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.

A comparative study of six European databases of medically oriented Web resources.

PubMed

Abad García, Francisca; González Teruel, Aurora; Bayo Calduch, Patricia; de Ramón Frias, Rosa; Castillo Blasco, Lourdes

2005-10-01

The paper describes six European medically oriented databases of Web resources, pertaining to five quality-controlled subject gateways, and compares their performance. The characteristics, coverage, procedure for selecting Web resources, record structure, searching possibilities, and existence of user assistance were described for each database. Performance indicators for each database were obtained by means of searches carried out using the key words, "myocardial infarction." Most of the databases originated in the 1990s in an academic or library context and include all types of Web resources of an international nature. Five databases use Medical Subject Headings. The number of fields per record varies between three and nineteen. The language of the search interfaces is mostly English, and some of them allow searches in other languages. In some databases, the search can be extended to Pubmed. Organizing Medical Networked Information, Catalogue et Index des Sites Médicaux Francophones, and Diseases, Disorders and Related Topics produced the best results. The usefulness of these databases as quick reference resources is clear. In addition, their lack of content overlap means that, for the user, they complement each other. Their continued survival faces three challenges: the instability of the Internet, maintenance costs, and lack of use in spite of their potential usefulness.

Integration of multiple DICOM Web servers into an enterprise-wide Web-based electronic medical record

NASA Astrophysics Data System (ADS)

Stewart, Brent K.; Langer, Steven G.; Martin, Kelly P.

1999-07-01

The purpose of this paper is to integrate multiple DICOM image webservers into the currently existing enterprises- wide web-browsable electronic medical record. Over the last six years the University of Washington has created a clinical data repository combining in a distributed relational database information from multiple departmental databases (MIND). A character cell-based view of this data called the Mini Medical Record (MMR) has been available for four years, MINDscape, unlike the text-based MMR. provides a platform independent, dynamic, web browser view of the MIND database that can be easily linked with medical knowledge resources on the network, like PubMed and the Federated Drug Reference. There are over 10,000 MINDscape user accounts at the University of Washington Academic Medical Centers. The weekday average number of hits to MINDscape is 35,302 and weekday average number of individual users is 1252. DICOM images from multiple webservers are now being viewed through the MINDscape electronic medical record.

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.

Google Scholar versus PubMed in locating primary literature to answer drug-related questions.

PubMed

Freeman, Maisha Kelly; Lauderdale, Stacy A; Kendrach, Michael G; Woolley, Thomas W

2009-03-01

Google Scholar linked more visitors to biomedical journal Web sites than did PubMed after the database's initial release; however, its usefulness in locating primary literature articles is unknown. To assess in both databases the availability of primary literature target articles; total number of citations; availability of free, full-text journal articles; and number of primary literature target articles retrieved by year within the first 100 citations of the search results. Drug information question reviews published in The Annals of Pharmacotherapy Drug Information Rounds column served as targets to determine the retrieval ability of Google Scholar and PubMed searches. Reviews printed in this column from January 2006 to June 2007 were eligible for study inclusion. Articles were chosen if at least 2 key words of the printed article were included in the PubMed Medical Subject Heading (MeSH) database, and these terms were searched in both databases. Twenty-two of 33 (67%) eligible Drug Information Rounds articles met the inclusion criteria. The median number of primary literature articles used in each of these articles was 6.5 (IQR 4.8, 8.3; mean +/- SD 8 +/- 5.4). No significant differences were found for the mean number of target primary literature articles located within the first 100 citations in Google Scholar and PubMed searches (5.1 +/- 3.9 vs 5.3 +/- 3.3; p = 0.868). Google Scholar searches located more total results than PubMed (2211.6 +/- 3999.5 vs 44.2 +/- 47.4; p = 0.019). The availability of free, full-text journal articles per Drug Information Rounds article was similar between the databases (1.8 +/- 1.7 vs 2.3 +/- 1.7; p = 0.325). More primary literature articles published prior to 2000 were located with Google Scholar searches compared with PubMed (62.8% vs 34.9%; p = 0.017); however, no statistically significant differences between the databases were observed for articles published after 2000 (66.4 vs 77.1; p = 0.074). No significant differences were identified in the number of target primary literature articles located between databases. PubMed searches yielded fewer total citations than Google Scholar results; however, PubMed appears to be more specific than Google Scholar for locating relevant primary literature articles.

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

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…

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.

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.

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

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.

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.

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

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...

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

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…

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…

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

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.

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

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

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.

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…

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.

DGIdb 3.0: a redesign and expansion of the drug-gene interaction database.

PubMed

Cotto, Kelsy C; Wagner, Alex H; Feng, Yang-Yang; Kiwala, Susanna; Coffman, Adam C; Spies, Gregory; Wollam, Alex; Spies, Nicholas C; Griffith, Obi L; Griffith, Malachi

2018-01-04

The drug-gene interaction database (DGIdb, www.dgidb.org) consolidates, organizes and presents drug-gene interactions and gene druggability information from papers, databases and web resources. DGIdb normalizes content from 30 disparate sources and allows for user-friendly advanced browsing, searching and filtering for ease of access through an intuitive web user interface, application programming interface (API) and public cloud-based server image. DGIdb v3.0 represents a major update of the database. Nine of the previously included 24 sources were updated. Six new resources were added, bringing the total number of sources to 30. These updates and additions of sources have cumulatively resulted in 56 309 interaction claims. This has also substantially expanded the comprehensive catalogue of druggable genes and anti-neoplastic drug-gene interactions included in the DGIdb. Along with these content updates, v3.0 has received a major overhaul of its codebase, including an updated user interface, preset interaction search filters, consolidation of interaction information into interaction groups, greatly improved search response times and upgrading the underlying web application framework. In addition, the expanded API features new endpoints which allow users to extract more detailed information about queried drugs, genes and drug-gene interactions, including listings of PubMed IDs, interaction type and other interaction metadata.

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

PubMed

Samuel, Hamman W; Zaïane, Osmar R

2017-01-01

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

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

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.

Plant Genome Resources at the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Smith-White, Brian; Chetvernin, Vyacheslav; Resenchuk, Sergei; Dombrowski, Susan M.; Pechous, Steven W.; Tatusova, Tatiana; Ostell, James

2005-01-01

The National Center for Biotechnology Information (NCBI) integrates data from more than 20 biological databases through a flexible search and retrieval system called Entrez. A core Entrez database, Entrez Nucleotide, includes GenBank and is tightly linked to the NCBI Taxonomy database, the Entrez Protein database, and the scientific literature in PubMed. A suite of more specialized databases for genomes, genes, gene families, gene expression, gene variation, and protein domains dovetails with the core databases to make Entrez a powerful system for genomic research. Linked to the full range of Entrez databases is the NCBI Map Viewer, which displays aligned genetic, physical, and sequence maps for eukaryotic genomes including those of many plants. A specialized plant query page allow maps from all plant genomes covered by the Map Viewer to be searched in tandem to produce a display of aligned maps from several species. PlantBLAST searches against the sequences shown in the Map Viewer allow BLAST alignments to be viewed within a genomic context. In addition, precomputed sequence similarities, such as those for proteins offered by BLAST Link, enable fluid navigation from unannotated to annotated sequences, quickening the pace of discovery. NCBI Web pages for plants, such as Plant Genome Central, complete the system by providing centralized access to NCBI's genomic resources as well as links to organism-specific Web pages beyond NCBI. PMID:16010002

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

"Spice," "kryptonite," "black mamba": an overview of brand names and marketing strategies of novel psychoactive substances on the web.

PubMed

Corazza, Ornella; Valeriani, Giuseppe; Bersani, Francesco Saverio; Corkery, John; Martinotti, Giovanni; Bersani, Giuseppe; Schifano, Fabrizio

2014-01-01

Abstract Introduction: Novel Psychoactive Substances (NPSs) are often sold online as "legal" and "safer" alternatives to International Controlled Drugs (ICDs) with captivating marketing strategies. Our aim was to review and summarize such strategies in terms of the appearance of the products, the brand names, and the latest trends in the illicit online marketplaces. Scientific data were searched in PsychInfo and Pubmed databases; results were integrated with an extensive monitoring of Internet (websites, online shops, chat rooms, fora, social networks) and media sources in nine languages (English, French, Farsi, Portuguese, Arabic, Russian, Spanish, and Chinese simplified/traditional) available from secure databases of the Global Public Health Intelligence Network. Evolving strategies for the online diffusion and the retail of NPSs have been identified, including discounts and periodic offers on chosen products. Advertisements and new brand names have been designed to attract customers, especially young people. An increased number of retailers have been recorded as well as new Web platforms and privacy systems. NPSs represent an unprecedented challenge in the field of public health with social, cultural, legal, and political implications. Web monitoring activities are essential for mapping the diffusion of NPSs and for supporting innovative Web-based prevention programmes.

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

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

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.

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.

Big Data in Health: a Literature Review from the Year 2005.

PubMed

de la Torre Díez, Isabel; Cosgaya, Héctor Merino; Garcia-Zapirain, Begoña; López-Coronado, Miguel

2016-09-01

The information stored in healthcare systems has increased over the last ten years, leading it to be considered Big Data. There is a wealth of health information ready to be analysed. However, the sheer volume raises a challenge for traditional methods. The aim of this article is to conduct a cutting-edge study on Big Data in healthcare from 2005 to the present. This literature review will help researchers to know how Big Data has developed in the health industry and open up new avenues for research. Information searches have been made on various scientific databases such as Pubmed, Science Direct, Scopus and Web of Science for Big Data in healthcare. The search criteria were "Big Data" and "health" with a date range from 2005 to the present. A total of 9724 articles were found on the databases. 9515 articles were discarded as duplicates or for not having a title of interest to the study. 209 articles were read, with the resulting decision that 46 were useful for this study. 52.6 % of the articles used were found in Science Direct, 23.7 % in Pubmed, 22.1 % through Scopus and the remaining 2.6 % through the Web of Science. Big Data has undergone extremely high growth since 2011 and its use is becoming compulsory in developed nations and in an increasing number of developing nations. Big Data is a step forward and a cost reducer for public and private healthcare.

Electronic Biomedical Literature Search for Budding Researcher

PubMed Central

Thakre, Subhash B.; Thakre S, Sushama S.; Thakre, Amol D.

2013-01-01

Search for specific and well defined literature related to subject of interest is the foremost step in research. When we are familiar with topic or subject then we can frame appropriate research question. Appropriate research question is the basis for study objectives and hypothesis. The Internet provides a quick access to an overabundance of the medical literature, in the form of primary, secondary and tertiary literature. It is accessible through journals, databases, dictionaries, textbooks, indexes, and e-journals, thereby allowing access to more varied, individualised, and systematic educational opportunities. Web search engine is a tool designed to search for information on the World Wide Web, which may be in the form of web pages, images, information, and other types of files. Search engines for internet-based search of medical literature include Google, Google scholar, Scirus, Yahoo search engine, etc., and databases include MEDLINE, PubMed, MEDLARS, etc. Several web-libraries (National library Medicine, Cochrane, Web of Science, Medical matrix, Emory libraries) have been developed as meta-sites, providing useful links to health resources globally. A researcher must keep in mind the strengths and limitations of a particular search engine/database while searching for a particular type of data. Knowledge about types of literature, levels of evidence, and detail about features of search engine as available, user interface, ease of access, reputable content, and period of time covered allow their optimal use and maximal utility in the field of medicine. Literature search is a dynamic and interactive process; there is no one way to conduct a search and there are many variables involved. It is suggested that a systematic search of literature that uses available electronic resource effectively, is more likely to produce quality research. PMID:24179937

Electronic biomedical literature search for budding researcher.

PubMed

Thakre, Subhash B; Thakre S, Sushama S; Thakre, Amol D

2013-09-01

Search for specific and well defined literature related to subject of interest is the foremost step in research. When we are familiar with topic or subject then we can frame appropriate research question. Appropriate research question is the basis for study objectives and hypothesis. The Internet provides a quick access to an overabundance of the medical literature, in the form of primary, secondary and tertiary literature. It is accessible through journals, databases, dictionaries, textbooks, indexes, and e-journals, thereby allowing access to more varied, individualised, and systematic educational opportunities. Web search engine is a tool designed to search for information on the World Wide Web, which may be in the form of web pages, images, information, and other types of files. Search engines for internet-based search of medical literature include Google, Google scholar, Scirus, Yahoo search engine, etc., and databases include MEDLINE, PubMed, MEDLARS, etc. Several web-libraries (National library Medicine, Cochrane, Web of Science, Medical matrix, Emory libraries) have been developed as meta-sites, providing useful links to health resources globally. A researcher must keep in mind the strengths and limitations of a particular search engine/database while searching for a particular type of data. Knowledge about types of literature, levels of evidence, and detail about features of search engine as available, user interface, ease of access, reputable content, and period of time covered allow their optimal use and maximal utility in the field of medicine. Literature search is a dynamic and interactive process; there is no one way to conduct a search and there are many variables involved. It is suggested that a systematic search of literature that uses available electronic resource effectively, is more likely to produce quality research.

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

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.

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.

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.

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

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.

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.

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.

Olelo: a web application for intuitive exploration of biomedical literature

PubMed Central

Niedermeier, Julian; Jankrift, Marcel; Tietböhl, Sören; Stachewicz, Toni; Folkerts, Hendrik; Uflacker, Matthias; Neves, Mariana

2017-01-01

Abstract Researchers usually query the large biomedical literature in PubMed via keywords, logical operators and filters, none of which is very intuitive. Question answering systems are an alternative to keyword searches. They allow questions in natural language as input and results reflect the given type of question, such as short answers and summaries. Few of those systems are available online but they experience drawbacks in terms of long response times and they support a limited amount of question and result types. Additionally, user interfaces are usually restricted to only displaying the retrieved information. For our Olelo web application, we combined biomedical literature and terminologies in a fast in-memory database to enable real-time responses to researchers’ queries. Further, we extended the built-in natural language processing features of the database with question answering and summarization procedures. Combined with a new explorative approach of document filtering and a clean user interface, Olelo enables a fast and intelligent search through the ever-growing biomedical literature. Olelo is available at http://www.hpi.de/plattner/olelo. PMID:28472397

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.

CNV-WebStore: online CNV analysis, storage and interpretation.

PubMed

Vandeweyer, Geert; Reyniers, Edwin; Wuyts, Wim; Rooms, Liesbeth; Kooy, R Frank

2011-01-05

Microarray technology allows the analysis of genomic aberrations at an ever increasing resolution, making functional interpretation of these vast amounts of data the main bottleneck in routine implementation of high resolution array platforms, and emphasising the need for a centralised and easy to use CNV data management and interpretation system. We present CNV-WebStore, an online platform to streamline the processing and downstream interpretation of microarray data in a clinical context, tailored towards but not limited to the Illumina BeadArray platform. Provided analysis tools include CNV analsyis, parent of origin and uniparental disomy detection. Interpretation tools include data visualisation, gene prioritisation, automated PubMed searching, linking data to several genome browsers and annotation of CNVs based on several public databases. Finally a module is provided for uniform reporting of results. CNV-WebStore is able to present copy number data in an intuitive way to both lab technicians and clinicians, making it a useful tool in daily clinical practice.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

2010-01-01

GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling 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 the NCBI Entrez retrieval system, 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 bi-monthly 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; Sayers, Eric W

2009-01-01

GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, 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(R) 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 the National Center for Biotechnology Information (NCBI) Entrez retrieval system, 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.

Response rate differences between web and alternative data collection methods for public health research: a systematic review of the literature.

PubMed

Blumenberg, Cauane; Barros, Aluísio J D

2018-07-01

To systematically review the literature and compare response rates (RRs) of web surveys to alternative data collection methods in the context of epidemiologic and public health studies. We reviewed the literature using PubMed, LILACS, SciELO, WebSM, and Google Scholar databases. We selected epidemiologic and public health studies that considered the general population and used two parallel data collection methods, being one web-based. RR differences were analyzed using two-sample test of proportions, and pooled using random effects. We investigated agreement using Bland-and-Altman, and correlation using Pearson's coefficient. We selected 19 studies (nine randomized trials). The RR of the web-based data collection was 12.9 percentage points (p.p.) lower (95% CI = - 19.0, - 6.8) than the alternative methods, and 15.7 p.p. lower (95% CI = - 24.2, - 7.3) considering only randomized trials. Monetary incentives did not reduce the RR differences. A strong positive correlation (r = 0.83) between the RRs was observed. Web-based data collection present lower RRs compared to alternative methods. However, it is not recommended to interpret this as a meta-analytical evidence due to the high heterogeneity of the studies.

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

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.

Medicinal properties of ‘true’ cinnamon (Cinnamomum zeylanicum): a systematic review

PubMed Central

2013-01-01

Background In traditional medicine Cinnamon is considered a remedy for respiratory, digestive and gynaecological ailments. In-vitro and in-vivo studies from different parts of the world have demonstrated numerous beneficial medicinal effects of Cinnamomum zeylanicum (CZ). This paper aims to systematically review the scientific literature and provide a comprehensive summary on the potential medicinal benefits of CZ. Methods A comprehensive systematic review was conducted in the following databases; PubMed, Web of Science, SciVerse Scopus for studies published before 31st December 2012. The following keywords were used: “Cinnamomum zeylanicum”, “Ceylon cinnamon”, “True cinnamon” and “Sri Lankan cinnamon”. To obtain additional data a manual search was performed using the reference lists of included articles. Results The literature search identified the following number of articles in the respective databases; PubMed=54, Web of Science=76 and SciVerse Scopus=591. Thirteen additional articles were identified by searching reference lists. After removing duplicates the total number of articles included in the present review is 70. The beneficial health effects of CZ identified were; a) anti-microbial and anti-parasitic activity, b) lowering of blood glucose, blood pressure and serum cholesterol, c) anti-oxidant and free-radical scavenging properties, d) inhibition of tau aggregation and filament formation (hallmarks of Alzheimer’s disease), e) inhibitory effects on osteoclastogenesis, f) anti-secretagogue and anti-gastric ulcer effects, g) anti-nociceptive and anti-inflammatory activity, h) wound healing properties and i) hepato-protective effects. The studies reported minimal toxic and adverse effects. Conclusions The available in-vitro and in-vivo evidence suggests that CZ has many beneficial health effects. However, since data on humans are sparse, randomized controlled trials in humans will be necessary to determine whether these effects have public health implications. PMID:24148965

The Mendeleev-Meyer force project.

PubMed

Santos, Sergio; Lai, Chia-Yun; Amadei, Carlo A; Gadelrab, Karim R; Tang, Tzu-Chieh; Verdaguer, Albert; Barcons, Victor; Font, Josep; Colchero, Jaime; Chiesa, Matteo

2016-10-14

Here we present the Mendeleev-Meyer Force Project which aims at tabulating all materials and substances in a fashion similar to the periodic table. The goal is to group and tabulate substances using nanoscale force footprints rather than atomic number or electronic configuration as in the periodic table. The process is divided into: (1) acquiring nanoscale force data from materials, (2) parameterizing the raw data into standardized input features to generate a library, (3) feeding the standardized library into an algorithm to generate, enhance or exploit a model to identify a material or property. We propose producing databases mimicking the Materials Genome Initiative, the Medical Literature Analysis and Retrieval System Online (MEDLARS) or the PRoteomics IDEntifications database (PRIDE) and making these searchable online via search engines mimicking Pubmed or the PRIDE web interface. A prototype exploiting deep learning algorithms, i.e. multilayer neural networks, is presented.

Where are Romanian biomedical journals now and what does the future hold for them? A scientometric analysis.

PubMed

Dumitrascu, Dan L

2018-01-01

There is a competition between scientific journals in order to achieve leadership in their scientific field. There are several Romanian biomedical journals which are published in English and a smaller number in Romanian. We need a periodical analysis of their visibility and ranking according to scientometric measures. We searched all biomedical journals indexed on international data bases: Web of Science, PubMed, Scopus, Embase, Google Scholar. We analyzed their evaluation factors. Several journals from Romania in the biomedical field are indexed in international databases. Their scientometric indexes are not high. The best journal was acquired by an international publisher and is no longer listed for Romania. There are several Romanian biomedical journals indexed in international databases that deserve periodical analysis. There is a need to improve their ranking.

The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies

PubMed Central

Cserhati, Matyas F.; Pandey, Sanjit; Beaudoin, James J.; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S.

2015-01-01

We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33 017 407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. Database URL: http://nntc-dcc.unmc.edu PMID:26228431

CBD: a biomarker database for colorectal cancer.

PubMed

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

2018-01-01

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

CBD: a biomarker database for colorectal cancer

PubMed Central

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

2018-01-01

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

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

PubMed

Grech, Victor

2016-01-01

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

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

PubMed

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

2011-02-01

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

Bosnian and Herzegovinian medical scientists in PubMed database.

PubMed

Masic, Izet

2013-01-01

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

The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies.

PubMed

Cserhati, Matyas F; Pandey, Sanjit; Beaudoin, James J; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S

2015-01-01

We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33,017,407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. © The Author(s) 2015. Published by Oxford University Press.

MGDB: a comprehensive database of genes involved in melanoma.

PubMed

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

2015-01-01

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

Using GenBank.

PubMed

Wheeler, David

2007-01-01

GenBank(R) is a comprehensive database of publicly available DNA sequences for more than 205,000 named organisms and for more than 60,000 within the embryophyta, obtained through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Daily data exchange with the European Molecular Biology Laboratory (EMBL) in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the National Center for Biotechnology Information (NCBI) retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases with taxonomy, genome, mapping, protein structure, and domain information and the biomedical journal literature through PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available through FTP. GenBank usage scenarios ranging from local analyses of the data available through FTP to online analyses supported by the NCBI Web-based tools are discussed. 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; Sayers, Eric W

2011-01-01

GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 380,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling 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 Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that 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.

rrndb: the Ribosomal RNA Operon Copy Number Database

PubMed Central

Klappenbach, Joel A.; Saxman, Paul R.; Cole, James R.; Schmidt, Thomas M.

2001-01-01

The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database containing annotated information on rRNA operon copy number among prokaryotes. Gene redundancy is uncommon in prokaryotic genomes, yet the rRNA genes can vary from one to as many as 15 copies. Despite the widespread use of 16S rRNA gene sequences for identification of prokaryotes, information on the number and sequence of individual rRNA genes in a genome is not readily accessible. In an attempt to understand the evolutionary implications of rRNA operon redundancy, we have created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms. Each entry (organism) in the rrndb contains detailed information linked directly to external websites including the Ribosomal Database Project, GenBank, PubMed and several culture collections. Data contained in the rrndb will be valuable to researchers investigating microbial ecology and evolution using 16S rRNA gene sequences. The rrndb web site is directly accessible on the WWW at http://rrndb.cme.msu.edu. PMID:11125085

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.

Sleep duration and overweight/obesity in children: implication for pediatric nursing

PubMed Central

Liu, Jianghong; Zhang, Angelina; Li, Linda

2012-01-01

Purpose The purpose of this study was to review evidence from the last 5 years (2006-2011) regarding a relationship between sleep duration and childhood overweight/obesity. Conclusions Among the 25 studies selected from PubMed and Web of Knowledge databases, all indicated significant associations between short sleep duration and childhood overweight/obesity. Studies explored a range of pediatric populations, methodologies, and potential contributing factors. Practice Implications Childhood sleep duration may be a modifiable risk factor in preventing obesity. In addition to identifying and assessing patients’ sleep habits, nurses play important roles as educators regarding the importance of adequate sleep and promoting it in children. PMID:22734873

PubMed searches: overview and strategies for clinicians.

PubMed

Lindsey, Wesley T; Olin, Bernie R

2013-04-01

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

Thailand mutation and variation database (ThaiMUT).

PubMed

Ruangrit, Uttapong; Srikummool, Metawee; Assawamakin, Anunchai; Ngamphiw, Chumpol; Chuechote, Suparat; Thaiprasarnsup, Vilasinee; Agavatpanitch, Gallissara; Pasomsab, Ekawat; Yenchitsomanus, Pa-Thai; Mahasirimongkol, Surakameth; Chantratita, Wasun; Palittapongarnpim, Prasit; Uyyanonvara, Bunyarit; Limwongse, Chanin; Tongsima, Sissades

2008-08-01

With the completion of the human genome project, novel sequencing and genotyping technologies had been utilized to detect mutations. Such mutations have continually been produced at exponential rate by researchers in various communities. Based on the population's mutation spectra, occurrences of Mendelian diseases are different across ethnic groups. A proportion of Mendelian diseases can be observed in some countries at higher rates than others. Recognizing the importance of mutation effects in Thailand, we established a National and Ethnic Mutation Database (NEMDB) for Thai people. This database, named Thailand Mutation and Variation database (ThaiMUT), offers a web-based access to genetic mutation and variation information in Thai population. This NEMDB initiative is an important informatics tool for both research and clinical purposes to retrieve and deposit human variation data. The mutation data cataloged in ThaiMUT database were derived from journal articles available in PubMed and local publications. In addition to collected mutation data, ThaiMUT also records genetic polymorphisms located in drug related genes. ThaiMUT could then provide useful information for clinical mutation screening services for Mendelian diseases and pharmacogenomic researches. ThaiMUT can be publicly accessed from http://gi.biotec.or.th/thaimut.

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

PubMed

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

2009-09-01

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

Tips and tricks for using the internet for professional purposes.

PubMed

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

2017-05-01

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

Diterpenes and Their Derivatives as Potential Anticancer Agents.

PubMed

Islam, Muhammad Torequl

2017-05-01

As therapeutic tools, diterpenes and their derivatives have gained much attention of the medicinal scientists nowadays. It is due to their pledging and important biological activities. This review congregates the anticancer diterpenes. For this, a search was made with selected keywords in PubMed, Science Direct, Web of Science, Scopus, The American Chemical Society and miscellaneous databases from January 2012 to January 2017 for the published articles. A total 28, 789 published articles were seen. Among them, 240 were included in this study. More than 250 important anticancer diterpenes and their derivatives were seen in the databases, acting in the different pathways. Some of them are already under clinical trials, while others are in the nonclinical and/or pre-clinical trials. In conclusion, diterpenes may be one of the lead molecules in the treatment of cancer. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Tips and tricks for using the internet for professional purposes

PubMed Central

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

2017-01-01

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

Accessing the medical devices market in Egypt and Saudi Arabia: a systematic review of policies and regulations.

PubMed

Gad, Mohamed; Kriza, Christine; Fidler, Armin; Kolominsky-Rabas, Peter

2016-07-01

Despite the significant medical devices market size in Egypt and Saudi Arabia, information regarding policies and regulations for medical devices market access is highly deficient. The aim of this paper is to provide a systematic review on market access policies and regulations in both countries, to allow safe and timely access to medical technology. The following databases were searched: PubMed, Science Direct, Scopus, and Al Manhal Arabic database. Additionally, the web portals of regulatory authorities of both countries were searched. There are 34 records included in the qualitative synthesis of this review. Expert commentary: Main findings include; adopted regulatory framework from reference countries, and interim main regulatory documents, In conclusion, the market access schemes are relatively structured. However, some recommendations are put forward to navigate towards a more comprehensive policy framework in both countries.

Meta-Analysis of Structured Triglyceride versus Physical Mixture Medium- and Long-Chain Triglycerides for PN in Liver Resection Patients.

PubMed

Zhao, Yajie; Wang, Chengfeng

2017-01-01

The use of total parenteral nutrition can affect liver function, causing a series of problems such as cholestasis. The aim of this meta-analysis was to compare structured triglyceride- (STG-) based lipid emulsions with physical medium-chain triglyceride (MCT)/long-chain triglyceride (LCT) mixtures in patients who had undergone liver surgery to identify any differences between these two types of parenteral nutrition. We searched the databases of PubMed, the Cochrane Library, Web of Science, EMBASE, and Chinese Biomedicine Database from January 2007 to March 2017 and included studies that compared STG-based lipid emulsions with physical MCT/LCT mixtures for surgical patients with liver disease. The STG was more beneficial than physical MCT/LCT on recovery of liver function and immune function. Therefore, STGs may represent a promising alternative to other types of lipid emulsions for hepatic surgery patients.

Pharmaceutical applications and phytochemical profile of Cinnamomum burmannii

PubMed Central

Al-Dhubiab, Bandar E.

2012-01-01

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

Acoustic rhinometry in mouth breathing patients: a systematic review.

PubMed

Melo, Ana Carolina Cardoso de; Gomes, Adriana de Oliveira de Camargo; Cavalcanti, Arlene Santos; Silva, Hilton Justino da

2015-01-01

When there is a change in the physiological pattern of nasal breathing, mouth breathing may already be present. The diagnosis of mouth breathing is related to nasal patency. One way to access nasal patency is by acoustic rhinometry. To systematically review the effectiveness of acoustic rhinometry for the diagnosis of patients with mouth breathing. Electronic databases LILACS, MEDLINE via PubMed and Bireme, SciELO, Web of Science, Scopus, PsycInfo, CINAHL, and Science Direct, from August to December 2013, were consulted. 11,439 articles were found: 30 from LILACS, 54 from MEDLINE via Bireme, 5558 from MEDLINE via PubMed, 11 from SciELO, 2056 from Web of Science, 1734 from Scopus, 13 from PsycInfo, 1108 from CINAHL, and 875 from Science Direct. Of these, two articles were selected. The heterogeneity in the use of equipment and materials for the assessment of respiratory mode in these studies reveals that there is not yet consensus in the assessment and diagnosis of patients with mouth breathing. According to the articles, acoustic rhinometry has been used for almost twenty years, but controlled studies attesting to the efficacy of measuring the geometry of nasal cavities for complementary diagnosis of respiratory mode are warranted. Copyright © 2014 Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial. Published by Elsevier Editora Ltda. All rights reserved.

Retrieving clinical evidence: a comparison of PubMed and Google Scholar for quick clinical searches.

PubMed

Shariff, Salimah Z; Bejaimal, Shayna Ad; Sontrop, Jessica M; Iansavichus, Arthur V; Haynes, R Brian; Weir, Matthew A; Garg, Amit X

2013-08-15

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

TMDB: a literature-curated database for small molecular compounds found from tea.

PubMed

Yue, Yi; Chu, Gang-Xiu; Liu, Xue-Shi; Tang, Xing; Wang, Wei; Liu, Guang-Jin; Yang, Tao; Ling, Tie-Jun; Wang, Xiao-Gang; Zhang, Zheng-Zhu; Xia, Tao; Wan, Xiao-Chun; Bao, Guan-Hu

2014-09-16

Tea is one of the most consumed beverages worldwide. The healthy effects of tea are attributed to a wealthy of different chemical components from tea. Thousands of studies on the chemical constituents of tea had been reported. However, data from these individual reports have not been collected into a single database. The lack of a curated database of related information limits research in this field, and thus a cohesive database system should necessarily be constructed for data deposit and further application. The Tea Metabolome database (TMDB), a manually curated and web-accessible database, was developed to provide detailed, searchable descriptions of small molecular compounds found in Camellia spp. esp. in the plant Camellia sinensis and compounds in its manufactured products (different kinds of tea infusion). TMDB is currently the most complete and comprehensive curated collection of tea compounds data in the world. It contains records for more than 1393 constituents found in tea with information gathered from 364 published books, journal articles, and electronic databases. It also contains experimental 1H NMR and 13C NMR data collected from the purified reference compounds or collected from other database resources such as HMDB. TMDB interface allows users to retrieve tea compounds entries by keyword search using compound name, formula, occurrence, and CAS register number. Each entry in the TMDB contains an average of 24 separate data fields including its original plant species, compound structure, formula, molecular weight, name, CAS registry number, compound types, compound uses including healthy benefits, reference literatures, NMR, MS data, and the corresponding ID from databases such as HMDB and Pubmed. Users can also contribute novel regulatory entries by using a web-based submission page. The TMDB database is freely accessible from the URL of http://pcsb.ahau.edu.cn:8080/TCDB/index.jsp. The TMDB is designed to address the broad needs of tea biochemists, natural products chemists, nutritionists, and members of tea related research community. The TMDB database provides a solid platform for collection, standardization, and searching of compounds information found in tea. As such this database will be a comprehensive repository for tea biochemistry and tea health research community.

Prevalence of suicidal ideation in Chinese college students: a meta-analysis.

PubMed

Li, Zhan-Zhan; Li, Ya-Ming; Lei, Xian-Yang; Zhang, Dan; Liu, Li; Tang, Si-Yuan; Chen, Lizhang

2014-01-01

About 1 million people worldwide commit suicide each year, and college students with suicidal ideation are at high risk of suicide. The prevalence of suicidal ideation in college students has been estimated extensively, but quantitative syntheses of overall prevalence are scarce, especially in China. Accurate estimates of prevalence are important for making public policy. In this paper, we aimed to determine the prevalence of suicidal ideation in Chinese college students. Databases including PubMed, Web of Knowledge, Chinese Web of Knowledge, Wangfang (Chinese database) and Weipu (Chinese database) were systematically reviewed to identify articles published between 2004 to July 2013, in either English or Chinese, reporting prevalence estimates of suicidal ideation among Chinese college students. The strategy also included a secondary search of reference lists of records retrieved from databases. Then the prevalence estimates were summarized using a random effects model. The effects of moderator variables on the prevalence estimates were assessed using a meta-regression model. A total of 41 studies involving 160339 college students were identified, and the prevalence ranged from 1.24% to 26.00%. The overall pooled prevalence of suicidal ideation among Chinese college students was 10.72% (95%CI: 8.41% to 13.28%). We noted substantial heterogeneity in prevalence estimates. Subgroup analyses showed that prevalence of suicidal ideation in females is higher than in males. The prevalence of suicidal ideation in Chinese college students is relatively high, although the suicide rate is lower compared with the entire society, suggesting the need for local surveys to inform the development of health services for college students.

Androgen-responsive gene database: integrated knowledge on androgen-responsive genes.

PubMed

Jiang, Mei; Ma, Yunsheng; Chen, Congcong; Fu, Xuping; Yang, Shu; Li, Xia; Yu, Guohua; Mao, Yumin; Xie, Yi; Li, Yao

2009-11-01

Androgen signaling plays an important role in many biological processes. Androgen Responsive Gene Database (ARGDB) is devoted to providing integrated knowledge on androgen-controlled genes. Gene records were collected on the basis of PubMed literature collections. More than 6000 abstracts and 950 original publications were manually screened, leading to 1785 human genes, 993 mouse genes, and 583 rat genes finally included in the database. All the collected genes were experimentally proved to be regulated by androgen at the expression level or to contain androgen-responsive regions. For each gene important details of the androgen regulation experiments were collected from references, such as expression change, androgen-responsive sequence, response time, tissue/cell type, experimental method, ligand identity, and androgen amount, which will facilitate further evaluation by researchers. Furthermore, the database was integrated with multiple annotation resources, including National Center for Biotechnology Information, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway, to reveal the biological characteristics and significance of androgen-regulated genes. The ARGDB web site is mainly composed of the Browse, Search, Element Scan, and Submission modules. It is user friendly and freely accessible at http://argdb.fudan.edu.cn. Preliminary analysis of the collected data was performed. Many disease pathways, such as prostate carcinogenesis, were found to be enriched in androgen-regulated genes. The discovered androgen-response motifs were similar to those in previous reports. The analysis results are displayed in the web site. In conclusion, ARGDB provides a unified gateway to storage, retrieval, and update of information on androgen-regulated genes.

Prevalence of Suicidal Ideation in Chinese College Students: A Meta-Analysis

PubMed Central

Li, Zhan-Zhan; Li, Ya-Ming; Lei, Xian-Yang; Zhang, Dan; Liu, Li; Tang, Si-Yuan; Chen, Lizhang

2014-01-01

Background About 1 million people worldwide commit suicide each year, and college students with suicidal ideation are at high risk of suicide. The prevalence of suicidal ideation in college students has been estimated extensively, but quantitative syntheses of overall prevalence are scarce, especially in China. Accurate estimates of prevalence are important for making public policy. In this paper, we aimed to determine the prevalence of suicidal ideation in Chinese college students. Objective and Methods Databases including PubMed, Web of Knowledge, Chinese Web of Knowledge, Wangfang (Chinese database) and Weipu (Chinese database) were systematically reviewed to identify articles published between 2004 to July 2013, in either English or Chinese, reporting prevalence estimates of suicidal ideation among Chinese college students. The strategy also included a secondary search of reference lists of records retrieved from databases. Then the prevalence estimates were summarized using a random effects model. The effects of moderator variables on the prevalence estimates were assessed using a meta-regression model. Results A total of 41 studies involving 160339 college students were identified, and the prevalence ranged from 1.24% to 26.00%. The overall pooled prevalence of suicidal ideation among Chinese college students was 10.72% (95%CI: 8.41% to 13.28%). We noted substantial heterogeneity in prevalence estimates. Subgroup analyses showed that prevalence of suicidal ideation in females is higher than in males. Conclusions The prevalence of suicidal ideation in Chinese college students is relatively high, although the suicide rate is lower compared with the entire society, suggesting the need for local surveys to inform the development of health services for college students. PMID:25285890

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.

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

PubMed Central

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

2013-01-01

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

Reducing heart disease through the vegetarian diet using primary prevention.

PubMed

Sticher, Megan A; Smith, Christine B; Davidson, Susan

2010-03-01

To evaluate research on the vegetarian diet for its safety, effectiveness in reducing heart disease, special considerations, contraindications, and its association with decreased cardiovascular disease risk. Selected research and evidence-based dietary guidelines found by searching CINAHL, PubMed, Ovid databases, and the World Wide Web. A carefully planned vegetarian diet with adequate supplementation may be effective for primary prevention of heart disease. The vegetarian diet is cost effective, safe, and relatively easy to implement. Improved dietary choices can help improve many chronic conditions. Guidelines for proper nutrition within a vegetarian lifestyle are readily accessible to patients and professionals alike. Referral to a dietitian is an appropriate option in primary care settings.

Biomarkers in sarcoidosis.

PubMed

Chopra, Amit; Kalkanis, Alexandros; Judson, Marc A

2016-11-01

Numerous biomarkers have been evaluated for the diagnosis, assessment of disease activity, prognosis, and response to treatment in sarcoidosis. In this report, we discuss the clinical and research utility of several biomarkers used to evaluate sarcoidosis. Areas covered: The sarcoidosis biomarkers discussed include serologic tests, imaging studies, identification of inflammatory cells and genetic analyses. Literature was obtained from medical databases including PubMed and Web of Science. Expert commentary: Most of the biomarkers examined in sarcoidosis are not adequately specific or sensitive to be used in isolation to make clinical decisions. However, several sarcoidosis biomarkers have an important role in the clinical management of sarcoidosis when they are coupled with clinical data including the results of other biomarkers.

Does honey have a role in paediatric wound management?

PubMed

Bittmann, Stefan; Luchter, Elisabeth; Thiel, Michael; Kameda, Genn; Hanano, Ralph; Längler, Alfred

Topical honey treatment has been shown to possess antimicrobial properties, promote autolytic debridement, stimulate growth of wound tissues to hasten healing, and to start the healing process in dormant wounds, stimulating anti-inflammatory activity that rapidly reduces pain, oedema and exudate production. This article provides an overview of the use of honey as a medicinal substance, particularly its use in wound treatment, and reviews the published data concerning honey as a form of complementary and alternative medicine in paediatric wound management. The literature reviewed was found by searching the PubMed, BIOSIS, and ISI Web of Science databases for the term honey. Exclusion criteria were articles where honey was used in a mixture with other therapeutic substances.

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

PubMed Central

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

2006-01-01

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

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.

A snapshot of 3649 Web-based services published between 1994 and 2017 shows a decrease in availability after 2 years.

PubMed

Osz, Ágnes; Pongor, Lorinc Sándor; Szirmai, Danuta; Gyorffy, Balázs

2017-12-08

The long-term availability of online Web services is of utmost importance to ensure reproducibility of analytical results. However, because of lack of maintenance following acceptance, many servers become unavailable after a short period of time. Our aim was to monitor the accessibility and the decay rate of published Web services as well as to determine the factors underlying trends changes. We searched PubMed to identify publications containing Web server-related terms published between 1994 and 2017. Automatic and manual screening was used to check the status of each Web service. Kruskall-Wallis, Mann-Whitney and Chi-square tests were used to evaluate various parameters, including availability, accessibility, platform, origin of authors, citation, journal impact factor and publication year. We identified 3649 publications in 375 journals of which 2522 (69%) were currently active. Over 95% of sites were running in the first 2 years, but this rate dropped to 84% in the third year and gradually sank afterwards (P < 1e-16). The mean half-life of Web services is 10.39 years. Working Web services were published in journals with higher impact factors (P = 4.8e-04). Services published before the year 2000 received minimal attention. The citation of offline services was less than for those online (P = 0.022). The majority of Web services provide analytical tools, and the proportion of databases is slowly decreasing. Conclusions. Almost one-third of Web services published to date went out of service. We recommend continued support of Web-based services to increase the reproducibility of published results. © The Author 2017. Published by Oxford University Press.

VIOLIN: vaccine investigation and online information network.

PubMed

Xiang, Zuoshuang; Todd, Thomas; Ku, Kim P; Kovacic, Bethany L; Larson, Charles B; Chen, Fang; Hodges, Andrew P; Tian, Yuying; Olenzek, Elizabeth A; Zhao, Boyang; Colby, Lesley A; Rush, Howard G; Gilsdorf, Janet R; Jourdian, George W; He, Yongqun

2008-01-01

Vaccines are among the most efficacious and cost-effective tools for reducing morbidity and mortality caused by infectious diseases. The vaccine investigation and online information network (VIOLIN) is a web-based central resource, allowing easy curation, comparison and analysis of vaccine-related research data across various human pathogens (e.g. Haemophilus influenzae, human immunodeficiency virus (HIV) and Plasmodium falciparum) of medical importance and across humans, other natural hosts and laboratory animals. Vaccine-related peer-reviewed literature data have been downloaded into the database from PubMed and are searchable through various literature search programs. Vaccine data are also annotated, edited and submitted to the database through a web-based interactive system that integrates efficient computational literature mining and accurate manual curation. Curated information includes general microbial pathogenesis and host protective immunity, vaccine preparation and characteristics, stimulated host responses after vaccination and protection efficacy after challenge. Vaccine-related pathogen and host genes are also annotated and available for searching through customized BLAST programs. All VIOLIN data are available for download in an eXtensible Markup Language (XML)-based data exchange format. VIOLIN is expected to become a centralized source of vaccine information and to provide investigators in basic and clinical sciences with curated data and bioinformatics tools for vaccine research and development. VIOLIN is publicly available at http://www.violinet.org.

Effectiveness of animal-assisted therapy: A systematic review of randomized controlled trials.

PubMed

Kamioka, Hiroharu; Okada, Shinpei; Tsutani, Kiichiro; Park, Hyuntae; Okuizumi, Hiroyasu; Handa, Shuichi; Oshio, Takuya; Park, Sang-Jun; Kitayuguchi, Jun; Abe, Takafumi; Honda, Takuya; Mutoh, Yoshiteru

2014-04-01

The objectives of this review were to summarize the evidence from randomized controlled trials (RCTs) on the effects of animal-assisted therapy (AAT). Studies were eligible if they were RCTs. Studies included one treatment group in which AAT was applied. We searched the following databases from 1990 up to October 31, 2012: MEDLINE via PubMed, CINAHL, Web of Science, Ichushi Web, GHL, WPRIM, and PsycINFO. We also searched all Cochrane Database up to October 31, 2012. Eleven RCTs were identified, and seven studies were about "Mental and behavioral disorders". Types of animal intervention were dog, cat, dolphin, bird, cow, rabbit, ferret, and guinea pig. The RCTs conducted have been of relatively low quality. We could not perform meta-analysis because of heterogeneity. In a study environment limited to the people who like animals, AAT may be an effective treatment for mental and behavioral disorders such as depression, schizophrenia, and alcohol/drug addictions, and is based on a holistic approach through interaction with animals in nature. To most effectively assess the potential benefits for AAT, it will be important for further research to utilize and describe (1) RCT methodology when appropriate, (2) reasons for non-participation, (3) intervention dose, (4) adverse effects and withdrawals, and (5) cost. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

The Protein-DNA Interface database

PubMed Central

2010-01-01

The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The database includes a simple functional classification of the protein-DNA complexes that consists of three hierarchical levels: Class, Type and Subtype. This classification has been defined and manually curated by humans based on the information gathered from several sources that include PDB, PubMed, CATH, SCOP and COPS. The current version of the database contains only structures with resolution of 2.5 Å or higher, accounting for a total of 922 entries. The major aim of this database is to contribute to the understanding of the main rules that underlie the molecular recognition process between DNA and proteins. To this end, the database is focused on each specific atomic interface rather than on the separated binding partners. Therefore, each entry in this database consists of a single and independent protein-DNA interface. We hope that PDIdb will be useful to many researchers working in fields such as the prediction of transcription factor binding sites in DNA, the study of specificity determinants that mediate enzyme recognition events, engineering and design of new DNA binding proteins with distinct binding specificity and affinity, among others. Finally, due to its friendly and easy-to-use web interface, we hope that PDIdb will also serve educational and teaching purposes. PMID:20482798

The Protein-DNA Interface database.

PubMed

Norambuena, Tomás; Melo, Francisco

2010-05-18

The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The database includes a simple functional classification of the protein-DNA complexes that consists of three hierarchical levels: Class, Type and Subtype. This classification has been defined and manually curated by humans based on the information gathered from several sources that include PDB, PubMed, CATH, SCOP and COPS. The current version of the database contains only structures with resolution of 2.5 A or higher, accounting for a total of 922 entries. The major aim of this database is to contribute to the understanding of the main rules that underlie the molecular recognition process between DNA and proteins. To this end, the database is focused on each specific atomic interface rather than on the separated binding partners. Therefore, each entry in this database consists of a single and independent protein-DNA interface.We hope that PDIdb will be useful to many researchers working in fields such as the prediction of transcription factor binding sites in DNA, the study of specificity determinants that mediate enzyme recognition events, engineering and design of new DNA binding proteins with distinct binding specificity and affinity, among others. Finally, due to its friendly and easy-to-use web interface, we hope that PDIdb will also serve educational and teaching purposes.

Dehydration in the Elderly: A Review Focused on Economic Burden.

PubMed

Frangeskou, M; Lopez-Valcarcel, B; Serra-Majem, L

2015-06-01

Dehydration is the most common fluid and electrolyte problem among elderly patients. It is reported to be widely prevalent and costly to individuals and to the health care system. The purpose of this review is to summarize the literature on the economic burden of dehydration in the elderly. A comprehensive search of several databases from database inception to November 2013, only in English language, was conducted. The databases included Pubmed and ISI Web of Science. The search terms «dehydration» / "hyponaremia" / "hypernatremia" AND «cost» AND «elderly» were used to search for comparative studies of the economic burden of dehydration. A total of 15 papers were identified. Dehydration in the elderly is an independent factor of higher health care expenditures. It is directly associated with an increase in hospital mortality, as well as with an increase in the utilization of ICU, short and long term care facilities, readmission rates and hospital resources, especially among those with moderate to severe hyponatremia. Dehydration represents a potential target for intervention to reduce healthcare expenditures and improve patients' quality of life.

The study of co-citation analysis and knowledge structure on healthcare domain

NASA Astrophysics Data System (ADS)

Chu, Kuo-Chung; Liu, Wen-I.; Tsai, Ming-Yu

2012-11-01

With the prevalence of Internet and digital archives, the online e-journal database facilitates scholars to search literature in a research domain, or to cross-search an inter-disciplined field; the key literature can be efficiently traced out. This study intends to build a Web-based citation analysis system, which consists of four modules, they are: 1) literature search module; (2) statistics module; (3) articles analysis module; and (4) co-citation analysis module. The system focuses on PubMed Central dataset that has 170,000 records. In a research domain, a specific keyword searches in terms of authors, journals, and core issues. In addition, we use data mining techniques for co-citation analysis. The results assist researchers with in-depth understanding of the domain knowledge. Having an automated system for co-citation analysis, it helps to understand changes, trends, and knowledge structure of research domain. For the best of our knowledge, the proposed system differentiates from existing online electronic retrieval database analysis function. Perhaps, the proposed system is going to be a value-added database of healthcare domain, and hope to contribute the researchers.

Construction of a database for published phase II/III drug intervention clinical trials for the period 2009-2014 comprising 2,326 records, 90 disease categories, and 939 drug entities.

