious warning for urgent action plan across the world. Knowledge production in this context could provide evidences for more efficient interventions. Aimed to that, we quantify the trend of diabetes research outputs of Middle East countries focusing on the scientific publication numbers, citations, and international collaboration. This scientometrics study was performed based on the systematic analysis through three international databases; ISI, PubMed, and Scopus from 1990 to 2012. International collaboration of Middle East countries and citations was analyzed based on Scopus. Diabetes' publications in Iran specifically were assessed, and frequent used terms were mapped by VOSviewer software. Over 23-year period, the number of diabetes publications and related citations in Middle East countries had increasing trend. The number of articles on diabetes in ISI, PubMed, and Scopus were respectively; 13,994, 11,336, and 20,707. Turkey, Israel, Iran, Saudi Arabia, and Egypt have devoted the five top competition positions. In addition, Israel, Turkey, and Iran were leading countries in citation analysis. The most collaborative country with Middle East countries was USA and within the region, the most collaborative country was Saudi Arabia. Iran in all databases stands on third position and produced 12.7% of diabetes publications within region. Regarding diabetes researches, the frequent used terms in Iranian articles were "effect," "woman," and "metabolic syndrome." Ascending trend of diabetes research outputs in Middle East countries is appreciated but encouraging to strategic planning for maintaining this trend, and more collaboration between researchers is needed to regional health promotion.

Occipital Nerve Stimulation for the Treatment of Patients With Medically Refractory Occipital Neuralgia: Congress of Neurological Surgeons Systematic Review and Evidence-Based Guideline.

PubMed

Sweet, Jennifer A; Mitchell, Laura S; Narouze, Samer; Sharan, Ashwini D; Falowski, Steven M; Schwalb, Jason M; Machado, Andre; Rosenow, Joshua M; Petersen, Erika A; Hayek, Salim M; Arle, Jeffrey E; Pilitsis, Julie G

2015-09-01

Occipital neuralgia (ON) is a disorder characterized by sharp, electrical, paroxysmal pain, originating from the occiput and extending along the posterior scalp, in the distribution of the greater, lesser, and/or third occipital nerve. Occipital nerve stimulation (ONS) constitutes a promising therapy for medically refractory ON because it is reversible with minimal side effects and has shown continued efficacy with long-term follow-up. To conduct a systematic literature review and provide treatment recommendations for the use of ONS for the treatment of patients with medically refractory ON. A systematic literature search was conducted using the PubMed database and the Cochrane Library to locate articles published between 1966 and April 2014 using MeSH headings and keywords relevant to ONS as a means to treat ON. A second literature search was conducted using the PubMed database and the Cochrane Library to locate articles published between 1966 and June 2014 using MeSH headings and keywords relevant to interventions that predict response to ONS in ON. The strength of evidence of each article that underwent full text review and the resulting strength of recommendation were graded according to the guidelines development methodology of the American Association of Neurological Surgeons/Congress of Neurological Surgeons Joint Guidelines Committee. Nine studies met the criteria for inclusion in this guideline. All articles provided Class III Level evidence. Based on the data derived from this systematic literature review, the following Level III recommendation can be made: the use of ONS is a treatment option for patients with medically refractory ON.

Where are we after 60 years of paragonimiasis research? A bibliometric assessment

PubMed Central

Culquichicón, Carlos; Hernández-Pacherres, Arturo; Labán-Seminario, L. Max; Cardona-Ospina, Jaime A.; Rodríguez-Morales, Alfonso J.

2018-01-01

SUMMARY Paragonimiasis is highly prevalent endemic foodborne disease in Southeast Asia and Latin America, and constitutes a major public health concern. A bibliometric analysis was performed about the worldwide scientific production of paragonimiasis. We browsed in the Science Citation Index-Expanded (SCI-E) (1957–2015), Scopus (1976–2015), Medline/PubMed/GoPubMed® (1970–2015), ScIELO (1981–2014) and LILACS (1985- 2011). All types of articles were included and categorized by year of publication, number, type of scientific article, city and institution of origin, international cooperation, scientific journal, impact factor, language of publication, authors and H index. In SCI-E, 1,028 manuscripts were recovered, while Japan (21.9%) and the USA (17.7%) were the countries with highest scientific production. In this database, Asian region studies received 5,454 citations (H index=32). In Scopus 2161 items were recovered, corresponding to 45.8% of Asian countries. Japan (18.2%) was the first with the University of Miyazaki (11.7% of the country); South Korea (9.5%) was second with the Seoul National University (11.2% of the country). In SciELO 29 items were found, with no contributions from the Asian region. In LILACS 1487 articles were found (22.9% covering Asia). Among the databases, the Journal of Parasitology (Impact factor=1.227) showed the highest number of manuscripts and “Agatsuma T”, from Japan, was the author with most records. Japan and South Korea lead global scientific production on paragonimiasis. By contrast, in Latin America, production has been extremely low especially in the last five years. PMID:28603233

Where are we after 60 years of paragonimiasis research? A bibliometric assessment.

PubMed

Culquichicón, Carlos; Hernández-Pacherres, Arturo; Labán-Seminario, L Max; Cardona-Ospina, Jaime A; Rodríguez-Morales, Alfonso J

2017-06-01

Paragonimiasis is highly prevalent endemic food-borne disease in Southeast Asia and Latin America, and constitutes a major public health concern. A bibliometric analysis was performed about the worldwide scientific production of paragonimiasis. We browsed in the Science Citation Index-Expanded (SCI-E) (1957-2015), Scopus (1976-2015), Medline/PubMed/GoPubMed® (1970-2015), ScIELO (1981-2014) and LILACS (1985-2011). All types of articles were included and categorized by year of publication, number, type of scientific article, city and institution of origin, international cooperation, scientific journal, impact factor, language of publication, authors and H index. In SCI-E, 1,028 manuscripts were recovered, while Japan (21.9%) and the USA (17.7%) were the countries with highest scientific production. In this database, Asian region studies received 5,454 citations (H index=32). In Scopus 2161 items were recovered, corresponding to 45.8% of Asian countries. Japan (18.2%) was the first with the University of Miyazaki (11.7% of the country); South Korea (9.5%) was second with the Seoul National University (11.2% of the country). In SciELO 29 items were found, with no contributions from the Asian region. In LILACS 1487 articles were found (22.9% covering Asia). Among the databases, the Journal of Parasitology (Impact factor=1.227) showed the highest number of manuscripts and "Agatsuma T", from Japan, was the author with most records. Japan and South Korea lead global scientific production on paragonimiasis. By contrast, in Latin America, production has been extremely low especially in the last five years.

A Neural Network Model of Individual Differences in Task Switching Abilities (Author’s Manuscript)

DTIC Science & Technology

2014-04-30

risk for schizophrenia . Proceedings of the National Academy of Sciences of the United States of America. 2001; 98:6917–6922. [PubMed: 11381111] Engle, RW...interference in verbal working memory. Neuropsychology . 2006; 20:511–528. [PubMed: 16938014] Herd SA, Banich MT, O’Reilly RC. Neural mechanisms of cognitive

Role of Polymerase Gamma Mutations in Breast Tumorigenesis

DTIC Science & Technology

2010-08-01

2005;309:481–484. [PubMed: 16020738] 47. Alonso A, Martin P, Albarran C, Aquilera B, Garcia O, Guzman A, et al. Detection of somatic mutations in the...Hum. Genet 2005;76:1081–1086. [PubMed: 15877282] 30. Spinazzola A, Viscomi C, Fernandez -Vizarra E, Carrara F, D’Adamo P, Calvo S, et al. MPV17

The Role of Polymerase Gamma Mutations in Breast Tumorigenesis

DTIC Science & Technology

2011-01-01

481–484. [PubMed: 16020738] 47. Alonso A, Martin P, Albarran C, Aquilera B, Garcia O, Guzman A, et al. Detection of somatic mutations in the...Hum. Genet 2005;76:1081–1086. [PubMed: 15877282] 30. Spinazzola A, Viscomi C, Fernandez -Vizarra E, Carrara F, D’Adamo P, Calvo S, et al. MPV17 encodes

[Neuromuscular electric stimulation therapy in otorhinolaryngology].