PubMed

Jeong, Sohyun; Han, Nayoung; Choi, Boyoon; Sohn, Minji; Song, Yun-Kyoung; Chung, Myeon-Woo; Na, Han-Sung; Ji, Eunhee; Kim, Hyunah; Rhew, Ki Yon; Kim, Therasa; Kim, In-Wha; Oh, Jung Mi

2016-06-01

To construct a database of published clinical drug trials suitable for use 1) as a research tool in accessing clinical trial information and 2) in evidence-based decision-making by regulatory professionals, clinical research investigators, and medical practitioners. Comprehensive information obtained from a search of design elements and results of clinical trials in peer reviewed journals using PubMed (http://www.ncbi.nlm.ih.gov/pubmed). The methodology to develop a structured database was devised by a panel composed of experts in medical, pharmaceutical, information technology, and members of Ministry of Food and Drug Safety (MFDS) using a step by step approach. A double-sided system consisting of user mode and manager mode served as the framework for the database; elements of interest from each trial were entered via secure manager mode enabling the input information to be accessed in a user-friendly manner (user mode). Information regarding methodology used and results of drug treatment were extracted as detail elements of each data set and then inputted into the web-based database system. Comprehensive information comprising 2,326 clinical trial records, 90 disease states, and 939 drugs entities and concerning study objectives, background, methods used, results, and conclusion could be extracted from published information on phase II/III drug intervention clinical trials appearing in SCI journals within the last 10 years. The extracted data was successfully assembled into a clinical drug trial database with easy access suitable for use as a research tool. The clinically most important therapeutic categories, i.e., cancer, cardiovascular, respiratory, neurological, metabolic, urogenital, gastrointestinal, psychological, and infectious diseases were covered by the database. Names of test and control drugs, details on primary and secondary outcomes and indexed keywords could also be retrieved and built into the database. The construction used in the database enables the user to sort and download targeted information as a Microsoft Excel spreadsheet. Because of the comprehensive and standardized nature of the clinical drug trial database and its ease of access it should serve as valuable information repository and research tool for accessing clinical trial information and making evidence-based decisions by regulatory professionals, clinical research investigators, and medical practitioners.

Application of the intelligent techniques in transplantation databases: a review of articles published in 2009 and 2010.

PubMed

Sousa, F S; Hummel, A D; Maciel, R F; Cohrs, F M; Falcão, A E J; Teixeira, F; Baptista, R; Mancini, F; da Costa, T M; Alves, D; Pisa, I T

2011-05-01

The replacement of defective organs with healthy ones is an old problem, but only a few years ago was this issue put into practice. Improvements in the whole transplantation process have been increasingly important in clinical practice. In this context are clinical decision support systems (CDSSs), which have reflected a significant amount of work to use mathematical and intelligent techniques. The aim of this article was to present consideration of intelligent techniques used in recent years (2009 and 2010) to analyze organ transplant databases. To this end, we performed a search of the PubMed and Institute for Scientific Information (ISI) Web of Knowledge databases to find articles published in 2009 and 2010 about intelligent techniques applied to transplantation databases. Among 69 retrieved articles, we chose according to inclusion and exclusion criteria. The main techniques were: Artificial Neural Networks (ANN), Logistic Regression (LR), Decision Trees (DT), Markov Models (MM), and Bayesian Networks (BN). Most articles used ANN. Some publications described comparisons between techniques or the use of various techniques together. The use of intelligent techniques to extract knowledge from databases of healthcare is increasingly common. Although authors preferred to use ANN, statistical techniques were equally effective for this enterprise. Copyright © 2011 Elsevier Inc. All rights reserved.

The NIF DISCO Framework: Facilitating Automated Integration of Neuroscience Content on the Web

PubMed Central

Marenco, Luis; Wang, Rixin; Shepherd, Gordon M.; Miller, Perry L.

2013-01-01

This paper describes the capabilities of DISCO, an extensible approach that supports integrative Web-based information dissemination. DISCO is a component of the Neuroscience Information Framework (NIF), an NIH Neuroscience Blueprint initiative that facilitates integrated access to diverse neuroscience resources via the Internet. DISCO facilitates the automated maintenance of several distinct capabilities using a collection of files 1) that are maintained locally by the developers of participating neuroscience resources and 2) that are “harvested” on a regular basis by a central DISCO server. This approach allows central NIF capabilities to be updated as each resource’s content changes over time. DISCO currently supports the following capabilities: 1) resource descriptions, 2) “LinkOut” to a resource’s data items from NCBI Entrez resources such as PubMed, 3) Web-based interoperation with a resource, 4) sharing a resource’s lexicon and ontology, 5) sharing a resource’s database schema, and 6) participation by the resource in neuroscience-related RSS news dissemination. The developers of a resource are free to choose which DISCO capabilities their resource will participate in. Although DISCO is used by NIF to facilitate neuroscience data integration, its capabilities have general applicability to other areas of research. PMID:20387131

The NIF DISCO Framework: facilitating automated integration of neuroscience content on the web.

PubMed

Marenco, Luis; Wang, Rixin; Shepherd, Gordon M; Miller, Perry L

2010-06-01

This paper describes the capabilities of DISCO, an extensible approach that supports integrative Web-based information dissemination. DISCO is a component of the Neuroscience Information Framework (NIF), an NIH Neuroscience Blueprint initiative that facilitates integrated access to diverse neuroscience resources via the Internet. DISCO facilitates the automated maintenance of several distinct capabilities using a collection of files 1) that are maintained locally by the developers of participating neuroscience resources and 2) that are "harvested" on a regular basis by a central DISCO server. This approach allows central NIF capabilities to be updated as each resource's content changes over time. DISCO currently supports the following capabilities: 1) resource descriptions, 2) "LinkOut" to a resource's data items from NCBI Entrez resources such as PubMed, 3) Web-based interoperation with a resource, 4) sharing a resource's lexicon and ontology, 5) sharing a resource's database schema, and 6) participation by the resource in neuroscience-related RSS news dissemination. The developers of a resource are free to choose which DISCO capabilities their resource will participate in. Although DISCO is used by NIF to facilitate neuroscience data integration, its capabilities have general applicability to other areas of research.

Information sources for obesity prevention policy research: a review of systematic reviews.

PubMed

Hanneke, Rosie; Young, Sabrina K

2017-08-08

Systematic identification of evidence in health policy can be time-consuming and challenging. This study examines three questions pertaining to systematic reviews on obesity prevention policy, in order to identify the most efficient search methods: (1) What percentage of the primary studies selected for inclusion in the reviews originated in scholarly as opposed to gray literature? (2) How much of the primary scholarly literature in this topic area is indexed in PubMed/MEDLINE? (3) Which databases index the greatest number of primary studies not indexed in PubMed, and are these databases searched consistently across systematic reviews? We identified systematic reviews on obesity prevention policy and explored their search methods and citations. We determined the percentage of scholarly vs. gray literature cited, the most frequently cited journals, and whether each primary study was indexed in PubMed. We searched 21 databases for all primary study articles not indexed in PubMed to determine which database(s) indexed the highest number of these relevant articles. In total, 21 systematic reviews were identified. Ten of the 21 systematic reviews reported searching gray literature, and 12 reviews ultimately included gray literature in their analyses. Scholarly articles accounted for 577 of the 649 total primary study papers. Of these, 495 (76%) were indexed in PubMed. Google Scholar retrieved the highest number of the remaining 82 non-PubMed scholarly articles, followed by Scopus and EconLit. The Journal of the American Dietetic Association was the most-cited journal. Researchers can maximize search efficiency by searching a small yet targeted selection of both scholarly and gray literature resources. A highly sensitive search of PubMed and those databases that index the greatest number of relevant articles not indexed in PubMed, namely multidisciplinary and economics databases, could save considerable time and effort. When combined with a gray literature search and additional search methods, including cited reference searching and consulting with experts, this approach could help maintain broad retrieval of relevant studies while improving search efficiency. Findings also have implications for designing specialized databases for public health research.

77 FR 39269 - Submission for OMB Review, Comment Request, Proposed Collection: IMLS Museum Web Database...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-02

..., Proposed Collection: IMLS Museum Web Database: MuseumsCount.gov AGENCY: Institute of Museum and Library... general public. Information such as name, address, phone, email, Web site, staff size, program details... Museum Web Database: MuseumsCount.gov collection. The 60-day notice for the IMLS Museum Web Database...

SeqHound: biological sequence and structure database as a platform for bioinformatics research

PubMed Central

2002-01-01

Background SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment. Results SeqHound is based on the National Center for Biotechnology Information data model and programming tools. It offers daily updated contents of all Entrez sequence databases in addition to 3-D structural data and information about sequence redundancies, sequence neighbours, taxonomy, complete genomes, functional annotation including Gene Ontology terms and literature links to PubMed. SeqHound is accessible via a web server through a Perl, C or C++ remote API or an optimized local API. It provides functionality necessary to retrieve specialized subsets of sequences, structures and structural domains. Sequences may be retrieved in FASTA, GenBank, ASN.1 and XML formats. Structures are available in ASN.1, XML and PDB formats. Emphasis has been placed on complete genomes, taxonomy, domain and functional annotation as well as 3-D structural functionality in the API, while fielded text indexing functionality remains under development. SeqHound also offers a streamlined WWW interface for simple web-user queries. Conclusions The system has proven useful in several published bioinformatics projects such as the BIND database and offers a cost-effective infrastructure for research. SeqHound will continue to develop and be provided as a service of the Blueprint Initiative at the Samuel Lunenfeld Research Institute. The source code and examples are available under the terms of the GNU public license at the Sourceforge site http://sourceforge.net/projects/slritools/ in the SLRI Toolkit. PMID:12401134

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

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

ChemiRs: a web application for microRNAs and chemicals.

PubMed

Su, Emily Chia-Yu; Chen, Yu-Sing; Tien, Yun-Cheng; Liu, Jeff; Ho, Bing-Ching; Yu, Sung-Liang; Singh, Sher

2016-04-18

MicroRNAs (miRNAs) are about 22 nucleotides, non-coding RNAs that affect various cellular functions, and play a regulatory role in different organisms including human. Until now, more than 2500 mature miRNAs in human have been discovered and registered, but still lack of information or algorithms to reveal the relations among miRNAs, environmental chemicals and human health. Chemicals in environment affect our health and daily life, and some of them can lead to diseases by inferring biological pathways. We develop a creditable online web server, ChemiRs, for predicting interactions and relations among miRNAs, chemicals and pathways. The database not only compares gene lists affected by chemicals and miRNAs, but also incorporates curated pathways to identify possible interactions. Here, we manually retrieved associations of miRNAs and chemicals from biomedical literature. We developed an online system, ChemiRs, which contains miRNAs, diseases, Medical Subject Heading (MeSH) terms, chemicals, genes, pathways and PubMed IDs. We connected each miRNA to miRBase, and every current gene symbol to HUGO Gene Nomenclature Committee (HGNC) for genome annotation. Human pathway information is also provided from KEGG and REACTOME databases. Information about Gene Ontology (GO) is queried from GO Online SQL Environment (GOOSE). With a user-friendly interface, the web application is easy to use. Multiple query results can be easily integrated and exported as report documents in PDF format. Association analysis of miRNAs and chemicals can help us understand the pathogenesis of chemical components. ChemiRs is freely available for public use at http://omics.biol.ntnu.edu.tw/ChemiRs .

A Tactical Framework for Cyberspace Situational Awareness

DTIC Science & Technology

2010-06-01

Command & Control 1. VOIP Telephone 2. Internet Chat 3. Web App ( TBMCS ) 4. Email 5. Web App (PEX) 6. Database (CAMS) 7. Database (ARMS) 8...Database (LogMod) 9. Resource (WWW) 10. Application (PFPS) Mission Planning 1. Application (PFPS) 2. Email 3. Web App ( TBMCS ) 4. Internet Chat...1. Web App (PEX) 2. Database (ARMS) 3. Web App ( TBMCS ) 4. Email 5. Database (CAMS) 6. VOIP Telephone 7. Application (PFPS) 8. Internet Chat 9

Community-acquired methicillin-resistant Staphylococcus aureus: a global problem.

PubMed

Evangelista, Síntia de Souza; de Oliveira, Adriana Cristina

2015-01-01

To describe the epidemiology of CA-MRSA cases in Brazil order to understand its occurrence, risk factors and forms of management in the country compared with the worldwide situation. Literature review and for articles selection considering the databases: Scopus, Science Direct, Isi Web of Knowledge, PubMed and BVS. Ten national articles describing 21 cases of CA-MRSA were identified, mostly in children, adolescents and adults with skin and soft tissue infection progressing to severe infections related to Oceania Southwest Pacific Clone (OSPC) leading to hospitalization. Conclusión: Although CA-MRSA is considered a global important microorganism we found a lack of published data about its epidemiology in Brazil, which hinder the design of the reality of the country against CA-MRSA.

Psychosocial job stress and immunity: a systematic review.

PubMed

Nakata, Akinori

2012-01-01

The purpose of this review was to provide current knowledge about the possible association between psychosocial job stress and immune parameters in blood, saliva, and urine. Using bibliographic databases (PubMed, PsychINFO, Web of Science, Medline) and the snowball method, 56 studies were found. In general, exposure to psychosocial job stress (high job demands, low job control, high job strain, job dissatisfaction, high effort-reward imbalance, overcommitment, burnout, unemployment, organizational downsizing, economic recession) had a measurable impact on immune parameters (reduced NK cell activity, NK and T cell subsets, CD4+/CD8+ ratio, and increased inflammatory markers). The evidence supports that psychosocial job stresses are related to disrupted immune responses but further research is needed to demonstrate cause-effect relationships.

Nutritional needs in the professional practice of swimming: a review

PubMed Central

Domínguez, Raúl; Jesús-Sánchez-Oliver, Antonio; Cuenca, Eduardo; Jodra, Pablo; Fernandes da Silva, Sandro; Mata-Ordóñez, Fernando

2017-01-01

[Purpose] Swimming requires developing a high aerobic and anaerobic capacity for strength and technical efficiency. The purpose of this study was to establish the nutritional requirements and dietary strategies that can optimize swimming performance. [Methods] Several related studies retrieved from the databases, Dialnet, Elsevier, Medline, Pubmed, and Web of Science, through keyword search strategies were reviewed. [Results] The recommended carbohydrate intake ranges between 6-10-12 g/kg/d, protein 2 g/kg/d, and fat should surpass 20-25% of the daily intake. [Conclusion] Performance can be optimized with a hydration plan, as well as adequate periodization of supplements, such as caffeine, creatine, sodium bicarbonate, B-alanine, beetroot juice, Vitamin D, bovine colostrum, and HMB. PMID:29370667

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.

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.

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

Nurses' roles in health promotion practice: an integrative review.

PubMed

Kemppainen, Virpi; Tossavainen, Kerttu; Turunen, Hannele

2013-12-01

Nurses play an important role in promoting public health. Traditionally, the focus of health promotion by nurses has been on disease prevention and changing the behaviour of individuals with respect to their health. However, their role as promoters of health is more complex, since they have multi-disciplinary knowledge and experience of health promotion in their nursing practice. This paper presents an integrative review aimed at examining the findings of existing research studies (1998-2011) of health promotion practice by nurses. Systematic computer searches were conducted of the Cochrane databases, Cinahl, PubMed, Web of Science, PsycINFO and Scopus databases, covering the period January 1998 to December 2011. Data were analysed and the results are presented using the concept map method of Novak and Gowin. The review found information on the theoretical basis of health promotion practice by nurses, the range of their expertise, health promotion competencies and the organizational culture associated with health promotion practice. Nurses consider health promotion important but a number of obstacles associated with organizational culture prevent effective delivery.

Mitigation of Fluorosis - A Review

PubMed Central

Dodamani, Arun S.; Jadhav, Harish C.; Naik, Rahul G.; Deshmukh, Manjiri A.

2015-01-01

Fluoride is required for normal development and growth of the body. It is found in plentiful quantity in environment and fluoride content in drinking water is largest contributor to the daily fluoride intake. The behaviour of fluoride ions in the human organism can be regarded as that of “double-edged sword”. Fluoride is beneficial in small amounts but toxic in large amounts. Excessive consumption of fluorides in various forms leads to development of fluorosis. Fluorosis is major health problem in 24 countries, including India, which lies in the geographical fluoride belt. Various technologies are being used to remove fluoride from water but still the problem has not been rooted out. The purpose of this paper is to review the available treatment modalities for fluorosis, available technologies for fluoride removal from water and ongoing fluorosis mitigation programs based on literature survey. Medline was the primary database used in the literature search. Other databases included: PubMed, Web of Science, Google Scholar, WHO, Ebscohost, Science Direct, Google Search Engine, etc. PMID:26266235

Nature-based experiences and health of cancer survivors.

PubMed

Ray, Heather; Jakubec, Sonya L

2014-11-01

Although exposure to, and interaction with, natural environments are recognized as health-promoting, little is understood about the use of nature contact in treatment and rehabilitation for cancer survivors. This narrative review summarizes the literature exploring the influence of nature-based experiences on survivor health. Key databases included CINAHL, EMBASE, Medline, Web of Science, PubMed, PsycArticles, ProQuest, and Cancerlit databases. Sixteen articles met inclusion criteria and were reviewed. Four major categories emerged: 1) Dragon boat racing may enhance breast cancer survivor quality of life, 2) Natural environment may counteract attentional fatigue in newly diagnosed breast cancer survivors, 3) Adventure programs provide a positive experience for children and adolescent survivors, fostering a sense of belonging and self-esteem, and 4) Therapeutic landscapes may decrease state-anxiety, improving survivor health. This review contributes to a better understanding of the therapeutic effects of nature-based experiences on cancer survivor health, providing a point of entry for future study. Copyright © 2014 Elsevier Ltd. All rights reserved.

Occupational Health and Safety in Aquaculture: Insights on Brazilian Public Policies.

PubMed

de Oliveira, Pedro Keller; Cavalli, Richard Souto; Kunert Filho, Hiran Castagnino; Carvalho, Daiane; Benedetti, Nadine; Rotta, Marco Aurélio; Peixoto Ramos, Augusto Sávio; de Brito, Kelly Cristina Tagliari; de Brito, Benito Guimarães; da Rocha, Andréa Ferretto; Stech, Marcia Regina; Cavalli, Lissandra Souto

2017-01-01

Aquaculture has many occupational hazards, including those that are physical, chemical, biological, ergonomic, and mechanical. The risks in aquaculture are inherent, as this activity requires particular practices. The objective of the present study was to show the risks associated with the aquaculture sector and present a critical overview on the Brazilian public policies concerning aquaculture occupational health. Methods include online research involved web searches and electronic databases including Pubmed, Google Scholar, Scielo and government databases. We conducted a careful revision of Brazilian labor laws related to occupational health and safety, rural workers, and aquaculture. The results and conclusion support the idea that aquaculture requires specific and well-established industry programs and policies, especially in developing countries. Aquaculture still lacks scientific research, strategies, laws, and public policies to boost the sector with regard to occupational health and safety. The establishment of a safe workplace in aquaculture in developing countries remains a challenge for all involved in employer-employee relationships.

HEALTH GeoJunction: place-time-concept browsing of health publications.

PubMed

MacEachren, Alan M; Stryker, Michael S; Turton, Ian J; Pezanowski, Scott

2010-05-18

The volume of health science publications is escalating rapidly. Thus, keeping up with developments is becoming harder as is the task of finding important cross-domain connections. When geographic location is a relevant component of research reported in publications, these tasks are more difficult because standard search and indexing facilities have limited or no ability to identify geographic foci in documents. This paper introduces HEALTH GeoJunction, a web application that supports researchers in the task of quickly finding scientific publications that are relevant geographically and temporally as well as thematically. HEALTH GeoJunction is a geovisual analytics-enabled web application providing: (a) web services using computational reasoning methods to extract place-time-concept information from bibliographic data for documents and (b) visually-enabled place-time-concept query, filtering, and contextualizing tools that apply to both the documents and their extracted content. This paper focuses specifically on strategies for visually-enabled, iterative, facet-like, place-time-concept filtering that allows analysts to quickly drill down to scientific findings of interest in PubMed abstracts and to explore relations among abstracts and extracted concepts in place and time. The approach enables analysts to: find publications without knowing all relevant query parameters, recognize unanticipated geographic relations within and among documents in multiple health domains, identify the thematic emphasis of research targeting particular places, notice changes in concepts over time, and notice changes in places where concepts are emphasized. PubMed is a database of over 19 million biomedical abstracts and citations maintained by the National Center for Biotechnology Information; achieving quick filtering is an important contribution due to the database size. Including geography in filters is important due to rapidly escalating attention to geographic factors in public health. The implementation of mechanisms for iterative place-time-concept filtering makes it possible to narrow searches efficiently and quickly from thousands of documents to a small subset that meet place-time-concept constraints. Support for a more-like-this query creates the potential to identify unexpected connections across diverse areas of research. Multi-view visualization methods support understanding of the place, time, and concept components of document collections and enable comparison of filtered query results to the full set of publications.

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

SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases.

PubMed

Schweiger, Dominik; Trajanoski, Zlatko; Pabinger, Stephan

2014-08-15

Semantic Web has established itself as a framework for using and sharing data across applications and database boundaries. Here, we present a web-based platform for querying biological Semantic Web databases in a graphical way. SPARQLGraph offers an intuitive drag & drop query builder, which converts the visual graph into a query and executes it on a public endpoint. The tool integrates several publicly available Semantic Web databases, including the databases of the just recently released EBI RDF platform. Furthermore, it provides several predefined template queries for answering biological questions. Users can easily create and save new query graphs, which can also be shared with other researchers. This new graphical way of creating queries for biological Semantic Web databases considerably facilitates usability as it removes the requirement of knowing specific query languages and database structures. The system is freely available at http://sparqlgraph.i-med.ac.at.

Effectiveness of horticultural therapy: a systematic review of randomized controlled trials.

PubMed

Kamioka, Hiroharu; Tsutani, Kiichiro; Yamada, Minoru; Park, Hyuntae; Okuizumi, Hiroyasu; Honda, Takuya; Okada, Shinpei; Park, Sang-Jun; Kitayuguchi, Jun; Abe, Takafumi; Handa, Shuichi; Mutoh, Yoshiteru

2014-10-01

To summarize the evidence from randomized controlled trials (RCTs) on the effects of horticultural therapy (HT). Studies were eligible if they were RCTs. Studies included one treatment group in which HT was applied. We searched the following databases from 1990 up to August 20, 2013: MEDLINE via PubMed, CINAHL, Web of Science, Ichushi-Web, GHL, WPRIM, and PsyclNFO. We also searched all Cochrane Database and Campbell Systematic Reviews up to September 20, 2013. Four studies met all inclusion criteria. The language of all eligible publications was English and Korean. Target diseases and/or symptoms were dementia, severe mental illness such as schizophrenia, bipolar disorder, and major depression, frail elderly in nursing home, and hemiplegic patients after stroke. These studies showed significant effectiveness in one or more outcomes for mental health and behavior. However, our review especially detected omissions of the following descriptions: method used to generate randomization, concealment, blinding, and intention-to-treat analysis. In addition, the results of this study suggested that the RCTs conducted have been of relatively low quality. Although there was insufficient evidence in the studies of HT due to poor methodological and reporting quality and heterogeneity, HT may be an effective treatment for mental and behavioral disorders such as dementia, schizophrenia, depression, and terminal-care for cancer. Copyright © 2014 Elsevier Ltd. All rights reserved.

Self-concept of left-behind children in China: a systematic review of the literature.

PubMed

Wang, X; Ling, L; Su, H; Cheng, J; Jin, L; Sun, Y-H

2015-05-01

The aim of our study was to systematically review studies which had compared self-concept in left-behind children with the general population of children in China. Relevant studies about self-concept of left-behind children in China published from 2004 to 2014 were sought by searching online databases including Chinese Biological Medicine Database (CBM), Chinese National Knowledge Infrastructure (CNKI), Wanfang Database, Vip Database, PubMed Database, Google Scholar and Web of Science. The methodological quality of the articles was assessed by using Newcastle-Ottawa Scale (NOS). Poled effect size and associated 95% confidence interval (CI) were calculated using the random effects model. Cochrane's Q was used to test for heterogeneity and I(2) index was used to determine the degree of heterogeneity. Nineteen studies involving 7758 left-behind children met the inclusion criteria and 15 studies were included in a meta-analysis. The results indicated that left-behind group had a lower score of self-concept and more psychological problems than the control group. The factors associated with self-concept in left-behind children were gender, age, grade and the relationships with parents, guardians and teachers. Left-behind children had lower self-concept and more mental health problems compared with the general population of children. The development of self-concept may be an important channel for promoting mental health of left-behind children. © 2014 John Wiley & Sons Ltd.

Effects of web-based interventions on cancer patients' symptoms: review of randomized trials.

PubMed

Fridriksdottir, N; Gunnarsdottir, S; Zoëga, S; Ingadottir, B; Hafsteinsdottir, E J G

2018-02-01

Symptom management is of high priority in cancer care. Information and communication technology allows interventions to be provided through the internet to enhance the delivery of care. This study aimed to review the effects of web-based interventions on cancer patients' symptoms. MEDLINE, PSychINFO, PubMed, CINAHL, and Cochrane databases were systematically searched. Included were randomized controlled trials (RCTs), pilot RCTs, or quasi-experimental (QE) studies focusing on web-based interventions in adult cancer patients with at least one outcome primary or secondary, in terms of symptoms, treatment side effects, or distress. Data were analyzed study by study. Twenty studies were identified. All web interventions included information, 16 included self-management support, 14 included self-monitoring, 13 included feedback/tailored information, 12 used communication with health-care professionals, and eight used communication with other patients. Overall, 13 studies reported positive symptom outcomes. Psychological distress was reported in eight studies with positive intervention effects in three. Symptoms of anxiety/depression were reported in ten studies with positive intervention effects in five. Somatic symptom severity was reported in ten studies with intervention effects found in six, and symptom distress was reported in six studies with intervention effects found in all. This review shows the promising potential of web-based interventions for cancer symptom management, although it was limited by considerable heterogeneity in the interventions tested and targeted outcomes. The multidimensional nature of symptoms was partly addressed; only one study was guided by a comprehensive theoretical model of cancer symptom management. It can only be speculated which web elements are important for effective symptom outcomes. Further testing is needed for web-based cancer symptom management.

[Bibliometric and thematic analysis of the scientific literature about omega-3 fatty acids indexed in international databases on health sciences].

PubMed

Sanz-Valero, J; Gil, Á; Wanden-Berghe, C; Martínez de Victoria, E

2012-11-01

To evaluate by bibliometric and thematic analysis the scientific literature on omega-3 fatty acids indexed in international databases on health sciences and to establish a comparative base for future analysis. Searches were conducted with the descriptor (MeSH, as Major Topic) "Fatty Acids, Omega-3" from the first date available until December 31, 2010. Databases consulted: MEDLINE (via PubMed), EMBASE, ISI Web of Knowledge, CINAHL and LILACS. The most common type of document was originals articles. Obsolescence was set at 5 years. The geographical distribution of authors who appear as first author was EEUU and the articles were written predominantly in English. The study population was 90.98% (95% CI 89.25 to 92.71) adult humans. The documents were classified into 59 subject areas and the most studied topic 16.24% (95% CI 14.4 to 18.04) associated with omega-3, was cardiovascular disease. This study indicates that the scientific literature on omega-3 fatty acids is a full force area of knowledge. The Anglo-Saxon institutions dominate the scientific production and it is mainly oriented to the study of cardiovascular disease.

Methanol poisoning among travellers to Indonesia.

PubMed

Giovanetti, Franco

2013-01-01

Common Travel Medicine sources generally do not provide information on the risk of methanol poisoning among travellers who visit Indonesia. The aim of this analysis was to increase knowledge on this topic through reports from bibliographic databases and Internet sources. Case reports and studies on methanol poisoning in Indonesia were retrieved through PubMed, Embase and Google Scholar database searching. The Google search was used to retrieve the Web Media articles reporting fatal and non-fatal methanol poisoning in Indonesia, in a timeframe from 01.01.2009 to 03.03.2013. Three case reports of methanol poisoning involving four travellers to Indonesia were found in bibliographic databases. The media sources searching identified 14 articles published online, reporting 22 cases of methanol poisoning among travellers after consumption of local alcohol beverages. The total number of death cases was 18. Some sources report also a large number of cases among the local population. Methanol poisoning is likely to be an emerging public health problem in Indonesia, with an associated morbidity and mortality among travellers and local people. Some strategies can be implemented to prevent or reduce harm among travellers. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

Just-in-time Database-Driven Web Applications

PubMed Central

2003-01-01

"Just-in-time" database-driven Web applications are inexpensive, quickly-developed software that can be put to many uses within a health care organization. Database-driven Web applications garnered 73873 hits on our system-wide intranet in 2002. They enabled collaboration and communication via user-friendly Web browser-based interfaces for both mission-critical and patient-care-critical functions. Nineteen database-driven Web applications were developed. The application categories that comprised 80% of the hits were results reporting (27%), graduate medical education (26%), research (20%), and bed availability (8%). The mean number of hits per application was 3888 (SD = 5598; range, 14-19879). A model is described for just-in-time database-driven Web application development and an example given with a popular HTML editor and database program. PMID:14517109

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.

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

PubMed

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

2018-04-01

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

Clinical Uncertainties, Health Service Challenges, and Ethical Complexities of HIV “Test-and-Treat”: A Systematic Review

PubMed Central

Shah, Kavita R.; Sarma, Karthik V.; Mahajan, Anish P.

2013-01-01

Despite the HIV “test-and-treat” strategy’s promise, questions about its clinical rationale, operational feasibility, and ethical appropriateness have led to vigorous debate in the global HIV community. We performed a systematic review of the literature published between January 2009 and May 2012 using PubMed, SCOPUS, Global Health, Web of Science, BIOSIS, Cochrane CENTRAL, EBSCO Africa-Wide Information, and EBSCO CINAHL Plus databases to summarize clinical uncertainties, health service challenges, and ethical complexities that may affect the test-and-treat strategy’s success. A thoughtful approach to research and implementation to address clinical and health service questions and meaningful community engagement regarding ethical complexities may bring us closer to safe, feasible, and effective test-and-treat implementation. PMID:23597344

Static Stretching of the Hamstring Muscle for Injury Prevention in Football Codes: a Systematic Review

PubMed Central

Rogan, Slavko; Wüst, Dirk; Schwitter, Thomas; Schmidtbleicher, Dietmar

2012-01-01

Purpose Hamstring injuries are common among football players. There is still disagreement regarding prevention. The aim of this review is to determine whether static stretching reduces hamstring injuries in football codes. Methods A systematic literature search was conducted on the online databases PubMed, PEDro, Cochrane, Web of Science, Bisp and Clinical Trial register. Study results were presented descriptively and the quality of the studies assessed were based on Cochrane's ‘risk of bias’ tool. Results The review identified 35 studies, including four analysis studies. These studies show deficiencies in the quality of study designs. Conclusion The study protocols are varied in terms of the length of intervention and follow-up. No RCT studies are available, however, RCT studies should be conducted in the near future. PMID:23785569

76 FR 1137 - Publicly Available Consumer Product Safety Information Database: Notice of Public Web Conferences

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-07

...: Notice of Public Web Conferences AGENCY: Consumer Product Safety Commission. ACTION: Notice. SUMMARY: The Consumer Product Safety Commission (``Commission,'' ``CPSC,'' or ``we'') is announcing two Web conferences... database (``Database''). The Web conferences will be webcast live from the Commission's headquarters in...

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.

Web-based infectious disease surveillance systems and public health perspectives: a systematic review.

PubMed

Choi, Jihye; Cho, Youngtae; Shim, Eunyoung; Woo, Hyekyung

2016-12-08

Emerging and re-emerging infectious diseases are a significant public health concern, and early detection and immediate response is crucial for disease control. These challenges have led to the need for new approaches and technologies to reinforce the capacity of traditional surveillance systems for detecting emerging infectious diseases. In the last few years, the availability of novel web-based data sources has contributed substantially to infectious disease surveillance. This study explores the burgeoning field of web-based infectious disease surveillance systems by examining their current status, importance, and potential challenges. A systematic review framework was applied to the search, screening, and analysis of web-based infectious disease surveillance systems. We searched PubMed, Web of Science, and Embase databases to extensively review the English literature published between 2000 and 2015. Eleven surveillance systems were chosen for evaluation according to their high frequency of application. Relevant terms, including newly coined terms, development and classification of the surveillance systems, and various characteristics associated with the systems were studied. Based on a detailed and informative review of the 11 web-based infectious disease surveillance systems, it was evident that these systems exhibited clear strengths, as compared to traditional surveillance systems, but with some limitations yet to be overcome. The major strengths of the newly emerging surveillance systems are that they are intuitive, adaptable, low-cost, and operated in real-time, all of which are necessary features of an effective public health tool. The most apparent potential challenges of the web-based systems are those of inaccurate interpretation and prediction of health status, and privacy issues, based on an individual's internet activity. Despite being in a nascent stage with further modification needed, web-based surveillance systems have evolved to complement traditional national surveillance systems. This review highlights ways in which the strengths of existing systems can be maintained and weaknesses alleviated to implement optimal web surveillance systems.

RESPIRATORY INFECTIONS RESEARCH IN AFGHANISTAN: BIBLIOMETRIC ANALYSIS WITH THE DATABASE PUBMED.

PubMed

Pilsczek, Florian H

2015-01-01

Infectious diseases research in a low-income country like Afghanistan is important. In this study an internet-based database Pubmed was used for bibliometric analysis of infectious diseases research activity. Research publications entries in PubMed were analysed according to number of publications, topic, publication type, and country of investigators. Between 2002-2011, 226 (77.7%) publications with the following research topics were identified: respiratory infections 3 (1.3%); parasites 8 (3.5%); diarrhoea 10 (4.4%); tuberculosis 10 (4.4%); human immunodeficiency virus (HIV) 11 (4.9%); multi-drug resistant bacteria (MDR) 18 (8.0%); polio 31 (13.7%); leishmania 31 (13.7%); malaria 46 (20.4%). From 2002-2011, 11 (4.9%) publications were basic science laboratory-based research studies. Between 2002-2011, 8 (3.5%) publications from Afghan institutions were identified. In conclusion, the internet-based database Pubmed can be consulted to collect data for guidance of infectious diseases research activity of low-income countries. The presented data suggest that infectious diseases research in Afghanistan is limited for respiratory infections research, has few studies conducted by Afghan institutions, and limited laboratory-based research contributions.

Medical mentoring via the evolving world wide web.

PubMed

Jaffer, Usman; Vaughan-Huxley, Eyston; Standfield, Nigel; John, Nigel W

2013-01-01

Mentoring, for physicians and surgeons in training, is advocated as an essential adjunct in work-based learning, providing support in career and non-career related issues. The World Wide Web (WWW) has evolved, as a technology, to become more interactive and person centric, tailoring itself to the individual needs of the user. This changing technology may open new avenues to foster mentoring in medicine. DESIGN, SYSTEMATIC REVIEW, MAIN OUTCOME MEASURES: A search of the MEDLINE database from 1950 to 2012 using the PubMed interface, combined with manual cross-referencing was performed using the following strategy: ("mentors"[MeSH Terms] OR "mentors"[All Fields] OR "mentor"[All Fields]) AND ("internet"[MeSH Terms] OR "internet"[All Fields]) AND ("medicine"[MeSH Terms] OR "medicine"[All Fields]) AND ("humans"[MeSH Terms] AND English[lang]). Abstracts were screened for relevance (UJ) to the topic; eligibility for inclusion was simply on screening for relevance to online mentoring and web-based technologies. Forty-five papers were found, of which 16 were relevant. All studies were observational in nature. To date, all medical mentoring applications utilizing the World Wide Web have enjoyed some success limited by Web 1.0 and 2.0 technologies. With the evolution of the WWW through 1.0, 2.0 and 3.0 generations, the potential for meaningful tele- and distance mentoring has greatly improved. Some engagement has been made with these technological advancements, however further work is required to fully realize the potential of these technologies. Copyright © 2012 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

76 FR 54807 - Notice of Proposed Information Collection: IMLS Museum Web Database: MuseumsCount.gov

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-02

...: IMLS Museum Web Database: MuseumsCount.gov AGENCY: Institute of Museum and Library Services, National..., and the general public. Information such as name, address, phone, e-mail, Web site, congressional...: IMLS Museum Web Database, MuseumsCount.gov . OMB Number: To be determined. Agency Number: 3137...

Evaluation models and criteria of the quality of hospital websites: a systematic review study

PubMed Central

Jeddi, Fatemeh Rangraz; Gilasi, Hamidreza; Khademi, Sahar

2017-01-01

Introduction Hospital websites are important tools in establishing communication and exchanging information between patients and staff, and thus should enjoy an acceptable level of quality. The aim of this study was to identify proper models and criteria to evaluate the quality of hospital websites. Methods This research was a systematic review study. The international databases such as Science Direct, Google Scholar, PubMed, Proquest, Ovid, Elsevier, Springer, and EBSCO together with regional database such as Magiran, Scientific Information Database, Persian Journal Citation Report (PJCR) and IranMedex were searched. Suitable keywords including website, evaluation, and quality of website were used. Full text papers related to the research were included. The criteria and sub criteria of the evaluation of website quality were extracted and classified. Results To evaluate the quality of the websites, various models and criteria were presented. The WEB-Q-IM, Mile, Minerva, Seruni Luci, and Web-Qual models were the designed models. The criteria of accessibility, content and apparent features of the websites, the design procedure, the graphics applied in the website, and the page’s attractions have been mentioned in the majority of studies. Conclusion The criteria of accessibility, content, design method, security, and confidentiality of personal information are the essential criteria in the evaluation of all websites. It is suggested that the ease of use, graphics, attractiveness and other apparent properties of websites are considered as the user-friendliness sub criteria. Further, the criteria of speed and accessibility of the website should be considered as sub criterion of efficiency. When determining the evaluation criteria of the quality of websites, attention to major differences in the specific features of any website is essential. PMID:28465807

Evaluation models and criteria of the quality of hospital websites: a systematic review study.

PubMed

Jeddi, Fatemeh Rangraz; Gilasi, Hamidreza; Khademi, Sahar

2017-02-01

Hospital websites are important tools in establishing communication and exchanging information between patients and staff, and thus should enjoy an acceptable level of quality. The aim of this study was to identify proper models and criteria to evaluate the quality of hospital websites. This research was a systematic review study. The international databases such as Science Direct, Google Scholar, PubMed, Proquest, Ovid, Elsevier, Springer, and EBSCO together with regional database such as Magiran, Scientific Information Database, Persian Journal Citation Report (PJCR) and IranMedex were searched. Suitable keywords including website, evaluation, and quality of website were used. Full text papers related to the research were included. The criteria and sub criteria of the evaluation of website quality were extracted and classified. To evaluate the quality of the websites, various models and criteria were presented. The WEB-Q-IM, Mile, Minerva, Seruni Luci, and Web-Qual models were the designed models. The criteria of accessibility, content and apparent features of the websites, the design procedure, the graphics applied in the website, and the page's attractions have been mentioned in the majority of studies. The criteria of accessibility, content, design method, security, and confidentiality of personal information are the essential criteria in the evaluation of all websites. It is suggested that the ease of use, graphics, attractiveness and other apparent properties of websites are considered as the user-friendliness sub criteria. Further, the criteria of speed and accessibility of the website should be considered as sub criterion of efficiency. When determining the evaluation criteria of the quality of websites, attention to major differences in the specific features of any website is essential.

Influence of Flavonoids on Mechanism of Modulation of Insulin Secretion.

PubMed

Soares, Juliana Mikaelly Dias; Pereira Leal, Ana Ediléia Barbosa; Silva, Juliane Cabral; Almeida, Jackson R G S; de Oliveira, Helinando Pequeno

2017-01-01

The development of alternatives for insulin secretion control in vivo or in vitro represents an important aspect to be investigated. In this direction, natural products have been progressively explored with this aim. In particular, flavonoids are potential candidates to act as insulin secretagogue. To study the influence of flavonoid on overall modulation mechanisms of insulin secretion. The research was conducted in the following databases and platforms: PubMed, Scopus, ISI Web of Knowledge, SciELO, LILACS, and ScienceDirect, and the MeSH terms used for the search were flavonoids, flavones, islets of Langerhans, and insulin-secreting cells. Twelve articles were included and represent the basis of discussion on mechanisms of insulin secretion of flavonoids. Papers in ISI Web of Knowledge were in number of 1, Scopus 44, PubMed 264, ScienceDirect 511, and no papers from LILACS and SciELO databases. According to the literature, the majority of flavonoid subclasses can modulate insulin secretion through several pathways, in an indication that corresponding molecule is a potential candidate for active materials to be applied in the treatment of diabetes. The action of natural products on insulin secretion represents an important investigation topic due to their importance in the diabetes controlIn addition to their typical antioxidant properties, flavonoids contribute to the insulin secretionThe modulation of insulin secretion is induced by flavonoids according to different mechanisms. Abbreviations used: K ATP channels: ATP-sensitive K + channels, GLUT4: Glucose transporter 4, ERK1/2: Extracellular signal-regulated protein kinases 1 and 2, L-VDCCs: L-type voltage-dependent Ca +2 channels, GLUT1: Glucose transporter 1, AMPK: Adenosine monophosphate-activated protein kinase, PTP1B: Protein tyrosine phosphatase 1B, GLUT2: Glucose transporter 2, cAMP: Cyclic adenosine monophosphate, PKA: Protein kinase A, PTK: Protein tyrosine kinase, CaMK II: Ca 2+ /calmodulin-dependent protein kinase II, GSIS: Glucose-stimulated insulin secretion, Insig-1: Insulin-induced gene 1, IRS-2: Insulin receptor substrate 2, PDX-1: Pancreatic and duodenal homeobox 1, SREBP-1c: Sterol regulatory element binding protein-1c, DMC: Dihydroxy-6'-methoxy-3',5'-dimethylchalcone, GLP-1: Glucagon-like peptide-1, GLP-1R: Glucagon-like peptide 1 receptor.

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/.

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

Evaluation Instruments for Quality of Life Related to Melasma: An Integrative Review.

PubMed

Pollo, Camila Fernandes; Meneguin, Silmara; Miot, Helio Amante

2018-05-21

The aim of this study was to analyze scientific production concerning the validation and cultural adaptation of quality of life evaluation instruments for patients with melasma and to offer a critical reflection on these methods. A literature review was performed based on a search of the Web of Science, Bireme, PubMed, Elsevier Scopus, and Google Scholar databases. All published articles from indexed periodicals in these electronic databases up to December 2015 were included. Eight articles were identified, of which only one (12.5%) referred to the development and validation of a specific instrument for evaluation of the quality of life of melasma patients. An additional six articles (75%) referred to transcultural adjustment and validation of the same instrument in other languages, and another (12.5%) article reported the development of a generic instrument for evaluation of quality of life in patients with pigment disorders. This review revealed only one specific instrument developed and validated in different cultures. Despite being widely used, this instrument did not follow the classic construction steps for psychometric instruments, which paves the way for future studies to develop novel instruments.

Effects of the Usage of l-Cysteine (l-Cys) on Human Health.

PubMed

Clemente Plaza, Noelia; Reig García-Galbis, Manuel; Martínez-Espinosa, Rosa María

2018-03-03

This review summarizes recent knowledge about the use of the amino acid l-Cysteine (l-Cys) through diet, nutritional supplements or drugs with the aim to improve human health or treat certain diseases. Three databases (PubMed, Scopus, and Web of Science) and different keywords have been used to create a database of documents published between 1950 and 2017 in scientific journals in English or Spanish. A total of 60,885 primary publications were ultimately selected to compile accurate information about the use of l-Cys in medicine and nutritional therapies and to identify the reported benefits of l-Cys on human health. The number of publications about the use of l-Cys for these purposes has increased significantly during the last two decades. This increase seems to be closely related to the rise of nutraceutical industries and personalized medicine. The main evidence reporting benefits of l-Cys usage is summarized. However, the lack of accurate information and studies based on clinical trials hampers consensus among authors. Thus, the debate about the role and effectiveness of supplements/drugs containing l-Cys is still open.

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.

Web resources for rare auto-inflammatory diseases: towards a common patient registry.

PubMed

Touitou, Isabelle; Hentgen, Véronique; Koné-Paut, Isabelle

2009-06-01

To review information resources on rare auto-inflammatory disorders (AIDs) for use by health care professionals, focusing particularly on patient registries. Using relevant key words, we surveyed the websites of several scientific societies of immunology, paediatrics and rheumatology, as well as Pubmed and specialized databases for AIDs. The Internet provides a wide variety of information related to AIDs. Moreover, several other initiatives have been undertaken to create new resources for professionals. We reviewed six patient registries for rare AIDs, taking a special interest in the submission questionnaire. We revealed a wide overlap between the items used in the questionnaires, whereas the currently available registries appeared inappropriate for AIDs patients with complex or undefined diagnosis. AIDs share common clinical features, pathophysiological pathways and therapeutic approaches. Although several resources are now available for rare AIDs, a unique and dedicated site gathering all aspects of these diseases as a whole is still lacking, i.e. covering research as well as the needs of AIDs patients and health care professionals. Our study thus advocates a merging of existing patient registries or the creation of a common database.

Evaluation Instruments for Quality of Life Related to Melasma: An Integrative Review

PubMed Central

Pollo, Camila Fernandes; Meneguin, Silmara; Miot, Helio Amante

2018-01-01

The aim of this study was to analyze scientific production concerning the validation and cultural adaptation of quality of life evaluation instruments for patients with melasma and to offer a critical reflection on these methods. A literature review was performed based on a search of the Web of Science, Bireme, PubMed, Elsevier Scopus, and Google Scholar databases. All published articles from indexed periodicals in these electronic databases up to December 2015 were included. Eight articles were identified, of which only one (12.5%) referred to the development and validation of a specific instrument for evaluation of the quality of life of melasma patients. An additional six articles (75%) referred to transcultural adjustment and validation of the same instrument in other languages, and another (12.5%) article reported the development of a generic instrument for evaluation of quality of life in patients with pigment disorders. This review revealed only one specific instrument developed and validated in different cultures. Despite being widely used, this instrument did not follow the classic construction steps for psychometric instruments, which paves the way for future studies to develop novel instruments. PMID:29791603

[Are antioxidant supplements effective in reducing delayed onset muscle soreness? A systematic review].

PubMed

Candia-Luján, Ramón; De Paz Fernández, José Antonio; Costa Moreira, Osvaldo

2014-10-05

In recent years, antioxidant supplements have become popular to counter the effects of free radicals and muscle damage symptoms, including delayed onset muscle soreness (DOMS). To conduct a systematic review in different databases to determine the effects of antioxidant supplements on DOMS. We conducted a search in databases; Cochrane, Pubmed, Scopus and SportDiscus and Web of Science (WOS). The words and acronyms used were; Delayed onset muscle soreness, exercise induced muscle damage, DOMS, EIMD, antioxidant and oxidative stress. 54 articles were identified of which 48 were retreived, all in English, 17 related to vitamin C and E, supplements polyphenolic correspond to fourteen, eleven other antioxidant supplements and six to commercial supplements, all of them used to diminish the DOMS and other variables. Both vitamins and commercial supplements have low effectiveness in reducing DOMS, while polyphenols and other antioxidant supplements show moderate to good effectiveness in combating DOMS. However, most of the studies have effectiveness in reducing other symptoms of muscle damage besides helping in the post-exercise recovery. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Web-Based Mindfulness Interventions for People With Physical Health Conditions: Systematic Review

PubMed Central

Toivonen, Kirsti I; Zernicke, Kristin

2017-01-01

Background Mindfulness-based interventions (MBIs) are becoming increasingly popular for helping people with physical health conditions. Expanding from traditional face-to-face program delivery, there is growing interest in Web-based application of MBIs, though Web-based MBIs for people with physical health conditions specifically have not been thoroughly reviewed to date. Objective The objective of this paper was to review Web-based MBIs for people with physical health conditions and to examine all outcomes reported (eg, efficacy or effectiveness for physical changes or psychological changes; feasibility). Methods Databases PubMed, PsycINFO, Science Direct, CINAHL Plus, and Web of Science were searched. Full-text English papers that described any Web-based MBI, examining any outcome, for people with chronic physical health conditions were included. Randomized, nonrandomized, controlled, and uncontrolled trials were all included. Extracted data included intervention characteristics, population characteristics, outcomes, and quality indicators. Intervention characteristics (eg, synchronicity and guidance) were examined as potential factors related to study outcomes. Results Of 435 publications screened, 19 published papers describing 16 studies were included. They examined Web-based MBIs for people with cancer, chronic pain or fibromyalgia, irritable bowel syndrome (IBS), epilepsy, heart disease, tinnitus, and acquired brain injury. Overall, most studies reported positive effects of Web-based MBIs compared with usual care on a variety of outcomes including pain acceptance, coping measures, and depressive symptoms. There were mixed results regarding the effectiveness of Web-based MBIs compared with active control treatment conditions such as cognitive behavioral therapy. Condition-specific symptoms (eg, cancer-related fatigue and IBS symptoms) targeted by treatment had the largest effect size improvements following MBIs. Results are inconclusive regarding physical variables. Conclusions Preliminary evidence suggests that Web-based MBIs may be helpful in alleviating symptom burden that those with physical health conditions can experience, particularly when interventions are tailored for specific symptoms. There was no evidence of differences between synchronous versus asynchronous or facilitated versus self-directed Web-based MBIs. Future investigations of Web-based MBIs should evaluate the effects of program adherence, effects on mindfulness levels, and whether synchronous or asynchronous, or facilitated or self-directed interventions elicit greater improvements. PMID:28860106

Development of a chemotherapy regimen interaction database for the mobile internet: detecting interactions with psychotropics through OncoRx-MI.