PubMed

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

2014-02-01

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

PGMapper: a web-based tool linking phenotype to genes.

PubMed

Xiong, Qing; Qiu, Yuhui; Gu, Weikuan

2008-04-01

With the availability of whole genome sequence in many species, linkage analysis, positional cloning and microarray are gradually becoming powerful tools for investigating the links between phenotype and genotype or genes. However, in these methods, causative genes underlying a quantitative trait locus, or a disease, are usually located within a large genomic region or a large set of genes. Examining the function of every gene is very time consuming and needs to retrieve and integrate the information from multiple databases or genome resources. PGMapper is a software tool for automatically matching phenotype to genes from a defined genome region or a group of given genes by combining the mapping information from the Ensembl database and gene function information from the OMIM and PubMed databases. PGMapper is currently available for candidate gene search of human, mouse, rat, zebrafish and 12 other species. Available online at http://www.genediscovery.org/pgmapper/index.jsp.

Database resources of the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Church, Deanna M.; Lash, Alex E.; Leipe, Detlef D.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M.; Tatusova, Tatiana A.; Wagner, Lukas; Rapp, Barbara A.

2001-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI’s Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, GeneMap’99, Human–Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP), SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheri­tance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov. PMID:11125038

[Use of multiple regression models in observational studies (1970-2013) and requirements of the STROBE guidelines in Spanish scientific journals].

PubMed

Real, J; Cleries, R; Forné, C; Roso-Llorach, A; Martínez-Sánchez, J M

In medicine and biomedical research, statistical techniques like logistic, linear, Cox and Poisson regression are widely known. The main objective is to describe the evolution of multivariate techniques used in observational studies indexed in PubMed (1970-2013), and to check the requirements of the STROBE guidelines in the author guidelines in Spanish journals indexed in PubMed. A targeted PubMed search was performed to identify papers that used logistic linear Cox and Poisson models. Furthermore, a review was also made of the author guidelines of journals published in Spain and indexed in PubMed and Web of Science. Only 6.1% of the indexed manuscripts included a term related to multivariate analysis, increasing from 0.14% in 1980 to 12.3% in 2013. In 2013, 6.7, 2.5, 3.5, and 0.31% of the manuscripts contained terms related to logistic, linear, Cox and Poisson regression, respectively. On the other hand, 12.8% of journals author guidelines explicitly recommend to follow the STROBE guidelines, and 35.9% recommend the CONSORT guideline. A low percentage of Spanish scientific journals indexed in PubMed include the STROBE statement requirement in the author guidelines. Multivariate regression models in published observational studies such as logistic regression, linear, Cox and Poisson are increasingly used both at international level, as well as in journals published in Spanish. Copyright © 2015 Sociedad Española de Médicos de Atención Primaria (SEMERGEN). Publicado por Elsevier España, S.L.U. All rights reserved.

Why Principal Investigators Funded by the U.S. National Institutes of Health Publish in the Public Library of Science Journals

ERIC Educational Resources Information Center

Pontika, Nancy

2015-01-01

Introduction: The National Institutes of Health public access policy requires the principal investigators of any Institutes-funded research to submit their manuscript to PubMed Central, and the open access publisher Public Library of Science submits all articles to PubMed Central, irrespective of funder. Whether the investigators, who made the…

The publication echo: effects of retrieving literature in PubMed by year of publication.

PubMed

Spreckelsen, Cord; Deserno, Thomas M; Spitzer, Klaus

2010-04-01

In PubMed search forms, the publication date refers to both the date of electronic and printed publication. This fact is documented in PubMed, but difficult to anticipate by the users and can provoke misinterpretations of search results. The Technical Note aims at systematically investing the effect (referred to as the publication echo), clarifying onset and extent of the publication echo, and comments on its impact. Papers with ambiguous publication dates are systematically retrieved and a trend analysis with seasonal decomposition on monthly publication data is performed. First doubled search results were found for 1999, their number since then rapidly increasing. Up to 17.6% of all articles of a year are found to be published electronically and in print, which can be before or afterwards. Maximum delay between the two dates is three years, except for one singular publication, where it is five years. Publication trends are exponential and linear when considering echoed and echo-cleaned data, respectively. As a conclusion, we suggest using a query formulation that unambiguously retrieves literature from PubMed by the date of publication. (c) 2010 Elsevier Ireland Ltd. All rights reserved.

Antileishmanial and Immunomodulatory Activity of Allium sativum (Garlic)

PubMed Central

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

2015-01-01

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

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

2007-01-01

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 240 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage (www.ncbi.nlm.nih.gov).

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

2005-01-01

GenBank is a comprehensive database that contains publicly available DNA sequences for more than 165,000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in the UK and the DNA Data Bank of Japan helps to ensure worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at http://www.ncbi.nlm.nih.gov.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

2006-01-01

GenBank (R) is a comprehensive database that contains publicly available DNA sequences for more than 205 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the Web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at www.ncbi.nlm.nih.gov.

Stem cells in bone diseases: current clinical practice.

PubMed

Beyth, Shaul; Schroeder, Josh; Liebergall, Meir

2011-01-01

Bone is an obvious candidate tissue for stem cell therapy. This review provides an update of existing stem cell-based clinical treatments for bone pathologies. A systematic computerized literature search was conducted. The following databases were accessed on 10 February 2011: NIH clinical trials database, PubMed, Ovid and Cochrane Reviews. Stem cell therapy offers new options for bone conditions, both acquired and inherited. There is still no agreement on the exact definition of 'mesenchymal stem cells'. Consequently, it is difficult to appreciate the effect of culture expansion and the feasibility of allogeneic transplantation. Based on the sound foundations of pre-clinical research, stem cell-based treatments and protocols have recently emerged. Well-designed prospective clinical trials are needed in order to establish and develop stem cell therapy for bone diseases.

Building an efficient curation workflow for the Arabidopsis literature corpus

PubMed Central

Li, Donghui; Berardini, Tanya Z.; Muller, Robert J.; Huala, Eva

2012-01-01

TAIR (The Arabidopsis Information Resource) is the model organism database (MOD) for Arabidopsis thaliana, a model plant with a literature corpus of about 39 000 articles in PubMed, with over 4300 new articles added in 2011. We have developed a literature curation workflow incorporating both automated and manual elements to cope with this flood of new research articles. The current workflow can be divided into two phases: article selection and curation. Structured controlled vocabularies, such as the Gene Ontology and Plant Ontology are used to capture free text information in the literature as succinct ontology-based annotations suitable for the application of computational analysis methods. We also describe our curation platform and the use of text mining tools in our workflow. Database URL: www.arabidopsis.org PMID:23221298

Primary Mucinous Cystadenocarcinoma of the Breast with Endocervical-Like Mucinous Epithelium

PubMed Central

Lin, Dong-Liang; Hu, Ji-Lin; Shao, Shi-Hong; Sun, Dong-Mei; Wang, Ji-Gang

2013-01-01

Summary Background Primary mucinous cystadenocarcinoma of the breast is an extremely rare entity. To the best of our knowledge, only 17 patients have been described in the PubMed database. Case Report Here, we report a primary breast mucinous cystadenocarcinoma with endocervical-like mucinous epithelium in a 62-year-old woman. The patient was followed for 5 months without any adjuvant treatment and she continues to be disease free. Conclusions Primary breast mucinous cystadenocarcinoma usually displays unique pathologic and immunohistochemical characteristics simulating its ovarian counterparts; it seems to have a good prognosis after complete resection. PMID:24550753

Physical well-being of oncology caregivers: an important quality-of-life domain.