PubMed

Yap, Kevin Yi-Lwern; Chui, Wai Keung; Chan, Alexandre

2011-09-01

Cancer patients are at high risks of drug-drug interactions (DDIs). Clinicians need to know the magnitude of DDIs so as to better manage their patients' drug therapies. We have previously created a novel interaction database for oncology prescriptions (OncoRx). In this project, we leverage on 3G networks to further develop this database into an iPhone-specific application for the mobile internet (OncoRx-MI). Data on anticancer drugs (ACDs), chemotherapy regimens (CRegs) and DDIs with psychotropics were compiled from various hardcopy and online resources, and published articles from PubMed, Scopus and Science Direct. The database and iPhone web documents were designed using Adobe Dreamweaver CS4 and associated with a combination of open-source programming scripts. OncoRx-MI currently detects over 5000 DDIs (69.3% pharmacokinetic, 30.7% pharmacodynamic) between 256 single-agent and combination CRegs with 51 psychotropic drugs. OncoRx-MI fits the iPhone screen configuration, and displays information regarding the regimen, pharmacokinetics of the drugs and detected DDIs in tabular format for improved usability. OncoRx-MI is the first mobile DDI application of its kind which detects interactions for combination CRegs. Future versions will include DDIs with other drug categories. Usability studies on its impact in clinical practice will also be carried out.

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.

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

dbDSM: a manually curated database for deleterious synonymous mutations.

PubMed

Wen, Pengbo; Xiao, Peng; Xia, Junfeng

2016-06-15

Synonymous mutations (SMs), which changed the sequence of a gene without directly altering the amino acid sequence of the encoded protein, were thought to have no functional consequences for a long time. They are often assumed to be neutral in models of mutation and selection and were completely ignored in many studies. However, accumulating experimental evidence has demonstrated that these mutations exert their impact on gene functions via splicing accuracy, mRNA stability, translation fidelity, protein folding and expression, and some of these mutations are implicated in human diseases. To the best of our knowledge, there is still no database specially focusing on disease-related SMs. We have developed a new database called dbDSM (database of Deleterious Synonymous Mutation), a continually updated database that collects, curates and manages available human disease-related SM data obtained from published literature. In the current release, dbDSM collects 1936 SM-disease association entries, including 1289 SMs and 443 human diseases from ClinVar, GRASP, GWAS Catalog, GWASdb, PolymiRTS database, PubMed database and Web of Knowledge. Additionally, we provided users a link to download all the data in the dbDSM and a link to submit novel data into the database. We hope dbDSM will be a useful resource for investigating the roles of SMs in human disease. dbDSM is freely available online at http://bioinfo.ahu.edu.cn:8080/dbDSM/index.jsp with all major browser supported. jfxia@ahu.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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.

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.

Centella asiatica (L.) Urban: From Traditional Medicine to Modern Medicine with Neuroprotective Potential.

PubMed

Orhan, Ilkay Erdogan

2012-01-01

This paper covers the studies relevant to neuroprotective activity of Centella asiatica (L.) Urban, also known as "Gotu Kola." The plant is native to the Southeast Asia and has been used traditionally as brain tonic in ayurvedic medicine. The neuroprotective effect of C. asiatica has been searched using the key words "Centella, Centella asiatica, gotu kola, Asiatic pennywort, neuroprotection, and memory" through the electronic databases including Sciencedirect, Web of Science, Scopus, Pubmed, and Google Scholar. According to the literature survey, C. asiatica (gotu kola) has been reported to have a comprehensive neuroprotection by different modes of action such as enzyme inhibition, prevention of amyloid plaque formation in Alzheimer's disease, dopamine neurotoxicity in Parkinson's disease, and decreasing oxidative stress. Therefore, C. asiatica could be suggested to be a desired phytopharmaceutical with neuroprotective effect emerged from traditional medicine.

[Interface between bioethics and international relations].

PubMed

Manchola-Castillo, Camilo; Garrafa, Volnei

2016-08-01

Recently, bioethics and international relations have gotten closer to one an other, probably as a result of the motivation of bioethics to intervene in global affairs. However, this relationship has only been on the practical level.This study's objective, through a literature review, is to highlight the huge potential that the epistemologies of both areas have to build a more fruitful dialogue. 18 articles relating both areas were retrieved from databases Scopus, Web of Science, Bireme and PubMed. The articles were then grouped in three categories of analysis: bioethics and global health; international organizations and bioethics; and international relations and bioethics. This study concludes that an epistemological approaching between these areas is desirable and proposes the establishment of two new areas of study: international relations in health and international relations from the South, drawing upon the conceptual basis developed by Latin-American bioethics.

Treatment of transverse patellar fractures: a comparison between metallic and non-metallic implants.

PubMed

Heusinkveld, Maarten H G; den Hamer, Anniek; Traa, Willeke A; Oomen, Pim J A; Maffulli, Nicola

2013-01-01

Several methods of transverse patellar fixation have been described. This study compares the clinical outcome and the occurrence of complications of various fixation methods. The databases PubMed, Web of Science, Science Direct, Google Scholar and Google were searched. A direct comparison between fixation techniques using mixed or non-metallic implants and metallic K-wire and tension band fixation shows no significant difference in clinical outcome between both groups. Additionally, studies reporting novel operation techniques show good clinical results. Studies describing the treatment of patients using non-metallic or mixed implants are fewer compared with those using metallic fixation. A large variety of clinical scoring systems were used for assessing the results of treatment, which makes direct comparison difficult. More data of fracture treatment using non-metallic or mixed implants is needed to achieve a more balanced comparison.

Endometrial cancer - reduce to the minimum. A new paradigm for adjuvant treatments?

PubMed Central

2011-01-01

Background Up to now, the role of adjuvant radiation therapy and the extent of lymph node dissection for early stage endometrial cancer are controversial. In order to clarify the current position of the given adjuvant treatment options, a systematic review was performed. Materials and methods Both, Pubmed and ISI Web of Knowledge database were searched using the following keywords and MESH headings: "Endometrial cancer", "Endometrial Neoplasms", "Endometrial Neoplasms/radiotherapy", "External beam radiation therapy", "Brachytherapy" and adequate combinations. Conclusion Recent data from randomized trials indicate that external beam radiation therapy - particularly in combination with extended lymph node dissection - or radical lymph node dissection increases toxicity without any improvement of overall survival rates. Thus, reduced surgical aggressiveness and limitation of radiotherapy to vaginal-vault-brachytherapy only is sufficient for most cases of early stage endometrial cancer. PMID:22118369

Listeriosis Phytotherapy

PubMed Central

Rafieian-Kopaei, Mahmoud; Saki, Kourosh; Bahmani, Mahmoud; Ghafourian, Sobhan; Sadeghifard, Nourkhoda; Taherikalani, Morovat

2015-01-01

Listeria monocytogenes can be found in many processed foods, raw milk, dairy products, meat and meat products such as sausages, beef and fish products, seafoods, eggs, fruits, and vegetables such as radish and cabbage. This article is a review study on the Iranian medicinal plants applied for treatment of listeriosis. Information of this review article was obtained by searching various key words such as Listeria monocytogenes, medicinal plants, plant extracts and essential oils among scientific articles published in databases of Google scholar, ISI Web of Knowledge, PubMed, Scopus, SID and Magiran. Thyme, German chamomile, great chamomile, yarrow, onion, oregano, nutmeg, sage, sagebrush, hyssop, rosemary, St John’s wort, safflower, ajowan, cumin, peppermint, shallot, anise, and parsnip are known antilisteriosis medicinal plants. Bioactive phytochemicals, antioxidants and monoterpenes, sesquiterpene, coumarin, flavonoids, tannins, saponins, alkaloids, and terpenoids are the main ingredients of antilisteriosis medicinal plants. PMID:26682768

Unintended Consequences of Sensor, Signal, and Imaging Informatics: New Problems and New Solutions.

PubMed

Hughes, C; Voros, S; Moreau-Gaudry, A

2016-11-10

This synopsis presents a selection for the IMIA (International Medical Informatics Association) Yearbook 2016 of excellent research in the broad field of Sensor, Signal and Imaging Informatics published in the year 2015, with a focus on Unintended consequences: new problems and new solutions. We performed a systematic initial selection and a double blind peer review process to find the best papers in this domain published in 2015, from the PubMed and Web of Science databases. The set of MesH keywords used was provided by experts. The constant advances in medical technology allow ever more relevant diagnostic and therapeutic approaches to be designed. Nevertheless, there is a need to acquire expert knowledge of these innovations in order to identify precociously new associated problems for which new solutions need to be designed and developed.

Experiences of Family Relationships Among Donor-Conceived Families: A Meta-Ethnography.

PubMed

Wyverkens, Elia; Van Parys, Hanna; Buysse, Ann

2015-09-01

In this qualitative evidence synthesis, we explore how family relationships are experienced by parents who used gamete donation to conceive. We systematically searched four databases (PubMed, Web of Science, PsycINFO, and ProQuest) for literature related to this topic and retrieved 25 studies. Through the analysis of the qualitative studies, a comprehensive synthesis and framework was constructed. Following the meta-ethnography approach of Noblit and Hare, four main themes were identified: (a) balancing the importance of genetic and social ties, (b) normalizing and legitimizing the family, (c) building strong family ties, and (d) minimizing the role of the donor. Underlying these four main themes, a sense of being "different" and "similar" at the same time was apparent. Findings are discussed in terms of their implications for studying and counseling donor-conceived families. © The Author(s) 2014.

The mirror neuron system in post-stroke rehabilitation

PubMed Central

2013-01-01

Different treatments for stroke patients have been proposed; among them the mirror therapy and motion imagery lead to functional recovery by providing a cortical reorganization. Up today the basic concepts of the current literature on mirror neurons and the major findings regarding the use of mirror therapy and motor imagery as potential tools to promote reorganization and functional recovery in post-stroke patients. Bibliographic research was conducted based on publications over the past thirteen years written in English in the databases Scielo, Pubmed/MEDLINE, ISI Web of Knowledge. The studies showed how the interaction among vision, proprioception and motor commands promotes the recruitment of mirror neurons, thus providing cortical reorganization and functional recovery of post-stroke patients. We conclude that the experimental advances on Mirror Neurons will bring new rational therapeutic approaches to post-stroke rehabilitation. PMID:24134862

The mirror neuron system in post-stroke rehabilitation.

PubMed

Carvalho, Diana; Teixeira, Silmar; Lucas, Marina; Yuan, Ti-Fei; Chaves, Fernanda; Peressutti, Caroline; Machado, Sergio; Bittencourt, Juliana; Menéndez-González, Manuel; Nardi, Antonio Egidio; Velasques, Bruna; Cagy, Mauricio; Piedade, Roberto; Ribeiro, Pedro; Arias-Carrión, Oscar

2013-10-17

Different treatments for stroke patients have been proposed; among them the mirror therapy and motion imagery lead to functional recovery by providing a cortical reorganization. Up today the basic concepts of the current literature on mirror neurons and the major findings regarding the use of mirror therapy and motor imagery as potential tools to promote reorganization and functional recovery in post-stroke patients. Bibliographic research was conducted based on publications over the past thirteen years written in English in the databases Scielo, Pubmed/MEDLINE, ISI Web of Knowledge. The studies showed how the interaction among vision, proprioception and motor commands promotes the recruitment of mirror neurons, thus providing cortical reorganization and functional recovery of post-stroke patients. We conclude that the experimental advances on Mirror Neurons will bring new rational therapeutic approaches to post-stroke rehabilitation.

Safranal: From an Aromatic Natural Product to a Rewarding Pharmacological Agent

PubMed Central

Rezaee, Ramin; Hosseinzadeh, Hossein

2013-01-01

Safranal, the main component of Crocus sativus essential oil, is thought to be the main cause of saffron unique odor. It is now about eighty years that this compound has been discovered and since then different scientific experiments have been done investigating its biological-pharmacological activities. Safranal effects in CNS have been more attractive to scientists and an escalating number of papers have been published regarding its neuropsychological effects. These promising properties of safranal propose its presence as a therapeutic agent in future, although there is a great need for further clinical trials and toxicological studies. In this review article, according to Scopus ®, Thomson Reuters Web of Knowledge®, Scientific Information Database (SID) ® and Pubmed ® all papers published until July 2012 were thoroughly discussed and a brief note of each study was prepared. PMID:23638289

Posttraumatic stress disorder and risk of obesity: systematic review and meta-analysis.

PubMed

Bartoli, Francesco; Crocamo, Cristina; Alamia, Alberto; Amidani, Francesca; Paggi, Elisabetta; Pini, Elena; Clerici, Massimo; Carrà, Giuseppe

2015-10-01

To examine the association between posttraumatic stress disorder (PTSD) and obesity in the literature to date. We systematically searched PubMed, Embase, Scopus, Web of Science, and ProQuest from database inception till September 2013. Search phrases combining the terms Obesity and Post-Traumatic Stress Disorder were used. We selected observational studies estimating obesity prevalence in samples of people with PTSD, as well as in comparison groups without PTSD. Obesity rates as well as demographic, clinical, and methodological variables were extracted from each publication or obtained directly from its authors. A total of 113, 395, 59, 115, and 400 records were generated from PubMed, Embase, Scopus, Web of Science, and ProQuest, respectively. Thirteen studies were eligible according to inclusion criteria. The pooled crude odds ratio (OR) and 95% confidence interval (CI) for obesity among people with PTSD, based on 589,781 subjects, was 1.55 (1.32-1.82). A large heterogeneity was found (I(2) = 90%), and risk of publication bias was statistically significant (P = .002). However,subgroup and sensitivity analyses including only studies with most accurate methods to assess obesity (OR = 1.35; 95% CI,1.05-1.74; I(2) = 47%) and PTSD (OR = 1.82; 95% CI, 1.33-2.50; I(2) = 75%) also confirmed the association between PTSD and obesity. Despite some limitations, individuals suffering from PTSD seem more likely, relative to controls, to suffer from obesity. As such, individuals with this comorbidity should be targeted for intensive prevention and treatment focused on both disorders. Future research is needed to identify the role of unknown factors and mediators that might clarify the nature of this association. © Copyright 2015 Physicians Postgraduate Press, Inc.

Using Web Ontology Language to Integrate Heterogeneous Databases in the Neurosciences

PubMed Central

Lam, Hugo Y.K.; Marenco, Luis; Shepherd, Gordon M.; Miller, Perry L.; Cheung, Kei-Hoi

2006-01-01

Integrative neuroscience involves the integration and analysis of diverse types of neuroscience data involving many different experimental techniques. This data will increasingly be distributed across many heterogeneous databases that are web-accessible. Currently, these databases do not expose their schemas (database structures) and their contents to web applications/agents in a standardized, machine-friendly way. This limits database interoperation. To address this problem, we describe a pilot project that illustrates how neuroscience databases can be expressed using the Web Ontology Language, which is a semantically-rich ontological language, as a common data representation language to facilitate complex cross-database queries. In this pilot project, an existing tool called “D2RQ” was used to translate two neuroscience databases (NeuronDB and CoCoDat) into OWL, and the resulting OWL ontologies were then merged. An OWL-based reasoner (Racer) was then used to provide a sophisticated query language (nRQL) to perform integrated queries across the two databases based on the merged ontology. This pilot project is one step toward exploring the use of semantic web technologies in the neurosciences. PMID:17238384

Bio-psycho-social factors affecting sexual self-concept: A systematic review.

PubMed

Potki, Robabeh; Ziaei, Tayebe; Faramarzi, Mahbobeh; Moosazadeh, Mahmood; Shahhosseini, Zohreh

2017-09-01

Nowadays, it is believed that mental and emotional aspects of sexual well-being are the important aspects of sexual health. Sexual self-concept is a major component of sexual health and the core of sexuality. It is defined as the cognitive perspective concerning the sexual aspects of 'self' and refers to the individual's self-perception as a sexual creature. The aim of this study was to assess the different factors affecting sexual self-concept. English electronic databases including PubMed, Scopus, Web of Science and Google Scholar as well as two Iranian databases including Scientific Information Database and Iranmedex were searched for English and Persian-language articles published between 1996 and 2016. Of 281 retrieved articles, 37 articles were finally included for writing this review article. Factors affecting sexual self-concept were categorized to biological, psychological and social factors. In the category of biological factors, age gender, marital status, race, disability and sexual transmitted infections are described. In the psychological category, the impact of body image, sexual abuse in childhood and mental health history are present. Lastly, in the social category, the roles of parents, peers and the media are discussed. As the development of sexual self-concept is influenced by multiple events in individuals' lives, to promotion of sexual self-concept, an integrated implementation of health policies is recommended.

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

PubMed Central

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

2017-01-01

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

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

PubMed

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

2017-08-31

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

Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems

PubMed Central

Boué, Stéphanie; Talikka, Marja; Westra, Jurjen Willem; Hayes, William; Di Fabio, Anselmo; Park, Jennifer; Schlage, Walter K.; Sewer, Alain; Fields, Brett; Ansari, Sam; Martin, Florian; Veljkovic, Emilija; Kenney, Renee; Peitsch, Manuel C.; Hoeng, Julia

2015-01-01

With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com PMID:25887162

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

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

PubMed Central

Turner, Brian; Razick, Sabry; Turinsky, Andrei L.; Vlasblom, James; Crowdy, Edgard K.; Cho, Emerson; Morrison, Kyle; Wodak, Shoshana J.

2010-01-01

We present iRefWeb, a web interface to protein interaction data consolidated from 10 public databases: BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MINT, MPact, MPPI and OPHID. iRefWeb enables users to examine aggregated interactions for a protein of interest, and presents various statistical summaries of the data across databases, such as the number of organism-specific interactions, proteins and cited publications. Through links to source databases and supporting evidence, researchers may gauge the reliability of an interaction using simple criteria, such as the detection methods, the scale of the study (high- or low-throughput) or the number of cited publications. Furthermore, iRefWeb compares the information extracted from the same publication by different databases, and offers means to follow-up possible inconsistencies. We provide an overview of the consolidated protein–protein interaction landscape and show how it can be automatically cropped to aid the generation of meaningful organism-specific interactomes. iRefWeb can be accessed at: http://wodaklab.org/iRefWeb. Database URL: http://wodaklab.org/iRefWeb/ PMID:20940177

On Building a Search Interface Discovery System

NASA Astrophysics Data System (ADS)

Shestakov, Denis

A huge portion of the Web known as the deep Web is accessible via search interfaces to myriads of databases on the Web. While relatively good approaches for querying the contents of web databases have been recently proposed, one cannot fully utilize them having most search interfaces unlocated. Thus, the automatic recognition of search interfaces to online databases is crucial for any application accessing the deep Web. This paper describes the architecture of the I-Crawler, a system for finding and classifying search interfaces. The I-Crawler is intentionally designed to be used in the deep web characterization surveys and for constructing directories of deep web resources.

Business Faculty Research: Satisfaction with the Web versus Library Databases

ERIC Educational Resources Information Center

Dewald, Nancy H.; Silvius, Matthew A.

2005-01-01

Business faculty members teaching at undergraduate campuses of the Pennsylvania State University were surveyed in order to assess their satisfaction with free Web sources and with subscription databases for their professional research. Although satisfaction with the Web's ease of use was higher than that for databases, overall satisfaction for…

Pub-Med-dot-com, here we come!

PubMed

Pulst, Stefan M

2016-08-01

As of April 8, 2016, articles in Neurology® Genetics can be searched using PubMed. Launched in 1996, PubMed is a search engine that accesses citations and abstracts of more than 26 million articles. Its primary sources include the MEDLINE database, which was started in the 1960s, and biomedical and life sciences journal articles that date back to 1946. In addition, PubMed accesses other sources, for example, citations to those life sciences journals that submit full-text articles to PubMed Central (PMC). PubMed Central was launched in 2000 as a free archive of biomedical and life science journals.

A Web-Based Database for Nurse Led Outreach Teams (NLOT) in Toronto.

PubMed

Li, Shirley; Kuo, Mu-Hsing; Ryan, David

2016-01-01

A web-based system can provide access to real-time data and information. Healthcare is moving towards digitizing patients' medical information and securely exchanging it through web-based systems. In one of Ontario's health regions, Nurse Led Outreach Teams (NLOT) provide emergency mobile nursing services to help reduce unnecessary transfers from long-term care homes to emergency departments. Currently the NLOT team uses a Microsoft Access database to keep track of the health information on the residents that they serve. The Access database lacks scalability, portability, and interoperability. The objective of this study is the development of a web-based database using Oracle Application Express that is easily accessible from mobile devices. The web-based database will allow NLOT nurses to enter and access resident information anytime and from anywhere.

ZifBASE: a database of zinc finger proteins and associated resources.

PubMed

Jayakanthan, Mannu; Muthukumaran, Jayaraman; Chandrasekar, Sanniyasi; Chawla, Konika; Punetha, Ankita; Sundar, Durai

2009-09-09

Information on the occurrence of zinc finger protein motifs in genomes is crucial to the developing field of molecular genome engineering. The knowledge of their target DNA-binding sequences is vital to develop chimeric proteins for targeted genome engineering and site-specific gene correction. There is a need to develop a computational resource of zinc finger proteins (ZFP) to identify the potential binding sites and its location, which reduce the time of in vivo task, and overcome the difficulties in selecting the specific type of zinc finger protein and the target site in the DNA sequence. ZifBASE provides an extensive collection of various natural and engineered ZFP. It uses standard names and a genetic and structural classification scheme to present data retrieved from UniProtKB, GenBank, Protein Data Bank, ModBase, Protein Model Portal and the literature. It also incorporates specialized features of ZFP including finger sequences and positions, number of fingers, physiochemical properties, classes, framework, PubMed citations with links to experimental structures (PDB, if available) and modeled structures of natural zinc finger proteins. ZifBASE provides information on zinc finger proteins (both natural and engineered ones), the number of finger units in each of the zinc finger proteins (with multiple fingers), the synergy between the adjacent fingers and their positions. Additionally, it gives the individual finger sequence and their target DNA site to which it binds for better and clear understanding on the interactions of adjacent fingers. The current version of ZifBASE contains 139 entries of which 89 are engineered ZFPs, containing 3-7F totaling to 296 fingers. There are 50 natural zinc finger protein entries ranging from 2-13F, totaling to 307 fingers. It has sequences and structures from literature, Protein Data Bank, ModBase and Protein Model Portal. The interface is cross linked to other public databases like UniprotKB, PDB, ModBase and Protein Model Portal and PubMed for making it more informative. A database is established to maintain the information of the sequence features, including the class, framework, number of fingers, residues, position, recognition site and physio-chemical properties (molecular weight, isoelectric point) of both natural and engineered zinc finger proteins and dissociation constant of few. ZifBASE can provide more effective and efficient way of accessing the zinc finger protein sequences and their target binding sites with the links to their three-dimensional structures. All the data and functions are available at the advanced web-based search interface http://web.iitd.ac.in/~sundar/zifbase.

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.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases.

PubMed

Wollbrett, Julien; Larmande, Pierre; de Lamotte, Frédéric; Ruiz, Manuel

2013-04-15

In recent years, a large amount of "-omics" data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases

PubMed Central

2013-01-01

Background In recent years, a large amount of “-omics” data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. Results We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. Conclusions BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic. PMID:23586394

The Woven EndoBridge (WEB) for endovascular therapy of intracranial aneurysms: Update of a systematic review with meta-analysis.

PubMed

Tau, Noam; Sadeh-Gonik, Udi; Aulagner, Gilles; Turjman, Francis; Gory, Benjamin; Armoiry, Xavier

2018-03-01

Endovascular treatment of wide-neck intracranial aneurysms (IAs) is challenging, especially in bifurcation location. The intra-saccular flow-disruptor Woven EndoBridge (WEB) offers a new concept of endovascular therapy for wide-neck IAs. We performed an update of a systematic review aimed to report the feasibility, effectiveness and safety of WEB device therapy. A systematic review was conducted using several electronic databases (including PUBMED and EMBASE), searching for studies published between October 2015 and December 2017 (those published between January 2010 and September 2015 were included in our initial systematic review). Outcomes were: success of implantation, peri-procedural complications, mortality, and adequate occlusion (complete occlusion or neck remnant). In total (initial review + update), 12 uncontrolled case-series studies were included, reporting outcomes for 940 patients (68.6% female; mean age, 57 years) harboring 962 IAs. Most IAs were wide-neck bifurcation aneurysms (75%-100%), mainly at middle cerebral artery (37%) and anterior communicating artery (24.6%). Feasibility was 97% (95% confidence interval [CI], 95%-99%), and 9% (95%CI, 5%-14%) of cases required additional treatment. There were 14% (95%CI, 9%-19%) peri-procedural complications. After a median clinical follow-up of 7 months, mortality was 5% (95%CI, 1%-10%) and was higher in series with larger proportions of ruptured IAs. At last angiographic follow-up (median, 7 months; range, 3-27.9 months), adequate occlusion rate was 81% (95%CI, 73%-88%). Although WEB showed high rates of adequate aneurysm occlusion at mid-term, procedure-related complications and mortality rates were not negligible. Future studies should compare the WEB device with other treatment options. Copyright © 2018 Elsevier B.V. All rights reserved.

Profiling online recreational/prescription drugs' customers and overview of drug vending virtual marketplaces.

PubMed

Orsolini, Laura; Francesconi, Giulia; Papanti, Duccio; Giorgetti, Arianna; Schifano, Fabrizio

2015-07-01

Internet and social networking sites play a significant role in the marketing and distribution of recreational/prescription drugs without restrictions. We aimed here at reviewing data relating to the profile of the online drug customer and at describing drug vending websites. The PubMed, Google Scholar, and Scopus databases were searched here in order to elicit data on the socio-demographic characteristics of the recreational marketplaces/online pharmacies' customers and the determinants relating to online drug purchasing activities. Typical online recreational drugs' customers seem to be Caucasian, men, in their 20s, highly educated, and using the web to impact as minimally as possible on their existing work/professional status. Conversely, people without any health insurance seemed to look at the web as a source of more affordable prescription medicines. Drug vending websites are typically presented here with a "no prescription required" approach, together with aggressive marketing strategies. The online availability of recreational/prescriptions drugs remains a public health concern. A more precise understanding of online vending sites' customers may well facilitate the drafting and implementation of proper prevention campaigns aimed at counteracting the increasing levels of online drug acquisition and hence intake activities. Copyright © 2015 John Wiley & Sons, Ltd.

From ontology selection and semantic web to an integrated information system for food-borne diseases and food safety.

PubMed

Yan, Xianghe; Peng, Yun; Meng, Jianghong; Ruzante, Juliana; Fratamico, Pina M; Huang, Lihan; Juneja, Vijay; Needleman, David S

2011-01-01

Several factors have hindered effective use of information and resources related to food safety due to inconsistency among semantically heterogeneous data resources, lack of knowledge on profiling of food-borne pathogens, and knowledge gaps among research communities, government risk assessors/managers, and end-users of the information. This paper discusses technical aspects in the establishment of a comprehensive food safety information system consisting of the following steps: (a) computational collection and compiling publicly available information, including published pathogen genomic, proteomic, and metabolomic data; (b) development of ontology libraries on food-borne pathogens and design automatic algorithms with formal inference and fuzzy and probabilistic reasoning to address the consistency and accuracy of distributed information resources (e.g., PulseNet, FoodNet, OutbreakNet, PubMed, NCBI, EMBL, and other online genetic databases and information); (c) integration of collected pathogen profiling data, Foodrisk.org ( http://www.foodrisk.org ), PMP, Combase, and other relevant information into a user-friendly, searchable, "homogeneous" information system available to scientists in academia, the food industry, and government agencies; and (d) development of a computational model in semantic web for greater adaptability and robustness.

Trends of infodemiology studies: a scoping review.

PubMed

Zeraatkar, Kimia; Ahmadi, Maryam

2018-06-01

The health care industry is rich in data and information. Web technologies, such as search engines and social media, have provided an opportunity for the management of user generated data in real time in the form of infodemiology studies. The aim of this study was to investigate infodemiology studies conducted during 2002-2016, and compare them based on developed, developing and in transition countries. This scoping review was conducted in 2017 with the help of the PRISMA guidelines. PubMed, Scopus, Science Direct, Web of Knowledge, Google Scholar, Wiley and Springer databases were searched between the years 2002 and 2016. Finally, 56 articles were included in the review and analysed. The initial infodemiology studies pertain to the quality assessment of the hospital's websites. Most of the studies were on developed countries, based on flu, and published in the Journal of Medical Internet Research. The infodemiology approach provides unmatched opportunities for the management of health data and information generated by the users. Using this potential will provide unique opportunities for the health information need assessment in real time by health librarians and thereby provide evidence based health information to the people. © 2018 Health Libraries Group.

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

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.

Understanding the productive author who published papers in medicine using National Health Insurance Database: A systematic review and meta-analysis.

PubMed

Chien, Tsair-Wei; Chang, Yu; Wang, Hsien-Yi

2018-02-01

Many researchers used National Health Insurance database to publish medical papers which are often retrospective, population-based, and cohort studies. However, the author's research domain and academic characteristics are still unclear.By searching the PubMed database (Pubmed.com), we used the keyword of [Taiwan] and [National Health Insurance Research Database], then downloaded 2913 articles published from 1995 to 2017. Social network analysis (SNA), Gini coefficient, and Google Maps were applied to gather these data for visualizing: the most productive author; the pattern of coauthor collaboration teams; and the author's research domain denoted by abstract keywords and Pubmed MESH (medical subject heading) terms.Utilizing the 2913 papers from Taiwan's National Health Insurance database, we chose the top 10 research teams shown on Google Maps and analyzed one author (Dr. Kao) who published 149 papers in the database in 2015. In the past 15 years, we found Dr. Kao had 2987 connections with other coauthors from 13 research teams. The cooccurrence abstract keywords with the highest frequency are cohort study and National Health Insurance Research Database. The most coexistent MESH terms are tomography, X-ray computed, and positron-emission tomography. The strength of the author research distinct domain is very low (Gini < 0.40).SNA incorporated with Google Maps and Gini coefficient provides insight into the relationships between entities. The results obtained in this study can be applied for a comprehensive understanding of other productive authors in the field of academics.

Facilitating Collaboration, Knowledge Construction and Communication with Web-Enabled Databases.

ERIC Educational Resources Information Center

McNeil, Sara G.; Robin, Bernard R.

This paper presents an overview of World Wide Web-enabled databases that dynamically generate Web materials and focuses on the use of this technology to support collaboration, knowledge construction, and communication. Database applications have been used in classrooms to support learning activities for over a decade, but, although business and…

Implementing a Dynamic Database-Driven Course Using LAMP

ERIC Educational Resources Information Center

Laverty, Joseph Packy; Wood, David; Turchek, John

2011-01-01

This paper documents the formulation of a database driven open source architecture web development course. The design of a web-based curriculum faces many challenges: a) relative emphasis of client and server-side technologies, b) choice of a server-side language, and c) the cost and efficient delivery of a dynamic web development, database-driven…

A Tutorial in Creating Web-Enabled Databases with Inmagic DB/TextWorks through ODBC.

ERIC Educational Resources Information Center

Breeding, Marshall

2000-01-01

Explains how to create Web-enabled databases. Highlights include Inmagic's DB/Text WebPublisher product called DB/TextWorks; ODBC (Open Database Connectivity) drivers; Perl programming language; HTML coding; Structured Query Language (SQL); Common Gateway Interface (CGI) programming; and examples of HTML pages and Perl scripts. (LRW)

Web Database Development: Implications for Academic Publishing.

ERIC Educational Resources Information Center

Fernekes, Bob

This paper discusses the preliminary planning, design, and development of a pilot project to create an Internet accessible database and search tool for locating and distributing company data and scholarly work. Team members established four project objectives: (1) to develop a Web accessible database and decision tool that creates Web pages on the…

Digging Deeper: The Deep Web.

ERIC Educational Resources Information Center

Turner, Laura

2001-01-01

Focuses on the Deep Web, defined as Web content in searchable databases of the type that can be found only by direct query. Discusses the problems of indexing; inability to find information not indexed in the search engine's database; and metasearch engines. Describes 10 sites created to access online databases or directly search them. Lists ways…

Do-It-Yourself: A Special Library's Approach to Creating Dynamic Web Pages Using Commercial Off-The-Shelf Applications

NASA Technical Reports Server (NTRS)

Steeman, Gerald; Connell, Christopher

2000-01-01

Many librarians may feel that dynamic Web pages are out of their reach, financially and technically. Yet we are reminded in library and Web design literature that static home pages are a thing of the past. This paper describes how librarians at the Institute for Defense Analyses (IDA) library developed a database-driven, dynamic intranet site using commercial off-the-shelf applications. Administrative issues include surveying a library users group for interest and needs evaluation; outlining metadata elements; and, committing resources from managing time to populate the database and training in Microsoft FrontPage and Web-to-database design. Technical issues covered include Microsoft Access database fundamentals, lessons learned in the Web-to-database process (including setting up Database Source Names (DSNs), redesigning queries to accommodate the Web interface, and understanding Access 97 query language vs. Standard Query Language (SQL)). This paper also offers tips on editing Active Server Pages (ASP) scripting to create desired results. A how-to annotated resource list closes out the paper.

Computer- and web-based interventions to promote healthy eating among children and adolescents: a systematic review.

PubMed

Hamel, Lauren M; Robbins, Lorraine B

2013-01-01

To: (1) determine the effect of computer- and web-based interventions on improving eating behavior (e.g. increasing fruit and vegetable consumption; decreasing fat consumption) and/or diet-related physical outcomes (e.g. body mass index) among children and adolescents; and (2) examine what elements enhance success. Children and adolescents are the heaviest they have ever been. Excess weight can carry into adulthood and result in chronic health problems. Because of the capacity to reach large audiences of children and adolescents to promote healthy eating, computer- and web-based interventions hold promise for helping to curb this serious trend. However, evidence to support this approach is lacking. Systematic review using guidelines from the Cochrane Effective Practice and Organisation of Care Group. The following databases were searched for studies from 1998-2011: CINAHL; PubMed; Cochrane; PsycINFO; ERIC; and Proquest. Fifteen randomized controlled trials or quasi-experimental studies were analysed in a systematic review. Although a majority of interventions resulted in statistically significant positive changes in eating behavior and/or diet-related physical outcomes, interventions that included post intervention follow-up, ranging from 3-18 months, showed that changes were not maintained. Elements, such as conducting the intervention at school or using individually tailored feedback, may enhance success. Computer- and web-based interventions can improve eating behavior and diet-related physical outcomes among children and adolescents, particularly when conducted in schools and individually tailored. These interventions can complement and support nursing efforts to give preventive care; however, maintenance efforts are recommended. © 2012 Blackwell Publishing Ltd.

WebEAV: automatic metadata-driven generation of web interfaces to entity-attribute-value databases.

PubMed

Nadkarni, P M; Brandt, C M; Marenco, L

2000-01-01

The task of creating and maintaining a front end to a large institutional entity-attribute-value (EAV) database can be cumbersome when using traditional client-server technology. Switching to Web technology as a delivery vehicle solves some of these problems but introduces others. In particular, Web development environments tend to be primitive, and many features that client-server developers take for granted are missing. WebEAV is a generic framework for Web development that is intended to streamline the process of Web application development for databases having a significant EAV component. It also addresses some challenging user interface issues that arise when any complex system is created. The authors describe the architecture of WebEAV and provide an overview of its features with suitable examples.

49 CFR 630.4 - Requirements.

Code of Federal Regulations, 2012 CFR

2012-10-01

... TRANSPORTATION NATIONAL TRANSIT DATABASE § 630.4 Requirements. (a) National Transit Database Reporting System... from the National Transit Database Web site located at http://www.ntdprogram.gov. These reference... Transit Database Web site and a notice of any significant changes to the reporting requirements specified...

49 CFR 630.4 - Requirements.

Code of Federal Regulations, 2011 CFR

2011-10-01

... TRANSPORTATION NATIONAL TRANSIT DATABASE § 630.4 Requirements. (a) National Transit Database Reporting System... from the National Transit Database Web site located at http://www.ntdprogram.gov. These reference... Transit Database Web site and a notice of any significant changes to the reporting requirements specified...

49 CFR 630.4 - Requirements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... TRANSPORTATION NATIONAL TRANSIT DATABASE § 630.4 Requirements. (a) National Transit Database Reporting System... from the National Transit Database Web site located at http://www.ntdprogram.gov. These reference... Transit Database Web site and a notice of any significant changes to the reporting requirements specified...

49 CFR 630.4 - Requirements.

Code of Federal Regulations, 2014 CFR

2014-10-01

... TRANSPORTATION NATIONAL TRANSIT DATABASE § 630.4 Requirements. (a) National Transit Database Reporting System... from the National Transit Database Web site located at http://www.ntdprogram.gov. These reference... Transit Database Web site and a notice of any significant changes to the reporting requirements specified...

49 CFR 630.4 - Requirements.

Code of Federal Regulations, 2013 CFR

2013-10-01

... TRANSPORTATION NATIONAL TRANSIT DATABASE § 630.4 Requirements. (a) National Transit Database Reporting System... from the National Transit Database Web site located at http://www.ntdprogram.gov. These reference... Transit Database Web site and a notice of any significant changes to the reporting requirements specified...

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.

Use of a secure Internet Web site for collaborative medical research.

PubMed

Marshall, W W; Haley, R W

2000-10-11

Researchers who collaborate on clinical research studies from diffuse locations need a convenient, inexpensive, secure way to record and manage data. The Internet, with its World Wide Web, provides a vast network that enables researchers with diverse types of computers and operating systems anywhere in the world to log data through a common interface. Development of a Web site for scientific data collection can be organized into 10 steps, including planning the scientific database, choosing a database management software system, setting up database tables for each collaborator's variables, developing the Web site's screen layout, choosing a middleware software system to tie the database software to the Web site interface, embedding data editing and calculation routines, setting up the database on the central server computer, obtaining a unique Internet address and name for the Web site, applying security measures to the site, and training staff who enter data. Ensuring the security of an Internet database requires limiting the number of people who have access to the server, setting up the server on a stand-alone computer, requiring user-name and password authentication for server and Web site access, installing a firewall computer to prevent break-ins and block bogus information from reaching the server, verifying the identity of the server and client computers with certification from a certificate authority, encrypting information sent between server and client computers to avoid eavesdropping, establishing audit trails to record all accesses into the Web site, and educating Web site users about security techniques. When these measures are carefully undertaken, in our experience, information for scientific studies can be collected and maintained on Internet databases more efficiently and securely than through conventional systems of paper records protected by filing cabinets and locked doors. JAMA. 2000;284:1843-1849.

Publication trend, resource utilization, and impact of the US National Cancer Database: A systematic review.

PubMed

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

2018-03-01

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

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.

PubMed

Kohany, Oleksiy; Gentles, Andrew J; Hankus, Lukasz; Jurka, Jerzy

2006-10-25

Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Updating and maintenance of the database requires specialized tools, which we have created and made available for use with Repbase, and which may be useful as a template for other curated databases. We describe the software tools RepbaseSubmitter and Censor, which are designed to facilitate updating and screening the content of Repbase. RepbaseSubmitter is a java-based interface for formatting and annotating Repbase entries. It eliminates many common formatting errors, and automates actions such as calculation of sequence lengths and composition, thus facilitating curation of Repbase sequences. In addition, it has several features for predicting protein coding regions in sequences; searching and including Pubmed references in Repbase entries; and searching the NCBI taxonomy database for correct inclusion of species information and taxonomic position. Censor is a tool to rapidly identify repetitive elements by comparison to known repeats. It uses WU-BLAST for speed and sensitivity, and can conduct DNA-DNA, DNA-protein, or translated DNA-translated DNA searches of genomic sequence. Defragmented output includes a map of repeats present in the query sequence, with the options to report masked query sequence(s), repeat sequences found in the query, and alignments. Censor and RepbaseSubmitter are available as both web-based services and downloadable versions. They can be found at http://www.girinst.org/repbase/submission.html (RepbaseSubmitter) and http://www.girinst.org/censor/index.php (Censor).

Methodological challenges when doing research that includes ethnic minorities: a scoping review.

PubMed

Morville, Anne-Le; Erlandsson, Lena-Karin

2016-11-01

There are challenging methodological issues in obtaining valid and reliable results on which to base occupational therapy interventions for ethnic minorities. The aim of this scoping review is to describe the methodological problems within occupational therapy research, when ethnic minorities are included. A thorough literature search yielded 21 articles obtained from the scientific databases PubMed, Cinahl, Web of Science and PsychInfo. Analysis followed Arksey and O'Malley's framework for scoping reviews, applying content analysis. The results showed methodological issues concerning the entire research process from defining and recruiting samples, the conceptual understanding, lack of appropriate instruments, data collection using interpreters to analyzing data. In order to avoid excluding the ethnic minorities from adequate occupational therapy research and interventions, development of methods for the entire research process is needed. It is a costly and time-consuming process, but the results will be valid and reliable, and therefore more applicable in clinical practice.

Centella asiatica (L.) Urban: From Traditional Medicine to Modern Medicine with Neuroprotective Potential

PubMed Central

Orhan, Ilkay Erdogan

2012-01-01

This paper covers the studies relevant to neuroprotective activity of Centella asiatica (L.) Urban, also known as “Gotu Kola.” The plant is native to the Southeast Asia and has been used traditionally as brain tonic in ayurvedic medicine. The neuroprotective effect of C. asiatica has been searched using the key words “Centella, Centella asiatica, gotu kola, Asiatic pennywort, neuroprotection, and memory” through the electronic databases including Sciencedirect, Web of Science, Scopus, Pubmed, and Google Scholar. According to the literature survey, C. asiatica (gotu kola) has been reported to have a comprehensive neuroprotection by different modes of action such as enzyme inhibition, prevention of amyloid plaque formation in Alzheimer's disease, dopamine neurotoxicity in Parkinson's disease, and decreasing oxidative stress. Therefore, C. asiatica could be suggested to be a desired phytopharmaceutical with neuroprotective effect emerged from traditional medicine. PMID:22666298

Inertial sensor-based methods in walking speed estimation: a systematic review.

PubMed

Yang, Shuozhi; Li, Qingguo

2012-01-01

Self-selected walking speed is an important measure of ambulation ability used in various clinical gait experiments. Inertial sensors, i.e., accelerometers and gyroscopes, have been gradually introduced to estimate walking speed. This research area has attracted a lot of attention for the past two decades, and the trend is continuing due to the improvement of performance and decrease in cost of the miniature inertial sensors. With the intention of understanding the state of the art of current development in this area, a systematic review on the exiting methods was done in the following electronic engines/databases: PubMed, ISI Web of Knowledge, SportDiscus and IEEE Xplore. Sixteen journal articles and papers in proceedings focusing on inertial sensor based walking speed estimation were fully reviewed. The existing methods were categorized by sensor specification, sensor attachment location, experimental design, and walking speed estimation algorithm.

van Manen's method and reduction in a phenomenological hermeneutic study.

PubMed

Heinonen, Kristiina

2015-03-01

To describe van Manen's method and concept of reduction in a study that used a phenomenological hermeneutic approach. Nurse researchers have used van Manen's method in different ways. Participants' lifeworlds are described in depth, but descriptions of reduction have been brief. The literature and knowledge review and manual search of research articles. Databases Web Science, PubMed, CINAHL and PsycINFO, without applying a time period, to identify uses of van Manen's method. This paper shows how van Manen's method has been used in nursing research and gives some examples of van Manen's reduction. Reduction enables us to conduct in-depth phenomenological hermeneutic research and understand people's lifeworlds. As there are many variations in adapting reduction, it is complex and confusing. This paper contributes to the discussion of phenomenology, hermeneutic study and reduction. It opens up reduction as a method for researchers to exploit.

Review of procedures used for the extraction of anti-cancer compounds from tropical plants.

PubMed

Pandey, Saurabh; Shaw, Paul N; Hewavitharana, Amitha K

2015-01-01

Tropical plants are important sources of anti-cancer lead molecules. According to the US National Cancer Institute, out of the 3000 plants identified as active against cancer using in vitro studies, 70% are of tropical origin. The extraction of bioactive compounds from the plant materials is a fundamental step whose efficiency is critical for the success of drug discovery efforts. There has been no review published of the extraction procedures of anti-cancer compounds from tropical plants and hence the following is a critical evaluation of such procedures undertaken prior to the use of these compounds in cancer cell line studies, during the last five years. It presents a comprehensive analysis of all approaches taken to extract anti-cancer compounds from various tropical plants. (Databases searched were PubMed, SciFinder, Web of Knowledge, Scopus, Embase and Google Scholar).

Cluster Analysis in Nursing Research: An Introduction, Historical Perspective, and Future Directions.

PubMed

Dunn, Heather; Quinn, Laurie; Corbridge, Susan J; Eldeirawi, Kamal; Kapella, Mary; Collins, Eileen G

2017-05-01

The use of cluster analysis in the nursing literature is limited to the creation of classifications of homogeneous groups and the discovery of new relationships. As such, it is important to provide clarity regarding its use and potential. The purpose of this article is to provide an introduction to distance-based, partitioning-based, and model-based cluster analysis methods commonly utilized in the nursing literature, provide a brief historical overview on the use of cluster analysis in nursing literature, and provide suggestions for future research. An electronic search included three bibliographic databases, PubMed, CINAHL and Web of Science. Key terms were cluster analysis and nursing. The use of cluster analysis in the nursing literature is increasing and expanding. The increased use of cluster analysis in the nursing literature is positioning this statistical method to result in insights that have the potential to change clinical practice.

OC29 - Caregiver burden in childhood asthma.

PubMed

Ekim, Ayfer

2016-05-09

Theme: Parenting/parenthood. As delivering care is an inherent part of becoming parents, providing high-level care to the child with health problems might be a burden for the caregiver. This systematic review investigated the effects of caregiver burden of parents who are primarily responsible for the caring of children with asthma. PubMed, CINAHL, Web of Science and Scopus databases were searched for the studies published between 2000-2015. Key search terms used were 'caregiver', 'burden, 'childhood asthma' and 'parent'. A total of 23 studies were examined for this review. Providing care to the child with asthma affects parents as caregivers negatively. Caregivers of the children with asthma often experience anxiety, fear, disappointment, grief, physical distress and low quality of life as the outcomes of caregiving burden. It is absolutely crucial to determine caregiver burden risks and protective factors since wellness level of caregivers affect the asthma management practices and decisions.

[High-intensity interval training for young athletes].

PubMed

Engel, Florian Azad; Sperlich, Billy

2014-06-01

A computer-based literature research during July 2013 using the electronic databases PubMed, MEDLINE, SPORTDiscus and Web of Science was performed to assess the effect of the high intensity interval training (HIIT) on sport performance in healthy children and adolescents. Studies examining the effect of HIIT on aerobic and anaerobic performance pre and post to HIIT-Interventions in children and adolescents (9-18 years) were included. The results indicate increased aerobic and anaerobic performance following two or three HIIT sessions per week for a period of five to ten weeks, additional to normal training. Results regarding long term effects following HIIT have not been documented so far. In addition, due to the physiological characteris-tics during HIIT protocols improved fatigue resistance has been demonstrated in children as compared to adults, which may be interpreted as a prerequisite for the applicability of HIIT in children.

Role of Proangiogenic Factors in Immunopathogenesis of Multiple Sclerosis.

PubMed

Hamid, Kabir Magaji; Mirshafiey, Abbas

2016-02-01

Angiogenesis is a complex and balanced process in which new blood vessels form from preexisting ones by sprouting, splitting, growth and remodeling. This phenomenon plays a vital role in many physiological and pathological processes. However, the disturbance in physiological process can play a role in pathogenesis of some chronic inflammatory diseases, including multiple sclerosis (MS) in human and its animal model. Although the relation between abnormal blood vessels and MS lesions was established in previous studies, but the role of pathological angiogenesis remains unclear. In this study, the link between proangiogenic factors and multiple sclerosis pathogenesis was examined by conducting a systemic review. Thus we searched the English medical literature via PubMed, ISI web of knowledge, Medline and virtual health library (VHL) databases. In this review, we describe direct and indirect roles of some proangiogenic factors in MS pathogenesis and report the association of these factors with pathological and inflammatory angiogenesis.