PubMed

Glajchen, Myra

2012-11-01

To provide an overview of research and practice related to the physical well-being of oncology caregivers. Literature retrieved through the PubMed and CINAHL databases. Caregivers play an important role in supporting people with cancer at every stage of the illness trajectory. Because caregiving is inherently stressful, caregivers should be routinely included in the assessment and treatment of patients with cancer. Oncology nurses are uniquely positioned to play a vital role in recognizing caregiver strain and intervening to break the cycle of unremitting physical and psychosocial burden. Copyright © 2012 Elsevier Inc. All rights reserved.

Current trends in laparoscopic groin hernia repair: A review

PubMed Central

Pahwa, Harvinder Singh; Kumar, Awanish; Agarwal, Prerit; Agarwal, Akshay Anand

2015-01-01

Hernia is a common problem of the modern world with its incidence more in developing countries. Inguinal hernia is the most common groin hernia repaired worldwide. With advancement in technology operative techniques of repair have also evolved. A PubMed and COCHRANE database search was accomplished in this regard to establish the current status of laparoscopic inguinal hernia repair in view of recent published literature. Published literature support that laparoscopic hernia repair is best suited for recurrent and bilateral inguinal hernia although it may be offered for primary inguinal hernia if expertise is available. PMID:26380826

Introducing meta-services for biomedical information extraction

PubMed Central

Leitner, Florian; Krallinger, Martin; Rodriguez-Penagos, Carlos; Hakenberg, Jörg; Plake, Conrad; Kuo, Cheng-Ju; Hsu, Chun-Nan; Tsai, Richard Tzong-Han; Hung, Hsi-Chuan; Lau, William W; Johnson, Calvin A; Sætre, Rune; Yoshida, Kazuhiro; Chen, Yan Hua; Kim, Sun; Shin, Soo-Yong; Zhang, Byoung-Tak; Baumgartner, William A; Hunter, Lawrence; Haddow, Barry; Matthews, Michael; Wang, Xinglong; Ruch, Patrick; Ehrler, Frédéric; Özgür, Arzucan; Erkan, Güneş; Radev, Dragomir R; Krauthammer, Michael; Luong, ThaiBinh; Hoffmann, Robert; Sander, Chris; Valencia, Alfonso

2008-01-01

We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; ). This prototype platform is a joint effort of 13 research groups and provides automatically generated annotations for PubMed/Medline abstracts. Annotation types cover gene names, gene IDs, species, and protein-protein interactions. The annotations are distributed by the meta-server in both human and machine readable formats (HTML/XML). This service is intended to be used by biomedical researchers and database annotators, and in biomedical language processing. The platform allows direct comparison, unified access, and result aggregation of the annotations. PMID:18834497

Mining the literature: new methods to exploit keyword profiles.

PubMed

Andrade-Navarro, Miguel A

2012-01-01

Bibliographic records in the PubMed database of biomedical literature are annotated with Medical Subject Headings (MeSH) by curators, which summarize the content of the articles. Two recent publications explain how to generate profiles of MeSH terms for a set of bibliographic records and to use them to define any given concept by its associated literature. These concepts can then be related by their keyword profiles, and this can be used, for example, to detect new associations between genes and inherited diseases. http://www.biomedcentral.com/1471-2105/13/249/abstracthttp://genomemedicine.com/content/4/9/75/abstract.

Management of hepatocellular carcinoma: an overview of major findings from meta-analyses

PubMed Central

Guo, Xiaozhong; Han, Guohong

2016-01-01

This paper aims to systematically review the major findings from meta-analyses comparing different treatment options for hepatocellular carcinoma (HCC). A total of 153 relevant papers were searched via the PubMed, EMBASE, and Cochrane library databases. They were classified according to the mainstay treatment modalities (i.e., liver transplantation, surgical resection, radiofrequency ablation, transarterial embolization or chemoembolization, sorafenib, and others). The primary outcome data, such as overall survival, diseases-free survival or recurrence-free survival, progression-free survival, and safety, were summarized. The recommendations and uncertainties regarding the treatment of HCC were also proposed. PMID:27167195

Treatment of cannabis use among people with psychotic or depressive disorders: a systematic review.

PubMed

Baker, Amanda L; Hides, Leanne; Lubman, Dan I

2010-03-01

This article systematically reviews the evidence from randomized controlled trials (RCTs) for pharmacologic and psychological approaches to the treatment of cannabis use among individuals with psychotic or depressive disorders. A systematic literature search was conducted using the PubMed and PsychINFO databases from inception to December 2008. Individual searches in cannabis use (search terms: marijuana, cannabis, marijuana abuse, cannabis abuse, marijuana usage, cannabis usage), mental disorders (search terms: mood disorders, affective disorders, anxiety disorders, anxiety, depressive disorder, depression, psychotic disorders, psychosis, mental disorders), and pharmacotherapy (search terms: medication, drug therapy, pharmacotherapy, psychopharmacology, clinical trials, drug trial, treatment trial) were conducted and limited to humans, adolescents and adults. A search combining the individual cannabis use, mental disorder and pharmacotherapy searches produced 1,713 articles (PubMed = 1,398; PsychINFO = 315). Combining the cannabis use and mental disorder searches while limiting them to English articles and RCTs produced a total of 286 articles (PubMed = 228; PsychINFO = 58). From this literature, there were 7 RCTs conducted among mental health clients that reported cannabis use outcomes using pharmacologic or psychological interventions. While few RCTs have been conducted, there is evidence that pharmacologic and psychological interventions are effective for reducing cannabis use in the short-term among people with psychotic disorders or depression. Although it is difficult to make evidence-based treatment recommendations due to the paucity of research in this area, available studies indicate that effectively treating the mental health disorder with standard pharmacotherapy may be associated with a reduction in cannabis use and that longer or more intensive psychological interventions rather than brief interventions may be required, particularly among heavier users of cannabis and those with more chronic mental disorders. Specific recommendations regarding the type and length of specific psychological treatments cannot be made at this time, although motivational interviewing and cognitive-behavioral therapy approaches appear most promising. (c) 2010 Physicians Postgraduate Press, Inc.

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

PubMed Central

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

2015-01-01

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

Use and Acceptance of Complementary and Alternative Medicine Among the General Population and Medical Personnel: A Systematic Review

PubMed Central

Frass, Michael; Strassl, Robert Paul; Friehs, Helmut; Müllner, Michael; Kundi, Michael; Kaye, Alan D.

2012-01-01

Background The interest in complementary and alternative medicine (CAM) has increased during the past decade and the attitude of the general public is mainly positive, but the debate about the clinical effectiveness of these therapies remains controversial among many medical professionals. Methods We conducted a systematic search of the existing literature utilizing different databases, including PubMed/Medline, PSYNDEX, and PsycLit, to research the use and acceptance of CAM among the general population and medical personnel. A special focus on CAM-referring literature was set by limiting the PubMed search to “Complementary Medicine” and adding two other search engines: CAMbase (www.cambase.de) and CAMRESEARCH (www.camresearch.net). These engines were used to reveal publications that at the time of the review were not indexed in PubMed. Results A total of 16 papers met the scope criteria. Prevalence rates of CAM in each of the included studies were between 5% and 74.8%. We found a higher utilization of homeopathy and acupuncture in German-speaking countries. Excluding any form of spiritual prayer, the data demonstrate that chiropractic manipulation, herbal medicine, massage, and homeopathy were the therapies most commonly used by the general population. We identified sex, age, and education as predictors of CAM utilization: More users were women, middle aged, and more educated. The ailments most often associated with CAM utilization included back pain or pathology, depression, insomnia, severe headache or migraine, and stomach or intestinal illnesses. Medical students were the most critical toward CAM. Compared to students of other professions (ie, nursing students: 44.7%, pharmacy students: 18.2%), medical students reported the least consultation with a CAM practitioner (10%). Conclusions The present data demonstrate an increase of CAM usage from 1990 through 2006 in all countries investigated. We found geographical differences, as well as differences between the general population and medical personnel. PMID:22438782