Evaluation of Primary/Preferred Language Data Collection

PubMed Central

Duong, Linh M.; Singh, Simple D.; Buchanan, Natasha; Phillips, Joan L; Cerlach, Ken

2015-01-01

A literature review was conducted to identify peer-reviewed articles related to primary/preferred language and interpreter-use data collection practices in hospitals, clinics, and outpatient settings to assess its completeness and quality. In January 2011, Embase (Ovid), MEDLINE (Ovid), PubMed, and Web of Science databases were searched for eligible studies. Primary and secondary inclusion criteria were applied to selected eligible articles. This extensive literature search yielded 768 articles after duplicates were removed. After primary and secondary inclusion criteria were applied, 28 eligible articles remained for data abstraction. All 28 articles in this review reported collecting primary/preferred language data, but only 18% (5/28) collected information on interpreter use. This review revealed that there remains variability in the way that primary/preferred language and interpreter use data are collected; all studies used various methodologies for evaluating and abstracting these data. Likewise, the sources from which the data were abstracted differed. PMID:23443456

Radish (Raphanus sativus) and Diabetes

PubMed Central

Banihani, Saleem Ali

2017-01-01

For more than three decades, various in vitro and in vivo studies have linked radishes with diabetes, though this link has not been discussed. This review systematically addresses and summarizes the effect of radishes on diabetes. We searched the Web of Science, PubMed, and EMBASE databases for English language articles from June 1987 through May 2017 using the key words “radish” and “diabetes,” and the references from particular reports were also considered if relevant. In summary, radish has been identified as having antidiabetic effects, making it favorable for those with diabetic conditions. This may be due to its ability to enhance the antioxidant defense mechanism and reduce the accumulation of free radicals, affect hormonal-induced glucose hemostasis, promote glucose uptake and energy metabolism, and reduce glucose absorption in the intestine. However, this summary requires further confirmation in research in vivo studies and clinical trials. PMID:28906451

Inertial Sensor-Based Methods in Walking Speed Estimation: A Systematic Review

PubMed Central

Yang, Shuozhi; Li, Qingguo

2012-01-01

Self-selected walking speed is an important measure of ambulation ability used in various clinical gait experiments. Inertial sensors, i.e., accelerometers and gyroscopes, have been gradually introduced to estimate walking speed. This research area has attracted a lot of attention for the past two decades, and the trend is continuing due to the improvement of performance and decrease in cost of the miniature inertial sensors. With the intention of understanding the state of the art of current development in this area, a systematic review on the exiting methods was done in the following electronic engines/databases: PubMed, ISI Web of Knowledge, SportDiscus and IEEE Xplore. Sixteen journal articles and papers in proceedings focusing on inertial sensor based walking speed estimation were fully reviewed. The existing methods were categorized by sensor specification, sensor attachment location, experimental design, and walking speed estimation algorithm. PMID:22778632

Effect of aromatherapy massage on pain in primary dysmenorrhea: A meta-analysis.

PubMed

Sut, Necdet; Kahyaoglu-Sut, Hatice

2017-05-01

This meta-analysis investigates the effect of aromatherapy massage on pain in primary dysmenorrhea. Randomized controlled trials were searched by keywords in several databases (Pubmed, ISI Web of Sciences, and Google Scholar). Six randomized controlled trials that included 362 participants with primary dysmenorrhea, comparing abdominal aromatherapy massage (n = 184) with massage with placebo oils (n = 178), were analyzed in the meta-analysis. The change in the visual analogue scale (VAS) pain score from the first menstruation cycle to the second cycle at the first menstruation day was used as the primary outcome. Aromatherapy massage with essential oils was superior to massage with placebo oils (standardized mean difference = -1.06 [95% CI: -1.55 to -0.55]). Abdominal aromatherapy massage with essential oils is an effective complementary method to relieve pain in primary dysmenorrhea. Copyright © 2017 Elsevier Ltd. All rights reserved.

What evidence is available on end-of-life (EOL) care and Latino elders? A literature review.

PubMed

Cruz-Oliver, Dulce M; Talamantes, Melissa; Sanchez-Reilly, Sandra

2014-02-01

Low-income and minority persons, such as Latinos, encounter substantial barriers in accessing effective end-of-life (EOL) care. This study intends to review current evidence on how to deliver EOL care to Latino elders. Literature search in PubMed and Ovid Web sites of articles indexed in Medline (1948-2011), Cochrane (2005-2011), Embase, and PsychInfo (1967-2011) databases. Articles were included if they contained (1) study participants' race/ethnicity, (2) adults or population older than 60 years, and (3) information related to EOL care. A total of 64 abstracts were reviewed, and 38 articles met the inclusion criteria. After reviewing the quality of evidence, 4 themes were identified and summarized: EOL preferences, hospice, Latino culture, and caregiving. Latino elders have traditional acculturation practices, face EOL decisions with family support, and, if educated, are receptive toward hospice and caregiver support.

Effectiveness of Traditional Chinese Acupuncture versus Sham Acupuncture: a Systematic Review

PubMed Central

Carlos, Luís; da Cruz, Lóris Aparecida Prado; Leopoldo, Vanessa Cristina; de Campos, Fabrício Ribeiro; de Almeida, Ana Maria; Silveira, Renata Cristina de Campos Pereira

2016-01-01

ABSTRACT Objective: to identify and synthesize the evidence from randomized clinical trials that tested the effectiveness of traditional Chinese acupuncture in relation to sham acupuncture for the treatment of hot flashes in menopausal women with breast cancer. Method: systematic review guided by the recommendations of the Cochrane Collaboration. Citations were searched in the following databases: MEDLINE via PubMed, Web of Science, CENTRAL, CINAHL, and LILACS. A combination of the following keywords was used: breast neoplasm, acupuncture, acupuncture therapy, acupuncture points, placebos, sham treatment, hot flashes, hot flushes, menopause, climacteric, and vasomotor symptoms. Results: a total of 272 studies were identified, five of which were selected and analyzed. Slight superiority of traditional acupuncture compared with sham acupuncture was observed; however, there were no strong statistical associations. Conclusions: the evidence gathered was not sufficient to affirm the effectiveness of traditional acupuncture compared with sham acupuncture. PMID:27533271

Evaluation of primary/preferred language data collection.

PubMed

Duong, Linh M; Singh, Simple D; Buchanan, Natasha; Phillips, Joan L; Gerlach, Ken

2012-01-01

A literature review was conducted to identify peer-reviewed articles related to primary/preferred language and interpreter-use data collection practices in hospitals, clinics, and outpatient settings to assess its completeness and quality. In January 2011, Embase (Ovid), MEDLINE (Ovid), PubMed, and Web of Science databases were searched for eligible studies. Primary and secondary inclusion criteria were applied to selected eligible articles. This extensive literature search yielded 768 articles after duplicates were removed. After primary and secondary inclusion criteria were applied, 28 eligible articles remained for data abstraction. All 28 articles in this review reported collecting primary/preferred language data, but only 18% (5/28) collected information on interpreter use. This review revealed that there remains variability in the way that primary/preferred language and interpreter use data are collected; all studies used various methodologies for evaluating and abstracting these data. Likewise, the sources from which the data were abstracted differed.

Protection motivation theory and physical activity in the general population: a systematic literature review.

PubMed

Bui, Linh; Mullan, Barbara; McCaffery, Kirsten

2013-01-01

An appropriate theoretical framework may be useful for guiding the development of physical activity interventions. This review investigates the effectiveness of the protection motivation theory (PMT), a model based on the cognitive mediation processes of behavioral change, in the prediction and promotion of physical activity participation. A literature search was conducted using the databases MEDLINE, PsycINFO, PubMed, and Web of Science, and a manual search was conducted on relevant reference lists. Studies were included if they tested or applied the PMT, measured physical activity, and sampled from healthy populations. A total of 20 studies were reviewed, grouped into four design categories: prediction, stage discrimination, experimental manipulation, and intervention. The results indicated that the PMT's coping appraisal construct of self-efficacy generally appears to be the most effective in predicting and promoting physical activity participation. In conclusion, the PMT shows some promise, however, there are still substantial gaps in the evidence.

A Review on Potential Mechanisms of Terminalia chebula in Alzheimer's Disease

PubMed Central

Afshari, Amir R.; Sadeghnia, Hamid R.; Mollazadeh, Hamid

2016-01-01

The current management of Alzheimer's disease (AD) focuses on acetylcholinesterase inhibitors (AChEIs) and NMDA receptor antagonists, although outcomes are not completely favorable. Hence, novel agents found in herbal plants are gaining attention as possible therapeutic alternatives. The Terminalia chebula (Family: Combretaceae) is a medicinal plant with a wide spectrum of medicinal properties and is reported to contain various biochemicals such as hydrolysable tannins, phenolic compounds, and flavonoids, so it may prove to be a good therapeutic alternative. In this research, we reviewed published scientific literature found in various databases: PubMed, Science Direct, Scopus, Web of Science, Scirus, and Google Scholar, with the keywords: T. chebula, AD, neuroprotection, medicinal plant, antioxidant, ellagitannin, gallotannin, gallic acid, chebulagic acid, and chebulinic acid. This review shows that T. chebula extracts and its constituents have AChEI and antioxidant and anti-inflammatory effects, all of which are currently relevant to the treatment of Alzheimer's disease. PMID:26941792

Uses of electromyography in dentistry: An overview with meta-analysis.

PubMed

Nishi, Shamima Easmin; Basri, Rehana; Alam, Mohammad Khursheed

2016-01-01

The purpose of this study was to review the uses of electromyography (EMG) in dentistry in the last few years in related research. EMG is an advanced technique to record and evaluate muscle activity. In the previous days, EMG was only used for medical sciences, but now EMG playing a tremendous role in medical as well as dental sector. Several electronic databases such as Google Scholar, PubMed, Science Direct, and Web of Science were systematically searched for studies published until July 2015. EMG can be used in both diagnosis and treatment purpose to record neuromuscular activity. In dentistry, we can utilize EMG to evaluate muscular activity in function such as chewing and biting or parafunctional activities such as clenching and bruxism. In case of TMJ and myofascial pain disorders, EMG widely is used in the last few years. EMG is one of biometric tests that occur in the modern evidence-based dentistry practice.

Listeriosis Phytotherapy: A Review Study on the Effectiveness of Iranian Medicinal Plants in Treatment of Listeriosis.

PubMed

Rafieian-Kopaei, Mahmoud; Saki, Kourosh; Bahmani, Mahmoud; Ghafourian, Sobhan; Sadeghifard, Nourkhoda; Taherikalani, Morovat

2015-12-17

Listeria monocytogenes can be found in many processed foods, raw milk, dairy products, meat and meat products such as sausages, beef and fish products, seafoods, eggs, fruits, and vegetables such as radish and cabbage. This article is a review study on the Iranian medicinal plants applied for treatment of listeriosis. Information of this review article was obtained by searching various key words such as Listeria monocytogenes, medicinal plants, plant extracts and essential oils among scientific articles published in databases of Google scholar, ISI Web of Knowledge, PubMed, Scopus, SID and Magiran. Thyme, German chamomile, great chamomile, yarrow, onion, oregano, nutmeg, sage, sagebrush, hyssop, rosemary, St John's wort, safflower, ajowan, cumin, peppermint, shallot, anise, and parsnip are known antilisteriosis medicinal plants. Bioactive phytochemicals, antioxidants and monoterpenes, sesquiterpene, coumarin, flavonoids, tannins, saponins, alkaloids, and terpenoids are the main ingredients of antilisteriosis medicinal plants. © The Author(s) 2015.

Applying World Wide Web technology to the study of patients with rare diseases.

PubMed

de Groen, P C; Barry, J A; Schaller, W J

1998-07-15

Randomized, controlled trials of sporadic diseases are rarely conducted. Recent developments in communication technology, particularly the World Wide Web, allow efficient dissemination and exchange of information. However, software for the identification of patients with a rare disease and subsequent data entry and analysis in a secure Web database are currently not available. To study cholangiocarcinoma, a rare cancer of the bile ducts, we developed a computerized disease tracing system coupled with a database accessible on the Web. The tracing system scans computerized information systems on a daily basis and forwards demographic information on patients with bile duct abnormalities to an electronic mailbox. If informed consent is given, the patient's demographic and preexisting medical information available in medical database servers are electronically forwarded to a UNIX research database. Information from further patient-physician interactions and procedures is also entered into this database. The database is equipped with a Web user interface that allows data entry from various platforms (PC-compatible, Macintosh, and UNIX workstations) anywhere inside or outside our institution. To ensure patient confidentiality and data security, the database includes all security measures required for electronic medical records. The combination of a Web-based disease tracing system and a database has broad applications, particularly for the integration of clinical research within clinical practice and for the coordination of multicenter trials.

High Temperature Superconducting Materials Database

National Institute of Standards and Technology Data Gateway

SRD 62 NIST High Temperature Superconducting Materials Database (Web, free access)   The NIST High Temperature Superconducting Materials Database (WebHTS) provides evaluated thermal, mechanical, and superconducting property data for oxides and other nonconventional superconductors.

HDAPD: a web tool for searching the disease-associated protein structures

PubMed Central

2010-01-01

Background The protein structures of the disease-associated proteins are important for proceeding with the structure-based drug design to against a particular disease. Up until now, proteins structures are usually searched through a PDB id or some sequence information. However, in the HDAPD database presented here the protein structure of a disease-associated protein can be directly searched through the associated disease name keyed in. Description The search in HDAPD can be easily initiated by keying some key words of a disease, protein name, protein type, or PDB id. The protein sequence can be presented in FASTA format and directly copied for a BLAST search. HDAPD is also interfaced with Jmol so that users can observe and operate a protein structure with Jmol. The gene ontological data such as cellular components, molecular functions, and biological processes are provided once a hyperlink to Gene Ontology (GO) is clicked. Further, HDAPD provides a link to the KEGG map such that where the protein is placed and its relationship with other proteins in a metabolic pathway can be found from the map. The latest literatures namely titles, journals, authors, and abstracts searched from PubMed for the protein are also presented as a length controllable list. Conclusions Since the HDAPD data content can be routinely updated through a PHP-MySQL web page built, the new database presented is useful for searching the structures for some disease-associated proteins that may play important roles in the disease developing process for performing the structure-based drug design to against the diseases. PMID:20158919

From Paper to Practice; Indexing Systems and Ethical Standards.

PubMed

Astaneh, Behrooz; Masoumi, Sarah

2018-04-01

Currently one of the main goals of editors is to attain a higher visibility for their journals. On the other hand, authors strive to publish their research in journals indexed in eminent databases such as Scopus, Thompson Reuters' Web of Science (ISI), Medline, etc. Therefore, clarifying the standards of indexing is of great importance. One of the most important issues in publication is the ethical considerations, which are mainly described by organizations, such as the International Committee of Medical Journal Editors and the Committee on Publication Ethics. In this study, we examined the ethical requirements of high impact databases for indexing journals to investigate whether they mention or mandate journals to adhere to publication ethics. We found that only Scopus mandated journals to state clear ethical policies on their website as a criterion for being indexed while Medline and Directory of Open Access Journals advised journals to adhere to ethics, not mandated, and Web of Science (ISI) and PubMed Central made no mention of ethics as a required criterion for indexing. Based on this short review, there seems to be a gap between the requirements of indexing systems and international guidelines for publication ethics. Currently, most indexing systems have only partially recommended journals to consider ethical issues. In such an atmosphere, we cannot expect journals or as a result, authors to professionally, completely, and whole heartedly implement ethical guidelines as a mandatory rule in their journals and research, when the indexing systems that most editors want to be indexed in and most authors want to be cited in do not mandate such guidelines.

What Do They Tell Their Students? Business Faculty Acceptance of the Web and Library Databases for Student Research

ERIC Educational Resources Information Center

Dewald, Nancy H.

2005-01-01

Business faculty were surveyed as to their use of free Web resources and subscription databases for their own and their students' research. A much higher percentage of respondents either require or encourage Web use by their students than require or encourage database use, though most also advise use of multiple sources.

Economic evaluations in gastroenterology in Brazil: A systematic review.

PubMed

de Paiva Haddad, Luciana Bertocco; Decimoni, Tassia Cristina; Turri, Jose Antonio; Leandro, Roseli; de Soárez, Patrícia Coelho

2016-02-06

To systematically review economic evaluations in gastroenterology, relating to Brazil, published between 1980 and 2013. We selected full and partial economic evaluations from among those retrieved by searching the following databases: MEDLINE (PubMed); Excerpta Medica; the Latin American and Caribbean Health Sciences Literature database; the Scientific Electronic Library Online; the database of the Centre for Reviews and Dissemination; the National Health Service (NHS) Economic Evaluation Database; the NHS Health Technology Assessment database; the Health Economics database of the Brazilian Virtual Library of Health; Scopus; Web of Science; and the Brazilian Network for the Evaluation of Health Technologies. Two researchers, working independently, selected the studies and extracted the data. We identified 535 health economic evaluations relating to Brazil and published in the 1980-2013 period. Of those 535 articles, only 40 dealt with gastroenterology. Full and partial economic evaluations respectively accounted for 23 (57.5%) and 17 (42.5%) of the 40 studies included. Among the 23 full economic evaluations, there were 11 cost-utility analyses, seven cost-effectiveness analyses, four cost-consequence analyses, and one cost-minimization analysis. Of the 40 studies, 25 (62.5%) evaluated medications; 7 (17.5%) evaluated procedures; and 3 (7.5%) evaluated equipment. Most (55%) of the studies were related to viral hepatitis, and most (63.4%) were published after 2010. Other topics included gastrointestinal cancer, liver transplantation, digestive diseases and hernias. Over the 33-year period examined, the number of such economic evaluations relating to Brazil, especially of those evaluating medications for the treatment of hepatitis, increased considerably. Further studies are needed in order to ensure that expenditures on health care in Brazil are made as fairly and efficiently as possible.

Economic evaluations in gastroenterology in Brazil: A systematic review

PubMed Central

de Paiva Haddad, Luciana Bertocco; Decimoni, Tassia Cristina; Turri, Jose Antonio; Leandro, Roseli; de Soárez, Patrícia Coelho

2016-01-01

AIM: To systematically review economic evaluations in gastroenterology, relating to Brazil, published between 1980 and 2013. METHODS: We selected full and partial economic evaluations from among those retrieved by searching the following databases: MEDLINE (PubMed); Excerpta Medica; the Latin American and Caribbean Health Sciences Literature database; the Scientific Electronic Library Online; the database of the Centre for Reviews and Dissemination; the National Health Service (NHS) Economic Evaluation Database; the NHS Health Technology Assessment database; the Health Economics database of the Brazilian Virtual Library of Health; Scopus; Web of Science; and the Brazilian Network for the Evaluation of Health Technologies. Two researchers, working independently, selected the studies and extracted the data. RESULTS: We identified 535 health economic evaluations relating to Brazil and published in the 1980-2013 period. Of those 535 articles, only 40 dealt with gastroenterology. Full and partial economic evaluations respectively accounted for 23 (57.5%) and 17 (42.5%) of the 40 studies included. Among the 23 full economic evaluations, there were 11 cost-utility analyses, seven cost-effectiveness analyses, four cost-consequence analyses, and one cost-minimization analysis. Of the 40 studies, 25 (62.5%) evaluated medications; 7 (17.5%) evaluated procedures; and 3 (7.5%) evaluated equipment. Most (55%) of the studies were related to viral hepatitis, and most (63.4%) were published after 2010. Other topics included gastrointestinal cancer, liver transplantation, digestive diseases and hernias. Over the 33-year period examined, the number of such economic evaluations relating to Brazil, especially of those evaluating medications for the treatment of hepatitis, increased considerably. CONCLUSION: Further studies are needed in order to ensure that expenditures on health care in Brazil are made as fairly and efficiently as possible. PMID:26855823

Structural Ceramics Database

National Institute of Standards and Technology Data Gateway

SRD 30 NIST Structural Ceramics Database (Web, free access)   The NIST Structural Ceramics Database (WebSCD) provides evaluated materials property data for a wide range of advanced ceramics known variously as structural ceramics, engineering ceramics, and fine ceramics.

Greater freedom of speech on Web 2.0 correlates with dominance of views linking vaccines to autism.

PubMed

Venkatraman, Anand; Garg, Neetika; Kumar, Nilay

2015-03-17

It is suspected that Web 2.0 web sites, with a lot of user-generated content, often support viewpoints that link autism to vaccines. We assessed the prevalence of the views supporting a link between vaccines and autism online by comparing YouTube, Google and Wikipedia with PubMed. Freedom of speech is highest on YouTube and progressively decreases for the others. Support for a link between vaccines and autism is most prominent on YouTube, followed by Google search results. It is far lower on Wikipedia and PubMed. Anti-vaccine activists use scientific arguments, certified physicians and official-sounding titles to gain credibility, while also leaning on celebrity endorsement and personalized stories. Online communities with greater freedom of speech lead to a dominance of anti-vaccine voices. Moderation of content by editors can offer balance between free expression and factual accuracy. Health communicators and medical institutions need to step up their activity on the Internet. Copyright © 2015 Elsevier Ltd. All rights reserved.

Web-Based Mindfulness Interventions for People With Physical Health Conditions: Systematic Review.

PubMed

Toivonen, Kirsti I; Zernicke, Kristin; Carlson, Linda E

2017-08-31

Mindfulness-based interventions (MBIs) are becoming increasingly popular for helping people with physical health conditions. Expanding from traditional face-to-face program delivery, there is growing interest in Web-based application of MBIs, though Web-based MBIs for people with physical health conditions specifically have not been thoroughly reviewed to date. The objective of this paper was to review Web-based MBIs for people with physical health conditions and to examine all outcomes reported (eg, efficacy or effectiveness for physical changes or psychological changes; feasibility). Databases PubMed, PsycINFO, Science Direct, CINAHL Plus, and Web of Science were searched. Full-text English papers that described any Web-based MBI, examining any outcome, for people with chronic physical health conditions were included. Randomized, nonrandomized, controlled, and uncontrolled trials were all included. Extracted data included intervention characteristics, population characteristics, outcomes, and quality indicators. Intervention characteristics (eg, synchronicity and guidance) were examined as potential factors related to study outcomes. Of 435 publications screened, 19 published papers describing 16 studies were included. They examined Web-based MBIs for people with cancer, chronic pain or fibromyalgia, irritable bowel syndrome (IBS), epilepsy, heart disease, tinnitus, and acquired brain injury. Overall, most studies reported positive effects of Web-based MBIs compared with usual care on a variety of outcomes including pain acceptance, coping measures, and depressive symptoms. There were mixed results regarding the effectiveness of Web-based MBIs compared with active control treatment conditions such as cognitive behavioral therapy. Condition-specific symptoms (eg, cancer-related fatigue and IBS symptoms) targeted by treatment had the largest effect size improvements following MBIs. Results are inconclusive regarding physical variables. Preliminary evidence suggests that Web-based MBIs may be helpful in alleviating symptom burden that those with physical health conditions can experience, particularly when interventions are tailored for specific symptoms. There was no evidence of differences between synchronous versus asynchronous or facilitated versus self-directed Web-based MBIs. Future investigations of Web-based MBIs should evaluate the effects of program adherence, effects on mindfulness levels, and whether synchronous or asynchronous, or facilitated or self-directed interventions elicit greater improvements. ©Kirsti I Toivonen, Kristin Zernicke, Linda E Carlson. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 31.08.2017.

Efficacy and Safety of Pedunculopontine Nuclei (PPN) Deep Brain Stimulation in the Treatment of Gait Disorders: A Meta-Analysis of Clinical Studies.

PubMed

Golestanirad, Laleh; Elahi, Behzad; Graham, Simon J; Das, Sunit; Wald, Lawrence L

2016-01-01

Pedunculopontine nucleus (PPN) has complex reciprocal connections with basal ganglia, especially with internal globus pallidus and substantia nigra, and it has been postulated that PPN stimulation may improve gait instability and freezing of gait. In this meta-analysis, we will assess the evidence for PPN deep brain stimulation in treatment of gait and motor abnormalities especially focusing on Parkinson disease patients. PubMed and Scopus electronic databases were searched for related studies published before February 2014. Medline (1966-2014), Embase (1974-2010), CINAHL, Web of Science, Scopus bibliographic, and Google Scholar databases (1960-2014) were also searched for studies investigating effect of PPN deep brain stimulation in treatment of postural and postural instability and total of ten studies met the inclusion criteria for this analysis. Our findings showed a significant improvement in postural instability (p<0.001) and motor symptoms of Parkinson disease on and off medications (p<0.05), but failed to show improvement in freezing of gait. Despite significant improvement in postural instability observed in included studies, evidence from current literature is not sufficient to generalize these findings to the majority of patients.

Review of telehealth stuttering management.

PubMed

Lowe, Robyn; O'Brian, Sue; Onslow, Mark

2013-01-01

Telehealth is the use of communication technology to provide health care services by means other than typical in-clinic attendance models. Telehealth is increasingly used for the management of speech, language and communication disorders. The aim of this article is to review telehealth applications to stuttering management. We conducted a search of peer-reviewed literature for the past 20 years using the Institute for Scientific Information Web of Science database, PubMed: The Bibliographic Database and a search for articles by hand. Outcomes for telehealth stuttering treatment were generally positive, but there may be a compromise of treatment efficiency with telehealth treatment of young children. Our search found no studies dealing with stuttering assessment procedures using telehealth models. No economic analyses of this delivery model have been reported. This review highlights the need for continued research about telehealth for stuttering management. Evidence from research is needed to inform the efficacy of assessment procedures using telehealth methods as well as guide the development of improved treatment procedures. Clinical and technical guidelines are urgently needed to ensure that the evolving and continued use of telehealth to manage stuttering does not compromise the standards of care afforded with standard in-clinic models.

The Efficacy of Equine-Assisted Activities and Therapies on Improving Physical Function.

PubMed

Rigby, B Rhett; Grandjean, Peter W

2016-01-01

To summarize the physical benefits of therapeutic horseback riding and hippotherapy and suggest directions for future research. Review of databases for peer-reviewed articles related to equine-assisted activities and therapies. Databases included MEDLINE via EBSCO, Web of Science, PubMed, Google Scholar, and Academic Search Complete. Articles were limited to those with full-text access published in English since 1987. Acute and residual improvements in physical benefits, such as gross motor function (e.g., walking, running, jumping), spasticity, muscle symmetry, posture, balance, and gait occur in adults and children with varying disabilities. The benefits appear to be greatest following multiweek interventions with one or more sessions per week. Modest acute cardiovascular responses are observed during equine-assisted activities and therapies with little or no evidence for training improvements in heart rate or blood pressure at rest or during riding. The present body of literature provides evidence that equine-assisted activities and therapies are an effective means of improving many measures of physical health. However, more controlled trials are urgently needed to strengthen the current knowledge base, establish dose-response characteristics of equine-assisted activities and therapies, and explore the physiologic basis for the promising results suggested from the literature.

Systematic review on strength training in Parkinson’s disease: an unsolved question

PubMed Central

Ramazzina, Ileana; Bernazzoli, Benedetta; Costantino, Cosimo

2017-01-01

The purpose of this study was to investigate the effectiveness of strength training, performed against a different resistance from body weight, in improving motor and nonmotor symptoms in patients with Parkinson’s disease (PD). The following electronic databases were searched: PubMed, Physiotherapy Evidence Database, Cochrane Central Register of Controlled Trials, Scopus, and Web of Science. The review was conducted and reported in accordance with the PRISMA statement. Thirteen high-quality randomized controlled trials were included. Strength training performed against external resistance is well tolerated and appears to be a suitable physical activity to improve both physical parameters and quality of life parameters of PD subjects. However, although the study intervention included strength training, only a few selected studies assessed the improvement of muscle strength. Despite the encouraging results, it is difficult to establish a correlation between strength training and the improvements made. Our review highlights the lack of common intent in terms of study design and the presence of different primary and secondary outcomes. Accordingly, further studies are needed to support the beneficial effects of different types of strength training in PD subjects and to underline the superiority of strength training in PD patients with respect to other training. PMID:28408811

The prognostic role of Leucine-rich repeat-containing G-protein-coupled receptor 5 in gastric cancer: A systematic review with meta-analysis.

PubMed

Huang, Tianchen; Qiu, Xinguang; Xiao, Jianan; Wang, Qingbing; Wang, Yanjun; Zhang, Yong; Bai, Dongxiao

2016-04-01

The prognostic value of Leucine-rich repeat-containing G-protein-coupled receptor 5 (LGR5) in gastric cancer remains controversial. To further investigate this relationship, we performed meta-analyses to systematically review the association between LGR5 expression and various clinical parameters in gastric cancer patients. Eligible studies from PubMed, Embase, Web of Science, CNKI (Chinese National Knowledge Infrastructure), Wangfang (Database of Chinese Ministry of Science & Technology) and CBM (China Biological Medicine) databases were evaluated to investigate the association of LGR5 expression with overall survival (OS) and clinicopathological features of gastric cancer. LGR5 overexpression was significantly associated with poor OS in patients with gastric cancer (HR 1.66, 95% CI 1.02-2.69). LGR5 overexpression was also significantly associated with TNM stage (TIII/TIV vs TI/TII: OR 5.42, 95% CI 1.02-28.72) and lymph node metastasis (positive vs negative: OR 2.30, 95% CI 1.06-5.0). Our meta-analysis indicates that LGR5 may be a predictive factor for invasion and metastasis, and poor prognosis in patients with gastric cancer. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Contribution of Latin American Countries to Cancer Research and Patent Generation: Recent Patents.

PubMed

Perez-Santos, Martin; Anaya-Ruiz, Maricruz; Bandala, Cindy

2017-01-01

Data mining publications and patent data can provide decision support for scientists, inventors and industry in the field of cancer research. The main objective of this article it to identify trends of research and patent generation productivity originating from Latin American countries in the field of cancer. Publications were collected from the Scopus, Web of Science, PubMed database; and patents were collected from Latipat Espacenet databases. Data from January 1, 2000 until December 31, 2014 were searched for documents with specific words in cancer as a ''topic'' and a list of 20 Latin American countries as affiliation country. A total of 12,989 items published and 244 patent applications including "cancer" were retrieved. Brazil, Mexico, Argentina, Chile and Peru were highest contributors in cancer research, while Brazil, Mexico, Cuba and Argentina were highest contributors in cancer patent applications. The analysis of the data from this study provides an overview of research and patent activity in Latin America in the cancer field, which can be useful to help health policy makers and people in academia to shape up cancer research in the future. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Effect of dietary intervention treatment on children with iron deficiency anemia in China: a meta-analysis.

PubMed

Sun, Jian; Zhang, Lei; Cui, Jing; Li, Shanshan; Lu, Hongting; Zhang, Yong; Li, Haiming; Sun, Jianping; Baloch, Zulqarnain

2018-05-10

Previous studies have shown beneficial effects of dietary approaches for iron deficiency anemia (IDA) control. This study was design to investigate the effect of dietary intervention treatment on children with iron deficiency anemia. We performed a systematic review of published dietary interventions effect on IDA treatment through meta-analysis. CBM, CNKI, Wanfang database, EMBASE, VIP, PubMed and Web of science database were searched to identify studies published between January, 1980 and December, 2016. Statistical analysis was performed by Revmen5.2 software. Initially we retrieved for 373 studies, and then 6 studies with a total of 676 individuals were included in the analysis according to the inclusion and exclusion criteria for meta-analysis. The overall pooled estimate of odds ratio [(OR), 95% confidence intervals (95% CI)] in the dietary intervention on children with iron deficiency anemia was 6.54 (95% CI: 3.48-12.31, Z = 5.82, p<0.001) and funnel plot is symmetric. Our meta-analysis suggested that dietary interventions are effective in improving the iron deficiency in children with iron deficiency anemia (IDA) and should be considered in the overall strategy of IDA management.

Comparison of local infiltration and epidural analgesia for postoperative pain control in total knee arthroplasty and total hip arthroplasty: A systematic review and meta-analysis

PubMed Central

Yan, Huan; Cang, Jing; Xue, Zhanggang; Lu, Jianfeng; Wang, Hao

2016-01-01

Pain management after total knee arthroplasty (TKA) and total hip arthroplasty should permit early mobilization with minimal pain. Local infiltration analgesia (LIA) is a new popular method for decreasing postoperative pain. The goal of this meta-analysis is to evaluate the efficacy of LIA in comparison with epidural analgesia. A literature search was performed in PubMed, EMBASE, the OVID database, Web of Science, and the Cochrane Library databases. The risk of bias was assessed using the Cochrane collaboration tool. Outcomes of interest included visual analog scale score, range of flexion, length of stay, and complications. Nine trials involving 537 patients met the inclusion criteria. LIA provides better pain relief and larger range of motion in TKA patients compared to epidural analgesia at the late postoperative period. No significant difference was observed in regard to the length of stay and complications. The current evidence shows that the use of local infiltration is effective for postoperative pain management in TKA patients. More high-quality randomized controlled trials with long-term follow-up are required for examining the long-term efficacy and safety of local infiltration. PMID:27209072

Comparison of local infiltration and epidural analgesia for postoperative pain control in total knee arthroplasty and total hip arthroplasty: A systematic review and meta-analysis.

PubMed

Yan, Huan; Cang, Jing; Xue, Zhanggang; Lu, Jianfeng; Wang, Hao

2016-11-10

Pain management after total knee arthroplasty (TKA) and total hip arthroplasty should permit early mobilization with minimal pain. Local infiltration analgesia (LIA) is a new popular method for decreasing postoperative pain. The goal of this meta-analysis is to evaluate the efficacy of LIA in comparison with epidural analgesia. A literature search was performed in PubMed, EMBASE, the OVID database, Web of Science, and the Cochrane Library databases. The risk of bias was assessed using the Cochrane collaboration tool. Outcomes of interest included visual analog scale score, range of flexion, length of stay, and complications. Nine trials involving 537 patients met the inclusion criteria. LIA provides better pain relief and larger range of motion in TKA patients compared to epidural analgesia at the late postoperative period. No significant difference was observed in regard to the length of stay and complications. The current evidence shows that the use of local infiltration is effective for postoperative pain management in TKA patients. More high-quality randomized controlled trials with long-term follow-up are required for examining the long-term efficacy and safety of local infiltration.

Barriers in the social and healthcare assistance for transgender persons: A systematic review of qualitative studies.

PubMed

Aylagas-Crespillo, Marina; García-Barbero, Óscar; Rodríguez-Martín, Beatriz

2017-11-01

To explore the barriers to requesting social and healthcare assistance perceived by transgender persons and professionals involved in the assistance. A meta-study, qualitative systematic review, of studies published in English or Spanish, exploring the barriers, perceived by transgender persons and social and healthcare professionals, that transgender persons have when they seek social and healthcare assistance was carried out in the following databases Medline (PubMed), Scopus, Web of Science, Spanish National Research Council, CUIDEN, ProQuest, PsycINFO and CINAHL. Two thousand two hundred and sixty-one articles were found in the databases searched. Seven articles met all inclusion criteria and were included in this review. The professionals highlight the uncertainty when treating transgender persons and their lack of training. Transgender persons highlight the lack of information and the sense of helplessness it creates. Perceptions of transphobia, the fragmentation of services, administrative barriers, the lack of cultural sensitivity and professional training are also considered barriers to assistance. The findings of this study provide key information for the design of plans and programmes to improve the quality of social and health care for transgender persons. Copyright © 2017 Elsevier España, S.L.U. All rights reserved.

Ocean Drilling Program: Janus Web Database

Science.gov Websites

in Janus Data Types and Examples Leg 199, sunrise. Janus Web Database ODP and IODP data are stored in as time permits (see Database Overview for available data). Data are available to everyone. There are

[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.

Bio-psycho-social factors affecting sexual self-concept: A systematic review

PubMed Central

Potki, Robabeh; Ziaei, Tayebe; Faramarzi, Mahbobeh; Moosazadeh, Mahmood; Shahhosseini, Zohreh

2017-01-01

Background Nowadays, it is believed that mental and emotional aspects of sexual well-being are the important aspects of sexual health. Sexual self-concept is a major component of sexual health and the core of sexuality. It is defined as the cognitive perspective concerning the sexual aspects of ‘self’ and refers to the individual’s self-perception as a sexual creature. Objective The aim of this study was to assess the different factors affecting sexual self-concept. Methods English electronic databases including PubMed, Scopus, Web of Science and Google Scholar as well as two Iranian databases including Scientific Information Database and Iranmedex were searched for English and Persian-language articles published between 1996 and 2016. Of 281 retrieved articles, 37 articles were finally included for writing this review article. Results Factors affecting sexual self-concept were categorized to biological, psychological and social factors. In the category of biological factors, age gender, marital status, race, disability and sexual transmitted infections are described. In the psychological category, the impact of body image, sexual abuse in childhood and mental health history are present. Lastly, in the social category, the roles of parents, peers and the media are discussed. Conclusion As the development of sexual self-concept is influenced by multiple events in individuals’ lives, to promotion of sexual self-concept, an integrated implementation of health policies is recommended. PMID:29038693

DrugQuest - a text mining workflow for drug association discovery.

PubMed

Papanikolaou, Nikolas; Pavlopoulos, Georgios A; Theodosiou, Theodosios; Vizirianakis, Ioannis S; Iliopoulos, Ioannis

2016-06-06

Text mining and data integration methods are gaining ground in the field of health sciences due to the exponential growth of bio-medical literature and information stored in biological databases. While such methods mostly try to extract bioentity associations from PubMed, very few of them are dedicated in mining other types of repositories such as chemical databases. Herein, we apply a text mining approach on the DrugBank database in order to explore drug associations based on the DrugBank "Description", "Indication", "Pharmacodynamics" and "Mechanism of Action" text fields. We apply Name Entity Recognition (NER) techniques on these fields to identify chemicals, proteins, genes, pathways, diseases, and we utilize the TextQuest algorithm to find additional biologically significant words. Using a plethora of similarity and partitional clustering techniques, we group the DrugBank records based on their common terms and investigate possible scenarios why these records are clustered together. Different views such as clustered chemicals based on their textual information, tag clouds consisting of Significant Terms along with the terms that were used for clustering are delivered to the user through a user-friendly web interface. DrugQuest is a text mining tool for knowledge discovery: it is designed to cluster DrugBank records based on text attributes in order to find new associations between drugs. The service is freely available at http://bioinformatics.med.uoc.gr/drugquest .

Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems.

PubMed

Boué, Stéphanie; Talikka, Marja; Westra, Jurjen Willem; Hayes, William; Di Fabio, Anselmo; Park, Jennifer; Schlage, Walter K; Sewer, Alain; Fields, Brett; Ansari, Sam; Martin, Florian; Veljkovic, Emilija; Kenney, Renee; Peitsch, Manuel C; Hoeng, Julia

2015-01-01

With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com © The Author(s) 2015. Published by Oxford University Press.

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

PubMed

McCormack, Gavin R; Virk, Jagdeep S

2014-09-01

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

The effectiveness of evidence-based nursing on development of nursing students' critical thinking: A meta-analysis.

PubMed

Cui, Chuyun; Li, Yufeng; Geng, Dongrong; Zhang, Hui; Jin, Changde

2018-06-01

The aim of this meta-analysis was to assess the effectiveness of evidence-based nursing (EBN) on the development of critical thinking for nursing students. A systematic literature review of original studies on randomized controlled trials was conducted. The relevant randomized controlled trials were retrieved from multiple electronic databases including Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, EMBASE, Web of Science, Cumulative Index to Nursing and Allied Health (CINAHL), Chinese BioMed Database (CBM), China National Knowledge Infrastructure (CNKI), and WanFang Database. In order to make a systematic evaluation, studies were selected according to inclusion and exclusion criteria, and then according to extracted data and assessed quality. The data extraction was completed by two independent reviewers, and the methodological quality assessment was completed by another two reviewers. All of the data was analyzed by the software RevMan5.3. A total of nine studies with 1079 nursing students were chosen in this systematic literature review. The result of this meta-analysis showed that the effectiveness of evidence-based nursing was superior to that of traditional teaching on nursing students' critical thinking. The results of this meta-analysis indicate that evidence-based nursing could help nursing students to promote their development of critical thinking. More researches with higher quality and larger sample size can be analyzed in the further. Copyright © 2018. Published by Elsevier Ltd.

Solution Kinetics Database on the Web

National Institute of Standards and Technology Data Gateway

SRD 40 NDRL/NIST Solution Kinetics Database on the Web (Web, free access)   Data for free radical processes involving primary radicals from water, inorganic radicals and carbon-centered radicals in solution, and singlet oxygen and organic peroxyl radicals in various solvents.

Beyond accuracy: creating interoperable and scalable text-mining web services.

PubMed

Wei, Chih-Hsuan; Leaman, Robert; Lu, Zhiyong

2016-06-15

The biomedical literature is a knowledge-rich resource and an important foundation for future research. With over 24 million articles in PubMed and an increasing growth rate, research in automated text processing is becoming increasingly important. We report here our recently developed web-based text mining services for biomedical concept recognition and normalization. Unlike most text-mining software tools, our web services integrate several state-of-the-art entity tagging systems (DNorm, GNormPlus, SR4GN, tmChem and tmVar) and offer a batch-processing mode able to process arbitrary text input (e.g. scholarly publications, patents and medical records) in multiple formats (e.g. BioC). We support multiple standards to make our service interoperable and allow simpler integration with other text-processing pipelines. To maximize scalability, we have preprocessed all PubMed articles, and use a computer cluster for processing large requests of arbitrary text. Our text-mining web service is freely available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmTools/#curl : Zhiyong.Lu@nih.gov. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.

Ocean Drilling Program: Privacy Policy

Science.gov Websites

and products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main web site ODP/TAMU Science Operator Home Ocean Drilling Program Privacy Policy The following is the privacy policy for the www-odp.tamu.edu web site. 1. Cookies are used in the Database portion of the web

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.

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

Innovative patient care practices using social media.

PubMed

Mattingly, T Joseph

2015-01-01

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

Breast volumetric analysis for aesthetic planning in breast reconstruction: a literature review of techniques

PubMed Central

Rozen, Warren Matthew; Spychal, Robert T.; Hunter-Smith, David J.

2016-01-01

Background Accurate volumetric analysis is an essential component of preoperative planning in both reconstructive and aesthetic breast procedures towards achieving symmetrization and patient-satisfactory outcome. Numerous comparative studies and reviews of individual techniques have been reported. However, a unifying review of all techniques comparing their accuracy, reliability, and practicality has been lacking. Methods A review of the published English literature dating from 1950 to 2015 using databases, such as PubMed, Medline, Web of Science, and EMBASE, was undertaken. Results Since Bouman’s first description of water displacement method, a range of volumetric assessment techniques have been described: thermoplastic casting, direct anthropomorphic measurement, two-dimensional (2D) imaging, and computed tomography (CT)/magnetic resonance imaging (MRI) scans. However, most have been unreliable, difficult to execute and demonstrate limited practicability. Introduction of 3D surface imaging has revolutionized the field due to its ease of use, fast speed, accuracy, and reliability. However, its widespread use has been limited by its high cost and lack of high level of evidence. Recent developments have unveiled the first web-based 3D surface imaging program, 4D imaging, and 3D printing. Conclusions Despite its importance, an accurate, reliable, and simple breast volumetric analysis tool has been elusive until the introduction of 3D surface imaging technology. However, its high cost has limited its wide usage. Novel adjunct technologies, such as web-based 3D surface imaging program, 4D imaging, and 3D printing, appear promising. PMID:27047788

A web-based genomic sequence database for the Streptomycetaceae: a tool for systematics and genome mining

USDA-ARS?s Scientific Manuscript database

The ARS Microbial Genome Sequence Database (http://199.133.98.43), a web-based database server, was established utilizing the BIGSdb (Bacterial Isolate Genomics Sequence Database) software package, developed at Oxford University, as a tool to manage multi-locus sequence data for the family Streptomy...

Collection Fusion Using Bayesian Estimation of a Linear Regression Model in Image Databases on the Web.

ERIC Educational Resources Information Center

Kim, Deok-Hwan; Chung, Chin-Wan

2003-01-01

Discusses the collection fusion problem of image databases, concerned with retrieving relevant images by content based retrieval from image databases distributed on the Web. Focuses on a metaserver which selects image databases supporting similarity measures and proposes a new algorithm which exploits a probabilistic technique using Bayesian…

The Web-Database Connection Tools for Sharing Information on the Campus Intranet.

ERIC Educational Resources Information Center

Thibeault, Nancy E.

This paper evaluates four tools for creating World Wide Web pages that interface with Microsoft Access databases: DB Gateway, Internet Database Assistant (IDBA), Microsoft Internet Database Connector (IDC), and Cold Fusion. The system requirements and features of each tool are discussed. A sample application, "The Virtual Help Desk"…

Adolescents' and young adults' transition experiences when transferring from paediatric to adult care: a qualitative metasynthesis.

PubMed

Fegran, Liv; Hall, Elisabeth O C; Uhrenfeldt, Lisbeth; Aagaard, Hanne; Ludvigsen, Mette Spliid

2014-01-01

The objective of this study was to synthesize qualitative studies of how adolescents and young adults with chronic diseases experience the transition from paediatric to adult hospital care. The review is designed as a qualitative metasynthesis and is following Sandelowski and Barroso's guidelines for synthesizing qualitative research. Literature searches were conducted in the databases PubMed, Ovid, Scopus, Cumulative Index to Nursing and Allied Health Literature (CINAHL), ISI Web of Science, and Nordic and German databases covering the period from 1999 to November 2010. In addition, forward citation snowball searching was conducted in the databases Ovid, CINAHL, ISI Web of Science, Scopus and Google Scholar. Of the 1143 records screened, 18 studies were included. Inclusion criteria were qualitative studies in English, German or Nordic languages on adolescents' and young adults' transition experiences when transferring from paediatric to adult care. There was no age limit, provided the focus was on the actual transfer process and participants had a chronic somatic disease. The studies were appraised as suitable for inclusion using a published appraisal tool. Data were analyzed into metasummaries and a metasynthesis according to established guidelines for synthesis of qualitative research. Four themes illustrating experiences of loss of familiar surroundings and relationships combined with insecurity and a feeling of being unprepared for what was ahead were identified: facing changes in significant relationships, moving from a familiar to an unknown ward culture, being prepared for transfer and achieving responsibility. Young adults' transition experiences seem to be comparable across diagnoses. Feelings of not belonging and of being redundant during the transfer process are striking. Health care professionals' appreciation of young adults' need to be acknowledged and valued as competent collaborators in their own transfer is crucial, and may protect them from additional health problems during a vulnerable phase. Further research including participants across various cultures and health care systems is needed. Copyright © 2013 Elsevier Ltd. All rights reserved.

An Overview of ARL’s Multimodal Signatures Database and Web Interface

DTIC Science & Technology

2007-12-01

ActiveX components, which hindered distribution due to license agreements and run-time license software to use such components. g. Proprietary...Overview The database consists of multimodal signature data files in the HDF5 format. Generally, each signature file contains all the ancillary...only contains information in the database, Web interface, and signature files that is releasable to the public. The Web interface consists of static

Analysis and Development of a Web-Enabled Planning and Scheduling Database Application

DTIC Science & Technology

2013-09-01

establishes an entity—relationship diagram for the desired process, constructs an operable database using MySQL , and provides a web- enabled interface for...development, develop, design, process, re- engineering, reengineering, MySQL , structured query language, SQL, myPHPadmin. 15. NUMBER OF PAGES 107 16...relationship diagram for the desired process, constructs an operable database using MySQL , and provides a web-enabled interface for the population of

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.