Accessing Biomedical Literature in the Current Information Landscape

PubMed Central

Khare, Ritu; Leaman, Robert; Lu, Zhiyong

2015-01-01

i. Summary Biomedical and life sciences literature is unique because of its exponentially increasing volume and interdisciplinary nature. Biomedical literature access is essential for several types of users including biomedical researchers, clinicians, database curators, and bibliometricians. In the past few decades, several online search tools and literature archives, generic as well as biomedicine-specific, have been developed. We present this chapter in the light of three consecutive steps of literature access: searching for citations, retrieving full-text, and viewing the article. The first section presents the current state of practice of biomedical literature access, including an analysis of the search tools most frequently used by the users, including PubMed, Google Scholar, Web of Science, Scopus, and Embase, and a study on biomedical literature archives such as PubMed Central. The next section describes current research and the state-of-the-art systems motivated by the challenges a user faces during query formulation and interpretation of search results. The research solutions are classified into five key areas related to text and data mining, text similarity search, semantic search, query support, relevance ranking, and clustering results. Finally, the last section describes some predicted future trends for improving biomedical literature access, such as searching and reading articles on portable devices, and adoption of the open access policy. PMID:24788259

The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis.

PubMed

Van Landeghem, Sofie; De Bodt, Stefanie; Drebert, Zuzanna J; Inzé, Dirk; Van de Peer, Yves

2013-03-01

Despite the availability of various data repositories for plant research, a wealth of information currently remains hidden within the biomolecular literature. Text mining provides the necessary means to retrieve these data through automated processing of texts. However, only recently has advanced text mining methodology been implemented with sufficient computational power to process texts at a large scale. In this study, we assess the potential of large-scale text mining for plant biology research in general and for network biology in particular using a state-of-the-art text mining system applied to all PubMed abstracts and PubMed Central full texts. We present extensive evaluation of the textual data for Arabidopsis thaliana, assessing the overall accuracy of this new resource for usage in plant network analyses. Furthermore, we combine text mining information with both protein-protein and regulatory interactions from experimental databases. Clusters of tightly connected genes are delineated from the resulting network, illustrating how such an integrative approach is essential to grasp the current knowledge available for Arabidopsis and to uncover gene information through guilt by association. All large-scale data sets, as well as the manually curated textual data, are made publicly available, hereby stimulating the application of text mining data in future plant biology studies.

Results of an assessment of information needs among speech-language pathologists and audiologists in Idaho.

PubMed

Guo, Ruiling; Bain, Barbara A; Willer, Janene

2008-04-01

The research assesses the information needs of speech-language pathologists (SLPs) and audiologists in Idaho and identifies specific needs for training in evidence-based practice (EBP) principles and searching EBP resources. A survey was developed to assess knowledge and skills in accessing information. Questionnaires were distributed to 217 members of the Idaho Speech-Language-Hearing Association, who were given multiple options to return the assessment survey (web, email, mail). Data were analyzed descriptively and statistically. The total response rate was 38.7% (84/217). Of the respondents, 87.0% (73/84) indicated insufficient knowledge and skills to search PubMed. Further, 47.6% (40/84) indicated limited knowledge of EBP. Of professionals responding, 52.4% (44/84) reported interest in learning more about EBP and 47.6% (40/84) reported interest in learning to search PubMed. SLPs and audiologists who graduated within the last 10 years were more likely to respond online, while those graduating prior to that time preferred to respond via hard copy. DISCUSSIONS/CONCLUSION: More effort should be made to ensure that SLPs and audiologists develop skills in locating information to support their practice. Results from this information needs assessment were used to design a training and outreach program on EBP and EBP database searching for SLPs and audiologists in Idaho.