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

Knowledge, skills and attitudes of hospital pharmacists in the use of information technology and electronic tools to support clinical practice: A Brazilian survey

PubMed Central

Vasconcelos, Hemerson Bruno da Silva; Woods, David John

2017-01-01

This study aimed to identify the knowledge, skills and attitudes of Brazilian hospital pharmacists in the use of information technology and electronic tools to support clinical practice. Methods: A questionnaire was sent by email to clinical pharmacists working public and private hospitals in Brazil. The instrument was validated using the method of Polit and Beck to determine the content validity index. Data (n = 348) were analyzed using descriptive statistics, Pearson's Chi-square test and Gamma correlation tests. Results: Pharmacists had 1–4 electronic devices for personal use, mainly smartphones (84.8%; n = 295) and laptops (81.6%; n = 284). At work, pharmacists had access to a computer (89.4%; n = 311), mostly connected to the internet (83.9%; n = 292). They felt competent (very capable/capable) searching for a web page/web site on a specific subject (100%; n = 348), downloading files (99.7%; n = 347), using spreadsheets (90.2%; n = 314), searching using MeSH terms in PubMed (97.4%; n = 339) and general searching for articles in bibliographic databases (such as Medline/PubMed: 93.4%; n = 325). Pharmacists did not feel competent in using statistical analysis software (somewhat capable/incapable: 78.4%; n = 273). Most pharmacists reported that they had not received formal education to perform most of these actions except searching using MeSH terms. Access to bibliographic databases was available in Brazilian hospitals, however, most pharmacists (78.7%; n = 274) reported daily use of a non-specific search engine such as Google. This result may reflect the lack of formal knowledge and training in the use of bibliographic databases and difficulty with the English language. The need to expand knowledge about information search tools was recognized by most pharmacists in clinical practice in Brazil, especially those with less time dedicated exclusively to clinical activity (Chi-square, p = 0.006). Conclusion: These results will assist in defining minimal competencies for the training of pharmacists in the field of information technology to support clinical practice. Knowledge and skill gaps are evident in the use of bibliographic databases, spreadsheets and statistical tools. PMID:29272292

Knowledge, skills and attitudes of hospital pharmacists in the use of information technology and electronic tools to support clinical practice: A Brazilian survey.

PubMed

Néri, Eugenie Desirèe Rabelo; Meira, Assuero Silva; Vasconcelos, Hemerson Bruno da Silva; Woods, David John; Fonteles, Marta Maria de França

2017-01-01

This study aimed to identify the knowledge, skills and attitudes of Brazilian hospital pharmacists in the use of information technology and electronic tools to support clinical practice. A questionnaire was sent by email to clinical pharmacists working public and private hospitals in Brazil. The instrument was validated using the method of Polit and Beck to determine the content validity index. Data (n = 348) were analyzed using descriptive statistics, Pearson's Chi-square test and Gamma correlation tests. Pharmacists had 1-4 electronic devices for personal use, mainly smartphones (84.8%; n = 295) and laptops (81.6%; n = 284). At work, pharmacists had access to a computer (89.4%; n = 311), mostly connected to the internet (83.9%; n = 292). They felt competent (very capable/capable) searching for a web page/web site on a specific subject (100%; n = 348), downloading files (99.7%; n = 347), using spreadsheets (90.2%; n = 314), searching using MeSH terms in PubMed (97.4%; n = 339) and general searching for articles in bibliographic databases (such as Medline/PubMed: 93.4%; n = 325). Pharmacists did not feel competent in using statistical analysis software (somewhat capable/incapable: 78.4%; n = 273). Most pharmacists reported that they had not received formal education to perform most of these actions except searching using MeSH terms. Access to bibliographic databases was available in Brazilian hospitals, however, most pharmacists (78.7%; n = 274) reported daily use of a non-specific search engine such as Google. This result may reflect the lack of formal knowledge and training in the use of bibliographic databases and difficulty with the English language. The need to expand knowledge about information search tools was recognized by most pharmacists in clinical practice in Brazil, especially those with less time dedicated exclusively to clinical activity (Chi-square, p = 0.006). These results will assist in defining minimal competencies for the training of pharmacists in the field of information technology to support clinical practice. Knowledge and skill gaps are evident in the use of bibliographic databases, spreadsheets and statistical tools.

PubMed had a higher sensitivity than Ovid-MEDLINE in the search for systematic reviews.

PubMed

Katchamart, Wanruchada; Faulkner, Amy; Feldman, Brian; Tomlinson, George; Bombardier, Claire

2011-07-01

To compare the performance of Ovid-MEDLINE vs. PubMed for identifying randomized controlled trials of methotrexate (MTX) in patients with rheumatoid arthritis (RA). We created search strategies for Ovid-MEDLINE and PubMed for a systematic review of MTX in RA. Their performance was evaluated using sensitivity, precision, and number needed to read (NNR). Comparing searches in Ovid-MEDLINE vs. PubMed, PubMed retrieved more citations overall than Ovid-MEDLINE; however, of the 20 citations that met eligibility criteria for the review, Ovid-MEDLINE retrieved 17 and PubMed 18. The sensitivity was 85% for Ovid-MEDLINE vs. 90% for PubMed, whereas the precision and NNR were comparable (precision: 0.881% for Ovid-MEDLINE vs. 0.884% for PubMed and NNR: 114 for Ovid-MEDLINE vs. 113 for PubMed). In systematic reviews of RA, PubMed has higher sensitivity than Ovid-MEDLINE with comparable precision and NNR. This study highlights the importance of well-designed database-specific search strategies. Copyright © 2010 Elsevier Inc. All rights reserved.

Antidepressants for depressive disorder in children and adolescents: a database of randomised controlled trials.

PubMed

Zhang, Yuqing; Zhou, Xinyu; Pu, Juncai; Zhang, Hanping; Yang, Lining; Liu, Lanxiang; Zhou, Chanjuan; Yuan, Shuai; Jiang, Xiaofeng; Xie, Peng

2018-05-31

In recent years, whether, when and how to use antidepressants to treat depressive disorder in children and adolescents has been hotly debated. Relevant evidence on this topic has increased rapidly. In this paper, we present the construction and content of a database of randomised controlled trials of antidepressants to treat depressive disorder in children and adolescents. This database can be freely accessed via our website and will be regularly updated. Major bibliographic databases (PubMed, the Cochrane Library, Web of Science, Embase, CINAHL, PsycINFO and LiLACS), international trial registers and regulatory agencies' websites were systematically searched for published and unpublished studies up to April 30, 2017. We included randomised controlled trials in which the efficacy or tolerability of any oral antidepressant was compared with that of a control group or any other treatment. In total, 7377 citations from bibliographical databases and 3289 from international trial registers and regulatory agencies' websites were identified. Of these, 53 trials were eligible for inclusion in the final database. Selected data were extracted from each study, including characteristics of the participants (the study population, setting, diagnostic criteria, type of depression, age, sex, and comorbidity), characteristics of the treatment conditions (the treatment conditions, general information, and detail of pharmacotherapy and psychotherapy) and study characteristics (the sponsor, country, number of sites, blinding method, sample size, treatment duration, depression scales, other scales, and primary outcome measure used, and side-effect monitoring method). Moreover, the risk of bias for each trial were assessed. This database provides information on nearly all randomised controlled trials of antidepressants in children and adolescents. By using this database, researchers can improve research efficiency, avoid inadvertent errors and easily focus on the targeted subgroups in which they are interested. For authors of subsequent reviews, they could only use this database to insure that they have completed a comprehensive review, rather than relied solely on the data from this database. We expect this database could help to promote research on evidence-based practice in the treatment of depressive disorder in children and adolescents. The database could be freely accessed in our website: http://xiepengteam.cn/research/evidence-based-medicine .

[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.

Results of an assessment of information needs among speech-language pathologists and audiologists in Idaho*

PubMed Central

Guo, Ruiling; Bain, Barbara A.; Willer, Janene

2008-01-01

Objectives: 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. Methods: 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. Results: 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. PMID:18379669

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.

Analysis and visualization of Arabidopsis thaliana GWAS using web 2.0 technologies.

PubMed

Huang, Yu S; Horton, Matthew; Vilhjálmsson, Bjarni J; Seren, Umit; Meng, Dazhe; Meyer, Christopher; Ali Amer, Muhammad; Borevitz, Justin O; Bergelson, Joy; Nordborg, Magnus

2011-01-01

With large-scale genomic data becoming the norm in biological studies, the storing, integrating, viewing and searching of such data have become a major challenge. In this article, we describe the development of an Arabidopsis thaliana database that hosts the geographic information and genetic polymorphism data for over 6000 accessions and genome-wide association study (GWAS) results for 107 phenotypes representing the largest collection of Arabidopsis polymorphism data and GWAS results to date. Taking advantage of a series of the latest web 2.0 technologies, such as Ajax (Asynchronous JavaScript and XML), GWT (Google-Web-Toolkit), MVC (Model-View-Controller) web framework and Object Relationship Mapper, we have created a web-based application (web app) for the database, that offers an integrated and dynamic view of geographic information, genetic polymorphism and GWAS results. Essential search functionalities are incorporated into the web app to aid reverse genetics research. The database and its web app have proven to be a valuable resource to the Arabidopsis community. The whole framework serves as an example of how biological data, especially GWAS, can be presented and accessed through the web. In the end, we illustrate the potential to gain new insights through the web app by two examples, showcasing how it can be used to facilitate forward and reverse genetics research. Database URL: http://arabidopsis.usc.edu/

School Gardens Enhance Academic Performance and Dietary Outcomes in Children.

PubMed

Berezowitz, Claire K; Bontrager Yoder, Andrea B; Schoeller, Dale A

2015-08-01

Schools face increasing demands to provide education on healthy living and improve core academic performance. Although these appear to be competing concerns, they may interact beneficially. This article focuses on school garden programs and their effects on students' academic and dietary outcomes. Database searches in CABI, Web of Science, Web of Knowledge, PubMed, Education Full Text, Education Resources Information Center (ERIC), and PsychINFO were conducted through May 2013 for peer-reviewed literature related to school-day garden interventions with measures of dietary and/or academic outcomes. Among 12 identified garden studies with dietary measures, all showed increases/improvements in predictors of fruit and vegetable (FV) consumption. Seven of these also included self-reported FV intake with 5 showing an increase and 2 showing no change. Four additional interventions that included a garden component measured academic outcomes; of these, 2 showed improvements in science achievement and 1 measured and showed improvements in math scores. This small set of studies offers evidence that garden-based learning does not negatively impact academic performance or FV consumption and may favorably impact both. Additional studies with more robust experimental designs and outcome measures are necessary to understand the effects of experiential garden-based learning on children's academic and dietary outcomes. © 2015, American School Health Association.

Harnessing the internet cloud for managing drug interactions with chemotherapy regimens in patients with cancer suffering from depression.

PubMed

Yap, Kevin Yi-Lwern; Ho, Yasmin Xiu Xiu; Chui, Wai Keung; Chan, Alexandre

2010-11-01

Concomitant use of anticancer drugs (ACDs) and antidepressants (ADs) in the treatment of depression in patients with cancer may result in potentially harmful drug-drug interactions (DDIs). It is crucial that clinicians make timely, accurate, safe and effective decisions regarding drug therapies in patients. The ubiquitous nature of the internet or "cloud" has enabled easy dissemination of DDI information, but there is currently no database dedicated to allow searching of ACD interactions by chemotherapy regimens. We describe the implementation of an AD interaction module to a previously published oncology-specific DDI database for clinicians which focuses on ACDs, single-agent and multiple-agent chemotherapy regimens. Drug- and DDI-related information were collated from drug information handbooks, databases, package inserts, and published literature from PubMed, Scopus and Science Direct. Web documents were constructed using Adobe software and programming scripts, and mounted on a domain served from the internet cloud. OncoRx is an oncology-specific DDI database whose structure is designed around all the major classes of ACDs and their frequently prescribed chemotherapy regimens. There are 117 ACDs and 256 regimens in OncoRx, and it can detect over 1 500 interactions with 21 ADs. Clinicians are provided with the pharmacokinetic parameters of the drugs, information on the regimens and details of the detected DDIs during an interaction search. OncoRx is the first database of its kind which allows detection of ACD and chemotherapy regimen interactions with ADs. This tool will assist clinicians in improving clinical response and reducing adverse effects based on the therapeutic and toxicity profiles of the drugs.

Web data mining

NASA Astrophysics Data System (ADS)

Wibonele, Kasanda J.; Zhang, Yanqing

2002-03-01

A web data mining system using granular computing and ASP programming is proposed. This is a web based application, which allows web users to submit survey data for many different companies. This survey is a collection of questions that will help these companies develop and improve their business and customer service with their clients by analyzing survey data. This web application allows users to submit data anywhere. All the survey data is collected into a database for further analysis. An administrator of this web application can login to the system and view all the data submitted. This web application resides on a web server, and the database resides on the MS SQL server.

Mining a Web Citation Database for Author Co-Citation Analysis.

ERIC Educational Resources Information Center

He, Yulan; Hui, Siu Cheung

2002-01-01

Proposes a mining process to automate author co-citation analysis based on the Web Citation Database, a data warehouse for storing citation indices of Web publications. Describes the use of agglomerative hierarchical clustering for author clustering and multidimensional scaling for displaying author cluster maps, and explains PubSearch, a…

Database of Novel and Emerging Adsorbent Materials

National Institute of Standards and Technology Data Gateway

SRD 205 NIST/ARPA-E Database of Novel and Emerging Adsorbent Materials (Web, free access)   The NIST/ARPA-E Database of Novel and Emerging Adsorbent Materials is a free, web-based catalog of adsorbent materials and measured adsorption properties of numerous materials obtained from article entries from the scientific literature. Search fields for the database include adsorbent material, adsorbate gas, experimental conditions (pressure, temperature), and bibliographic information (author, title, journal), and results from queries are provided as a list of articles matching the search parameters. The database also contains adsorption isotherms digitized from the cataloged articles, which can be compared visually online in the web application or exported for offline analysis.

MoccaDB - an integrative database for functional, comparative and diversity studies in the Rubiaceae family

PubMed Central

Plechakova, Olga; Tranchant-Dubreuil, Christine; Benedet, Fabrice; Couderc, Marie; Tinaut, Alexandra; Viader, Véronique; De Block, Petra; Hamon, Perla; Campa, Claudine; de Kochko, Alexandre; Hamon, Serge; Poncet, Valérie

2009-01-01

Background In the past few years, functional genomics information has been rapidly accumulating on Rubiaceae species and especially on those belonging to the Coffea genus (coffee trees). An increasing number of expressed sequence tag (EST) data and EST- or genomic-derived microsatellite markers have been generated, together with Conserved Ortholog Set (COS) markers. This considerably facilitates comparative genomics or map-based genetic studies through the common use of orthologous loci across different species. Similar genomic information is available for e.g. tomato or potato, members of the Solanaceae family. Since both Rubiaceae and Solanaceae belong to the Euasterids I (lamiids) integration of information on genetic markers would be possible and lead to more efficient analyses and discovery of key loci involved in important traits such as fruit development, quality, and maturation, or adaptation. Our goal was to develop a comprehensive web data source for integrated information on validated orthologous markers in Rubiaceae. Description MoccaDB is an online MySQL-PHP driven relational database that houses annotated and/or mapped microsatellite markers in Rubiaceae. In its current release, the database stores 638 markers that have been defined on 259 ESTs and 379 genomic sequences. Marker information was retrieved from 11 published works, and completed with original data on 132 microsatellite markers validated in our laboratory. DNA sequences were derived from three Coffea species/hybrids. Microsatellite markers were checked for similarity, in vitro tested for cross-amplification and diversity/polymorphism status in up to 38 Rubiaceae species belonging to the Cinchonoideae and Rubioideae subfamilies. Functional annotation was provided and some markers associated with described metabolic pathways were also integrated. Users can search the database for marker, sequence, map or diversity information through multi-option query forms. The retrieved data can be browsed and downloaded, along with protocols used, using a standard web browser. MoccaDB also integrates bioinformatics tools (CMap viewer and local BLAST) and hyperlinks to related external data sources (NCBI GenBank and PubMed, SOL Genomic Network database). Conclusion We believe that MoccaDB will be extremely useful for all researchers working in the areas of comparative and functional genomics and molecular evolution, in general, and population analysis and association mapping of Rubiaceae and Solanaceae species, in particular. PMID:19788737

ARIANE: integration of information databases within a hospital intranet.

PubMed

Joubert, M; Aymard, S; Fieschi, D; Volot, F; Staccini, P; Robert, J J; Fieschi, M

1998-05-01

Large information systems handle massive volume of data stored in heterogeneous sources. Each server has its own model of representation of concepts with regard to its aims. One of the main problems end-users encounter when accessing different servers is to match their own viewpoint on biomedical concepts with the various representations that are made in the databases servers. The aim of the project ARIANE is to provide end-users with easy-to-use and natural means to access and query heterogeneous information databases. The objectives of this research work consist in building a conceptual interface by means of the Internet technology inside an enterprise Intranet and to propose a method to realize it. This method is based on the knowledge sources provided by the Unified Medical Language System (UMLS) project of the US National Library of Medicine. Experiments concern queries to three different information servers: PubMed, a Medline server of the NLM; Thériaque, a French database on drugs implemented in the Hospital Intranet; and a Web site dedicated to Internet resources in gastroenterology and nutrition, located at the Faculty of Medicine of Nice (France). Accessing to each of these servers is different according to the kind of information delivered and according to the technology used to query it. Dealing with health care professional workstation, the authors introduced in the ARIANE project quality criteria in order to attempt a homogeneous and efficient way to build a query system able to be integrated in existing information systems and to integrate existing and new information sources.

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

PubMed Central

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

2018-01-01

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

Wenjing decoction (herbal medicine) for the treatment of primary dysmenorrhea: a systematic review and meta-analysis.

PubMed

Gao, Li; Jia, Chunhua; Zhang, Heng; Ma, Cuilan

2017-10-01

Wenjing decoction is a well-accepted traditional Chinese medicine for the treatment of primary dysmenorrhea in East Asia, but its clinical effectiveness and risk have not been adequately assessed. In this paper, we conducted a systematic review and meta-analysis to evaluate the efficacy of Wenjing decoction for the treatment of primary dysmenorrhea. Eight databases were used in our research: the Cochrane Library, the Web of Science, PubMed, EMBASE, the Chinese Biomedical Literature Database (CBM), the Chinese National Knowledge Infrastructure (CNKI), the Chinese Scientific Journal Database, and the Wan-fang Database. The following search terms were used: (Wenjing decoction OR Wenjing formula OR Wenjing tang) AND (primary dysmenorrhea OR dysmenorrhea OR painful menstruation) AND (randomized controlled trial). No language limitation was used. A total of 18 studies, including 1736 patients, were included in the meta-analysis. Wenjing decoction was shown to be significantly better than nonsteroidal anti-inflammatory drugs for the improvement of primary dysmenorrhea according to the clinical effective rate (RR 1.41, 95% CI 1.24-1.61), the visual analogue scale (MD -1.77, 95% CI -2.69 to -0.84), and the pain scale for dysmenorrhea (MD -1.81, 95% CI -2.41 to -1.22). The results supported the clinical use of Wenjing decoction for the treatment of primary dysmenorrhea. However, the quality of the evidence for this finding was low due to a high risk of bias in the included studies. Therefore, well-designed randomized controlled trials are still needed to further evaluate the efficacy of Wenjing decoction for the treatment of primary dysmenorrhea.

THE ECOTOX DATABASE AND ECOLOGICAL SOIL SCREENING LEVEL (ECO-SSL) WEB SITES

EPA Science Inventory

The EPA's ECOTOX database (http://www.epa.gov/ecotox/) provides a web browser search interface for locating aquatic and terrestrial toxic effects information. Data on more than 8100 chemicals and 5700 terrestrial and aquatic species are included in the database. Information is ...

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

Picturing the Heart

MedlinePlus

... Links for Students Glossary Government Resources Kids.gov – Science Information and services on the web from government agencies, ... and educational organizations. Science.gov Gateway to government science information and research results. PubMed Central Free full-text ...

Nuclear Medicine

MedlinePlus

... VIEW MORE RELATED NEWS Government Resources Kids.gov – Science Information and services on the web from government agencies, ... and educational organizations. Science.gov Gateway to government science information and research results. PubMed Central Free full-text ...

Factors Associated With Suicidal Attempts in Iran: A Systematic Review.

PubMed

Hakim Shooshtari, Mitra; Malakouti, Seyyed Kazem; Panaghi, Leili; Mohseni, Shohreh; Mansouri, Naghmeh; Rahimi Movaghar, Afarin

2016-03-01

Suicide prevention is a health service priority. Some surveys have assessed suicidal behaviors and potential risk factors. The current paper aimed to gather information about etiology of suicide attempts in Iran. Pubmed, ISI web of science, PsychInfo, IranPsych, IranMedex, IranDoc as well as gray literature were searched. By electronic and gray literature search, 128 articles were enrolled in this paper. Pubmed, ISI web of science, PsychInfo, IranPsych, IranMedex, IranDoc were searched for electronic search. After reading the abstracts, 84 studies were excluded and full texts of 44 articles were reviewed critically. Pubmed, ISI web of science, PsychInfo, IranPsych, IranMedex, IranDoc as well as gray literature were searched to find any study about etiologic factors of suicide attempt in Iran. Depressive disorder was the most common diagnosis in suicide attempters that is 45% of the evaluated cases had depression. One study that had used Minnesota multiphasic personality inventory (MMPI) found that Histrionics in females and Schizophrenia and Paranoia in males were significantly influential. Family conflicts with 50.7% and conflict with parents with 44% were two effective psychosocial factors in suicidal attempts. In around one fourth (28.7%) of the cases, conflict with spouse was the main etiologic factor. According to the methodological limitations, outcomes should be generalized cautiously. Further studies will help to plan preventive strategies for suicidal attempts; therefore, continued researches should be conducted to fill the data gaps.

What Makes a Successful Survey? A Systematic Review of Surveys Used in Anterior Cruciate Ligament Reconstruction.

PubMed

Ekhtiari, Seper; Kay, Jeffrey; de Sa, Darren; Simunovic, Nicole; Musahl, Volker; Peterson, Devin C; Ayeni, Olufemi R

2017-05-01

To characterize and assess the methodological quality of patient and physician surveys related to anterior cruciate ligament reconstruction, and to analyze the factors influencing response rate. The databases MEDLINE, Embase, and PubMed were searched from database inception to search date and screened in duplicate for relevant studies. Data regarding survey characteristics, response rates, and distribution methods were extracted. A previously published list of recommendations for high-quality surveys in orthopaedics was used as a scale to assess survey quality (12 items scored 0, 1, or 2; maximum score = 24). Of the initial 1,276 studies, 53 studies published between 1986 and 2016 met the inclusion criteria. Sixty-four percent of studies were distributed to physicians, compared with 32% distributed to patients and less than 4% to coaches. The median number of items in each survey was 10.5, and the average response rate was 73% (range: 18% to 100%). In-person distribution was the most common method (40%), followed by web-based methods (28%) and mail (25%). Response rates were highest for surveys targeted at patients (77%, P < .0001) and those delivered in-person (94%, P < .0001). The median quality score was 12/24 (range = 8.5/24 to 21/24). There was high inter-rater agreement using the quality scale (intraclass correlation coefficient = 0.92), but there was no correlation with the response rate (Rho = -0.01, P = .97). Response rates vary based on target audience and distribution methods, with patients responding at a significantly higher rate than physicians and in-person distribution yielding significantly higher response rates than web or mail surveys. Level IV, systematic review of Level IV studies. Copyright © 2017 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Assessing the quality of study reports on spa therapy based on randomized controlled trials by the spa therapy checklist (SPAC).

PubMed

Kamioka, Hiroharu; Tsutani, Kiichiro; Maeda, Masaharu; Hayasaka, Shinya; Okuizum, Hiroyasu; Goto, Yasuaki; Okada, Shinpei; Kitayuguchi, Jun; Abe, Takafumi

2014-11-01

The purpose of this study was to assess the quality of study reports on spa therapy based on randomized controlled trials by the spa therapy and balneotherapy checklist (SPAC), and to show the relationship between SPAC score and the characteristics of publication. We searched the following databases from 1990 up to September 30, 2013: MEDLINE via PubMed, CINAHL, Web of Science, Ichushi Web, Global Health Library, the Western Pacific Region Index Medicus, PsycINFO, and the Cochrane Database of Systematic Reviews. We used the SPAC to assess the quality of reports on spa therapy and balneotherapy trials (SPAC) that was developed using the Delphi consensus method. Fifty-one studies met all inclusion criteria. Forty studies (78%) were about "Diseases of the musculoskeletal system and connective)". The total SPAC score (full-mark; 19 pts) was 10.8 ± 2.3 pts (mean ± SD). The items for which a description was lacking (very poor; <50%) in many studies were as follows: "locations of spa facility where the data were collected"; "pH"; "scale of bathtub"; "presence of other facility and exposure than bathing (sauna, steam bath, etc.)"; "qualification and experience of care provider"; "Instructions about daily life" and "adherence". We clarified that there was no relationship between the publish period, languages, and the impact factor (IF) for the SPAC score. In order to prevent flawed description, SPAC could provide indispensable information for researchers who are going to design a research protocol according to each disease. Copyright © 2014 Elsevier Ltd. All rights reserved.

Do spatiotemporal parameters and gait variability differ across the lifespan of healthy adults? A systematic review.

PubMed

Herssens, Nolan; Verbecque, Evi; Hallemans, Ann; Vereeck, Luc; Van Rompaey, Vincent; Saeys, Wim

2018-06-12

Aging is often associated with changes in the musculoskeletal system, peripheral and central nervous system. These age-related changes often result in mobility problems influencing gait performance. Compensatory strategies are used as a way to adapt to these physiological changes. The aim of this review is to investigate the differences in spatiotemporal and gait variability measures throughout the healthy adult life. This systematic review was conducted according to the PRISMA guidelines and registered in the PROSPERO database (no. CRD42017057720). Databases MEDLINE (Pubmed), Web of Science (Web of Knowledge), Cochrane Library and ScienceDirect were systematically searched until March 2018. Eighteen of the 3195 original studies met the eligibility criteria and were included in this review. The majority of studies reported spatiotemporal and gait variability measures in adults above the age of 65, followed by the young adult population, information of middle-aged adults is lacking. Spatiotemporal parameters and gait variability measures were extracted from 2112 healthy adults between 18 and 98 years old and, in general, tend to deteriorate with increasing age. Variability measures were only reported in an elderly population and show great variety between studies. The findings of this review suggest that most spatiotemporal parameters significantly differ across different age groups. Elderly populations show a reduction of preferred walking speed, cadence, step and stride length, all related to a more cautious gait, while gait variability measures remain stable over time. A preliminary framework of normative reference data is provided, enabling insights into the influence of aging on spatiotemporal parameters, however spatiotemporal parameters of middle-aged adults should be investigated more thoroughly. Copyright © 2018 Elsevier B.V. All rights reserved.

Virtual Reality Applications for Stress Management Training in the Military.

PubMed

Pallavicini, Federica; Argenton, Luca; Toniazzi, Nicola; Aceti, Luciana; Mantovani, Fabrizia

2016-12-01

Stress Management Training programs are increasingly being adopted in the military field for resilience empowerment and primary stress prevention. In the last several years, advanced technologies (virtual reality in particular) have been integrated in order to develop more innovative and effective stress training programs for military personnel, including soldiers, pilots, and other aircrew professionals. This systematic review describes experimental studies that have been conducted in recent years to test the effectiveness of virtual reality-based Stress Management Training programs developed for military personnel. This promising state-of-the-art technology has the potential to be a successful new approach in empowering soldiers and increasing their resilience to stress. To provide an overview from 2001 to 2016 of the application of virtual reality for Stress Management Training programs developed for the military, a computer-based search for relevant publications was performed in several databases. Databases used in the search were PsycINFO, Web of Science (Web of Knowledge), PubMed, and Medline. The search string was: ("Virtual Reality") AND ("Military") AND ["Stress Training" OR ("Stress Management")]. There were 14 studies that met the inclusion criteria and were included in the review. The main observation to be drawn from this review is that virtual reality can provide interactive Stress Management Training to decrease levels of perceived stress and negative affect in military personnel. This technology appears to be a promising tool for assessing individuals' resilience to stress and for identifying the impact that stress can have on physiological reactivity and performance.Pallavicini F, Argenton L, Toniazzi N, Aceti L, Mantovani F. Virtual realtiy applications for stress management training in the military. Aerosp Med Hum Perform. 2016; 87(12):1021-1030.

Evaluation of the content and accessibility of web sites for accredited orthopaedic sports medicine fellowships.

PubMed

Mulcahey, Mary K; Gosselin, Michelle M; Fadale, Paul D

2013-06-19

The Internet is a common source of information for orthopaedic residents applying for sports medicine fellowships, with the web sites of the American Orthopaedic Society for Sports Medicine (AOSSM) and the San Francisco Match serving as central databases. We sought to evaluate the web sites for accredited orthopaedic sports medicine fellowships with regard to content and accessibility. We reviewed the existing web sites of the ninety-five accredited orthopaedic sports medicine fellowships included in the AOSSM and San Francisco Match databases from February to March 2012. A Google search was performed to determine the overall accessibility of program web sites and to supplement information obtained from the AOSSM and San Francisco Match web sites. The study sample consisted of the eighty-seven programs whose web sites connected to information about the fellowship. Each web site was evaluated for its informational value. Of the ninety-five programs, fifty-one (54%) had links listed in the AOSSM database. Three (3%) of all accredited programs had web sites that were linked directly to information about the fellowship. Eighty-eight (93%) had links listed in the San Francisco Match database; however, only five (5%) had links that connected directly to information about the fellowship. Of the eighty-seven programs analyzed in our study, all eighty-seven web sites (100%) provided a description of the program and seventy-six web sites (87%) included information about the application process. Twenty-one web sites (24%) included a list of current fellows. Fifty-six web sites (64%) described the didactic instruction, seventy (80%) described team coverage responsibilities, forty-seven (54%) included a description of cases routinely performed by fellows, forty-one (47%) described the role of the fellow in seeing patients in the office, eleven (13%) included call responsibilities, and seventeen (20%) described a rotation schedule. Two Google searches identified direct links for 67% to 71% of all accredited programs. Most accredited orthopaedic sports medicine fellowships lack easily accessible or complete web sites in the AOSSM or San Francisco Match databases. Improvement in the accessibility and quality of information on orthopaedic sports medicine fellowship web sites would facilitate the ability of applicants to obtain useful information.

[A systematic evaluation of application of the web-based cancer database].

PubMed

Huang, Tingting; Liu, Jialin; Li, Yong; Zhang, Rui

2013-10-01

In order to support the theory and practice of the web-based cancer database development in China, we applied a systematic evaluation to assess the development condition of the web-based cancer databases at home and abroad. We performed computer-based retrieval of the Ovid-MEDLINE, Springerlink, EBSCOhost, Wiley Online Library and CNKI databases, the papers of which were published between Jan. 1995 and Dec. 2011, and retrieved the references of these papers by hand. We selected qualified papers according to the pre-established inclusion and exclusion criteria, and carried out information extraction and analysis of the papers. Eventually, searching the online database, we obtained 1244 papers, and checking the reference lists, we found other 19 articles. Thirty-one articles met the inclusion and exclusion criteria and we extracted the proofs and assessed them. Analyzing these evidences showed that the U.S.A. counted for 26% in the first place. Thirty-nine percent of these web-based cancer databases are comprehensive cancer databases. As for single cancer databases, breast cancer and prostatic cancer are on the top, both counting for 10% respectively. Thirty-two percent of the cancer database are associated with cancer gene information. For the technical applications, MySQL and PHP applied most widely, nearly 23% each.

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

PubMed Central

2013-01-01

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

A simple method for serving Web hypermaps with dynamic database drill-down

PubMed Central

Boulos, Maged N Kamel; Roudsari, Abdul V; Carson, Ewart R

2002-01-01

Background HealthCyberMap aims at mapping parts of health information cyberspace in novel ways to deliver a semantically superior user experience. This is achieved through "intelligent" categorisation and interactive hypermedia visualisation of health resources using metadata, clinical codes and GIS. HealthCyberMap is an ArcView 3.1 project. WebView, the Internet extension to ArcView, publishes HealthCyberMap ArcView Views as Web client-side imagemaps. The basic WebView set-up does not support any GIS database connection, and published Web maps become disconnected from the original project. A dedicated Internet map server would be the best way to serve HealthCyberMap database-driven interactive Web maps, but is an expensive and complex solution to acquire, run and maintain. This paper describes HealthCyberMap simple, low-cost method for "patching" WebView to serve hypermaps with dynamic database drill-down functionality on the Web. Results The proposed solution is currently used for publishing HealthCyberMap GIS-generated navigational information maps on the Web while maintaining their links with the underlying resource metadata base. Conclusion The authors believe their map serving approach as adopted in HealthCyberMap has been very successful, especially in cases when only map attribute data change without a corresponding effect on map appearance. It should be also possible to use the same solution to publish other interactive GIS-driven maps on the Web, e.g., maps of real world health problems. PMID:12437788

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

[A web-based integrated clinical database for laryngeal cancer].

PubMed

E, Qimin; Liu, Jialin; Li, Yong; Liang, Chuanyu

2014-08-01

To establish an integrated database for laryngeal cancer, and to provide an information platform for laryngeal cancer in clinical and fundamental researches. This database also meet the needs of clinical and scientific use. Under the guidance of clinical expert, we have constructed a web-based integrated clinical database for laryngeal carcinoma on the basis of clinical data standards, Apache+PHP+MySQL technology, laryngeal cancer specialist characteristics and tumor genetic information. A Web-based integrated clinical database for laryngeal carcinoma had been developed. This database had a user-friendly interface and the data could be entered and queried conveniently. In addition, this system utilized the clinical data standards and exchanged information with existing electronic medical records system to avoid the Information Silo. Furthermore, the forms of database was integrated with laryngeal cancer specialist characteristics and tumor genetic information. The Web-based integrated clinical database for laryngeal carcinoma has comprehensive specialist information, strong expandability, high feasibility of technique and conforms to the clinical characteristics of laryngeal cancer specialties. Using the clinical data standards and structured handling clinical data, the database can be able to meet the needs of scientific research better and facilitate information exchange, and the information collected and input about the tumor sufferers are very informative. In addition, the user can utilize the Internet to realize the convenient, swift visit and manipulation on the database.

Ocean Drilling Program: TAMU Staff Directory

Science.gov Websites

products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main web site Employment Opportunities ODP | Search | Database | Drilling | Publications | Science | Cruise Info | Public

SNPversity: a web-based tool for visualizing diversity

PubMed Central

Schott, David A; Vinnakota, Abhinav G; Portwood, John L; Andorf, Carson M

2018-01-01

Abstract Many stand-alone desktop software suites exist to visualize single nucleotide polymorphism (SNP) diversity, but web-based software that can be easily implemented and used for biological databases is absent. SNPversity was created to answer this need by building an open-source visualization tool that can be implemented on a Unix-like machine and served through a web browser that can be accessible worldwide. SNPversity consists of a HDF5 database back-end for SNPs, a data exchange layer powered by TASSEL libraries that represent data in JSON format, and an interface layer using PHP to visualize SNP information. SNPversity displays data in real-time through a web browser in grids that are color-coded according to a given SNP’s allelic status and mutational state. SNPversity is currently available at MaizeGDB, the maize community’s database, and will be soon available at GrainGenes, the clade-oriented database for Triticeae and Avena species, including wheat, barley, rye, and oat. The code and documentation are uploaded onto github, and they are freely available to the public. We expect that the tool will be highly useful for other biological databases with a similar need to display SNP diversity through their web interfaces. Database URL: https://www.maizegdb.org/snpversity PMID:29688387

Construction of a Linux based chemical and biological information system.

PubMed

Molnár, László; Vágó, István; Fehér, András

2003-01-01

A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

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

The system is developed to collect, process, store and present the information provided by the radio frequency identification (RFID) devices. The system contains three parts, the application software, the database and the web page. The application software manages multiple RFID devices, such as readers and portals, simultaneously. It communicates with the devices through application programming interface (API) provided by the device vendor. The application software converts data collected by the RFID readers and portals to readable information. It is capable of encrypting data using 256 bits advanced encryption standard (AES). The application software has a graphical user interface (GUI). Themore » GUI mimics the configurations of the nucler material storage sites or transport vehicles. The GUI gives the user and system administrator an intuitive way to read the information and/or configure the devices. The application software is capable of sending the information to a remote, dedicated and secured web and database server. Two captured screen samples, one for storage and transport, are attached. The database is constructed to handle a large number of RFID tag readers and portals. A SQL server is employed for this purpose. An XML script is used to update the database once the information is sent from the application software. The design of the web page imitates the design of the application software. The web page retrieves data from the database and presents it in different panels. The user needs a user name combined with a password to access the web page. The web page is capable of sending e-mail and text messages based on preset criteria, such as when alarm thresholds are excceeded. A captured screen sample is attached. The application software is designed to be installed on a local computer. The local computer is directly connected to the RFID devices and can be controlled locally or remotely. There are multiple local computers managing different sites or transport vehicles. The control from remote sites and information transmitted to a central database server is through secured internet. The information stored in the central databaser server is shown on the web page. The users can view the web page on the internet. A dedicated and secured web and database server (https) is used to provide information security.« less

Ionic Liquids Database- (ILThermo)

National Institute of Standards and Technology Data Gateway

SRD 147 NIST Ionic Liquids Database- (ILThermo) (Web, free access)   IUPAC Ionic Liquids Database, ILThermo, is a free web research tool that allows users worldwide to access an up-to-date data collection from the publications on experimental investigations of thermodynamic, and transport properties of ionic liquids as well as binary and ternary mixtures containing ionic liquids.

FirstSearch and NetFirst--Web and Dial-up Access: Plus Ca Change, Plus C'est la Meme Chose?

ERIC Educational Resources Information Center

Koehler, Wallace; Mincey, Danielle

1996-01-01

Compares and evaluates the differences between OCLC's dial-up and World Wide Web FirstSearch access methods and their interfaces with the underlying databases. Also examines NetFirst, OCLC's new Internet catalog, the only Internet tracking database from a "traditional" database service. (Author/PEN)

Ocean Drilling Program: Web Site Access Statistics

Science.gov Websites

and products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main See statistics for JOIDES members. See statistics for Janus database. 1997 October November December accessible only on www-odp.tamu.edu. ** End of ODP, start of IODP. Privacy Policy ODP | Search | Database

XCOM: Photon Cross Sections Database

National Institute of Standards and Technology Data Gateway

SRD 8 XCOM: Photon Cross Sections Database (Web, free access)   A web database is provided which can be used to calculate photon cross sections for scattering, photoelectric absorption and pair production, as well as total attenuation coefficients, for any element, compound or mixture (Z <= 100) at energies from 1 keV to 100 GeV.

Web 2.0 applications in medicine: trends and topics in the literature.

PubMed

Boudry, Christophe

2015-04-01

The World Wide Web has changed research habits, and these changes were further expanded when "Web 2.0" became popular in 2005. Bibliometrics is a helpful tool used for describing patterns of publication, for interpreting progression over time, and the geographical distribution of research in a given field. Few studies employing bibliometrics, however, have been carried out on the correlative nature of scientific literature and Web 2.0. The aim of this bibliometric analysis was to provide an overview of Web 2.0 implications in the biomedical literature. The objectives were to assess the growth rate of literature, key journals, authors, and country contributions, and to evaluate whether the various Web 2.0 applications were expressed within this biomedical literature, and if so, how. A specific query with keywords chosen to be representative of Web 2.0 applications was built for the PubMed database. Articles related to Web 2.0 were downloaded in Extensible Markup Language (XML) and were processed through developed hypertext preprocessor (PHP) scripts, then imported to Microsoft Excel 2010 for data processing. A total of 1347 articles were included in this study. The number of articles related to Web 2.0 has been increasing from 2002 to 2012 (average annual growth rate was 106.3% with a maximum of 333% in 2005). The United States was by far the predominant country for authors, with 514 articles (54.0%; 514/952). The second and third most productive countries were the United Kingdom and Australia, with 87 (9.1%; 87/952) and 44 articles (4.6%; 44/952), respectively. Distribution of number of articles per author showed that the core population of researchers working on Web 2.0 in the medical field could be estimated at approximately 75. In total, 614 journals were identified during this analysis. Using Bradford's law, 27 core journals were identified, among which three (Studies in Health Technology and Informatics, Journal of Medical Internet Research, and Nucleic Acids Research) produced more than 35 articles related to Web 2.0 over the period studied. A total of 274 words in the field of Web 2.0 were found after manual sorting of the 15,878 words appearing in title and abstract fields for articles. Word frequency analysis reveals "blog" as the most recurrent, followed by "wiki", "Web 2.0", "social media", "Facebook", "social networks", "blogger", "cloud computing", "Twitter", and "blogging". All categories of Web 2.0 applications were found, indicating the successful integration of Web 2.0 into the biomedical field. This study shows that the biomedical community is engaged in the use of Web 2.0 and confirms its high level of interest in these tools. Therefore, changes in the ways researchers use information seem to be far from over.

Transition to a Unified System: Using Perl To Drive Library Databases and Enhance Web Site Functionality.

ERIC Educational Resources Information Center

Fagan, Judy Condit

2001-01-01

Discusses the need for libraries to routinely redesign their Web sites, and presents a case study that describes how a Perl-driven database at Southern Illinois University's library improved Web site organization and patron access, simplified revisions, and allowed staff unfamiliar with HTML to update content. (Contains 56 references.) (Author/LRW)

Effects of auditory cues on gait initiation and turning in patients with Parkinson's disease.

PubMed

Gómez-González, J; Martín-Casas, P; Cano-de-la-Cuerda, R

2016-12-08

To review the available scientific evidence about the effectiveness of auditory cues during gait initiation and turning in patients with Parkinson's disease. We conducted a literature search in the following databases: Brain, PubMed, Medline, CINAHL, Scopus, Science Direct, Web of Science, Cochrane Database of Systematic Reviews, Cochrane Library Plus, CENTRAL, Trip Database, PEDro, DARE, OTseeker, and Google Scholar. We included all studies published between 2007 and 2016 and evaluating the influence of auditory cues on independent gait initiation and turning in patients with Parkinson's disease. The methodological quality of the studies was assessed with the Jadad scale. We included 13 studies, all of which had a low methodological quality (Jadad scale score≤2). In these studies, high-intensity, high-frequency auditory cues had a positive impact on gait initiation and turning. More specifically, they 1) improved spatiotemporal and kinematic parameters; 2) decreased freezing, turning duration, and falls; and 3) increased gait initiation speed, muscle activation, and gait speed and cadence in patients with Parkinson's disease. We need studies of better methodological quality to establish the Parkinson's disease stage in which auditory cues are most beneficial, as well as to determine the most effective type and frequency of the auditory cue during gait initiation and turning in patients with Parkinson's disease. Copyright © 2016 Sociedad Española de Neurología. Publicado por Elsevier España, S.L.U. All rights reserved.

MicroRNAs for osteosarcoma in the mouse: a meta-analysis

PubMed Central

Chang, Junli; Yao, Min; Li, Yimian; Zhao, Dongfeng; Hu, Shaopu; Cui, Xuejun; Liu, Gang; Shi, Qi; Wang, Yongjun; Yang, Yanping

2016-01-01

Osteosarcoma (OS) is the most common primary malignant bone carcinoma with high morbidity that happens mainly in children and young adults. As the key components of gene-regulatory networks, microRNAs (miRNAs) control many critical pathophysiological processes, including initiation and progression of cancers. The objective of this study is to summarize and evaluate the potential of miRNAs as targets for prevention and treatment of OS in mouse models, and to explore the methodological quality of current studies. We searched PubMed, Web of Science, Embase, Wan Fang Database, VIP Database, China Knowledge Resource Integrated Database, and Chinese BioMedical since their beginning date to 10 May 2016. Two reviewers separately screened the controlled studies, which estimate the effects of miRNAs on osteosarcoma in mice. A pair-wise analysis was performed. Thirty six studies with enough randomization were selected and included in the meta-analysis. We found that blocking oncogenic or restoring decreased miRNAs in cancer cells could significantly suppress the progression of OS in vivo, as assessed by tumor volume and tumor weight. This meta-analysis suggests that miRNAs are potential therapeutic targets for OS and correction of the altered expression of miRNAs significantly suppresses the progression of OS in mouse models, however, the overall methodological quality of studies included here was low, and more animal studies with the rigourous design must be carried out before a miRNA-based treatment could be translated from animal studies to clinical trials. PMID:27852052

Identification and management of elder physical abuse in the routine of dentistry - a systematic review.

PubMed

Silva, Luanderson O; Souza-Silva, Bianca N; de Alcântara Rodrigues, José Lucas; Rigo, Lilian; Cericato, Graziela O; Franco, Ademir; Paranhos, Luiz R

2017-03-01

To perform a systematic search in the literature in order to verify whether the dentists are able to identify and manage cases elder physical abuse. Dentists may play an important legal role contributing to the management of abused patients through the identification of injuries in their face, head and neck. The present systematic review was performed following the PRISMA Statement and was registered in the PROSPERO database. A search was conducted in the following electronic databases: PubMed, LILACS, SciELO, Embase, Web of Science, OpenGrey, Google Scholar. Specifically, the last two databases were used to search the 'grey literature'. The research question was based on the PVO strategy for systematic exploratory review. Two examiners determined the eligibility criteria for selecting the studies and performed all the research steps. The initial search resulted in 842 studies, from which eight were considered eligible. Six studies used questionnaires to assess the perception, knowledge and attitudes of dentists towards the identification and management of cases of elder abuse, while two studies assessed this information through personal interviews. Two studies were rated as high quality, while six studies reached moderate quality. Male and female dentists were assessed separately in six studies. Only three studies specified the aggressor. The dentists revealed insufficient knowledge on elder abuse. Most of the dentists are not able to identify and manage these cases in the clinical routine. © 2016 John Wiley & Sons A/S and The Gerodontology Association. Published by John Wiley & Sons Ltd.

Guidelines on the irritable bowel syndrome: mechanisms and practical management

PubMed Central

Spiller, R; Aziz, Q; Creed, F; Emmanuel, A; Houghton, L; Hungin, P; Jones, R; Kumar, D; Rubin, G; Trudgill, N; Whorwell, P

2007-01-01

Background IBS affects 5–11% of the population of most countries. Prevalence peaks in the third and fourth decades, with a female predominance. Aim To provide a guide for the assessment and management of adult patients with irritable bowel syndrome. Methods Members of the Clinical Services Committee of The British Society of Gastroenterology were allocated particular areas to produce review documents. Literature searching included systematic searches using electronic databases such as Pubmed, EMBASE, MEDLINE, Web of Science, and Cochrane databases and extensive personal reference databases. Results Patients can usefully be classified by predominant bowel habit. Few investigations are needed except when diarrhoea is a prominent feature. Alarm features may warrant further investigation. Adverse psychological features and somatisation are often present. Ascertaining the patients' concerns and explaining symptoms in simple terms improves outcome. IBS is a heterogeneous condition with a range of treatments, each of which benefits a small proportion of patients. Treatment of associated anxiety and depression often improves bowel and other symptoms. Randomised placebo controlled trials show benefit as follows: cognitive behavioural therapy and psychodynamic interpersonal therapy improve coping; hypnotherapy benefits global symptoms in otherwise refractory patients; antispasmodics and tricyclic antidepressants improve pain; ispaghula improves pain and bowel habit; 5‐HT3 antagonists improve global symptoms, diarrhoea, and pain but may rarely cause unexplained colitis; 5‐HT4 agonists improve global symptoms, constipation, and bloating; selective serotonin reuptake inhibitors improve global symptoms. Conclusions Better ways of identifying which patients will respond to specific treatments are urgently needed. PMID:17488783

Effect of various Danshen injections on patients with coronary heart disease after percutaneous coronary intervention: A protocol for a systematic review and network meta-analysis.

PubMed

Zhu, Zehao; Wang, Yuanping; Liao, Weilin; Li, Huimin; Wang, Dawei

2018-06-01

Patients with coronary heart disease (CHD) who undergo percutaneous coronary intervention (PCI) have a certain risk of vascular complications, including coronary restenosis and thrombosis. Many recent randomized controlled trials have reported that Danshen injection (DSI) combined with conventional Western medicine can significantly reduce the occurrence of major cardiovascular adverse events in patients with CHD after PCI. However, there are many types of DSIs, and no study has yet compared each type. Therefore, we propose a study protocol for the systematic evaluation of the efficacy of various DSIs in the treatment of CHD after PCI. We will search the following electronic databases for randomized controlled trials evaluating the effect of DSI in patients with CHD after PCI: PubMed, Embase, Web of Science, Cochrane Library, Scopus, Ovid Evidence-Based Medicine Reviews, China National Knowledge Infrastructure, and Chinese Biomedicine Literature Database. Each database will be searched from inception to April 2018. The entire process will include study selection, data extraction, risk of bias assessment, pairwise meta-analyses, and network meta-analyses. This proposed study will compare the efficacy of different DSIs in the treatment of patients with CHD after PCI. The outcomes will include major cardiovascular adverse events and left ventricular ejection fraction. This proposed systematic review will evaluate the different advantages of various types of DSIs in the treatment of patients with CHD after PCI. PROSPERO (registration number: CRD42018092705).

The impact of mHealth interventions on health systems: a systematic review protocol.

PubMed

Fortuin, Jill; Salie, Faatiema; Abdullahi, Leila H; Douglas, Tania S

2016-11-25

Mobile health (mHealth) has been described as a health enabling tool that impacts positively on the health system in terms of improved access, quality and cost of health care. The proposed systematic review will examine the impact of mHealth on health systems by assessing access, quality and cost of health care as indicators. The systematic review will include literature from various sources including published and unpublished/grey literature. The databases to be searched include: PubMed, Cochrane Library, Google Scholar, NHS Health Technology Assessment Database and Web of Science. The reference lists of studies will be screened and conference proceedings searched for additional eligible reports. Literature to be included will have mHealth as the primary intervention. Two authors will independently screen the search output, select studies and extract data; discrepancies will be resolved by consensus and discussion with the assistance of the third author. The systematic review will inform policy makers, investors, health professionals, technologists and engineers about the impact of mHealth in strengthening the health system. In particular, it will focus on three metrics to determine whether mHealth strengthens the health system, namely quality of, access to and cost of health care services. Systematic review registration: PROSPERO CRD42015026070.

Implants in disabled patients: A review and update

PubMed Central

Romero-Pérez, María J.; Mang-de la Rosa, María R.; López-Jimenez, Julián; Fernández-Feijoo, Javier

2014-01-01

The range of indications for dental implants has broadened enormously owing to their predictability and the improvement of patient satisfaction in terms of stability, comfort, aesthetics and functionality. The aim of this article is to review those indications in patients with mental or physical disabilities as the difficulty to cope with oral hygiene often leads to teeth extraction, adding edentulousness to the impairments already present. Following that goal, available literature in Pubmed database, Scopus, Web of Knowledge and The Cochrane Library database about dental implants placement in these patients has been reviewed, assessing the variables of each study: number of patients, sex, average age, oral hygiene, parafunctional habits, impairment, bone quality, protocol of implant surgery, necessity of deep intravenous sedation or general anesthesia, follow-up period and number of failures. The comparison with studies involving other patient populations without mental or physical impediments did not show statistically significant differences in terms of the failure rate recorded. Although there is not much literature available, the results of this review seem to suggest that osseointegrated oral implants could be a therapeutic option in patients who suffer from any physical or psychological impairment. The success of an oral rehabilitation depends mainly on an adequate selection of the patients. Key words:Implants, disabled, sedation. PMID:24608221

Contribution of food prices and diet cost to socioeconomic disparities in diet quality and health: a systematic review and analysis

PubMed Central

Drewnowski, Adam

2015-01-01

Context: It is well established in the literature that healthier diets cost more than unhealthy diets. Objective: The aim of this review was to examine the contribution of food prices and diet cost to socioeconomic inequalities in diet quality. Data Sources: A systematic literature search of the PubMed, Google Scholar, and Web of Science databases was performed. Study Selection: Publications linking food prices, dietary quality, and socioeconomic status were selected. Data Extraction: Where possible, review conclusions were illustrated using a French national database of commonly consumed foods and their mean retail prices. Data Synthesis: Foods of lower nutritional value and lower-quality diets generally cost less per calorie and tended to be selected by groups of lower socioeconomic status. A number of nutrient-dense foods were available at low cost but were not always palatable or culturally acceptable to the low-income consumer. Acceptable healthier diets were uniformly associated with higher costs. Food budgets in poverty were insufficient to ensure optimum diets. Conclusions: Socioeconomic disparities in diet quality may be explained by the higher cost of healthy diets. Identifying food patterns that are nutrient rich, affordable, and appealing should be a priority to fight social inequalities in nutrition and health. PMID:26307238

Prevalence of Food Insecurity in Iran: A Systematic Review and Meta-analysis.

PubMed

Behzadifar, Meysam; Behzadifar, Masoud; Abdi, Shadi; Malekzadeh, Reza; Arab Salmani, Masoumeh; Ghoreishinia, Gholamreza; Falahi, Ebrahim; Mirzaei, Masoud; Shams Biranvand, Nabi; Sayehmiri, Kourosh

2016-04-01

Food security is one of the main factors of individual and social health. It is of such importance that the World Bank and Food and Agriculture Organization (FAO) announced it as one of the Millennium Development Goals. This study aimed to report the prevalence of food insecurity in Iran. We searched English databases including; Scopus, Ovid, Web of Science, PubMed and Google Scholar and also Iranian databases; SID, Magiran and IranMedex for words Iran, food insecurity, and prevalence up to August 2015. The pooled food insecurity prevalence was calculated using Der-Simonian test. All analyses were performed using random effects model with 95% CI. We assessed heterogeneity of the studies using sub-group and meta-regression analyses. A total of 31 studies were included. The prevalence of food insecurity was 49% among households (95% CI: %40-%59), 67% in children (95% CI: %63-%70), 61% in mothers (95% CI: %35-%88), 49% in adolescents (95% CI: %33-%66) and 65% in the elderly (95% CI: %44-%86). The prevalence of food insecurity is high in Iran. Fiscal policies should promote the nutritional knowledge of household members and also support the households to meet their nutritional needs. This plan should give priority to mid and low socioeconomic groups.

Letrozole versus clomiphene citrate in polycystic ovary syndrome: a meta-analysis of randomized controlled trials.

PubMed

Hu, Shifu; Yu, Qiong; Wang, Yingying; Wang, Mei; Xia, Wei; Zhu, Changhong

2018-05-01

Polycystic ovary syndrome (PCOS) is a common endocrine disturbance affecting women in the reproductive age group. The present study aimed to compare the effects of letrozole (LE) and clomiphene citrate (CC) for ovulation induction in women with PCOS. The PUBMED, Web of Science, and EMBASE databases were screened systematically for randomized controlled trials (RCTs) published from database inception to July 2017. Eleven RCTs involving 2255 patients were included, and data were independently extracted and analyzed using 95% risk ratios (RRs) and confidence intervals (CIs) based on a random- or fixed-effect model (as appropriate). Meta-analyses of nine RCTs comparing LE and CC ovulation induction, followed by timed intercourse, indicated that the former significantly increased the ovulation rate (RR = 1.18; 95% CI 1.03-1.36, P = 0.01), pregnancy rate (RR = 1.34; 95% CI 1.09-1.64, P = 0.006), and live birth rate (RR = 1.55; 95% CI 1.28-1.88, P < 0.00001). However, LE and CC did not differ significantly in terms of the multiple pregnancy and abortion rates. Furthermore, LE for ovulation induction significantly improved the pregnancy rate after IUI. LE is superior to CC for ovulation induction in patients with PCOS.

Contribution of food prices and diet cost to socioeconomic disparities in diet quality and health: a systematic review and analysis.

PubMed

Darmon, Nicole; Drewnowski, Adam

2015-10-01

It is well established in the literature that healthier diets cost more than unhealthy diets. The aim of this review was to examine the contribution of food prices and diet cost to socioeconomic inequalities in diet quality. A systematic literature search of the PubMed, Google Scholar, and Web of Science databases was performed. Publications linking food prices, dietary quality, and socioeconomic status were selected. Where possible, review conclusions were illustrated using a French national database of commonly consumed foods and their mean retail prices. Foods of lower nutritional value and lower-quality diets generally cost less per calorie and tended to be selected by groups of lower socioeconomic status. A number of nutrient-dense foods were available at low cost but were not always palatable or culturally acceptable to the low-income consumer. Acceptable healthier diets were uniformly associated with higher costs. Food budgets in poverty were insufficient to ensure optimum diets. Socioeconomic disparities in diet quality may be explained by the higher cost of healthy diets. Identifying food patterns that are nutrient rich, affordable, and appealing should be a priority to fight social inequalities in nutrition and health. © The Author(s) 2015. Published by Oxford University Press on behalf of the International Life Sciences Institute.

Effect of Virtual Reality on Postural and Balance Control in Patients with Stroke: A Systematic Literature Review.

PubMed

Chen, Ling; Lo, Wai Leung Ambrose; Mao, Yu Rong; Ding, Ming Hui; Lin, Qiang; Li, Hai; Zhao, Jiang Li; Xu, Zhi Qin; Bian, Rui Hao; Huang, Dong Feng

2016-01-01

Objective . To critically evaluate the studies that were conducted over the past 10 years and to assess the impact of virtual reality on static and dynamic balance control in the stroke population. Method . A systematic review of randomized controlled trials published between January 2006 and December 2015 was conducted. Databases searched were PubMed, Scopus, and Web of Science. Studies must have involved adult patients with stroke during acute, subacute, or chronic phase. All included studies must have assessed the impact of virtual reality programme on either static or dynamic balance ability and compared it with a control group. The Physiotherapy Evidence Database (PEDro) scale was used to assess the methodological quality of the included studies. Results . Nine studies were included in this systematic review. The PEDro scores ranged from 4 to 9 points. All studies, except one, showed significant improvement in static or dynamic balance outcomes group. Conclusions . This review provided moderate evidence to support the fact that virtual reality training is an effective adjunct to standard rehabilitation programme to improve balance for patients with chronic stroke. The effect of VR training in balance recovery is less clear in patients with acute or subacute stroke. Further research is required to investigate the optimum training intensity and frequency to achieve the desired outcome.

The Effect of Music on the Spirituality of Patients: A Systematic Review.

PubMed

Alvarenga, Willyane de Andrade; Leite, Ana Carolina Andrade Biaggi; Oliveira, Marina Sanches; Nascimento, Lucila Castanheira; Silva-Rodrigues, Fernanda Machado; Nunes, Michelle Darezzo Rodrigues; Carvalho, Emilia Campos de

2018-06-01

Although some studies have suggested that music can positively affect physical and psychological variables, few have evaluated its effects on spirituality. This study aimed to evaluate the effects of musical interventions on the spirituality of patients, regardless of diagnoses. This was a systematic literature review that followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) recommendations conducted through a relevant search of terms in six databases (PubMed, Web of Science, CINAHL, PsycINFO, ScienceDirect, and LILACS) without temporal delimitation. Experimental or quasi-experimental studies were included, involving participants regardless of diagnoses, to assess the effect of music on spirituality, either through musical intervention as music medicine or through music therapy. The methodological quality of included studies was evaluated using the Physiotherapy Evidence Database scale. A total of 147 studies were identified; 7 met the inclusion criteria. Five studies were randomized controlled trials involving six music therapists leading the musical intervention with the active participation of patients. The interventions used were heterogeneous. Three studies were associated with improved spirituality after the intervention. Four studies used measurements to evaluate spiritual well-being. This review did not allow ascertaining the positive impact of music intervention on spirituality in patients, which motivates further research.

['Clinical auditing', a novel tool for quality assessment in surgical oncology].

PubMed

van Leersum, Nicoline J; Kolfschoten, Nikki E; Klinkenbijl, Jean H G; Tollenaar, Rob A E M; Wouters, Michel W J M

2011-01-01

To determine whether systematic audit and feedback of information about the process and outcomes improve the quality of surgical care. Systematic literature review. Embase, PubMed, and Web of Science databases were searched for publications on 'quality assessment' and 'surgery'. The references of the publications found were examined as well. Publications were included in the review if the effect of auditing on the quality of surgical care had been investigated. In the databases 2415 publications were found. After selection, 28 publications describing the effect of auditing, whether or not combined with a quality improvement project, on guideline adherence or indications of outcomes of care were included. In 21 studies, a statistically significant positive effect of auditing was reported. In 5 studies a positive effect was found, but this was either not significant or statistical significance was not determined. In 2 studies no effect was observed. 5 studies compared the combination of auditing with a quality improvement project with auditing alone; 4 of these reported an additional effect of the quality improvement project. Audit and feedback of quality information seem to have a positive effect on the quality of surgical care. The use of quality information from audits for the purpose of a quality improvement project can enhance the positive effect of the audit.

Prevalence of pterygium in Iran: a systematic review and meta-analysis study

PubMed Central

Yasemi, Masoud; Bamdad, Shahram; Sarokhani, Diana; Sarokhani, Mandana; Sayemiri, Kourosh

2017-01-01

Background and aim Pterygium is one of the most prevalent pathologies involving the cornea, which can lead to various vision signs and even reduction in eyesight. No accurate estimate has been reported about the prevalence of pterygium in Iran. Hence, this study aimed to determine the pterygium prevalence in Iran by meta-analysis method. Methods Searching for data of the last eleven years (from 2004 to 2015) was conducted using the keywords of pterygium, eye, and Iran in International and domestic indexing services and databases including Iranmedex, Scientific Information Database (SID), Magiran, Irandoc, Medlib, IranPsych, Science Direct, Web of Science (Thomson Reuters), PubMed, and Scopus. The data were analyzed using the meta-analysis method (the random effects model). The disharmony of the studies was investigated using the I2 index. The data were analyzed by STATA Ver.11 software. Results In 5 studies conducted in Iran, with a sample size of 10,838 people between 2004 and 2015, the extent of the prevalence was estimated to be 11% (95% CI: 3 to 18%). Also, the prevalence of pterygium in women and men was 18% and 13%, respectively. Conclusion According to the published reports from Iran and its comparison with other points in the world, the prevalence of pterygium in Iran is high, especially among women. PMID:29560142

Positive psychology interventions in breast cancer. A systematic review.

PubMed

Casellas-Grau, Anna; Font, Antoni; Vives, Jaume

2014-01-01

Positive psychology is an emerging area of empirical study, not only in clinical, but also in health psychology. The present systematic review aims to synthesize the evidence about the positive psychology interventions utilized in breast cancer. Relevant studies were identified via Pubmed, PsycINFO, Web of Science, Scopus, Cochrane, CINAHL, Wiley Online Library, TDX, and DIALNET databases (up to April 2013). Only those papers focused on interventions related to positive psychology and carried out on breast cancer patients were included. Of the 7266 articles found through databases, 16 studies were finally included in this review. Five groups of therapies were found: mindfulness-based approaches, expression of positive emotions, spiritual interventions, hope therapy, and meaning-making interventions. These specific interventions promoted positive changes in breast cancer participants, such as enhanced quality of life, well-being, hope, benefit finding, or optimism. However, the disparity of the interventions and some methodological issues limit the outcomes. Some studies provided relevant evidence about the clear development of positive aspects from the breast cancer experience. Positive interventions applied to patients and survivors of breast cancer were found to be able to promote positive aspects. A global consensus of a positive therapies classification is needed to take one more step in structuring positive psychology. Copyright © 2013 John Wiley & Sons, Ltd.

Critical appraisal of systematic reviews on the effect of a history of periodontitis on dental implant loss.

PubMed

Faggion, Clovis Mariano; Giannakopoulos, Nikolaos Nikitas

2013-05-01

To perform a systematic critical appraisal of the methodological quality of systematic reviews on the effect of a history of periodontitis on dental implant loss. PubMed, the Cochrane database for systematic reviews, the DARE, Biosis Preview, CINAHL, Web of Science, and LILACS electronic databases were searched on 16th June 2012, independently and in duplicate, for systematic reviews and meta-analyses related to dental implants for patients with and without a history of periodontitis. Manual searching of the reference lists of included papers was also conducted. The methodological quality of these systematic reviews was assessed by use of the AMSTAR and R-AMSTAR checklists. Before quality assessment was initiated, the reviewers were calibrated until they achieved excellent agreement. Sixty-eight papers were initially retrieved. Of these, nine systematic reviews and three meta-analyses were included. Some domains, for example, "characteristics of the included studies" were satisfied in both checklists. In contrast, domains such as "comprehensive literature search" and "assessment of likelihood of publication bias" were rarely met. Much methodological variability was encountered in the selected reviews. To furnish readers with a more comprehensive assessment of the evidence, authors should observe higher standards when conducting and reporting their reviews. © 2013 John Wiley & Sons A/S.

The Importance of Species Name Synonyms in Literature Searches.

PubMed

Guala, Gerald F

2016-01-01

The synonyms of biological species names are shown to be an important component in comprehensive searches of electronic scientific literature databases but they are not well leveraged within the major literature databases examined. For accepted or valid species names in the Integrated Taxonomic Information System (ITIS) which have synonyms in the system, and which are found in citations within PLoS, PMC, PubMed or Scopus, both the percentage of species for which citations will not be found if synonyms are not used, and the percentage increase in number of citations found by including synonyms are very often substantial. However, there is no correlation between the number of synonyms per species and the magnitude of the effect. Further, the number of citations found does not generally increase proportionally to the number of synonyms available. Users looking for literature on specific species across all of the resources investigated here are often missing large numbers of citations if they are not manually augmenting their searches with synonyms. Of course, missing citations can have serious consequences by effectively hiding critical information. Literature searches should include synonym relationships and a new web service in ITIS, with examples of how to apply it to this issue, was developed as a result of this study, and is here announced, to aide in this.

The importance of species name synonyms in literature searches

USGS Publications Warehouse

Guala, Gerald

2016-01-01

The synonyms of biological species names are shown to be an important component in comprehensive searches of electronic scientific literature databases but they are not well leveraged within the major literature databases examined. For accepted or valid species names in the Integrated Taxonomic Information System (ITIS) which have synonyms in the system, and which are found in citations within PLoS, PMC, PubMed or Scopus, both the percentage of species for which citations will not be found if synonyms are not used, and the percentage increase in number of citations found by including synonyms are very often substantial. However, there is no correlation between the number of synonyms per species and the magnitude of the effect. Further, the number of citations found does not generally increase proportionally to the number of synonyms available. Users looking for literature on specific species across all of the resources investigated here are often missing large numbers of citations if they are not manually augmenting their searches with synonyms. Of course, missing citations can have serious consequences by effectively hiding critical information. Literature searches should include synonym relationships and a new web service in ITIS, with examples of how to apply it to this issue, was developed as a result of this study, and is here announced, to aide in this.

Antepartum Care of Women Who Are Obese During Pregnancy: Systematic Review of the Current Evidence.

PubMed

Carlson, Nicole S; Leslie, Sharon Lynn; Dunn, Alexis

2018-05-14

Nearly 40% of US women of childbearing age are obese. Obesity during pregnancy is associated with multiple risks for both the woman and fetus, yet clinicians often feel unprepared to provide optimal antepartum care for this group of women. We collected and reviewed current evidence concerning antepartum care of women who are obese during pregnancy. We conducted a systematic review using PRISMA guidelines. Current evidence relating to the pregnancy care of women with a prepregnancy body mass index of 30kg/m 2 or higher was identified using MEDLINE databases via PubMed, Embase, and Web of Science Core Collection between January 2012 and February 2018. A total of 354 records were located after database searches, of which 63 met inclusion criteria. Topic areas for of included studies were: pregnancy risk and outcomes related to obesity, communication between women and health care providers, gestational weight gain and activity/diet, diabetic disorders, hypertensive disorders, obstructive sleep apnea, mental health, pregnancy imaging and measurement, late antepartum care, and preparation for labor and birth. Midwives and other health care providers can provide better antepartum care to women who are obese during pregnancy by incorporating evidence from the most current clinical investigations. © 2018 by the American College of Nurse-Midwives.

The musculoskeletal consequences of breast reconstruction using the latissimus dorsi muscle for women following mastectomy for breast cancer: A critical review.

PubMed

Blackburn, N E; Mc Veigh, J G; Mc Caughan, E; Wilson, I M

2018-03-01

Breast reconstruction using the latissimus dorsi (LD) flap following mastectomy is an important management option in breast cancer. However, one common, but often ignored, complication following LD flap is shoulder dysfunction. The aim of this critical review was to comprehensively assess the musculoskeletal impact of LD breast reconstruction and evaluate the functional outcome following surgery. Five electronic databases were searched including; Medline, Embase, CINAHL Plus (Cumulative Index to Nursing and Allied Health), PubMed and Web of Science. Databases were searched from 2006 to 2016, and only full text, English language articles were included. Twenty-two observational studies and two surveys were reviewed with sample sizes ranging from six to 206 participants. The majority of studies had small sample sizes and were retrospective in nature. Nevertheless, there is evidence to suggest that there is some degree of weakness and reduced mobility at the shoulder following LD muscle transfer. The literature demonstrates that there is considerable morbidity in the immediate post-operative period with functional recovery varying between studies. The majority of work tends to be limited and often gives conflicting results; therefore, further investigation is required in order to determine underlying factors that contribute to a reduction in function and activities of daily living. © 2017 John Wiley & Sons Ltd.

Lidocaine dose-response effect on postoperative cognitive deficit: meta-analysis and meta-regression.

PubMed

Habibi, Mohammad Reza; Habibi, Valiollah; Habibi, Ali; Soleimani, Aria

2018-04-01

The true influence of the perioperative intravenous lidocaine on the development of postoperative cognitive deficit (POCD) in coronary artery bypass grafting (CABG) remains controversial. The principal aim is to undertake a meta-regression to determine whether moderator variables mediate the relationship between lidocaine and POCD. Areas covered: We searched the Web of Science, PubMed database, Scopus and the Cochrane Library database (up to June 2017) and systematically reviewed a list of retrieved articles. Our final review includes only randomized controlled trials (RCTs) that compared infusion of lidocaine and placebo during cardiopulmonary bypass (CPB). Mantel-Haenszel risk ratio (MH RR) and corresponding 95% confidence interval (CI) was used to report the overall effect and meta-regression analysis. A total of 688 patients in five RCTs were included. POCD occurred in 34% of all cases. Perioperative lidocaine reduces POCD (MH RR 0.702 (95% CI: 0.541-0.909). Younger age, male gender, longer CPB and higher concentration of lidocaine significantly mediate the relationship between lidocaine and POCD in favour of the neuroprotective effect of lidocaine. Expert commentary: The neuroprotective effect of lidocaine on POCD is consistent in spite of longer CPB time. A higher concentration of lidocaine strengthened the neuroprotective effect of lidocaine.

ITS-90 Thermocouple Database

National Institute of Standards and Technology Data Gateway

SRD 60 NIST ITS-90 Thermocouple Database (Web, free access)   Web version of Standard Reference Database 60 and NIST Monograph 175. The database gives temperature -- electromotive force (emf) reference functions and tables for the letter-designated thermocouple types B, E, J, K, N, R, S and T. These reference functions have been adopted as standards by the American Society for Testing and Materials (ASTM) and the International Electrotechnical Commission (IEC).

THGS: a web-based database of Transmembrane Helices in Genome Sequences

PubMed Central

Fernando, S. A.; Selvarani, P.; Das, Soma; Kumar, Ch. Kiran; Mondal, Sukanta; Ramakumar, S.; Sekar, K.

2004-01-01

Transmembrane Helices in Genome Sequences (THGS) is an interactive web-based database, developed to search the transmembrane helices in the user-interested gene sequences available in the Genome Database (GDB). The proposed database has provision to search sequence motifs in transmembrane and globular proteins. In addition, the motif can be searched in the other sequence databases (Swiss-Prot and PIR) or in the macromolecular structure database, Protein Data Bank (PDB). Further, the 3D structure of the corresponding queried motif, if it is available in the solved protein structures deposited in the Protein Data Bank, can also be visualized using the widely used graphics package RASMOL. All the sequence databases used in the present work are updated frequently and hence the results produced are up to date. The database THGS is freely available via the world wide web and can be accessed at http://pranag.physics.iisc.ernet.in/thgs/ or http://144.16.71.10/thgs/. PMID:14681375

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.

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.

A Summary of New Findings on the Biological Effects of Selenium in Selected Animal Species—A Critical Review

PubMed Central

Hosnedlova, Bozena; Kepinska, Marta; Skalickova, Sylvie; Fernandez, Carlos; Ruttkay-Nedecky, Branislav; Malevu, Thembinkosi Donald; Sochor, Jiri; Baron, Mojmir; Melcova, Magdalena; Zidkova, Jarmila; Kizek, Rene

2017-01-01

Selenium is an essential trace element important for many physiological processes, especially for the functions of immune and reproductive systems, metabolism of thyroid hormones, as well as antioxidant defense. Selenium deficiency is usually manifested by an increased incidence of retention of placenta, metritis, mastitis, aborts, lowering fertility and increased susceptibility to infections. In calves, lambs and kids, the selenium deficiency demonstrates by WMD (white muscle disease), in foals and donkey foals, it is associated with incidence of WMD and yellow fat disease, and in pigs it causes VESD (vitamin E/selenium deficiency) syndrome. The prevention of these health disorders can be achieved by an adequate selenium supplementation to the diet. The review summarizes the survey of knowledge on selenium, its biological significance in the organism, the impact of its deficiency in mammalian livestock (comparison of ruminants vs. non-ruminants, herbivore vs. omnivore) and possibilities of its peroral administration. The databases employed were as follows: Web of Science, PubMed, MEDLINE and Google Scholar. PMID:29065468

The Distinction of Amyloid-β Protein Precursor (AβPP) Ratio in Platelet Between Alzheimer's Disease Patients and Controls: A Systematic Review and Meta-Analysis.

PubMed

Shi, Yachen; Gu, Lihua; Alsharif, Abdul Azeez; Zhang, Zhijun

2017-01-01

To systematically assess the clinical significance of platelet amyloid-β protein precursor (AβPP) ratio between Alzheimer's disease (AD) patients and controls. 14 articles were selected in this analysis by search of databases including PubMed and Web of Science up to December 2016. Random effects models were used to calculate the standardized mean difference (SMD). Subgroup analyses were used to detect the cause of heterogeneity. The result showed a significant drop in platelet AβPP ratio in AD patients compared to controls [SMD: -1.871; 95% CI: (-2.33, -1.41); p < 0.001; I2 = 88.0% ]. Subgroup analysis revealed races or the quality of studies may be the cause of high heterogeneity. This meta-analysis concluded that there is a close association between platelet AβPP ratio and AD. It is necessary to design a sizable sample study to further support that platelet AβPP ratio can be a biomarker of AD.

Critical factors for the success of orthodontic mini-implants: a systematic review.

PubMed

Chen, Yan; Kyung, Hee Moon; Zhao, Wen Ting; Yu, Won Jae

2009-03-01

This systematic review was undertaken to discuss factors that affect mini-implants as direct and indirect orthodontic anchorage. The data were collected from electronic databases (Medline [Entrez PubMed], Embase, Web of Science, Cochrane Library, and All Evidence Based Medicine Reviews). Randomized clinical trials, prospective and retrospective clinical studies, and clinical trials concerning the properties, affective factors, and requirements of mini-implants were considered. The titles and abstracts that appeared to fulfill the initial selection criteria were collected by consensus, and the original articles were retrieved and evaluated with a methodologic checklist. A hand search of key orthodontic journals was performed to identify recent unindexed literature. The search strategy resulted in 596 articles. By screening titles and abstracts, 126 articles were identified. After the exclusion criteria were applied, 16 articles remained. The analyzed results of the literature were divided into 2 topics: placement-related and loading-related factors. Mini-implants are effective as anchorage, and their success depends on proper initial mechanical stability and loading quality and quantity.

Nonmotor Symptoms in Parkinson Disease: A Descriptive Review on Social Cognition Ability.

PubMed

Palmeri, Rosanna; Lo Buono, Viviana; Corallo, Francesco; Foti, Maria; Di Lorenzo, Giuseppe; Bramanti, Placido; Marino, Silvia

2017-03-01

Parkinson disease (PD) is a neurodegenerative disorder characterized by motor and nonmotor symptoms. Nonmotor symptoms include cognitive deficits and impairment in emotions recognition ability associated with loss of dopaminergic neurons in the substantia nigra and with alteration in frontostriatal circuits. In this review, we analyzed the studies on social cognition ability in patients with PD. We searched on PubMed and Web of Science databases and screening references of included studied and review articles for additional citations. From initial 260 articles, only 18 met search criteria. A total of 496 patients were compared with 514 health controls, through 16 different tests that assessed some subcomponents of social cognition, such as theory of mind, decision-making, and emotional face recognition. Studies on cognitive function in patients with PD have focused on executive function. Patients with PD showed impairment in social cognition from the earliest stages of disease. This ability seems to not be significantly associated with other cognitive functions.

An integrative review of the efficacy of motivational interviewing in HIV management.

PubMed

Dillard, Phillip K; Zuniga, Julie Ann; Holstad, Marcia M

2017-04-01

The purpose of this integrative review is to examine the use of motivational interviewing (MI) to improve health outcomes in persons living with HIV (PLWH). We reviewed the existing literature, using the PRISMA model. The PubMed, Web of Science, Embase, and CINAHL databases were searched for all relevant studies, using the terms HIV, AIDS, and motivational interviewing. Of 239 articles identified initially, 19 met our criteria for synthesis. These studies were conducted throughout the world, including the U.S., Thailand, and South Africa. In general, studies that used MI, either alone or in conjunction with other interventions, reported improved adherence, decreased depression, and decreased risky sexual behaviors. This review demonstrates a positive relationship between MI-based interventions and behavioral change, which may lead to improved health outcomes in PLWH. Motivational interviewing can be an effective method of therapeutic communication for PLWH, who struggle with adherence, depression, and risky sexual behaviors. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Gender dysphoria and autism spectrum disorder: A narrative review.

PubMed

Van Der Miesen, Anna I R; Hurley, Hannah; De Vries, Annelou L C

2016-01-01

The current literature shows growing evidence of a link between gender dysphoria (GD) and autism spectrum disorder (ASD). This study reviews the available clinical and empirical data. A systematic search of the literature was conducted using the following databases: PubMed, Web of Science, PsycINFO and Scopus; utilizing different combinations of the following search terms: autism, autism spectrum disorder (ASD), Asperger's disorder (AD), co-morbidity, gender dysphoria (GD), gender identity disorder (GID), transgenderism and transsexualism. In total, 25 articles and reports were selected and discussed. Information was grouped by found co-occurrence rates, underlying hypotheses and implications for diagnosis and treatment. GD and ASD were found to co-occur frequently - sometimes characterized by atypical presentation of GD, which makes a correct diagnosis and determination of treatment options for GD difficult. Despite these challenges there are several case reports describing gender affirming treatment of co-occurring GD in adolescents and adults with ASD. Various underlying hypotheses for the link between GD and ASD were suggested, but almost all of them lack evidence.

Hybrid robotic systems for upper limb rehabilitation after stroke: A review.

PubMed

Resquín, Francisco; Cuesta Gómez, Alicia; Gonzalez-Vargas, Jose; Brunetti, Fernando; Torricelli, Diego; Molina Rueda, Francisco; Cano de la Cuerda, Roberto; Miangolarra, Juan Carlos; Pons, José Luis

2016-11-01

In recent years the combined use of functional electrical stimulation (FES) and robotic devices, called hybrid robotic rehabilitation systems, has emerged as a promising approach for rehabilitation of lower and upper limb motor functions. This paper presents a review of the state of the art of current hybrid robotic solutions for upper limb rehabilitation after stroke. For this aim, studies have been selected through a search using web databases: IEEE-Xplore, Scopus and PubMed. A total of 10 different hybrid robotic systems were identified, and they are presented in this paper. Selected systems are critically compared considering their technological components and aspects that form part of the hybrid robotic solution, the proposed control strategies that have been implemented, as well as the current technological challenges in this topic. Additionally, we will present and discuss the corresponding evidences on the effectiveness of these hybrid robotic therapies. The review also discusses the future trends in this field. Copyright © 2016 IPEM. Published by Elsevier Ltd. All rights reserved.

The role of physical activity and heart rate variability for the control of work related stress.

PubMed

Tonello, Laís; Rodrigues, Fábio B; Souza, Jeniffer W S; Campbell, Carmen S G; Leicht, Anthony S; Boullosa, Daniel A

2014-01-01

Physical activity (PA) and exercise are often used as tools to reduce stress and therefore the risk for developing cardiovascular diseases (CVD). Meanwhile, heart rate variability (HRV) has been utilized to assess both stress and PA or exercise influences. The objective of the present review was to examine the current literature in regards to workplace stress, PA/exercise and HRV to encourage further studies. We considered original articles from known databases (PubMed, ISI Web of Knowledge) over the last 10 years that examined these important factors. A total of seven studies were identified with workplace stress strongly associated with reduced HRV in workers. Longitudinal workplace PA interventions may provide a means to improve worker stress levels and potentially cardiovascular risk with mechanisms still to be clarified. Future studies are recommended to identify the impact of PA, exercise, and fitness on stress levels and HRV in workers and their subsequent influence on cardiovascular health.

Clostridium difficile infection in low- and middle-human development index countries: a systematic review.

PubMed

Forrester, Joseph D; Cai, Lawrence Z; Mbanje, Chenesa; Rinderknecht, Tanya N; Wren, Sherry M

2017-10-01

To describe the impact and epidemiology of Clostridium difficile infection (CDI) in low- and middle-human development index (LMHDI) countries. Prospectively registered, systematic literature review of existing literature in the PubMed, Ovid and Web of Science databases describing the epidemiology and management of C. difficile in LMHDI countries. Risk factors were compared between studies when available. Of the 218 abstracts identified after applying search criteria, 25 studies were reviewed in detail. The weighted pooled infection rate among symptomatic non-immunosuppressed inpatients was 15.8% (95% CI 12.1-19.5%) and was 10.1% (95% CI 3.0-17.2%) among symptomatic outpatients. Subgroup analysis of immunosuppressed patient populations revealed pooled infection rates similar to non-immunosuppressed patient populations. Risk factor analysis was infrequently performed. While the percentages of patients with CDI in LMHDI countries among the reviewed studies are lower than expected, there remains a paucity of epidemiologic data evaluating burden of C. difficile infection in these settings. © 2017 John Wiley & Sons Ltd.

Neuropsychological assessment in migraine patients: a descriptive review on cognitive implications.

PubMed

Foti, Maria; Lo Buono, Viviana; Corallo, Francesco; Palmeri, Rosanna; Bramanti, Placido; Marino, Silvia

2017-04-01

Migraine is considered a disabling disorder with highly prevalence in population. Recent studies report that migraine patients have a cognitive decline associated to structural brain alterations. We search on PubMed and Web of Science databases and screening references of included studies and review articles for additional citations. From 519 studies identified, only 16 met the inclusion criteria. All studies were conducted on 1479 migraineurs (190 non-migraine headache and 11,978 controls subject) and examined the association between migraine and cognitive impairment. The results are discordant. Indeed, while cognitive deficits during the attack of migraine are now recognized, only few studies confirmed the presence of cognitive impairment in migraine patients. Given the prevalence of migraine in the population (especially among women), and the early age of the population, an association between migraine and cognitive impairment could have substantial public health implications. Future studies should determine if specific migraine characteristics, for example, attack frequency, may impact the association between migraine and cognitive decline.

Cyberbullying and adolescent mental health: systematic review.

PubMed

Bottino, Sara Mota Borges; Bottino, Cássio M C; Regina, Caroline Gomez; Correia, Aline Villa Lobo; Ribeiro, Wagner Silva

2015-03-01

Cyberbullying is a new form of violence that is expressed through electronic media and has given rise to concern for parents, educators and researchers. In this paper, an association between cyberbullying and adolescent mental health will be assessed through a systematic review of two databases: PubMed and Virtual Health Library (BVS). The prevalence of cyberbullying ranged from 6.5% to 35.4%. Previous or current experiences of traditional bullying were associated with victims and perpetrators of cyberbullying. Daily use of three or more hours of Internet, web camera, text messages, posting personal information and harassing others online were associated with cyberbullying. Cybervictims and cyberbullies had more emotional and psychosomatic problems, social difficulties and did not feel safe and cared for in school. Cyberbullying was associated with moderate to severe depressive symptoms, substance use, ideation and suicide attempts. Health professionals should be aware of the violent nature of interactions occurring in the virtual environment and its harm to the mental health of adolescents.

Use of information communication technology and stress, burnout, and mental health in older, middle-aged, and younger workers - results from a systematic review.

PubMed

Berg-Beckhoff, Gabriele; Nielsen, Grace; Ladekjær Larsen, Eva

2017-04-01

The aim of this systematic review is to summarise quantitative studies in occupational settings observing the association between Information communication technology (ICT) and stress, and burnout, considering age as an effect modifier. A systematic review using PRISMA guidelines was conducted through the following bibliographic databases: PubMed, Web of Science, Psycinfo, and the Cochrane Library. Inclusion criteria were occupational settings and content relevant to our research question. Risk of bias was assessed using the Newcastle-Ottawa scale. Two interventional, 4 cohorts, and 29 cross-sectional studies were found. ICT use in occupational settings was associated with stress seen in cross-sectional studies, but not in interventional studies. There was a concordant association with ICT and burnout in different study designs. Overall, there were no linear trends between age and technostress. We suggest that the observed associations were mostly present in the middle-aged working population and that these associations need to be supported in further studies.

African Americans' Perceptions of Pain and Pain Management: A Systematic Review.

PubMed

Booker, Staja Q

2016-01-01

The purpose of this systematic review is to explore the perceptions of acute, persistent, and disease-specific pain and treatment options held by adult African Americans. Underassessment and undermanagement of pain in African Americans has been well documented; however, the cultural continuum of pain perceptions and their influence on pain assessment and management has not been synthesized. Electronic database searches of the Cumulative Index for Nursing and Allied Health Literature and PubMed, Web-based searches of the pain-specific journals plus a manual search of reference lists identified 41 relevant articles addressing perceptions of pain and/or pain management. Analysis of the literature revealed six themes: (a) meaning of pain, (b) description of pain, (c) coping with pain, (d) impact of pain, (e) patient-provider relationship, and (f) treatment approaches. These findings warrant further research and indicate the need for more precise evaluation of pain in African Americans, highlighting an imperative to incorporate cultural patterns into pain management practice and education. © The Author(s) 2014.

Magnesium Levels in Drinking Water and Coronary Heart Disease Mortality Risk: A Meta-Analysis.

PubMed

Jiang, Lei; He, Pengcheng; Chen, Jiyan; Liu, Yong; Liu, Dehui; Qin, Genggeng; Tan, Ning

2016-01-02

Epidemiological studies have demonstrated inconsistent associations between drinking water magnesium levels and risk of mortality from coronary heart disease (CHD); thus, a meta-analysis was performed to assess the association between them. Relevant studies were searched by the databases of Cochrane, EMBASE, PubMed and Web of Knowledge. Pooled relative risks (RR) with their 95% CI were calculated to assess this association using a random-effects model. Finally, nine articles with 10 studies involving 77,821 CHD cases were used in this study. Our results revealed an inverse association between drinking water magnesium level and CHD mortality (RR = 0.89, 95% CI = 0.79-0.99, I² = 70.6). Nine of the 10 studies came from Europe, and the association was significant between drinking water magnesium level and the risk of CHD mortality (RR = 0.83, 95% CI = 0.69-0.98). In conclusion, drinking water magnesium level was significantly inversely associated with CHD mortality.

Magnesium Levels in Drinking Water and Coronary Heart Disease Mortality Risk: A Meta-Analysis

PubMed Central

Jiang, Lei; He, Pengcheng; Chen, Jiyan; Liu, Yong; Liu, Dehui; Qin, Genggeng; Tan, Ning

2016-01-01

Epidemiological studies have demonstrated inconsistent associations between drinking water magnesium levels and risk of mortality from coronary heart disease (CHD); thus, a meta-analysis was performed to assess the association between them. Relevant studies were searched by the databases of Cochrane, EMBASE, PubMed and Web of Knowledge. Pooled relative risks (RR) with their 95% CI were calculated to assess this association using a random-effects model. Finally, nine articles with 10 studies involving 77,821 CHD cases were used in this study. Our results revealed an inverse association between drinking water magnesium level and CHD mortality (RR = 0.89, 95% CI = 0.79–0.99, I2 = 70.6). Nine of the 10 studies came from Europe, and the association was significant between drinking water magnesium level and the risk of CHD mortality (RR = 0.83, 95% CI = 0.69–0.98). In conclusion, drinking water magnesium level was significantly inversely associated with CHD mortality. PMID:26729158

Finding similar nucleotide sequences using network BLAST searches.

PubMed

Ladunga, Istvan

2009-06-01

The Basic Local Alignment Search Tool (BLAST) is a keystone of bioinformatics due to its performance and user-friendliness. Beginner and intermediate users will learn how to design and submit blastn and Megablast searches on the Web pages at the National Center for Biotechnology Information. We map nucleic acid sequences to genomes, find identical or similar mRNA, expressed sequence tag, and noncoding RNA sequences, and run Megablast searches, which are much faster than blastn. Understanding results is assisted by taxonomy reports, genomic views, and multiple alignments. We interpret expected frequency thresholds, biological significance, and statistical significance. Weak hits provide no evidence, but hints for further analyses. We find genes that may code for homologous proteins by translated BLAST. We reduce false positives by filtering out low-complexity regions. Parsed BLAST results can be integrated into analysis pipelines. Links in the output connect to Entrez, PUBMED, structural, sequence, interaction, and expression databases. This facilitates integration with a wide spectrum of biological knowledge.

4G/5G polymorphism of plasminogen activator inhibitor-1 gene is associated with polycystic ovary syndrome in Chinese patients: a meta-analysis.

PubMed

Wang, Li-Hong; Wang, Li-Mei; Zhou, Na

2015-09-01

To date, case-control studies on the association between a single-nucleotide polymorphism (SNP) in the plasminogen activator inhibitor-1 (PAI-1) gene and polycystic ovary syndrome (PCOS) have provided controversial results. The electronic databases PubMed, Embase, Web of Science, and CNKI (China National Knowledge Infrastructure) were searched for studies to include in the present meta-analysis. The fixed effects and random effects models showed that the 4G allele was associated with a risk of PCOS compared with the 5G allele in Chinese patients (OR = 2.05; 95 % CI = 1.56-2.69), but not in Caucasian patients (OR = 1.05; 95 % CI = 0.81-1.37). The contrast of homozygotes and the recessive and dominant models produced the same pattern of results as the allele contrast. Our pooled data suggest evidence for a major role of PAI-1 gene 4G/5G polymorphism in the pathogenesis of PCOS among Chinese patients.

The IJHPR publishes its 100th article, and other momentous milestones.

PubMed

Rosen, Bruce; Israeli, Avi

2013-12-19

The Israel Journal of Health Policy Research (IJHPR) was launched in January 2012 and it is now publishing its 100th article. It was accepted into PubMed after only six months of publication and it has now also been accepted by Thomson Reuters for inclusion in the Web of Science as well as the Social Science Citation Index. It is rare for a new journal to reach these milestones at such an early stage in its development.One of the key factors in the journal's acceptance into these prestigious databases has been its unique national/international approach - exploring both what Israel can learn from health systems in other countries and what other countries can learn from Israeli health care. Another key factor has been its ability to attract high quality contributions from virtually all of the Israeli universities and research centers involved in health policy. A third important factor has been the journal's ability to engage leading international scholars as contributors and/or editorial board members.

Natural Products and Complementary Therapies for Chemotherapy-Induced Peripheral Neuropathy: A Systematic Review

PubMed Central

Brami, Cloé; Bao, Ting; Deng, Gary

2015-01-01

Chemotherapy-induced peripheral neuropathy (CIPN) is a serious dose-limiting side-effect without any FDA-approved treatment option. Prior reviews focus mostly on pharmacological interventions, but nonpharmaceutical interventions have also been evaluated. A Web of Science and PubMed database search to identify relevant RCTs from January 2005 to May 2015 included the terms: CIPN, cancer; and supplements, vitamin E, goshajinkigan, kampo, acetyl-L-carnitine, carnitine, alpha-lipoic acid, omega-3, glutamine, or glutamate; or massage, acupuncture, mind-body practice, yoga, meditation, Tai-Chi, physical activity, or exercise. Of 1465 publications screened, 12 RCTs evaluated natural products and one evaluated electroacupuncture. Vitamin E may help prevent CIPN. L-glutamine, goshajinkigan, and omega-3 are also promising. Acetyl-L-carnitine may worsen CIPN and alpha-lipoic acid activity is unknown. Electroacupuncture was not superior to placebo. No RCTs were published regarding other complementary therapies, although some studies mention positive incidental findings. Natural products and complementary therapies deserve further investigation, given the lack of effective CIPN interventions. PMID:26652982

Systematic Review and Meta-analysis of the Impact of Restaurant Menu Calorie Labeling

PubMed Central

Tobias, Deirdre K.; Cradock, Angie L.; Batchelder, Holly; Gortmaker, Steven L.

2015-01-01

We conducted a systematic review and meta-analysis evaluating the relationship between menu calorie labeling and calories ordered or purchased in the PubMed, Web of Science, PolicyFile, and PAIS International databases through October 2013. Among 19 studies, menu calorie labeling was associated with a −18.13 kilocalorie reduction ordered per meal with significant heterogeneity across studies (95% confidence interval = −33.56, −2.70; P = .021; I2 = 61.0%). However, among 6 controlled studies in restaurant settings, labeling was associated with a nonsignificant −7.63 kilocalorie reduction (95% confidence interval = −21.02, 5.76; P = .264; I2 = 9.8%). Although current evidence does not support a significant impact on calories ordered, menu calorie labeling is a relatively low-cost education strategy that may lead consumers to purchase slightly fewer calories. These findings are limited by significant heterogeneity among nonrestaurant studies and few studies conducted in restaurant settings. PMID:25790388

Effect of intervention programs in schools to reduce screen time: a meta-analysis.

PubMed

Friedrich, Roberta Roggia; Polet, Jéssica Pinto; Schuch, Ilaine; Wagner, Mário Bernardes

2014-01-01

to evaluate the effects of intervention program strategies on the time spent on activities such as watching television, playing videogames, and using the computer among schoolchildren. a search for randomized controlled trials available in the literature was performed in the following electronic databases: PubMed, Lilacs, Embase, Scopus, Web of Science, and Cochrane Library using the following Keywords randomized controlled trial, intervention studies, sedentary lifestyle, screen time, and school. A summary measure based on the standardized mean difference was used with a 95% confidence interval. a total of 1,552 studies were identified, of which 16 were included in the meta-analysis. The interventions in the randomized controlled trials (n=8,785) showed a significant effect in reducing screen time, with a standardized mean difference (random effect) of: -0.25 (-0.37, -0.13), p<0.01. interventions have demonstrated the positive effects of the decrease of screen time among schoolchildren. Copyright © 2014 Sociedade Brasileira de Pediatria. Published by Elsevier Editora Ltda. All rights reserved.

Preventing Suicide Among Inpatients

PubMed Central

Sakinofsky, Isaac

2014-01-01

Objective Inpatient suicide comprises a proportionately small but clinically important fraction of suicide. This study is intended as a qualitative analysis of the comprehensive English literature, highlighting what is known and what can be done to prevent inpatient suicide. Method: A systematic search was conducted on the Cochrane Library, PubMed, Embase, Web of Knowledge, and a personal database for articles on cohort series, preferably controlled, of inpatient suicide (not deliberate self-harm or attempted suicide, unless they also dealt specifically with suicide data). Results: A qualitative discussion is presented, based on the findings of the literature searched. Conclusions: The bulk of inpatient suicides actually occur not on the ward but off premises, when the patient was on leave or had absconded. Peaks occur shortly after admission and discharge. It is possible to reduce suicide risk on the ward by having a safe environment, optimizing patient visibility, supervising patients appropriately, careful assessment, awareness of and respect for suicide risk, good teamwork and communication, and adequate clinical treatment. PMID:24881161

The Significance of Scalp Involvement in Pemphigus: A Literature Review

PubMed Central

Sar-Pomian, Marta; Rudnicka, Lidia

2018-01-01

Scalp is a unique location for pemphigus because of the abundance of desmogleins localized in hair follicles. Scalp involvement is observed in up to 60% of patients in the course of pemphigus. The lesions may occasionally lead to alopecia. Unforced removal of anagen hairs in a pull test is a sign of high disease activity. Direct immunofluorescence of plucked hair bulbs is considered a reliable diagnostic method in patients with pemphigus. Follicular acantholysis is a characteristic histopathological feature of pemphigus lesions localized on the scalp. Trichoscopy may serve as a supplementary method in the diagnosis of pemphigus. This review summarizes the most recent data concerning scalp involvement in pemphigus vulgaris and pemphigus foliaceus. A systematic literature search was conducted in three medical databases: PubMed, Embase, and Web of Science. The analysis included literature data about desmoglein distribution in hair follicles, as well as information about clinical manifestations, histopathology, immunopathology, and trichoscopy of scalp lesions in pemphigus and their response to treatment. PMID:29770335

Aerobic exercise effects upon cognition in Mild Cognitive Impairment: A systematic review of randomized controlled trials.

PubMed

Cammisuli, D M; Innocenti, A; Franzoni, F; Pruneti, C

2017-07-01

Several studies have shown that physical activity has positive effects on cognition in healthy older adults without cognitive complains but lesser is known about the effectiveness of aerobic exercise in patients suffering from Mild Cognitive Impairment (MCI). The aim of the present study was to systematically review the evidence from randomized controlled trials (RCTs) about the effects of aerobic exercise upon cognition in MCI patients. To this end, PubMed, Cochrane and Web of Science databases were analytically searched for RCTs including aerobic exercise interventions for MCI patients. There is evidence that aerobic exercise improves cognition in MCI patients. Overall research reported moderate effects for global cognition, logical memory, inhibitory control and divided attention. Due to methodological limitations of the investigated studies, findings should be interpreted with caution. Standardized training protocols, larger scale interventions and follow-ups may also provide better insight into the preventive effects of aerobic exercise on cognitive deterioration in MCI and its conversion into dementia.

Long Noncoding RNA H19 in Digestive System Cancers: A Meta-Analysis of Its Association with Pathological Features.

PubMed

Lin, Yang; Xu, Lijian; Wei, Wei; Zhang, Xiaohui; Ying, Rongchao

2016-01-01

Long noncoding RNA (lncRNA) H19 has been reported to be upregulated in malignant digestive tumors, but its clinical relevance is not yet established. The meta-analysis was to investigate the association between H19 expression and pathological features of digestive system cancers. The databases of PubMed, EMBase, Web of Science, CNKI, and WanFang were searched for the related studies. A total of 478 patients from 6 studies were finally included. The meta-analysis showed that the patient group of high H19 expression had a higher risk of poorly differentiated grade, deep tumor invasion (T2 stage or more), lymph node metastasis, and advanced TNM stage than the group of low H19 expression, although there was no difference between them in terms of distant metastasis. Therefore, the high expression of lncRNA H19 might predict poor oncological outcomes of patients with digestive system cancers.

Current Applications and Future Perspectives of the Use of 3D Printing in Anatomical Training and Neurosurgery

PubMed Central

Baskaran, Vivek; Štrkalj, Goran; Štrkalj, Mirjana; Di Ieva, Antonio

2016-01-01

3D printing is a form of rapid prototyping technology, which has led to innovative new applications in biomedicine. It facilitates the production of highly accurate three dimensional objects from substrate materials. The inherent accuracy and other properties of 3D printing have allowed it to have exciting applications in anatomy education and surgery, with the specialty of neurosurgery having benefited particularly well. This article presents the findings of a literature review of the Pubmed and Web of Science databases investigating the applications of 3D printing in anatomy and surgical education, and neurosurgery. A number of applications within these fields were found, with many significantly improving the quality of anatomy and surgical education, and the practice of neurosurgery. They also offered advantages over existing approaches and practices. It is envisaged that the number of useful applications will rise in the coming years, particularly as the costs of this technology decrease and its uptake rises. PMID:27445707

Current Applications and Future Perspectives of the Use of 3D Printing in Anatomical Training and Neurosurgery.

PubMed

Baskaran, Vivek; Štrkalj, Goran; Štrkalj, Mirjana; Di Ieva, Antonio

2016-01-01

3D printing is a form of rapid prototyping technology, which has led to innovative new applications in biomedicine. It facilitates the production of highly accurate three dimensional objects from substrate materials. The inherent accuracy and other properties of 3D printing have allowed it to have exciting applications in anatomy education and surgery, with the specialty of neurosurgery having benefited particularly well. This article presents the findings of a literature review of the Pubmed and Web of Science databases investigating the applications of 3D printing in anatomy and surgical education, and neurosurgery. A number of applications within these fields were found, with many significantly improving the quality of anatomy and surgical education, and the practice of neurosurgery. They also offered advantages over existing approaches and practices. It is envisaged that the number of useful applications will rise in the coming years, particularly as the costs of this technology decrease and its uptake rises.

Is carpal tunnel syndrome related to computer exposure at work? A review and meta-analysis.

PubMed

Mediouni, Zakia; de Roquemaurel, Alexis; Dumontier, Christian; Becour, Bertrand; Garrabe, Hélène; Roquelaure, Yves; Descatha, Alexis

2014-02-01

A meta-analysis on epidemiological studies was undertaken to assess association between carpal tunnel syndrome (CTS) and computer work. Four databases (PubMed, Embase, Web of Science, and Base de Donnees de Sante Publique) were searched with cross-references from published reviews. We included recent studies, original epidemiological studies for which the association was assessed with blind reviewing with control group. Relevant associations were extracted, and a metarisk was calculated using the generic variance approach (meta-odds ratio [meta-OR]). Six studies met the criteria for inclusion. Results are contradictory because of heterogeneous work exposure. The meta-OR for computer use was 1.67 (95% confidence interval [CI], 0.79 to 3.55). The meta-OR for keyboarding was 1.11 (95% CI, 0.62 to 1.98) and for mouse 1.94 (95% CI, 0.90 to 4.21). It was not possible to show an association between computer use and CTS, although some particular work circumstances may be associated with CTS.

[Systematic review on the physical activity level and nutritional status of Brazilian children].

PubMed

Graziele Bento, Gisele; Cascaes da Silva, Franciele; Gonçalves, Elizandra; Domingos Dos Santos, Patrícia; da Silva, Rudney

2016-08-01

Objective To systematically review the literature on the prevalence and the factors associated with physical activity level and nutritional status of Brazilian children. Methods The electronic database MEDLINE (via PubMed), SciELO, SCOPUS and Web of Science were selected. The search strategy included the descriptors proposed in the Medical Subject Headings (MeSH): "Motor Activity", "Activities", "Nutritional Status", "Overweight", "Obesity", "Body Mass Index", "Child", "Brazil". Results The search allowed the identification of 141 articles, of which 16 studies were considered potentially relevant and were included in the review. Conclusions Studies about nutritional status and physical activity levels in Brazilian children are still scarce, but the work on this has increased in recent years, especially those that use cross designs, as well as questionnaires to measure physical activity; BMI for nutritional status is still widely used. Furthermore, studies that analyzed the amount of hours designated to sedentary behaviors such as watching TV, playing video-games and using the computer, found that these activities took more than two hours every day.

Lean thinking in health and nursing: an integrative literature review 1

PubMed Central

Magalhães, Aline Lima Pestana; Erdmann, Alacoque Lorenzini; da Silva, Elza Lima; dos Santos, José Luís Guedes

2016-01-01

ABSTRACT Objectives: to demonstrate the scientific knowledge developed on lean thinking in health, highlighting the impact and contributions in health care and nursing. Method: an integrative literature review in the PubMed, CINAHL, Scopus, Web of Science, Emerald, LILACS and SciELO electronic library databases, from 2006 to 2014, with syntax keywords for each data base, in which 47 articles were selected for analysis. Results: the categories were developed from the quality triad proposed by Donabedian: structure, process and outcome. Lean thinking is on the rise in health surveys, particularly internationally, especially in the USA and UK, improving the structure, process and outcome of care and management actions. However, it is an emerging theme in nursing. Conclusion: this study showed that the use of lean thinking in the context of health has a transforming effect on care and organizational aspects, promoting advantages in terms of quality, safety and efficiency of health care and nursing focused on the patient. PMID:27508906

Laparoscopic-assisted vaginal hysterectomy vs abdominal hysterectomy for benign disease: a meta-analysis of randomized controlled trials.

PubMed

Yi, Yue-xiong; Zhang, Wei; Zhou, Qi; Guo, Wan-ru; Su, Yu

2011-11-01

The objective of this meta-analysis was to assess whether laparoscopic-assisted vaginal hysterectomy achieves better clinical results compared with abdominal hysterectomy. Medline (PubMed), EMBASE, Web of Science, ProQuest, Cochrane Library and China Biological Medicine Database were searched to identify randomized controlled trials that compared laparoscopic-assisted vaginal hysterectomy with abdominal hysterectomy. Twenty-three trials were studied and the analysis was performed using Review Manager Version 5 and R Version 2.11.1. The results showed that laparoscopic-assisted vaginal hysterectomy was associated with a longer operation time, less blood loss, shorter hospital stay, smaller haemoglobin drop, less postoperative pain, quicker return to normal activities and fewer peri-operative complications. Quality of life is likely to be the key outcome to evaluate the approach for hysterectomy, but further research is needed. For suitable patients and surgeons, laparoscopic-assisted vaginal hysterectomy is a better choice than abdominal hysterectomy. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Motivation in pediatric motor rehabilitation: A systematic search of the literature using the self-determination theory as a conceptual framework.

PubMed

Meyns, Pieter; Roman de Mettelinge, Tine; van der Spank, Judith; Coussens, Marieke; Van Waelvelde, Hilde

2017-03-09

Motivation is suggested as an important factor in pediatric motor rehabilitation. Therefore, we reviewed the existing evidence of (motivational) motor rehabilitation paradigms, and how motivation influences rehabilitation outcome using self-determination theory as conceptual framework. PubMed and Web-of-Science databases were systematically searched until June 2015. Data were independently extracted and critiqued for quality by three authors. Studies reporting motivational aspects were included. Most studies examined new technology (e.g., virtual reality [VR]). Out of 479 records, three RCT, six case-control, and six non-comparative studies were included with mixed quality. Motivation was rarely reported. Training individualization to the child's capabilities with more variety seemed promising to increase motivation. Motivation increased when the exercises seemed helpful for daily activities. Motivation in pediatric rehabilitation should be comprehensively assessed within a theoretical framework as there are indications that motivated children have better rehabilitation outcomes, depending on the aspect of motivation.

Management of advanced gastric cancer: An overview of major findings from meta-analysis

PubMed Central

Cai, Danxian; Li, Wende; Hui, Jialiang; Liu, Chuan; Zhao, Yanxia; Li, Guoxin

2016-01-01

This study aims to provide an overview of different treatment for advanced gastric cancer. In the present study, we systematically reviewed the major findings from relevant meta-analyses. A total of 54 relevant papers were searched via the PubMed, Web of Science, and Google scholar databases. They were classified according to the mainstay treatment modalities such as surgery, chemotherapy and others. Primary outcomes including overall survival, response rate, disease-free survival, recurrence-free survival, progression-free survival, time-to-progression, time-to failure, recurrence and safety were summarized. The recommendations and uncertainties regarding the treatment of advanced gastric cancer were also proposed. It was suggested that laparoscopic gastrectomy was a safe and technical alternative to open gastrectomy. Besides, neoadjuvant chemotherapy and adjuvant chemotherapy were thought to benefit the survival over surgery alone. And it was demonstrated in the study that targeted therapy like anti-angiogenic and anti-HER2 agents but anti-EGFR agent might have a significant survival benefit. PMID:27655725

Financial outcomes of transoral robotic surgery: A narrative review.

PubMed

Othman, Sammy; McKinnon, Brian J

2018-04-03

To determine the current cost impact and financial outcomes of transoral robotic surgery in Otolaryngology. A narrative review of the literature with a defined search strategy using Pubmed, MEDLINE, CINAHL, and Web of Science. Using keywords ENT or otolaryngology, cost or economic, transoral robotic surgery or TORs, searches were performed in Pubmed, MEDLINE, CINAHL, and Web of Science and reviewed by the authors for inclusion and analysis. Six total papers were deemed appropriate for analysis. All addressed cost impact of transoral robotic surgery (TORs) as compared to open surgical methods in treating oropharyngeal cancer and/or the identification of the primary tumor within unknown primary squamous cell carcinoma. Results showed TORs to be cost-effective. Transoral robotic surgery is currently largely cost effective for both treatment and diagnostic procedures. However, further studies are needed to qualify long-term data. Copyright © 2018. Published by Elsevier Inc.

NNDC Data Services

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

Tuli, J.K.; Sonzogni,A.

The National Nuclear Data Center has provided remote access to some of its resources since 1986. The major databases and other resources available currently through NNDC Web site are summarized. The National Nuclear Data Center (NNDC) has provided remote access to the nuclear physics databases it maintains and to other resources since 1986. With considerable innovation access is now mostly through the Web. The NNDC Web pages have been modernized to provide a consistent state-of-the-art style. The improved database services and other resources available from the NNOC site at www.nndc.bnl.govwill be described.

Comparing Unique Title Coverage of Web of Science and Scopus in Earth and Atmospheric Sciences

ERIC Educational Resources Information Center

Barnett, Philip; Lascar, Claudia

2012-01-01

The current journal titles in earth and atmospheric sciences, that are unique to each of two databases, Web of Science and Scopus, were identified using different methods. Comparing by subject category shows that Scopus has hundreds of unique titles, and Web of Science just 16. The titles unique to each database have low SCImago Journal Rank…

Generic HTML Form Processor: A versatile PHP script to save web-collected data into a MySQL database.

PubMed

Göritz, Anja S; Birnbaum, Michael H

2005-11-01

The customizable PHP script Generic HTML Form Processor is intended to assist researchers and students in quickly setting up surveys and experiments that can be administered via the Web. This script relieves researchers from the burdens of writing new CGI scripts and building databases for each Web study. Generic HTML Form Processor processes any syntactically correct HTML forminput and saves it into a dynamically created open-source database. We describe five modes for usage of the script that allow increasing functionality but require increasing levels of knowledge of PHP and Web servers: The first two modes require no previous knowledge, and the fifth requires PHP programming expertise. Use of Generic HTML Form Processor is free for academic purposes, and its Web address is www.goeritz.net/brmic.

Turning Access into a web-enabled secure information system for clinical trials.

PubMed

Dongquan Chen; Chen, Wei-Bang; Soong, Mayhue; Soong, Seng-Jaw; Orthner, Helmuth F

2009-08-01

Organizations that have limited resources need to conduct clinical studies in a cost-effective, but secure way. Clinical data residing in various individual databases need to be easily accessed and secured. Although widely available, digital certification, encryption, and secure web server, have not been implemented as widely, partly due to a lack of understanding of needs and concerns over issues such as cost and difficulty in implementation. The objective of this study was to test the possibility of centralizing various databases and to demonstrate ways of offering an alternative to a large-scale comprehensive and costly commercial product, especially for simple phase I and II trials, with reasonable convenience and security. We report a working procedure to transform and develop a standalone Access database into a secure Web-based secure information system. For data collection and reporting purposes, we centralized several individual databases; developed, and tested a web-based secure server using self-issued digital certificates. The system lacks audit trails. The cost of development and maintenance may hinder its wide application. The clinical trial databases scattered in various departments of an institution could be centralized into a web-enabled secure information system. The limitations such as the lack of a calendar and audit trail can be partially addressed with additional programming. The centralized Web system may provide an alternative to a comprehensive clinical trial management system.

Google Scholar is not enough to be used alone for systematic reviews.

PubMed

Giustini, Dean; Boulos, Maged N Kamel

2013-01-01

Google Scholar (GS) has been noted for its ability to search broadly for important references in the literature. Gehanno et al. recently examined GS in their study: 'Is Google scholar enough to be used alone for systematic reviews?' In this paper, we revisit this important question, and some of Gehanno et al.'s other findings in evaluating the academic search engine. The authors searched for a recent systematic review (SR) of comparable size to run search tests similar to those in Gehanno et al. We selected Chou et al. (2013) contacting the authors for a list of publications they found in their SR on social media in health. We queried GS for each of those 506 titles (in quotes "), one by one. When GS failed to retrieve a paper, or produced too many results, we used the allintitle: command to find papers with the same title. Google Scholar produced records for ~95% of the papers cited by Chou et al. (n=476/506). A few of the 30 papers that were not in GS were later retrieved via PubMed and even regular Google Search. But due to its different structure, we could not run searches in GS that were originally performed by Chou et al. in PubMed, Web of Science, Scopus and PsycINFO®. Identifying 506 papers in GS was an inefficient process, especially for papers using similar search terms. Has Google Scholar improved enough to be used alone in searching for systematic reviews? No. GS' constantly-changing content, algorithms and database structure make it a poor choice for systematic reviews. Looking for papers when you know their titles is a far different issue from discovering them initially. Further research is needed to determine when and how (and for what purposes) GS can be used alone. Google should provide details about GS' database coverage and improve its interface (e.g., with semantic search filters, stored searching, etc.). Perhaps then it will be an appropriate choice for systematic reviews.

Towards eliminating malaria in high endemic countries: the roles of community health workers and related cadres and their challenges in integrated community case management for malaria: a systematic review.

PubMed

Sunguya, Bruno F; Mlunde, Linda B; Ayer, Rakesh; Jimba, Masamine

2017-01-03

Human resource for health crisis has impaired global efforts against malaria in highly endemic countries. To address this, the World Health Organization (WHO) recommended scaling-up of community health workers (CHWs) and related cadres owing to their documented success in malaria and other disease prevention and management. Evidence is inconsistent on the roles and challenges they encounter in malaria interventions. This systematic review aims to summarize evidence on roles and challenges of CHWs and related cadres in integrated community case management for malaria (iCCM). This systematic review retrieved evidence from PubMed, CINAHL, ISI Web of Knowledge, and WHO regional databases. Terms extracted from the Boolean phrase used for PubMed were also used in other databases. The review included studies with Randomized Control Trial, Quasi-experimental, Pre-post interventional, Longitudinal and cohort, Cross-sectional, Case study, and Secondary data analysis. Because of heterogeneity, only narrative synthesis was conducted for this review. A total of 66 articles were eligible for analysis out of 1380 studies retrieved. CHWs and related cadre roles in malaria interventions included: malaria case management, prevention including health surveillance and health promotion specific to malaria. Despite their documented success, CHWs and related cadres succumb to health system challenges. These are poor and unsustainable finance for iCCM, workforce related challenges, lack of and unsustainable supply of medicines and diagnostics, lack of information and research, service delivery and leadership challenges. Community health workers and related cadres had important preventive, case management and promotive roles in malaria interventions. To enable their effective integration into the health systems, the identified challenges should be addressed. They include: introducing sustainable financing on iCCM programmes, tailoring their training to address the identified gaps, improving sustainable supply chain management of malaria drugs and diagnostics, and addressing regulatory challenges in the local contexts.

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.

A Web-based open-source database for the distribution of hyperspectral signatures

NASA Astrophysics Data System (ADS)

Ferwerda, J. G.; Jones, S. D.; Du, Pei-Jun

2006-10-01

With the coming of age of field spectroscopy as a non-destructive means to collect information on the physiology of vegetation, there is a need for storage of signatures, and, more importantly, their metadata. Without the proper organisation of metadata, the signatures itself become limited. In order to facilitate re-distribution of data, a database for the storage & distribution of hyperspectral signatures and their metadata was designed. The database was built using open-source software, and can be used by the hyperspectral community to share their data. Data is uploaded through a simple web-based interface. The database recognizes major file-formats by ASD, GER and International Spectronics. The database source code is available for download through the hyperspectral.info web domain, and we happily invite suggestion for additions & modification for the database to be submitted through the online forums on the same website.

Factors Associated With Suicidal Attempts in Iran: A Systematic Review

PubMed Central

Hakim Shooshtari, Mitra; Malakouti, Seyyed Kazem; Panaghi, Leili; Mohseni, Shohreh; Mansouri, Naghmeh; Rahimi Movaghar, Afarin

2016-01-01

Context: Suicide prevention is a health service priority. Some surveys have assessed suicidal behaviors and potential risk factors. Objectives: The current paper aimed to gather information about etiology of suicide attempts in Iran. Data Sources: Pubmed, ISI web of science, PsychInfo, IranPsych, IranMedex, IranDoc as well as gray literature were searched. Study Selection: By electronic and gray literature search, 128 articles were enrolled in this paper. Pubmed, ISI web of science, PsychInfo, IranPsych, IranMedex, IranDoc were searched for electronic search. After reading the abstracts, 84 studies were excluded and full texts of 44 articles were reviewed critically. Data Extraction: Pubmed, ISI web of science, PsychInfo, IranPsych, IranMedex, IranDoc as well as gray literature were searched to find any study about etiologic factors of suicide attempt in Iran. Results: Depressive disorder was the most common diagnosis in suicide attempters that is 45% of the evaluated cases had depression. One study that had used Minnesota multiphasic personality inventory (MMPI) found that Histrionics in females and Schizophrenia and Paranoia in males were significantly influential. Family conflicts with 50.7% and conflict with parents with 44% were two effective psychosocial factors in suicidal attempts. In around one fourth (28.7%) of the cases, conflict with spouse was the main etiologic factor. Conclusions: According to the methodological limitations, outcomes should be generalized cautiously. Further studies will help to plan preventive strategies for suicidal attempts; therefore, continued researches should be conducted to fill the data gaps. PMID:27284284

MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.

PubMed

Hayashi, Takanori; Matsuzaki, Yuri; Yanagisawa, Keisuke; Ohue, Masahito; Akiyama, Yutaka

2018-05-08

Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Therefore, rigid body protein-protein docking calculations for two protein structures are expected to allow elucidation of PPIs different from known complexes in terms of 3D structures because known PPI information is not explicitly required. We have developed rapid PPI prediction software based on protein-protein docking, called MEGADOCK. In order to fully utilize the benefits of computational PPI predictions, it is necessary to construct a comprehensive database to gather prediction results and their predicted 3D complex structures and to make them easily accessible. Although several databases exist that provide predicted PPIs, the previous databases do not contain a sufficient number of entries for the purpose of discovering novel PPIs. In this study, we constructed an integrated database of MEGADOCK PPI predictions, named MEGADOCK-Web. MEGADOCK-Web provides more than 10 times the number of PPI predictions than previous databases and enables users to conduct PPI predictions that cannot be found in conventional PPI prediction databases. In MEGADOCK-Web, there are 7528 protein chains and 28,331,628 predicted PPIs from all possible combinations of those proteins. Each protein structure is annotated with PDB ID, chain ID, UniProt AC, related KEGG pathway IDs, and known PPI pairs. Additionally, MEGADOCK-Web provides four powerful functions: 1) searching precalculated PPI predictions, 2) providing annotations for each predicted protein pair with an experimentally known PPI, 3) visualizing candidates that may interact with the query protein on biochemical pathways, and 4) visualizing predicted complex structures through a 3D molecular viewer. MEGADOCK-Web provides a huge amount of comprehensive PPI predictions based on docking calculations with biochemical pathways and enables users to easily and quickly assess PPI feasibilities by archiving PPI predictions. MEGADOCK-Web also promotes the discovery of new PPIs and protein functions and is freely available for use at http://www.bi.cs.titech.ac.jp/megadock-web/ .

Accessibility and quality of online information for pediatric orthopaedic surgery fellowships.

PubMed

Davidson, Austin R; Murphy, Robert F; Spence, David D; Kelly, Derek M; Warner, William C; Sawyer, Jeffrey R

2014-12-01

Pediatric orthopaedic fellowship applicants commonly use online-based resources for information on potential programs. Two primary sources are the San Francisco Match (SF Match) database and the Pediatric Orthopaedic Society of North America (POSNA) database. We sought to determine the accessibility and quality of information that could be obtained by using these 2 sources. The online databases of the SF Match and POSNA were reviewed to determine the availability of embedded program links or external links for the included programs. If not available in the SF Match or POSNA data, Web sites for listed programs were located with a Google search. All identified Web sites were analyzed for accessibility, content volume, and content quality. At the time of online review, 50 programs, offering 68 positions, were listed in the SF Match database. Although 46 programs had links included with their information, 36 (72%) of them simply listed http://www.sfmatch.org as their unique Web site. Ten programs (20%) had external links listed, but only 2 (4%) linked directly to the fellowship web page. The POSNA database does not list any links to the 47 programs it lists, which offer 70 positions. On the basis of a Google search of the 50 programs listed in the SF Match database, web pages were found for 35. Of programs with independent web pages, all had a description of the program and 26 (74%) described their application process. Twenty-nine (83%) listed research requirements, 22 (63%) described the rotation schedule, and 12 (34%) discussed the on-call expectations. A contact telephone number and/or email address was provided by 97% of programs. Twenty (57%) listed both the coordinator and fellowship director, 9 (26%) listed the coordinator only, 5 (14%) listed the fellowship director only, and 1 (3%) had no contact information given. The SF Match and POSNA databases provide few direct links to fellowship Web sites, and individual program Web sites either do not exist or do not effectively convey information about the programs. Improved accessibility and accurate information online would allow potential applicants to obtain information about pediatric fellowships in a more efficient manner.

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.

WebEAV

PubMed Central

Nadkarni, Prakash M.; Brandt, Cynthia M.; Marenco, Luis

2000-01-01

The task of creating and maintaining a front end to a large institutional entity-attribute-value (EAV) database can be cumbersome when using traditional client-server technology. Switching to Web technology as a delivery vehicle solves some of these problems but introduces others. In particular, Web development environments tend to be primitive, and many features that client-server developers take for granted are missing. WebEAV is a generic framework for Web development that is intended to streamline the process of Web application development for databases having a significant EAV component. It also addresses some challenging user interface issues that arise when any complex system is created. The authors describe the architecture of WebEAV and provide an overview of its features with suitable examples. PMID:10887163

Anatomy and histology of apical support: a literature review concerning cardinal and uterosacral ligaments.

PubMed

Ramanah, Rajeev; Berger, Mitchell B; Parratte, Bernard M; DeLancey, John O L

2012-11-01

The objective of this work was to collect and summarize relevant literature on the anatomy, histology, and imaging of apical support of the upper vagina and the uterus provided by the cardinal (CL) and uterosacral (USL) ligaments. A literature search in English, French, and German languages was carried out with the keywords apical support, cardinal ligament, transverse cervical ligament, Mackenrodt ligament, parametrium, paracervix, retinaculum uteri, web, uterosacral ligament, and sacrouterine ligament in the PubMed database. Other relevant journal and textbook articles were sought by retrieving references cited in previous PubMed articles. Fifty references were examined in peer-reviewed journals and textbooks. The USL extends from the S2 to the S4 vertebra region to the dorsal margin of the uterine cervix and/or to the upper third of the posterior vaginal wall. It has a superficial and deep component. Autonomous nerve fibers are a major constituent of the deep USL. CL is defined as a perivascular sheath with a proximal insertion around the origin of the internal iliac artery and a distal insertion on the cervix and/or vagina. It is divided into a cranial (vascular) and a caudal (neural) portions. Histologically, it contains mainly vessels, with no distinct band of connective tissue. Both the deep USL and the caudal CL are closely related to the inferior hypogastric plexus. USL and CL are visceral ligaments, with mesentery-like structures containing vessels, nerves, connective tissue, and adipose tissue.

Application and outcomes of therapy combining transcranial direct current stimulation and virtual reality: a systematic review.

PubMed

Massetti, Thais; Crocetta, Tânia Brusque; Silva, Talita Dias da; Trevizan, Isabela Lopes; Arab, Claudia; Caromano, Fátima Aparecida; Monteiro, Carlos Bandeira de Mello

2017-08-01

To evaluate the methods and major outcomes of transcranial direct current stimulation (tDCS) combined with virtual reality (VR) therapy in randomized controlled trials. A systematic review was performed following PRISMA guidelines using PubMed, PubMed Central, Web of Science and CAPES periodic databases, with no time restriction. The studies were screened for the following inclusion criteria: human subjects, combination of VR and tDCS methods, and randomized controlled study design. All potentially relevant articles were independently reviewed by two researchers, who reached a consensus on which articles met the inclusion criteria. The PEDro scale was used to evaluate the studies. Eleven studies were included, all of which utilized a variety of tDCS and VR application methods. The main outcomes were found to be beneficial in intervention groups of different populations, including improvements in body sway, gait, stroke recovery, pain management and vegetative reactions. The use of tDCS combined with VR showed positive results in both healthy and impaired patients. Future studies with larger sample sizes and homogeneous participants are required to confirm the benefits of tDCS and VR. Implications for Rehabilitation tDCS with VR intervention can be an alternative to traditional rehabilitation programs. tDCS with VR is a promising type of intervention with a variety of positive effects. Application of tDCS with VR is appropriated to both healthy and impaired patients. There is no consensus of tDCS with VR application.

Anatomy and histology of apical support: a literature review concerning cardinal and uterosacral ligaments

PubMed Central

Ramanah, Rajeev; Berger, Mitchell B.; Parratte, Bernard M.

2014-01-01

The objective of this work was to collect and summarize relevant literature on the anatomy, histology, and imaging of apical support of the upper vagina and the uterus provided by the cardinal (CL) and uterosacral (USL) ligaments. A literature search in English, French, and German languages was carried out with the keywords apical support, cardinal ligament, transverse cervical ligament, Mackenrodt ligament, parametrium, paracervix, retinaculum uteri, web, uterosacral ligament, and sacrouterine ligament in the PubMed database. Other relevant journal and textbook articles were sought by retrieving references cited in previous PubMed articles. Fifty references were examined in peer-reviewed journals and textbooks. The USL extends from the S2 to the S4 vertebra region to the dorsal margin of the uterine cervix and/or to the upper third of the posterior vaginal wall. It has a superficial and deep component. Autonomous nerve fibers are a major constituent of the deep USL. CL is defined as a perivascular sheath with a proximal insertion around the origin of the internal iliac artery and a distal insertion on the cervix and/or vagina. It is divided into a cranial (vascular) and a caudal (neural) portions. Histologically, it contains mainly vessels, with no distinct band of connective tissue. Both the deep USL and the caudal CL are closely related to the inferior hypogastric plexus. USL and CL are visceral ligaments, with mesentery-like structures containing vessels, nerves, connective tissue, and adipose tissue. PMID:22618209

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

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

TryTransDB: A web-based resource for transport proteins in Trypanosomatidae.

PubMed

Sonar, Krushna; Kabra, Ritika; Singh, Shailza

2018-03-12

TryTransDB is a web-based resource that stores transport protein data which can be retrieved using a standalone BLAST tool. We have attempted to create an integrated database that can be a one-stop shop for the researchers working with transport proteins of Trypanosomatidae family. TryTransDB (Trypanosomatidae Transport Protein Database) is a web based comprehensive resource that can fire a BLAST search against most of the transport protein sequences (protein and nucleotide) from Trypanosomatidae family organisms. This web resource further allows to compute a phylogenetic tree by performing multiple sequence alignment (MSA) using CLUSTALW suite embedded in it. Also, cross-linking to other databases helps in gathering more information for a certain transport protein in a single website.

Using Web Database Tools To Facilitate the Construction of Knowledge in Online Courses.

ERIC Educational Resources Information Center

McNeil, Sara G.; Robin, Bernard R.

This paper presents an overview of database tools that dynamically generate World Wide Web materials and focuses on the use of these tools to support research activities, as well as teaching and learning. Database applications have been used in classrooms to support learning activities for over a decade, but, although business and e-commerce have…

Database Organisation in a Web-Enabled Free and Open-Source Software (foss) Environment for Spatio-Temporal Landslide Modelling

NASA Astrophysics Data System (ADS)

Das, I.; Oberai, K.; Sarathi Roy, P.

2012-07-01

Landslides exhibit themselves in different mass movement processes and are considered among the most complex natural hazards occurring on the earth surface. Making landslide database available online via WWW (World Wide Web) promotes the spreading and reaching out of the landslide information to all the stakeholders. The aim of this research is to present a comprehensive database for generating landslide hazard scenario with the help of available historic records of landslides and geo-environmental factors and make them available over the Web using geospatial Free & Open Source Software (FOSS). FOSS reduces the cost of the project drastically as proprietary software's are very costly. Landslide data generated for the period 1982 to 2009 were compiled along the national highway road corridor in Indian Himalayas. All the geo-environmental datasets along with the landslide susceptibility map were served through WEBGIS client interface. Open source University of Minnesota (UMN) mapserver was used as GIS server software for developing web enabled landslide geospatial database. PHP/Mapscript server-side application serve as a front-end application and PostgreSQL with PostGIS extension serve as a backend application for the web enabled landslide spatio-temporal databases. This dynamic virtual visualization process through a web platform brings an insight into the understanding of the landslides and the resulting damage closer to the affected people and user community. The landslide susceptibility dataset is also made available as an Open Geospatial Consortium (OGC) Web Feature Service (WFS) which can be accessed through any OGC compliant open source or proprietary GIS Software.

Metadata tables to enable dynamic data modeling and web interface design: the SEER example.

PubMed

Weiner, Mark; Sherr, Micah; Cohen, Abigail

2002-04-01

A wealth of information addressing health status, outcomes and resource utilization is compiled and made available by various government agencies. While exploration of the data is possible using existing tools, in general, would-be users of the resources must acquire CD-ROMs or download data from the web, and upload the data into their own database. Where web interfaces exist, they are highly structured, limiting the kinds of queries that can be executed. This work develops a web-based database interface engine whose content and structure is generated through interaction with a metadata table. The result is a dynamically generated web interface that can easily accommodate changes in the underlying data model by altering the metadata table, rather than requiring changes to the interface code. This paper discusses the background and implementation of the metadata table and web-based front end and provides examples of its use with the NCI's Surveillance, Epidemiology and End-Results (SEER) database.

CUNY+ Web: Usability Study of the Web-Based GUI Version of the Bibliographic Database of the City University of New York (CUNY).

ERIC Educational Resources Information Center

Oulanov, Alexei; Pajarillo, Edmund J. Y.

2002-01-01

Describes the usability evaluation of the CUNY (City University of New York) information system in Web and Graphical User Interface (GUI) versions. Compares results to an earlier usability study of the basic information database available on CUNY's wide-area network and describes the applicability of the previous usability instrument to this…

The integrated web service and genome database for agricultural plants with biotechnology information.

PubMed

Kim, Changkug; Park, Dongsuk; Seol, Youngjoo; Hahn, Jangho

2011-01-01

The National Agricultural Biotechnology Information Center (NABIC) constructed an agricultural biology-based infrastructure and developed a Web based relational database for agricultural plants with biotechnology information. The NABIC has concentrated on functional genomics of major agricultural plants, building an integrated biotechnology database for agro-biotech information that focuses on genomics of major agricultural resources. This genome database provides annotated genome information from 1,039,823 records mapped to rice, Arabidopsis, and Chinese cabbage.

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.

A decade of Web Server updates at the Bioinformatics Links Directory: 2003-2012.

PubMed

Brazas, Michelle D; Yim, David; Yeung, Winston; Ouellette, B F Francis

2012-07-01

The 2012 Bioinformatics Links Directory update marks the 10th special Web Server issue from Nucleic Acids Research. Beginning with content from their 2003 publication, the Bioinformatics Links Directory in collaboration with Nucleic Acids Research has compiled and published a comprehensive list of freely accessible, online tools, databases and resource materials for the bioinformatics and life science research communities. The past decade has exhibited significant growth and change in the types of tools, databases and resources being put forth, reflecting both technology changes and the nature of research over that time. With the addition of 90 web server tools and 12 updates from the July 2012 Web Server issue of Nucleic Acids Research, the Bioinformatics Links Directory at http://bioinformatics.ca/links_directory/ now contains an impressive 134 resources, 455 databases and 1205 web server tools, mirroring the continued activity and efforts of our field.

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.

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.

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

Full-participation of students with physical disabilities in science and engineering laboratories.

PubMed

Jeannis, Hervens; Joseph, James; Goldberg, Mary; Seelman, Katherine; Schmeler, Mark; Cooper, Rory A

2018-02-01

To conduct a literature review identifying barriers and facilitators students with physical disabilities (SwD-P) may encounter in science and engineering (S&E) laboratories. Publications were identified from 1991 to 2015 in ERIC, web of science via web of knowledge, CINAHL, SCOPUS, IEEEXplore, engineering village, business source complete and PubMed databases using search terms and synonyms for accommodations, advanced manufacturing, additive manufacturing, assistive technology (AT), barriers, engineering, facilitators, instructor, laboratory, STEM education, science, students with disabilities and technology. Twenty-two of the 233 publications that met the review's inclusion criteria were examined. Barriers and facilitators were grouped based on the international classification of functioning, disability and health framework (ICF). None of the studies directly found barriers or facilitators to SwD-P in science or engineering laboratories within postsecondary environments. The literature is not clear on the issues specifically related to SwD-P. Given these findings, further research (e.g., surveys or interviews) should be conducted to identify more details to obtain more substantial information on the barriers that may prevent SwD-P from fully participating in S&E instructional laboratories. Implications for Rehabilitation Students with disabilities remain underrepresented going into STEM careers. A need exist to help uncover barriers students with disabilities encounter in STEM laboratory. Environments. Accommodations and strategies that facilitate participation in STEM laboratory environments are promising for students with disabilities.

Acute effects of exercise on mood and EEG activity in healthy young subjects: a systematic review.

PubMed

Lattari, Eduardo; Portugal, Eduardo; Moraes, Helena; Machado, Sérgio; Santos, Tony M; Deslandes, Andrea C

2014-01-01

Electroencephalography has been used to establish the relationship among cortical activity, exercise and mood, such as asymmetry, absolute and relative power. The purpose of this study was to systematically review the influence of cortical activity on mood state induced by exercise. The Preferred Reporting Items in Systematic reviews and Meta-Analyses was followed in this study. The studies were retrieved from MEDLINE/PubMed, ISI Web of Knowledge and SciELO. Search was conducted in all databases using the following terms: EEG asymmetry, sLORETA, exercise, with affect, mood and emotions. Based on the defined criteria, a total of 727 articles were found in the search conducted in the literature (666 in Pubmed, 54 in ISI Web of Science, 2 in SciELO and 5 in other data sources). Total of 11 studies were selected which properly met the criteria for this review. Nine out of 11 studies used the frontal asymmetry, four used absolute and relative power and one used sLORETA. With regard to changes in cortical activity and mood induced by exercise, six studies attributed this result to different intensities, one to duration, one to type of exercise and one to fitness level. In general, EEG measures showed contradictory evidence of its ability to predict or modulate psychological mood states through exercise intervention.

Digital hand atlas and computer-aided bone age assessment via the Web

NASA Astrophysics Data System (ADS)

Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente

1999-07-01

A frequently used assessment method of bone age is atlas matching by a radiological examination of a hand image against a reference set of atlas patterns of normal standards. We are in a process of developing a digital hand atlas with a large standard set of normal hand and wrist images that reflect the skeletal maturity, race and sex difference, and current child development. The digital hand atlas will be used for a computer-aided bone age assessment via Web. We have designed and partially implemented a computer-aided diagnostic (CAD) system for Web-based bone age assessment. The system consists of a digital hand atlas, a relational image database and a Web-based user interface. The digital atlas is based on a large standard set of normal hand an wrist images with extracted bone objects and quantitative features. The image database uses a content- based indexing to organize the hand images and their attributes and present to users in a structured way. The Web-based user interface allows users to interact with the hand image database from browsers. Users can use a Web browser to push a clinical hand image to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, will be extracted and compared with patterns from the atlas database to assess the bone age. The relevant reference imags and the final assessment report will be sent back to the user's browser via Web. The digital atlas will remove the disadvantages of the currently out-of-date one and allow the bone age assessment to be computerized and done conveniently via Web. In this paper, we present the system design and Web-based client-server model for computer-assisted bone age assessment and our initial implementation of the digital atlas database.

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.

The integrated web service and genome database for agricultural plants with biotechnology information

PubMed Central

Kim, ChangKug; Park, DongSuk; Seol, YoungJoo; Hahn, JangHo

2011-01-01

The National Agricultural Biotechnology Information Center (NABIC) constructed an agricultural biology-based infrastructure and developed a Web based relational database for agricultural plants with biotechnology information. The NABIC has concentrated on functional genomics of major agricultural plants, building an integrated biotechnology database for agro-biotech information that focuses on genomics of major agricultural resources. This genome database provides annotated genome information from 1,039,823 records mapped to rice, Arabidopsis, and Chinese cabbage. PMID:21887015

Integrated Functional and Executional Modelling of Software Using Web-Based Databases

NASA Technical Reports Server (NTRS)

Kulkarni, Deepak; Marietta, Roberta

1998-01-01

NASA's software subsystems undergo extensive modification and updates over the operational lifetimes. It is imperative that modified software should satisfy safety goals. This report discusses the difficulties encountered in doing so and discusses a solution based on integrated modelling of software, use of automatic information extraction tools, web technology and databases. To appear in an article of Journal of Database Management.

COMPUTER-AIDED SCIENCE POLICY ANALYSIS AND RESEARCH (WEBCASPAR)

EPA Science Inventory

WebCASPAR is a database system containing information about academic science and engineering resources and is available on the World Wide Web. Included in the database is information from several of SRS's academic surveys plus information from a variety of other sources, includin...

Effectiveness of Traditional Chinese Acupuncture versus Sham Acupuncture: a Systematic Review.

PubMed

Carlos, Luís; Cruz, Lóris Aparecida Prado da; Leopoldo, Vanessa Cristina; Campos, Fabrício Ribeiro de; Almeida, Ana Maria de; Silveira, Renata Cristina de Campos Pereira

2016-08-15

to identify and synthesize the evidence from randomized clinical trials that tested the effectiveness of traditional Chinese acupuncture in relation to sham acupuncture for the treatment of hot flashes in menopausal women with breast cancer. systematic review guided by the recommendations of the Cochrane Collaboration. Citations were searched in the following databases: MEDLINE via PubMed, Web of Science, CENTRAL, CINAHL, and LILACS. A combination of the following keywords was used: breast neoplasm, acupuncture, acupuncture therapy, acupuncture points, placebos, sham treatment, hot flashes, hot flushes, menopause, climacteric, and vasomotor symptoms. a total of 272 studies were identified, five of which were selected and analyzed. Slight superiority of traditional acupuncture compared with sham acupuncture was observed; however, there were no strong statistical associations. the evidence gathered was not sufficient to affirm the effectiveness of traditional acupuncture compared with sham acupuncture. identificar e sintetizar as evidências oriundas de ensaios clínicos randomizados que testaram a efetividade da acupuntura tradicional chinesa em relação à sham acupuntura para o tratamento dos fogachos em mulheres com câncer de mama no climatério. revisão sistemática guiada pelas recomendações da Colaboração Cochrane. A busca foi realizada nas bases de dados: MEDLINE via PubMed, Web of Science, CENTRAL Cochrane, CINAHL e LILACS. Adotou-se a combinação dos descritores: breast neoplasm, acupuncture, acupuncture therapy, acupuncture points, placebos, sham treatment, hot flashes, hot flushes, menopause, climacteric, vasomotor symptoms. foram identificados 272 estudos, sendo 5 selecionados e analisados. Foi observada discreta superioridade da acupuntura tradicional em relação à sham, entretanto, sem fortes associações estatísticas. as evidências obtidas não foram suficientes para afirmar quanto à efetividade da acupuntura tradicional em relação à sham. Identificar y sintetizar la evidencia de un ensayo clínico aleatorizado que examinó la eficacia de la acupuntura tradicional en relación a la acupuntura sham para el tratamiento de sofocos en las mujeres menopáusicas con cáncer de mama. Revisión sistemática guiada por las recomendaciones de la Colaboración Cochrane. Las referencias bibliográficas se buscaron en las siguientes bases de datos: MEDLINE vía PubMed, Web of Science, Cochrane Central Register of Controlled Trials (CENTRAL), CINAHL y LILACS. Se utilizó una combinación de las siguientes palabras clave: breast neoplasm, acupuncture, acupuncture therapy, acupuncture points, placebos, sham treatment, hot flashes, hot flushes, menopause, climacteric, vasomotor symptoms. Se identificó un total de 272 estudios, cinco de los cuales fueron seleccionados y analizados. Se encontró una ligera superioridad de la acupuntura tradicional comparada con la acupuntura sham; sin embargo, no se encontraron asociaciones estadísticas fuertes. La evidencia obtenida no fue suficiente para confirmar la eficacia de la acupuntura tradicional comparada con la acupuntura sham.

EpiCollect: linking smartphones to web applications for epidemiology, ecology and community data collection.

PubMed

Aanensen, David M; Huntley, Derek M; Feil, Edward J; al-Own, Fada'a; Spratt, Brian G

2009-09-16

Epidemiologists and ecologists often collect data in the field and, on returning to their laboratory, enter their data into a database for further analysis. The recent introduction of mobile phones that utilise the open source Android operating system, and which include (among other features) both GPS and Google Maps, provide new opportunities for developing mobile phone applications, which in conjunction with web applications, allow two-way communication between field workers and their project databases. Here we describe a generic framework, consisting of mobile phone software, EpiCollect, and a web application located within www.spatialepidemiology.net. Data collected by multiple field workers can be submitted by phone, together with GPS data, to a common web database and can be displayed and analysed, along with previously collected data, using Google Maps (or Google Earth). Similarly, data from the web database can be requested and displayed on the mobile phone, again using Google Maps. Data filtering options allow the display of data submitted by the individual field workers or, for example, those data within certain values of a measured variable or a time period. Data collection frameworks utilising mobile phones with data submission to and from central databases are widely applicable and can give a field worker similar display and analysis tools on their mobile phone that they would have if viewing the data in their laboratory via the web. We demonstrate their utility for epidemiological data collection and display, and briefly discuss their application in ecological and community data collection. Furthermore, such frameworks offer great potential for recruiting 'citizen scientists' to contribute data easily to central databases through their mobile phone.

Protein Information Resource: a community resource for expert annotation of protein data

PubMed Central

Barker, Winona C.; Garavelli, John S.; Hou, Zhenglin; Huang, Hongzhan; Ledley, Robert S.; McGarvey, Peter B.; Mewes, Hans-Werner; Orcutt, Bruce C.; Pfeiffer, Friedhelm; Tsugita, Akira; Vinayaka, C. R.; Xiao, Chunlin; Yeh, Lai-Su L.; Wu, Cathy

2001-01-01

The Protein Information Resource, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the most comprehensive and expertly annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database. To provide timely and high quality annotation and promote database interoperability, the PIR-International employs rule-based and classification-driven procedures based on controlled vocabulary and standard nomenclature and includes status tags to distinguish experimentally determined from predicted protein features. The database contains about 200 000 non-redundant protein sequences, which are classified into families and superfamilies and their domains and motifs identified. Entries are extensively cross-referenced to other sequence, classification, genome, structure and activity databases. The PIR web site features search engines that use sequence similarity and database annotation to facilitate the analysis and functional identification of proteins. The PIR-Inter­national databases and search tools are accessible on the PIR web site at http://pir.georgetown.edu/ and at the MIPS web site at http://www.mips.biochem.mpg.de. The PIR-International Protein Sequence Database and other files are also available by FTP. PMID:11125041

Evaluating Web-Based Nursing Education's Effects: A Systematic Review and Meta-Analysis.

PubMed

Kang, Jiwon; Seomun, GyeongAe

2017-09-01

This systematic review and meta-analysis investigated whether using web-based nursing educational programs increases a participant's knowledge and clinical performance. We performed a meta-analysis of studies published between January 2000 and July 2016 and identified through RISS, CINAHL, ProQuest Central, Embase, the Cochrane Library, and PubMed. Eleven studies were eligible for inclusion in this analysis. The results of the meta-analysis demonstrated significant differences not only for the overall effect but also specifically for blended programs and short (2 weeks or 4 weeks) intervention periods. To present more evidence supporting the effectiveness of web-based nursing educational programs, further research is warranted.

Construction and validation of a web-based epidemiological database for inflammatory bowel diseases in Europe An EpiCom study.

PubMed

Burisch, Johan; Cukovic-Cavka, Silvija; Kaimakliotis, Ioannis; Shonová, Olga; Andersen, Vibeke; Dahlerup, Jens F; Elkjaer, Margarita; Langholz, Ebbe; Pedersen, Natalia; Salupere, Riina; Kolho, Kaija-Leena; Manninen, Pia; Lakatos, Peter Laszlo; Shuhaibar, Mary; Odes, Selwyn; Martinato, Matteo; Mihu, Ion; Magro, Fernando; Belousova, Elena; Fernandez, Alberto; Almer, Sven; Halfvarson, Jonas; Hart, Ailsa; Munkholm, Pia

2011-08-01

The EpiCom-study investigates a possible East-West-gradient in Europe in the incidence of IBD and the association with environmental factors. A secured web-based database is used to facilitate and centralize data registration. To construct and validate a web-based inception cohort database available in both English and Russian language. The EpiCom database has been constructed in collaboration with all 34 participating centers. The database was translated into Russian using forward translation, patient questionnaires were translated by simplified forward-backward translation. Data insertion implies fulfillment of international diagnostic criteria, disease activity, medical therapy, quality of life, work productivity and activity impairment, outcome of pregnancy, surgery, cancer and death. Data is secured by the WinLog3 System, developed in cooperation with the Danish Data Protection Agency. Validation of the database has been performed in two consecutive rounds, each followed by corrections in accordance with comments. The EpiCom database fulfills the requirements of the participating countries' local data security agencies by being stored at a single location. The database was found overall to be "good" or "very good" by 81% of the participants after the second validation round and the general applicability of the database was evaluated as "good" or "very good" by 77%. In the inclusion period January 1st -December 31st 2010 1336 IBD patients have been included in the database. A user-friendly, tailor-made and secure web-based inception cohort database has been successfully constructed, facilitating remote data input. The incidence of IBD in 23 European countries can be found at www.epicom-ecco.eu. Copyright © 2011 European Crohn's and Colitis Organisation. All rights reserved.

Upgrades to the TPSX Material Properties Database

NASA Technical Reports Server (NTRS)

Squire, T. H.; Milos, F. S.; Partridge, Harry (Technical Monitor)

2001-01-01

The TPSX Material Properties Database is a web-based tool that serves as a database for properties of advanced thermal protection materials. TPSX provides an easy user interface for retrieving material property information in a variety of forms, both graphical and text. The primary purpose and advantage of TPSX is to maintain a high quality source of often used thermal protection material properties in a convenient, easily accessible form, for distribution to government and aerospace industry communities. Last year a major upgrade to the TPSX web site was completed. This year, through the efforts of researchers at several NASA centers, the Office of the Chief Engineer awarded funds to update and expand the databases in TPSX. The FY01 effort focuses on updating correcting the Ames and Johnson thermal protection materials databases. In this session we will summarize the improvements made to the web site last year, report on the status of the on-going database updates, describe the planned upgrades for FY02 and FY03, and provide a demonstration of TPSX.

Village Green Project: Web-accessible Database

EPA Science Inventory

The purpose of this web-accessible database is for the public to be able to view instantaneous readings from a solar-powered air monitoring station located in a public location (prototype pilot test is outside of a library in Durham County, NC). The data are wirelessly transmitte...

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.

The Brainomics/Localizer database.

PubMed

Papadopoulos Orfanos, Dimitri; Michel, Vincent; Schwartz, Yannick; Pinel, Philippe; Moreno, Antonio; Le Bihan, Denis; Frouin, Vincent

2017-01-01

The Brainomics/Localizer database exposes part of the data collected by the in-house Localizer project, which planned to acquire four types of data from volunteer research subjects: anatomical MRI scans, functional MRI data, behavioral and demographic data, and DNA sampling. Over the years, this local project has been collecting such data from hundreds of subjects. We had selected 94 of these subjects for their complete datasets, including all four types of data, as the basis for a prior publication; the Brainomics/Localizer database publishes the data associated with these 94 subjects. Since regulatory rules prevent us from making genetic data available for download, the database serves only anatomical MRI scans, functional MRI data, behavioral and demographic data. To publish this set of heterogeneous data, we use dedicated software based on the open-source CubicWeb semantic web framework. Through genericity in the data model and flexibility in the display of data (web pages, CSV, JSON, XML), CubicWeb helps us expose these complex datasets in original and efficient ways. Copyright © 2015 Elsevier Inc. All rights reserved.

Relax with CouchDB - Into the non-relational DBMS era of Bioinformatics

PubMed Central

Manyam, Ganiraju; Payton, Michelle A.; Roth, Jack A.; Abruzzo, Lynne V.; Coombes, Kevin R.

2012-01-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. PMID:22609849

CREDO: a structural interactomics database for drug discovery

PubMed Central

Schreyer, Adrian M.; Blundell, Tom L.

2013-01-01

CREDO is a unique relational database storing all pairwise atomic interactions of inter- as well as intra-molecular contacts between small molecules and macromolecules found in experimentally determined structures from the Protein Data Bank. These interactions are integrated with further chemical and biological data. The database implements useful data structures and algorithms such as cheminformatics routines to create a comprehensive analysis platform for drug discovery. The database can be accessed through a web-based interface, downloads of data sets and web services at http://www-cryst.bioc.cam.ac.uk/credo. Database URL: http://www-cryst.bioc.cam.ac.uk/credo PMID:23868908

Web 2.0 Applications in Medicine: Trends and Topics in the Literature

PubMed Central

2015-01-01

Background The World Wide Web has changed research habits, and these changes were further expanded when “Web 2.0” became popular in 2005. Bibliometrics is a helpful tool used for describing patterns of publication, for interpreting progression over time, and the geographical distribution of research in a given field. Few studies employing bibliometrics, however, have been carried out on the correlative nature of scientific literature and Web 2.0. Objective The aim of this bibliometric analysis was to provide an overview of Web 2.0 implications in the biomedical literature. The objectives were to assess the growth rate of literature, key journals, authors, and country contributions, and to evaluate whether the various Web 2.0 applications were expressed within this biomedical literature, and if so, how. Methods A specific query with keywords chosen to be representative of Web 2.0 applications was built for the PubMed database. Articles related to Web 2.0 were downloaded in Extensible Markup Language (XML) and were processed through developed hypertext preprocessor (PHP) scripts, then imported to Microsoft Excel 2010 for data processing. Results A total of 1347 articles were included in this study. The number of articles related to Web 2.0 has been increasing from 2002 to 2012 (average annual growth rate was 106.3% with a maximum of 333% in 2005). The United States was by far the predominant country for authors, with 514 articles (54.0%; 514/952). The second and third most productive countries were the United Kingdom and Australia, with 87 (9.1%; 87/952) and 44 articles (4.6%; 44/952), respectively. Distribution of number of articles per author showed that the core population of researchers working on Web 2.0 in the medical field could be estimated at approximately 75. In total, 614 journals were identified during this analysis. Using Bradford’s law, 27 core journals were identified, among which three (Studies in Health Technology and Informatics, Journal of Medical Internet Research, and Nucleic Acids Research) produced more than 35 articles related to Web 2.0 over the period studied. A total of 274 words in the field of Web 2.0 were found after manual sorting of the 15,878 words appearing in title and abstract fields for articles. Word frequency analysis reveals “blog” as the most recurrent, followed by “wiki”, “Web 2.0”, ”social media”, “Facebook”, “social networks”, “blogger”, “cloud computing”, “Twitter”, and “blogging”. All categories of Web 2.0 applications were found, indicating the successful integration of Web 2.0 into the biomedical field. Conclusions This study shows that the biomedical community is engaged in the use of Web 2.0 and confirms its high level of interest in these tools. Therefore, changes in the ways researchers use information seem to be far from over. PMID:25842175

Columba: an integrated database of proteins, structures, and annotations.

PubMed

Trissl, Silke; Rother, Kristian; Müller, Heiko; Steinke, Thomas; Koch, Ina; Preissner, Robert; Frömmel, Cornelius; Leser, Ulf

2005-03-31

Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annotation. Compiling such sets using current web resources is tedious because the necessary data are spread over many different databases. To facilitate this task, we have created COLUMBA, an integrated database of annotations of protein structures. COLUMBA currently integrates twelve different databases, including PDB, KEGG, Swiss-Prot, CATH, SCOP, the Gene Ontology, and ENZYME. The database can be searched using either keyword search or data source-specific web forms. Users can thus quickly select and download PDB entries that, for instance, participate in a particular pathway, are classified as containing a certain CATH architecture, are annotated as having a certain molecular function in the Gene Ontology, and whose structures have a resolution under a defined threshold. The results of queries are provided in both machine-readable extensible markup language and human-readable format. The structures themselves can be viewed interactively on the web. The COLUMBA database facilitates the creation of protein structure data sets for many structure-based studies. It allows to combine queries on a number of structure-related databases not covered by other projects at present. Thus, information on both many and few protein structures can be used efficiently. The web interface for COLUMBA is available at http://www.columba-db.de.

Content and Accessibility of Shoulder and Elbow Fellowship Web Sites in the United States.

PubMed

Young, Bradley L; Oladeji, Lasun O; Cichos, Kyle; Ponce, Brent

2016-01-01

Increasing numbers of training physicians are using the Internet to gather information about graduate medical education programs. The content and accessibility of web sites that provide this information have been demonstrated to influence applicants' decisions. Assessments of orthopedic fellowship web sites including sports medicine, pediatrics, hand and spine have found varying degrees of accessibility and material. The purpose of this study was to evaluate the accessibility and content of the American Shoulder and Elbow Surgeons (ASES) fellowship web sites (SEFWs). A complete list of ASES programs was obtained from a database on the ASES web site. The accessibility of each SEFWs was assessed by the existence of a functioning link found in the database and through Google®. Then, the following content areas of each SEFWs were evaluated: fellow education, faculty/previous fellow information, and recruitment. At the time of the study, 17 of the 28 (60.7%) ASES programs had web sites accessible through Google®, and only five (17.9%) had functioning links in the ASES database. Nine programs lacked a web site. Concerning web site content, the majority of SEFWs contained information regarding research opportunities, research requirements, case descriptions, meetings and conferences, teaching responsibilities, attending faculty, the application process, and a program description. Fewer than half of the SEFWs provided information regarding rotation schedules, current fellows, previous fellows, on-call expectations, journal clubs, medical school of current fellows, residency of current fellows, employment of previous fellows, current research, and previous research. A large portion of ASES fellowship programs lacked functioning web sites, and even fewer provided functioning links through the ASES database. Valuable information for potential applicants was largely inadequate across present SEFWs.

Accessing the SEED genome databases via Web services API: tools for programmers.

PubMed

Disz, Terry; Akhter, Sajia; Cuevas, Daniel; Olson, Robert; Overbeek, Ross; Vonstein, Veronika; Stevens, Rick; Edwards, Robert A

2010-06-14

The SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between genomes and other clues to accurately and efficiently annotate microbial genomes. The backend is used as the foundation for many genome annotation tools, such as the Rapid Annotation using Subsystems Technology (RAST) server for whole genome annotation, the metagenomics RAST server for random community genome annotations, and the annotation clearinghouse for exchanging annotations from different resources. In addition to a web user interface, the SEED also provides Web services based API for programmatic access to the data in the SEED, allowing the development of third-party tools and mash-ups. The currently exposed Web services encompass over forty different methods for accessing data related to microbial genome annotations. The Web services provide comprehensive access to the database back end, allowing any programmer access to the most consistent and accurate genome annotations available. The Web services are deployed using a platform independent service-oriented approach that allows the user to choose the most suitable programming platform for their application. Example code demonstrate that Web services can be used to access the SEED using common bioinformatics programming languages such as Perl, Python, and Java. We present a novel approach to access the SEED database. Using Web services, a robust API for access to genomics data is provided, without requiring large volume downloads all at once. The API ensures timely access to the most current datasets available, including the new genomes as soon as they come online.

The GLIMS Glacier Database

NASA Astrophysics Data System (ADS)

Raup, B. H.; Khalsa, S. S.; Armstrong, R.

2007-12-01

The Global Land Ice Measurements from Space (GLIMS) project has built a geospatial and temporal database of glacier data, composed of glacier outlines and various scalar attributes. These data are being derived primarily from satellite imagery, such as from ASTER and Landsat. Each "snapshot" of a glacier is from a specific time, and the database is designed to store multiple snapshots representative of different times. We have implemented two web-based interfaces to the database; one enables exploration of the data via interactive maps (web map server), while the other allows searches based on text-field constraints. The web map server is an Open Geospatial Consortium (OGC) compliant Web Map Server (WMS) and Web Feature Server (WFS). This means that other web sites can display glacier layers from our site over the Internet, or retrieve glacier features in vector format. All components of the system are implemented using Open Source software: Linux, PostgreSQL, PostGIS (geospatial extensions to the database), MapServer (WMS and WFS), and several supporting components such as Proj.4 (a geographic projection library) and PHP. These tools are robust and provide a flexible and powerful framework for web mapping applications. As a service to the GLIMS community, the database contains metadata on all ASTER imagery acquired over glacierized terrain. Reduced-resolution of the images (browse imagery) can be viewed either as a layer in the MapServer application, or overlaid on the virtual globe within Google Earth. The interactive map application allows the user to constrain by time what data appear on the map. For example, ASTER or glacier outlines from 2002 only, or from Autumn in any year, can be displayed. The system allows users to download their selected glacier data in a choice of formats. The results of a query based on spatial selection (using a mouse) or text-field constraints can be downloaded in any of these formats: ESRI shapefiles, KML (Google Earth), MapInfo, GML (Geography Markup Language) and GMT (Generic Mapping Tools). This "clip-and-ship" function allows users to download only the data they are interested in. Our flexible web interfaces to the database, which includes various support layers (e.g. a layer to help collaborators identify satellite imagery over their region of expertise) will facilitate enhanced analysis to be undertaken on glacier systems, their distribution, and their impacts on other Earth systems.

Web application for detailed real-time database transaction monitoring for CMS condition data

NASA Astrophysics Data System (ADS)

de Gruttola, Michele; Di Guida, Salvatore; Innocente, Vincenzo; Pierro, Antonio

2012-12-01

In the upcoming LHC era, database have become an essential part for the experiments collecting data from LHC, in order to safely store, and consistently retrieve, a wide amount of data, which are produced by different sources. In the CMS experiment at CERN, all this information is stored in ORACLE databases, allocated in several servers, both inside and outside the CERN network. In this scenario, the task of monitoring different databases is a crucial database administration issue, since different information may be required depending on different users' tasks such as data transfer, inspection, planning and security issues. We present here a web application based on Python web framework and Python modules for data mining purposes. To customize the GUI we record traces of user interactions that are used to build use case models. In addition the application detects errors in database transactions (for example identify any mistake made by user, application failure, unexpected network shutdown or Structured Query Language (SQL) statement error) and provides warning messages from the different users' perspectives. Finally, in order to fullfill the requirements of the CMS experiment community, and to meet the new development in many Web client tools, our application was further developed, and new features were deployed.

WebCSD: the online portal to the Cambridge Structural Database

PubMed Central

Thomas, Ian R.; Bruno, Ian J.; Cole, Jason C.; Macrae, Clare F.; Pidcock, Elna; Wood, Peter A.

2010-01-01

WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer. PMID:22477776

Comparisons of citations in Web of Science, Scopus, and Google Scholar for articles published in general medical journals.

PubMed

Kulkarni, Abhaya V; Aziz, Brittany; Shams, Iffat; Busse, Jason W

2009-09-09

Until recently, Web of Science was the only database available to track citation counts for published articles. Other databases are now available, but their relative performance has not been established. To compare the citation count profiles of articles published in general medical journals among the citation databases of Web of Science, Scopus, and Google Scholar. Cohort study of 328 articles published in JAMA, Lancet, or the New England Journal of Medicine between October 1, 1999, and March 31, 2000. Total citation counts for each article up to June 2008 were retrieved from Web of Science, Scopus, and Google Scholar. Article characteristics were analyzed in linear regression models to determine interaction with the databases. Number of citations received by an article since publication and article characteristics associated with citation in databases. Google Scholar and Scopus retrieved more citations per article with a median of 160 (interquartile range [IQR], 83 to 324) and 149 (IQR, 78 to 289), respectively, than Web of Science (median, 122; IQR, 66 to 241) (P < .001 for both comparisons). Compared with Web of Science, Scopus retrieved more citations from non-English-language sources (median, 10.2% vs 4.1%) and reviews (30.8% vs 18.2%), and fewer citations from articles (57.2% vs 70.5%), editorials (2.1% vs 5.9%), and letters (0.8% vs 2.6%) (all P < .001). On a log(10)-transformed scale, fewer citations were found in Google Scholar to articles with declared industry funding (nonstandardized regression coefficient, -0.09; 95% confidence interval [CI], -0.15 to -0.03), reporting a study of a drug or medical device (-0.05; 95% CI, -0.11 to 0.01), or with group authorship (-0.29; 95% CI, -0.35 to -0.23). In multivariable analysis, group authorship was the only characteristic that differed among the databases; Google Scholar had significantly fewer citations to group-authored articles (-0.30; 95% CI, -0.36 to -0.23) compared with Web of Science. Web of Science, Scopus, and Google Scholar produced quantitatively and qualitatively different citation counts for articles published in 3 general medical journals.

A radiology department intranet: development and applications.

PubMed

Willing, S J; Berland, L L

1999-01-01

An intranet is a "private Internet" that uses the protocols of the World Wide Web to share information resources within a company or with the company's business partners and clients. The hardware requirements for an intranet begin with a dedicated Web server permanently connected to the departmental network. The heart of a Web server is the hypertext transfer protocol (HTTP) service, which receives a page request from a client's browser and transmits the page back to the client. Although knowledge of hypertext markup language (HTML) is not essential for authoring a Web page, a working familiarity with HTML is useful, as is knowledge of programming and database management. Security can be ensured by using scripts to write information in hidden fields or by means of "cookies." Interfacing databases and database management systems with the Web server and conforming the user interface to HTML syntax can be achieved by means of the common gateway interface (CGI), Active Server Pages (ASP), or other methods. An intranet in a radiology department could include the following types of content: on-call schedules, work schedules and a calendar, a personnel directory, resident resources, memorandums and discussion groups, software for a radiology information system, and databases.

BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers.

PubMed

Meyer, Michael J; Geske, Philip; Yu, Haiyuan

2016-05-15

Biological sequence databases are integral to efforts to characterize and understand biological molecules and share biological data. However, when analyzing these data, scientists are often left holding disparate biological currency-molecular identifiers from different databases. For downstream applications that require converting the identifiers themselves, there are many resources available, but analyzing associated loci and variants can be cumbersome if data is not given in a form amenable to particular analyses. Here we present BISQUE, a web server and customizable command-line tool for converting molecular identifiers and their contained loci and variants between different database conventions. BISQUE uses a graph traversal algorithm to generalize the conversion process for residues in the human genome, genes, transcripts and proteins, allowing for conversion across classes of molecules and in all directions through an intuitive web interface and a URL-based web service. BISQUE is freely available via the web using any major web browser (http://bisque.yulab.org/). Source code is available in a public GitHub repository (https://github.com/hyulab/BISQUE). haiyuan.yu@cornell.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A community effort to construct a gravity database for the United States and an associated Web portal

USGS Publications Warehouse

Keller, Gordon R.; Hildenbrand, T.G.; Kucks, R.; Webring, M.; Briesacher, A.; Rujawitz, K.; Hittleman, A.M.; Roman, D.R.; Winester, D.; Aldouri, R.; Seeley, J.; Rasillo, J.; Torres, R.; Hinze, W. J.; Gates, A.; Kreinovich, V.; Salayandia, L.

2006-01-01

Potential field data (gravity and magnetic measurements) are both useful and costeffective tools for many geologic investigations. Significant amounts of these data are traditionally in the public domain. A new magnetic database for North America was released in 2002, and as a result, a cooperative effort between government agencies, industry, and universities to compile an upgraded digital gravity anomaly database, grid, and map for the conterminous United States was initiated and is the subject of this paper. This database is being crafted into a data system that is accessible through a Web portal. This data system features the database, software tools, and convenient access. The Web portal will enhance the quality and quantity of data contributed to the gravity database that will be a shared community resource. The system's totally digital nature ensures that it will be flexible so that it can grow and evolve as new data, processing procedures, and modeling and visualization tools become available. Another goal of this Web-based data system is facilitation of the efforts of researchers and students who wish to collect data from regions currently not represented adequately in the database. The primary goal of upgrading the United States gravity database and this data system is to provide more reliable data that support societal and scientific investigations of national importance. An additional motivation is the international intent to compile an enhanced North American gravity database, which is critical to understanding regional geologic features, the tectonic evolution of the continent, and other issues that cross national boundaries. ?? 2006 Geological Society of America. All rights reserved.

7 CFR 3430.55 - Technical reporting.

Code of Federal Regulations, 2010 CFR

2010-01-01

... the Current Research Information System (CRIS). (b) Initial Documentation in the CRIS Database... identification of equipment purchased with any Federal funds under the award and any subsequent use of such equipment. (e) CRIS Web Site Via Internet. The CRIS database is available to the public on the worldwide web...

Online Islamic Organizations and Measuring Web Effectiveness

DTIC Science & Technology

2004-12-01

Internet Research 13 (2003) : 17-26. Retrived from ProQuest online database on 15 May 2004. Lee, Jae-Kwan. “A model for monitoring public sector...Web site strategy.” Internet Research : Electronic Networking Applications and Policy 13 (2003) : 259-266. Retrieved from Emerad online database on

Contraception supply chain challenges: a review of evidence from low- and middle-income countries.

PubMed

Mukasa, Bakali; Ali, Moazzam; Farron, Madeline; Van de Weerdt, Renee

2017-10-01

To identify and assess factors determining the functioning of supply chain systems for modern contraception in low- and middle-income countries (LMICs), and to identify challenges contributing to contraception stockouts that may lead to unmet need. Scientific databases and grey literature were searched including Database of Abstracts of Reviews of Effectiveness (DARE), PubMed, MEDLINE, POPLINE, CINAHL, Academic Search Complete, Science Direct, Web of Science, Cochrane Central, Google Scholar, WHO databases and websites of key international organisations. Studies indicated that supply chain system inefficiencies significantly affect availability of modern FP and contraception commodities in LMICs, especially in rural public facilities where distribution barriers may be acute. Supply chain failures or bottlenecks may be attributed to: weak and poorly institutionalized logistic management information systems (LMIS), poor physical infrastructures in LMICs, lack of trained and dedicated staff for supply chain management, inadequate funding, and rigid government policies on task sharing. However, there is evidence that implementing effective LMISs and involving public and private providers will distribution channels resulted in reduction in medical commodities' stockout rates. Supply chain bottlenecks contribute significantly to persistent high stockout rates for modern contraceptives in LMICs. Interventions aimed at enhancing uptake of contraceptives to reduce the problem of unmet need in LMICs should make strong commitments towards strengthening these countries' health commodities supply chain management systems. Current evidence is limited and additional, and well-designed implementation research on contraception supply chain systems is warranted to gain further understanding and insights on the determinants of supply chain bottlenecks and their impact on stockouts of contraception commodities.

Gun policy and serious mental illness: priorities for future research and policy.

PubMed

McGinty, Emma Elizabeth; Webster, Daniel W; Barry, Colleen L

2014-01-01

In response to recent mass shootings, policy makers have proposed multiple policies to prevent persons with serious mental illness from having guns. The political debate about these proposals is often uninformed by research. To address this gap, this review article summarizes the research related to gun restriction policies that focus on serious mental illness. Gun restriction policies were identified by researching the THOMAS legislative database, state legislative databases, prior review articles, and the news media. PubMed, PsycINFO, and Web of Science databases were searched for publications between 1970 and 2013 that addressed the relationship between serious mental illness and violence, the effectiveness of gun policies focused on serious mental illness, the potential for such policies to exacerbate negative public attitudes, and the potential for gun restriction policies to deter mental health treatment seeking. Limited research suggests that federal law restricting gun possession by persons with serious mental illness may prevent gun violence from this population. Promotion of policies to prevent persons with serious mental illness from having guns does not seem to exacerbate negative public attitudes toward this group. Little is known about how restricting gun possession among persons with serious mental illness affects suicide risk or mental health treatment seeking. Future studies should examine how gun restriction policies for serious mental illness affect suicide, how such policies are implemented by states, how persons with serious mental illness perceive policies that restrict their possession of guns, and how gun restriction policies influence mental health treatment seeking among persons with serious mental illness.

Robotic Gait Training for Individuals With Cerebral Palsy: A Systematic Review and Meta-Analysis.

PubMed

Carvalho, Igor; Pinto, Sérgio Medeiros; Chagas, Daniel das Virgens; Praxedes Dos Santos, Jomilto Luiz; de Sousa Oliveira, Tainá; Batista, Luiz Alberto

2017-11-01

To identify the effects of robotic gait training practices in individuals with cerebral palsy. The search was performed in the following electronic databases: PubMed, Embase, Medline (OvidSP), Cochrane Database of Systematic Reviews, Web of Science, Scopus, Compendex, IEEE Xplore, ScienceDirect, Academic Search Premier, and Physiotherapy Evidence Database. Studies were included if they fulfilled the following criteria: (1) they investigated the effects of robotic gait training, (2) they involved patients with cerebral palsy, and (3) they enrolled patients classified between levels I and IV using the Gross Motor Function Classification System. The information was extracted from the selected articles using the descriptive-analytical method. The Critical Review Form for Quantitative Studies was used to quantitate the presence of critical components in the articles. To perform the meta-analysis, the effects of the intervention were quantified by effect size (Cohen d). Of the 133 identified studies, 10 met the inclusion criteria. The meta-analysis showed positive effects on gait speed (.21 [-.09, .51]), endurance (.21 [-.06, .49]), and gross motor function in dimension D (.18 [-.10, .45]) and dimension E (0.12 [-.15, .40]). The results obtained suggest that this training benefits people with cerebral palsy, specifically by increasing walking speed and endurance and improving gross motor function. For future studies, we suggest investigating device configuration parameters and conducting a large number of randomized controlled trials with larger sample sizes and individuals with homogeneous impairment. Copyright © 2017 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Nursing students' satisfaction with bilingual teaching in nursing courses in China: A meta-analysis.

PubMed

Cai, Chunlian; Zhang, Chunmei; Wang, Yan; Xiong, Lina; Jin, Yanfei; Jin, Changde

2016-09-01

The aim of this meta-analysis is to systematically evaluate nursing students' satisfaction with the textbooks, teachers, teaching methods and overall teaching result in nursing bilingual teaching in China. The relevant cross-sectional studies were retrieved from multiple electronic databases including PubMed, Web of Science, Chinese BioMed Database (CBM), China National Knowledge Infrastructure (CNKI) and WanFang Database from inception to August 2015. Studies that measured students' satisfaction with textbooks, teachers, teaching methods, overall teaching result in nursing bilingual teaching in China as outcomes were included. The data were independently extracted using a standardized form and analyzed by STATA (version12.0). A total of thirty-four studies, including 3533 nursing students, were eligible for inclusion in the review. Meta-analyses revealed that nursing students' satisfaction rate of textbooks was 64%, 95%CI (46%, 82%), teachers' teaching attitude was 88%, 95%CI (84%, 92%), teachers' oral expression was 60%, 95%CI (38%, 81%), teachers' pronunciation was 90%, 95%CI (86%, 94%), teachers' teaching ability was 71%, 95%CI (60%, 82%), teaching methods was 69%, 95%CI (52%, 86%) and overall teaching result was 80%, 95%CI (68%, 92%). Our results show that nursing students' satisfaction with the textbooks, teachers, teaching methods and overall teaching result is not high in nursing bilingual teaching in China. These findings suggest that future directions for improving bilingual teaching in China include establishing suitable bilingual teaching material, training teaching faculty members and adopting proper teaching methods. Copyright © 2016 Elsevier Ltd. All rights reserved.

Efficacy of hypopressive abdominal gymnastics in rehabilitating the pelvic floor of women: A systematic review.

PubMed

Ruiz de Viñaspre Hernández, R

2017-12-13

Hypopressive abdominal gymnastics has been proposed as a new paradigm in rehabilitating the pelvic floor. Its claims contraindicate the recommendation for pelvic floor muscle training during the postpartum period. To determine whether hypopressive abdominal gymnastics is more effective than pelvic floor muscle training or other alternative conservative treatments for rehabilitating the pelvic floor. We consulted the databases of the Cumulative Index to Nursing and Allied Health Literature (CINAHL), the Cochrane Library, Latin American and Caribbean Health Sciences Literature (LILACS), Physiotherapy Evidence Database (PEDro), PubMed, Scopus, Trip Database and Web of Science. We selected systematic reviews, clinical trials and analytical studies that assessed the efficacy of hypopressive abdominal gymnastics in women. The measured outcomes were the strengthening of the pelvic floor muscles, the incidence of urine incontinence or prolapse and symptom remission. We included 4 clinical trials, whose quality was measured with the PEDro scale. Hypopressive gymnastics is less effective than pelvic floor muscle training for activating pelvic floor muscles, achieving closure of the levator hiatus of the anus and increasing pelvic floor muscle thickness, strength and resistance. The evidence reviewed does not support the recommendation for hypopressive abdominal gymnastics for strengthening the pelvic floor either during the postpartum period or outside that period. Pelvic floor muscle training remains the first-line treatment for pelvic floor dysfunction. There is a lack of quality clinical trials that have evaluated the efficacy of hypopressive abdominal gymnastics. Copyright © 2017 AEU. Publicado por Elsevier España, S.L.U. All rights reserved.

The impact and measurement of social dysfunction in late-life depression: an evaluation of current methods with a focus on wearable technology.

PubMed

Hodgetts, Sophie; Gallagher, Peter; Stow, Daniel; Ferrier, I Nicol; O'Brien, John T

2017-03-01

Depression is known to negatively impact social functioning, with patients commonly reporting difficulties maintaining social relationships. Moreover, a large body of evidence suggests poor social functioning is not only present in depression but that social functioning is an important factor in illness course and outcome. In addition, good social relationships can play a protective role against the onset of depressive symptoms, particularly in late-life depression. However, the majority of research in this area has employed self-report measures of social function. This approach is problematic, as due to their reliance on memory, such measures are prone to error from the neurocognitive impairments of depression, as well as mood-congruent biases. Narrative review based on searches of the Web of Science and PubMed database(s) from the start of the databases, until the end of 2015. The present review provides an overview of the literature on social functioning in (late-life) depression and discusses the potential for new technologies to improve the measurement of social function in depressed older adults. In particular, the use of wearable technology to collect direct, objective measures of social activity, such as physical activity and speech, is considered. In order to develop a greater understanding of social functioning in late-life depression, future research should include the development and validation of more direct, objective measures in conjunction with subjective self-report measures. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

CliniWeb: managing clinical information on the World Wide Web.

PubMed

Hersh, W R; Brown, K E; Donohoe, L C; Campbell, E M; Horacek, A E

1996-01-01

The World Wide Web is a powerful new way to deliver on-line clinical information, but several problems limit its value to health care professionals: content is highly distributed and difficult to find, clinical information is not separated from non-clinical information, and the current Web technology is unable to support some advanced retrieval capabilities. A system called CliniWeb has been developed to address these problems. CliniWeb is an index to clinical information on the World Wide Web, providing a browsing and searching interface to clinical content at the level of the health care student or provider. Its database contains a list of clinical information resources on the Web that are indexed by terms from the Medical Subject Headings disease tree and retrieved with the assistance of SAPHIRE. Limitations of the processes used to build the database are discussed, together with directions for future research.

Information System through ANIS at CeSAM

NASA Astrophysics Data System (ADS)

Moreau, C.; Agneray, F.; Gimenez, S.

2015-09-01

ANIS (AstroNomical Information System) is a web generic tool developed at CeSAM to facilitate and standardize the implementation of astronomical data of various kinds through private and/or public dedicated Information Systems. The architecture of ANIS is composed of a database server which contains the project data, a web user interface template which provides high level services (search, extract and display imaging and spectroscopic data using a combination of criteria, an object list, a sql query module or a cone search interfaces), a framework composed of several packages, and a metadata database managed by a web administration entity. The process to implement a new ANIS instance at CeSAM is easy and fast : the scientific project has to submit data or a data secure access, the CeSAM team installs the new instance (web interface template and the metadata database), and the project administrator can configure the instance with the web ANIS-administration entity. Currently, the CeSAM offers through ANIS a web access to VO compliant Information Systems for different projects (HeDaM, HST-COSMOS, CFHTLS-ZPhots, ExoDAT,...).

Analysis Tool Web Services from the EMBL-EBI.

PubMed

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

2013-07-01

Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.

Analysis Tool Web Services from the EMBL-EBI

PubMed Central

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

2013-01-01

Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods. PMID:23671338

The use of eHealth to promote physical activity in cancer survivors: a systematic review.

PubMed

Haberlin, Ciarán; O'Dwyer, Tom; Mockler, David; Moran, Jonathan; O'Donnell, Dearbhaile M; Broderick, Julie

2018-06-16

Achieving adequate levels of physical activity (PA) and avoiding sedentary behaviour are particularly important in cancer survivors. eHealth, which includes, but is not limited to, the delivery of health information through Internet and mobile technologies, is an emerging concept in healthcare which may present opportunities to improve PA in cancer survivors. The aim of this systematic review was to explore the effects of eHealth in the promotion of PA among cancer survivors. Suitable articles were searched using PubMed, CINAHL, EMBASE, PsychInfo, Web of Science and SCOPUS databases using a combination of keywords and medical subject headings. Articles were included if they described an eHealth intervention designed to improve PA in cancer survivors. Two reviewers screened studies for inclusion. In total, 1065 articles were considered. Ten studies met eligibility criteria. A variety of platforms designed to increase PA were described in these studies: web application (app) (n = 5), web and mobile application (n = 2), mobile app (n = 1), website only (n = 1), e-mail based (n = 1). All studies measured PA using self-report outcome measures with the exception of one study which measured steps using a Fitbit. Meta-analysis was not performed because of variations in study design and interventions. All studies reported improvements in PA, with 8/10 studies reporting statistically significant changes. The use of eHealth to promote PA in cancer survivors is a relatively new concept, which is supported by the recent emergent evidence described in this review. eHealth shows promise as a means of promoting and increasing daily PA, but further high-quality, longer term studies are needed to establish the feasibility and effectiveness of eHealth platforms aimed at that goal.

Internet delivered diabetes self-management education: a review.

PubMed

Pereira, Katherine; Phillips, Beth; Johnson, Constance; Vorderstrasse, Allison

2015-01-01

Diabetes self-management education is a cornerstone of successful diabetes management. Various methods have been used to reach the increasing numbers of patients with diabetes, including Internet-based education. The purpose of this article is to review various delivery methods of Internet diabetes education that have been evaluated, as well as their effectiveness in improving diabetes-related outcomes. Literature was identified in the Cumulative Index to Nursing and Allied Health Literature (CINAHL), PubMed, Medline, EBSCO, the Cochrane Library, and the Web of Science databases through searches using the following terms: "type 2 diabetes AND internet/web based AND education" and "type 2 diabetes AND diabetes self-management education (DSME) AND web-based/internet OR technology assisted education." The search was limited to English language articles published in the last 10 years. The search yielded 111 articles; of these, 14 met criteria for inclusion in this review. Nine studies were randomized controlled trials, and study lengths varied from 2 weeks to 24 months, for a total of 2,802 participants. DSME delivered via the Internet is effective at improving measures of glycemic control and diabetes knowledge compared with usual care. In addition, results demonstrate that improved eating habits and increased attendance at clinic appointments occur after the online DSME, although engagement and usage of Internet materials waned over time. Interventions that included an element of interaction with healthcare providers were seen as attractive to participants. Internet-delivered diabetes education has the added benefit of easier access for many individuals, and patients can self-pace themselves through materials. More research on the cost-benefits of Internet diabetes education and best methods to maintain patient engagement are needed, along with more studies assessing the long-term impact of Internet-delivered DSME.

Web-Based Versus Usual Care and Other Formats of Decision Aids to Support Prostate Cancer Screening Decisions: Systematic Review and Meta-Analysis.

PubMed

Baptista, Sofia; Teles Sampaio, Elvira; Heleno, Bruno; Azevedo, Luís Filipe; Martins, Carlos

2018-06-26

Prostate cancer is a leading cause of cancer among men. Because screening for prostate cancer is a controversial issue, many experts in the field have defended the use of shared decision making using validated decision aids, which can be presented in different formats (eg, written, multimedia, Web). Recent studies have concluded that decision aids improve knowledge and reduce decisional conflict. This meta-analysis aimed to investigate the impact of using Web-based decision aids to support men's prostate cancer screening decisions in comparison with usual care and other formats of decision aids. We searched PubMed, CINAHL, PsycINFO, and Cochrane CENTRAL databases up to November 2016. This search identified randomized controlled trials, which assessed Web-based decision aids for men making a prostate cancer screening decision and reported quality of decision-making outcomes. Two reviewers independently screened citations for inclusion criteria, extracted data, and assessed risk of bias. Using a random-effects model, meta-analyses were conducted pooling results using mean differences (MD), standardized mean differences (SMD), and relative risks (RR). Of 2406 unique citations, 7 randomized controlled trials met the inclusion criteria. For risk of bias, selective outcome reporting and participant/personnel blinding were mostly rated as unclear due to inadequate reporting. Based on seven items, two studies had high risk of bias for one item. Compared to usual care, Web-based decision aids increased knowledge (SMD 0.46; 95% CI 0.18-0.75), reduced decisional conflict (MD -7.07%; 95% CI -9.44 to -4.71), and reduced the practitioner control role in the decision-making process (RR 0.50; 95% CI 0.31-0.81). Web-based decision aids compared to printed decision aids yielded no differences in knowledge, decisional conflict, and participation in decision or screening behaviors. Compared to video decision aids, Web-based decision aids showed lower average knowledge scores (SMD -0.50; 95% CI -0.88 to -0.12) and a slight decrease in prostate-specific antigen screening (RR 1.12; 95% CI 1.01-1.25). According to this analysis, Web-based decision aids performed similarly to alternative formats (ie, printed, video) for the assessed decision-quality outcomes. The low cost, readiness, availability, and anonymity of the Web can be an advantage for increasing access to decision aids that support prostate cancer screening decisions among men. ©Sofia Baptista, Elvira Teles Sampaio, Bruno Heleno, Luís Filipe Azevedo, Carlos Martins. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 26.06.2018.

Deep Web video

ScienceCinema

None Available

2018-02-06

To make the web work better for science, OSTI has developed state-of-the-art technologies and services including a deep web search capability. The deep web includes content in searchable databases available to web users but not accessible by popular search engines, such as Google. This video provides an introduction to the deep web search engine.

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

GALT protein database, a bioinformatics resource for the management and analysis of structural features of a galactosemia-related protein and its mutants.

PubMed

d'Acierno, Antonio; Facchiano, Angelo; Marabotti, Anna

2009-06-01

We describe the GALT-Prot database and its related web-based application that have been developed to collect information about the structural and functional effects of mutations on the human enzyme galactose-1-phosphate uridyltransferase (GALT) involved in the genetic disease named galactosemia type I. Besides a list of missense mutations at gene and protein sequence levels, GALT-Prot reports the analysis results of mutant GALT structures. In addition to the structural information about the wild-type enzyme, the database also includes structures of over 100 single point mutants simulated by means of a computational procedure, and the analysis to each mutant was made with several bioinformatics programs in order to investigate the effect of the mutations. The web-based interface allows querying of the database, and several links are also provided in order to guarantee a high integration with other resources already present on the web. Moreover, the architecture of the database and the web application is flexible and can be easily adapted to store data related to other proteins with point mutations. GALT-Prot is freely available at http://bioinformatica.isa.cnr.it/GALT/.

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/.

Efficacy and Safety of L-Carnitine Treatment for Chronic Heart Failure: A Meta-Analysis of Randomized Controlled Trials.

PubMed

Song, Xiaolong; Qu, Huiyan; Yang, Zongguo; Rong, Jingfeng; Cai, Wan; Zhou, Hua

2017-01-01

Background . Whether additional benefit can be achieved with the use of L-carnitine (L-C) in patients with chronic heart failure (CHF) remains controversial. We therefore performed a meta-analysis of randomized controlled trials (RCTs) to evaluate the effects of L-C treatment in CHF patients. Methods . Pubmed, Ovid Embase, Web of Science, and Cochrane Library databases, Chinese National Knowledge Infrastructure (CNKI) database, Wanfang database, Chinese Biomedical (CBM) database, and Chinese Science and Technology Periodicals database (VIP) until September 30, 2016, were identified. Studies that met the inclusion criteria were systematically evaluated by two reviewers independently. Results . 17 RCTs with 1625 CHF patients were included in this analysis. L-C treatment in CHF was associated with considerable improvement in overall efficacy (OR = 3.47, P < 0.01), left ventricular ejection fraction (LVEF) (WMD: 4.14%, P = 0.01), strike volume (SV) (WMD: 8.21 ml, P = 0.01), cardiac output (CO) (WMD: 0.88 L/min, P < 0.01), and E/A (WMD: 0.23, P < 0.01). Moreover, treatment with L-C also resulted in significant decrease in serum levels of BNP (WMD: -124.60 pg/ml, P = 0.01), serum levels of NT-proBNP (WMD: -510.36 pg/ml, P < 0.01), LVESD (WMD: -4.06 mm, P < 0.01), LVEDD (WMD: -4.79 mm, P < 0.01), and LVESV (WMD: -20.16 ml, 95% CI: -35.65 to -4.67, P < 0.01). However, there were no significant differences in all-cause mortality, 6-minute walk, and adverse events between L-C and control groups. Conclusions . L-C treatment is effective for CHF patients in improving clinical symptoms and cardiac functions, decreasing serum levels of BNP and NT-proBNP. And it has a good tolerance.

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

PubMed

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

2016-03-11

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

Systematic review and technological overview of the antimicrobial activity of Tagetes minuta and future perspectives.

PubMed

Santos, Daniela Coelho Dos; Schneider, Lara Rodrigues; da Silva Barboza, Andressa; Diniz Campos, Ângela; Lund, Rafael Guerra

2017-08-17

The antimicrobial potential of Tagetes minuta was correlated with its traditional use as antibacterial, insecticidal, biocide, disinfectant, anthelminthic, antifungal, and antiseptic agent as well as its use in urinary tract infections. This study aimed to systematically review articles and patents regarding the antimicrobial activity of T. minuta and give rise to perspectives on this plant as a potential antimicrobial agent. A literature search of studies published between 1997 and 2015 was conducted over five databases: MedLine (PubMed), Web of Science, Scopus, Google Scholar, Portal de Periódicos Capes and SciFinder, grey literature was explored using the System for Information on Dissertations database, and theses were searched using the ProQuest Dissertations and Theses Full text database and the Periódicos Capes Theses database. Additionally, the following databases for patents were analysed: United States Patent and Trademark Office (USPTO), Google Patents, National Institute of Industrial Property (INPI) and Espacenet patent search (EPO). The data were tabulated and analysed using Microsoft Office Excel 2010. After title screening, 51 studies remained and this number decreased to 26 after careful examinations of the abstracts. The full texts of these 26 studies were assessed to check if they were eligible. Among them, 3 were excluded for not having full text access, and 11 were excluded because they did not fit the inclusion criteria, which left 10 articles for this systematic review. The same process was conducted for the patent search, resulting in 4 patents being included in this study. Recent advances highlighted by this review may shed light on future directions of studies concerning T. minuta as a novel antimicrobial agent, which should be repeatedly proven in future animal and clinical studies. Although more evidence on its specificity and clinical efficacy are necessary to support its clinical use, T. minuta is expected to be a highly effective, safe and affordable treatment for infectious diseases. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database.

PubMed

Miao, Zhichao; Westhof, Eric

2016-07-08

RBscore&NBench combines a web server, RBscore and a database, NBench. RBscore predicts RNA-/DNA-binding residues in proteins and visualizes the prediction scores and features on protein structures. The scoring scheme of RBscore directly links feature values to nucleic acid binding probabilities and illustrates the nucleic acid binding energy funnel on the protein surface. To avoid dataset, binding site definition and assessment metric biases, we compared RBscore with 18 web servers and 3 stand-alone programs on 41 datasets, which demonstrated the high and stable accuracy of RBscore. A comprehensive comparison led us to develop a benchmark database named NBench. The web server is available on: http://ahsoka.u-strasbg.fr/rbscorenbench/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

S/MARt DB: a database on scaffold/matrix attached regions.

PubMed

Liebich, Ines; Bode, Jürgen; Frisch, Matthias; Wingender, Edgar

2002-01-01

S/MARt DB, the S/MAR transaction database, is a relational database covering scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins that are involved in the chromosomal attachment to the nuclear scaffold. The data are mainly extracted from original publications, but a World Wide Web interface for direct submissions is also available. S/MARt DB is closely linked to the TRANSFAC database on transcription factors and their binding sites. It is freely accessible through the World Wide Web (http://transfac.gbf.de/SMARtDB/) for non-profit research.

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.

Prognostic significance of pretreatment plasma fibrinogen level in patients with digestive system tumors: a meta-analysis.

PubMed

Ji, Rui; Ren, Qian; Bai, Suyang; Wang, Yuping; Zhou, Yongning

2018-06-01

High pretreatment levels of plasma fibrinogen have been widely reported to be a potential predictor of prognosis in digestive system tumors; however, the conclusions are not consistent. Therefore, we performed a meta-analysis to comprehensively assess the prognostic roles of high pretreatment plasma fibrinogen levels in digestive system tumors. We searched for eligible studies in the PubMed, Embase, and Web of Science electronic databases for publications from the database inception to 1 September 2017. The endpoints of interest included overall survival, disease-free survival, and recurrence-free survival. We investigated the relationship between fibrinogenemia and overall survival in colorectal cancer (10 studies), gastric cancer (6), pancreatic cancer (6), hepatocellular carcinoma (7), and esophageal squamous cell carcinoma (10); the pooled results indicated that fibrinogenemia was significantly related to a worse overall survival (hazard ratio (HR) 1.73; 95% confidence interval (CI) 1.52, 1.97; P <0.001; HR 1.71; 95% CI 1.28, 2.28; P <0.001; HR 1.57; 95% CI 1.13, 2.17; P = 0.007; HR 1.89; 95% CI 1.57, 2.27; P <0.001, and HR 1.67; 95% CI 1.35, 2.07; P <0.001). Taken together, an increased pretreatment plasma fibrinogen level was related to worse survival in digestive system tumors, indicating that it could be a useful prognostic marker in these types of tumors.

The SPO11-C631T gene polymorphism and male infertility risk: a meta-analysis.

PubMed

Ren, Zheng-Ju; Ren, Peng-Wei; Yang, Bo; Liao, Jian; Liu, Sheng-Zhuo; Fang, Kun; Ren, Shang-Qing; Liu, Liang-Ren; Dong, Qiang

2017-11-01

To evaluate the association between the SPO11 gene C631T polymorphism and the risk of male infertility. We conducted a search on PubMed, Embase, Web of Science, Chinese National Knowledge Infrastructure (CNKI), China biology medical literature database (CBM), VIP, and Chinese literature database (Wan Fang) on 31 March 2016. Odds ratio (OR) and 95% confidence interval (95%CI) were used to assess the strength of associations. A total of five studies including 542 cases and 510 controls were involved in this meta-analysis. The pooled results indicated that the SPO11 gene C631T polymorphism was significantly associated with increased risk of male infertility (TT + CT vs. CC: OR = 4.14, 95%CI = 2.48-6.89; CT vs. CC: OR = 4.34, 95%CI = 2.56-7.34; T vs. C: OR = 4.35, 95%CI = 2.58-7.34). Subgroup analysis of different countries proved the relationship between SPO11 gene C631T polymorphism and male infertility risk in Chinese, but not in Iranian peoples. In conclusion, this study suggested that SPO11 gene C631T polymorphism may contribute as a genetic factor susceptible to cause male infertility. Furthermore, more large sample and representative population-based cases and well-matched controls are needed to validate our results.

Effect of ankle-foot orthosis on postural control after stroke: a systematic review.

PubMed

Guerra Padilla, M; Molina Rueda, F; Alguacil Diego, I M

2014-09-01

Stroke is currently the main cause of permanent disability in adults. The impairments are a combination of sensory, motor, cognitive and emotional changes that result in restrictions on the ability to perform basic activities of daily living (BADL). Postural control is affected and causes problems with static and dynamic balance, thus increasing the risk of falls and secondary injuries. The purpose of this review was to compile the literature to date, and assess the impact of ankle-foot orthosis (AFO) on postural control and gait in individuals who have suffered a stroke. The review included randomised and controlled trials that examined the effects of AFO in stroke patients between 18 and 80 years old, with acute or chronic evolution. No search limits on the date of the studies were included, and the search lasted until April 2011. The following databases were used: Pubmed, Trip Database, Cochrane library, Embase, ISI Web Knowledge, CINHAL and PEDro. Intervention succeeded in improving some gait parameters, such as speed and cadence. However it is not clear if there was improvement in the symmetry, postural sway or balance. Because of the limitations of this systematic review, due to the clinical diversity of the studies and the methodological limitations, 0these results should be considered with caution. Copyright © 2011 Sociedad Española de Neurología. Published by Elsevier Espana. All rights reserved.

Quantitative instruments used to assess children's sense of smell: a review article.

PubMed

Moura, Raissa Gomes Fonseca; Cunha, Daniele Andrade; Gomes, Ana Carolina de Lima Gusmão; Silva, Hilton Justino da

2014-01-01

To systematically gather from the literature available the quantitative instruments used to assess the sense of smell in studies carried out with children. The present study included a survey in the Pubmed and Bireme platforms and in the databases of MedLine, Lilacs, regional SciELO and Web of Science, followed by selection and critical analysis of the articles found and chosen. We selected original articles related to the topic in question, conducted only with children in Portuguese, English, and Spanish. We excluded studies addressing other phases of human development, exclusively or concurrently with the pediatric population; studies on animals; literature review articles; dissertations; book chapters; case study articles; and editorials. A book report protocol was created for this study, including the following information: author, department, year, location, population/sample, age, purpose of the study, methods, and main results. We found 8,451 articles by typing keywords and identifiers. Out of this total, 5,928 were excluded by the title, 2,366 by the abstract, and 123 after we read the full text. Thus, 34 articles were selected, of which 28 were repeated in the databases, totalizing 6 articles analyzed in this review. We observed a lack of standardization of the quantitative instruments used to assess children's sense of smell, with great variability in the methodology of the tests, which reduces the effectiveness and reliability of the results.