Essential oils, their therapeutic properties, and implication in dentistry: A review

PubMed Central

Dagli, Namrata; Dagli, Rushabh; Mahmoud, Rasha Said; Baroudi, Kusai

2015-01-01

Background: Antibacterial treatments currently used for treatment cause several side effects, and bacterial resistance to the antibiotics is also increasing. Therefore, there is need to find better alternatives. Essential oils (EOs) have been used for treatment of various ailments since ancient times and have gained popularity over the years. Safety and efficacy of EOs have been proved by several clinical trials. This review gives an overview on the EOs, their uses, and adverse effects. Materials and Methods: A literature search was performed in the PubMed for clinical trial studies and review articles on EOs published up to February 2015. The search was performed during March 2015. The following keywords were used: “Lavender essential oil,” “cinnamon oil,” “clove oil,” “eucalyptus oil,” “peppermint oil,” “lemon EOs,” and “tea tree oil.” Results: Total 70 relevant articles were found in PubMed database. After screening of abstracts, 52 articles were selected to be included in the present review. Conclusion: On the basis of the available information, it can be concluded that EOs have the potential to be developed as preventive or therapeutic agents for various oral diseases, but further clinical trials are required to establish their safety and efficacy. PMID:26539382

From Mind to Body: Is Mental Practice Effective on Strength Gains? A Meta-Analysis.

PubMed

Manochio, João Paulo; Lattari, Eduardo; Portugal, Eduardo Matta Mello; Monteiro-Junior, Renato Sobral; Paes, Flávia; Budde, Henning; de Tarso Veras Farinatti, Paulo; Arias-Carrión, Oscar; Wegner, Mirko; Carta, Mauro Giovanni; Mura, Gioia; Ferreira Rocha, Nuno Barbosa; Almada, Leonardo Ferreira; Nardi, Antonio Egidio; Yuan, Ti-Fei; Machado, Sergio

2015-01-01

Mental practice is an internal reproduction of a motor act (whose intention is to promote learning and improving motor skills). Some studies have shown that other cognitive strategies also increase the strength and muscular resistance in healthy people by the enhancement of the performance during dynamic tasks. Mental training sessions may be primordial to improving muscle strength in different subjects. The aim of this study was to systematically review and meta-analiyze studies that assessed whether mental practice is effective in improving muscular strength. We conducted an electronic-computed search in Pub-Med/Medline and ISI Web of Knowledge, Scielo and manual searchs, searching papers written in English between 1991 and 2014. There were 44 studies in Pub-Med/Medline, 631 in ISI Web of Knowledge, 11 in Scielo and 3 in manual searchs databases. After exclusion of studies for duplicate, unrelated to the topic by title and summary, different samples and methodologies, a meta-analysis of 4 studies was carried out to identify the dose-response relationship. We did not find evidence that mental practice is effective in increasing strength in healthy individuals. There is no evidence that mental practice alone can be effective to induce strength gains or to optimize the training effects.

Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.

PubMed

Druzinsky, Robert E; Balhoff, James P; Crompton, Alfred W; Done, James; German, Rebecca Z; Haendel, Melissa A; Herrel, Anthony; Herring, Susan W; Lapp, Hilmar; Mabee, Paula M; Muller, Hans-Michael; Mungall, Christopher J; Sternberg, Paul W; Van Auken, Kimberly; Vinyard, Christopher J; Williams, Susan H; Wall, Christine E

2016-01-01

In recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required. Here we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repository for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). We compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar. Our tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities.