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At least 343 records · Page 19Linked to original sources

Development and evaluation of evidence-based nursing (EBN) filters and related databases.

OBJECTIVES: Difficulties encountered in the retrieval of evidence-based nursing (EBN) literature and recognition of terminology, research focus, and design differences between evidence-based medicine and nursing led to the realization that nursing needs its own filter strategies for evidence-based practice. This article describes the development and evaluation of filters that facilitate evidence-based nursing searches. METHODS: An inductive, multistep methodology was employed. A sleep search strategy was developed for uniform application to all filters for filter development and evaluation purposes. An EBN matrix was next developed as a framework to illustrate conceptually the placement of nursing-sensitive filters along two axes: horizontally, an adapted nursing process, and vertically, levels of evidence. Nursing diagnosis, patient outcomes, and primary data filters were developed recursively. Through an interface with the PubMed search engine, the EBN matrix filters were inserted into a database that executes filter searches, retrieves citations, and stores and updates retrieved citations sets hourly. For evaluation purposes, the filters were subjected to sensitivity and specificity analyses and retrieval set comparisons. Once the evaluation was complete, hyperlinks providing access to any one or a combination of completed filters to the EBN matrix were created. Subject searches on any topic may be applied to the filters, which interface with PubMed. RESULTS: Sensitivity and specificity for the combined nursing diagnosis and primary data filter were 64% and 99%, respectively; for the patient outcomes filter, the results were 75% and 71%, respectively. Comparisons were made between the EBN matrix filters (nursing diagnosis and primary data) and PubMed's Clinical Queries (diagnosis and sensitivity) filters. Additional comparisons examined publication types and indexing differences. Review articles accounted for the majority of the publication type differences, because "review" was accepted by the CQ but was "NOT'd" by the EBN filter. Indexing comparisons revealed that although the term "nursing diagnosis" is in Medical Subject Headings (MeSH), the nursing diagnoses themselves (e.g., sleep deprivation, disturbed sleep pattern) are not indexed as nursing diagnoses. As a result, abstracts deemed to be appropriate nursing diagnosis by the EBN filter were not accepted by the CQ diagnosis filter. CONCLUSIONS: The EBN filter capture of desired articles may be enhanced by further refinement to achieve a greater degree of filter sensitivity. Retrieval set comparisons revealed publication type differences and indexing issues. The EBN matrix filter "NOT'd" out "review," while the CQ filter did not. Indexing issues were identified that explained the retrieval of articles deemed appropriate by the EBN filter matrix but not included in the CQ retrieval. These results have MeSH definition and indexing implications as well as implications for clinical decision support in nursing practice.

Databases, Bibliographic↗

Internet resources for family physicians.

PROBLEM BEING ADDRESSED: The internet has experienced tremendous growth over the past few years and has many resources in the field of family medicine. However, many family physicians remain unaware of how the Internet can be used to enhance their practice and of how to gain access to this powerful tool. OBJECTIVE OF PROGRAM: To characterize components of the Internet, to explore how family physicians can use the Internet to enhance practice, and to increase awareness of how to gain access to Internet sites relevant to family medicine. MAIN COMPONENTS OF THE PROGRAM: An on-line search through the World Wide Web was conducted using multiple search engines including Lycos, WebCrawler, OpenText, and Yahoo as well as a conventional MEDLINE search of Internet publications for the past 5 years. A website containing an evolving selection of resources can be found at http:@dfcm 18.med.utoronto.ca/anthes/hpgdfcm1.htm. CONCLUSION: The Internet has useful applications and resources for family physicians including rapid communication between physicians, access to medical literature, continuing medical education programs, and lists of patient support and discussion groups.

Attitude to Computers↗

Configuration space analysis of common cost functions in radiotherapy beam-weight optimization algorithms.

The successful implementation of downhill search engines in radiotherapy optimization algorithms depends on the absence of local minima in the search space. Such techniques are much faster than stochastic optimization methods but may become trapped in local minima if they exist. A technique known as 'configuration space analysis' was applied to examine the search space of cost functions used in radiotherapy beam-weight optimization algorithms. A downhill-simplex beam-weight optimization algorithm was run repeatedly to produce a frequency distribution of final cost values. By plotting the frequency distribution as a function of final cost, the existence of local minima can be determined. Common cost functions such as the quadratic deviation of dose to the planning target volume (PTV), integral dose to organs-at-risk (OARs), dose-threshold and dose-volume constraints for OARs were studied. Combinations of the cost functions were also considered. The simple cost function terms such as the quadratic PTV dose and integral dose to OAR cost function terms are not susceptible to local minima. In contrast, dose-threshold and dose-volume OAR constraint cost function terms are able to produce local minima in the example case studied.

Algorithms↗

The Celera Discovery System.

The Celera Discovery System (CDS) is a web-accessible research workbench for mining genomic and related biological information. Users have access to the human and mouse genome sequences with annotation presented in summary form in BioMolecule Reports for genes, transcripts and proteins. Over 40 additional databases are available, including sequence, mapping, mutation, genetic variation, mRNA expression, protein structure, motif and classification data. Data are accessible by browsing reports, through a variety of interactive graphical viewers, and by advanced query capability provided by the LION SRS search engine. A growing number of sequence analysis tools are available, including sequence similarity, pattern searching, multiple sequence alignment and Hidden Markov Model search. A user workspace keeps track of queries and analyses. CDS is widely used by the academic research community and requires a subscription for access. The system and academic pricing information are available at http://cds.celera.com.

Animals↗

Peritoneal catheters and exit-site practices toward optimum peritoneal access: a review of current developments.

OBJECTIVE: This review updates the 1998 International Society for Peritoneal Dialysis (ISPD) recommendations for peritoneal dialysis catheters and exit-site practices (Gokal R, et al. Peritoneal catheters and exit-site practices toward optimum peritonealaccess: 1998 update. Perit Dial Int 1998; 18:11-33.) DESIGN DATA SOURCES: The Ovid and PubMed search engines were used to review the Medline databases of January 1980 through June 2003. Searches were restricted to human data; primary key word searches included dialysis, peritoneal dialysis, and continuous ambulatory peritoneal dialysis cross referenced with access, catheter, dialysis catheter, peritoneal dialysis catheter, and Tenckhoff catheter. Related searches were provided via the PubMed related articles link. STUDY SELECTION: Reports were selected if they provided identifiable information on catheter design, catheter placement technique, and survival or placement complications. Reports without such data were excluded from review. Each study was then categorized by its characteristics: single-center or multicenter; retrospective or prospective; controlled trial, with or without random patient assignment; or review article. MAIN RESULTS: There are few randomized controlled evaluations testing how catheter design and/or placement influence long-term survival and function, and these are typically conducted at a single center. The majority of reports represent retrospective single-center experiences, and these are supplemented by occasional multicenter data registries. CONCLUSIONS: There is substantial variability in catheter outcomes between centers, and this variability is more closely correlated with operator and center characteristics than with catheter design. Some catheter designs appear to impact long-term catheter success, and, in some cases, specific patient characteristics and dialysis formats combine with specific catheter designs to influence catheter survival. Most reporters prefer two-cuff designs and placement of the deep cuff at an intramuscular location. Intramuscular cuff placement results in fewer pericatheter leaks and hernias, but makes catheter removal more difficult. High-risk patients (those with previous pelvic surgery) benefit from visual inspection of the peritoneum during catheter placement, and in randomized controlled trials, catheters with pre-shaped arcuate subcutaneous segments ("swan neck" designs) reduce the risk of early drainage failure via "migration."

Catheterization↗

Health information-seeking behaviour in adolescence: the place of the internet.

The internet is one of a range of health information sources available to adolescents. It is recognised that young people have difficulties accessing traditional health services; in theory, the internet offers them confidential and convenient access to an unprecedented level of information about a diverse range of subjects. This could redress adolescents' state of relative health 'information poverty', compared to adults. This paper seeks to explore United Kingdom (UK) and United States (US) adolescents' perceptions and experiences of using the internet to find information about health and medicines, in the context of the other health information sources that are available to them. The study involved a series of 26 single-gender focus groups with 157 English-speaking students aged 11-19 years from the UK and the US. Many students reported that the internet was their primary general information source. Information sources were defined during analysis in terms of previous experience of the source, saliency of the available information, and credibility of the source (defined in terms of expertise, trustworthiness and empathy). Most focus group participants had extensive personal experience with the internet and some information providers therein (notably search engines). Internet health information was regarded generally as salient. Its saliency was increased through active searching and personalisation. Perceived credibility of the internet varied because expertise and trustworthiness were sometimes difficult to determine, and empathy could be facilitated through online communities but the individual could control disclosure. The internet combines positive features of traditional lay and professional, personal and impersonal sources. Although it is unlikely to supplant the role of trusted peers and adults, the internet has found an important place among adolescents' repertory of health information sources.

Adolescent↗

Effectiveness of retrieval in similarity searches of chemical databases: a review of performance measures.

This article reviews measures for evaluating the effectiveness of similarity searches in chemical databases, drawing principally upon the many measures that have been described previously for evaluating the performance of text search engines. The use of the various measures is exemplified by fragment-based 2D similarity searches on several databases for which both structural and bioactivity data are available. It is concluded that the cumulative recall and G-H score measures are the most useful of those tested.

Chemical Phenomena↗

[Clinical practice guideline on peritoneal carcinomatosis treatment using surgical cytoreduction and hyperthermic intraoperative intraperitoneal chemotherapy].

In 2005, the Comité de l'évolution des pratiques en oncologie (CEPO) took it upon itself to develop a clinical practice guideline to determine the clinical value of surgical cytoreduction followed by hyperthermic intraoperative intraperitoneal chemotherapy (HIPEC) for treating peritoneal carcinomatosis stemming from colorectal cancer, cancers of the appendix and stomach, pseudomyxoma peritonei, and mesothelioma of the peritoneum. A review of the scientific literature was performed using the PubMed search engine. The period covered extended from January 1990 to January 2006, inclusively. The scientific literature search was limited to clinical trials (minimum phase II) and organizations elaborating clinical practice recommendations. Twenty-six studies were identified. Of these, only one was phase III. Although some of these studies have demonstrated a benefit from this treatment in terms of patient survival, HIPEC remains a complex procedure whose optimal use is uncertain. Given the morbidity and mortality associated with this treatment, this procedure requires a high level of expertise. Considering the evidence available, the CEPO recommends: 1) that complete cytoreduction followed by HIPEC be used in a clinical research context only, preferably in the presence of an isolated peritoneal carcinomatosis stemming from colorectal cancer, cancer of the appendix, peritoneal pseudomyxoma, or mesothelioma of the peritoneum; 2) that studies be conducted only in specialized centers with the necessary expertise and technical resources.

Antineoplastic Agents↗

Large-gel two-dimensional electrophoresis-matrix assisted laser desorption/ionization-time of flight-mass spectrometry: an analytical challenge for studying complex protein mixtures.

The large-gel two-dimensional electrophoresis (2-DE) technique, developed by Klose and co-workers over the past 25 years, provides the resolving power necessary to separate crude proteome extracts of higher eukaryotes. Matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) provides the sample throughput necessary to identify thousands of different protein species in an adequate time period. Spot excision, in situ proteolysis, and extraction of the cleavage products from the gel matrix, peptide purification and concentration as well as the mass spectrometric sample preparation are the crucial steps that interface the two analytical techniques. Today, these routines and not the mass spectrometric instrumentation determine how many protein digests can be analyzed per day per instrument. The present paper focuses on this analytical interface and reports on an integrated protocol and technology developed in our laboratory. Automated identification of proteins in sequence databases by mass spectrometric peptide mapping requires a powerful search engine that makes full use of the information contained in the experimental data, and scores the search results accordingly. This challenge is heading a second part of the paper.

Animals↗

Improved classification of mass spectrometry database search results using newer machine learning approaches.

Manual analysis of mass spectrometry data is a current bottleneck in high throughput proteomics. In particular, the need to manually validate the results of mass spectrometry database searching algorithms can be prohibitively time-consuming. Development of software tools that attempt to quantify the confidence in the assignment of a protein or peptide identity to a mass spectrum is an area of active interest. We sought to extend work in this area by investigating the potential of recent machine learning algorithms to improve the accuracy of these approaches and as a flexible framework for accommodating new data features. Specifically we demonstrated the ability of boosting and random forest approaches to improve the discrimination of true hits from false positive identifications in the results of mass spectrometry database search engines compared with thresholding and other machine learning approaches. We accommodated additional attributes obtainable from database search results, including a factor addressing proton mobility. Performance was evaluated using publically available electrospray data and a new collection of MALDI data generated from purified human reference proteins.

Amino Acid Sequence↗

IndexToolkit: an open source toolbox to index protein databases for high-throughput proteomics.

UNLABELLED: A software package, IndexToolkit, aimed at overcoming the disadvantage of FASTA-format databases for frequent searching, is developed to utilize an indexing strategy to substantially accelerate sequence queries. IndexToolkit includes user-friendly tools and an Application Programming Interface (API) to facilitate indexing, storage and retrieval of protein sequence databases. As open source, it provides a sequence-retrieval developing framework, which is easily extensible for high-speed-request proteomic applications, such as database searching or modification discovering. We applied IndexToolkit to database searching engine pFind to demonstrate its effect. Experimental studies show that IndexToolkit is able to support significantly faster searches of protein database. AVAILABILITY: The IndexToolkit is free to use under the open source GNU GPL license. The source code and the compiled binary can be freely accessed through the website http://pfind.jdl.ac.cn/IndexToolkit. In this website, the more detailed information including screenshots and documentations for users and developers is also available.

Database Management Systems↗

Pharmacotherapy of xerostomia in primary Sjögren's syndrome.

We reviewed the current literature concerning the treatment of dry mouth in patients with primary Sjögren's syndrome (SJS). Computerized MEDLINE search engines were used with the terms Sjögren, xerostomia, dry mouth, and treatment. References from key articles were searched, and all pertinent articles were procured and reviewed. Primary SJS is an uncommon but serious disorder. Dry mouth caused by SJS can lead to dental erosion, dysphagia, oral infections, and discomfort. Preventing these complications is of paramount importance. Pharmacotherapy is limited to topical saliva substitutes, which are considered first, followed by muscarinic stimulators such as pilocarpine or cevimeline, if required. Immunosuppressive therapy is being investigated. Patients should have regular oral and dental examinations to detect complications. Satisfaction with the efficacy and tolerability of treatment should be monitored frequently. The clinician may have to use a trial-and-error approach to determine a successful regimen.

Humans↗

Analysis of Internet sites for headache.

The Internet is capable of providing an unprecedented amount of information to both physicians and patients interested in headache. To assess the status of headache information on the Internet (as of January 2000), a search for 'headache' was performed using 10 leading Internet search engines. The number of web pages identified ranged from 4419 (WebCrawler) to 506 426 (Northern Light). The 'average' search yielded nearly 150 000 web page listings for 'headache'. The content was then reviewed of the top 10 listed web pages for each search (i.e. a total of 100 page listings). The results demonstrate that, at the present time, Internet-based information on headache is extensive but poorly organized. Editorial review of this potential valuable resource is required in order to maximize its utility in headache education and management.

Headache↗

AHMII: Agent to Help Microbial Information Integration.

Reproducibility is the key to science. Therefore, the fidelity of organisms, particularly type strains, used in molecular biology must be authenticated before embarking on a series of experiments. In the case of microbes the authentic strain can be obtained from a culture collection. However, tracking down a culture collection that possesses the strain can be an arduous task. With this in mind we have developed a one-stop search engine for bacteria, fungi, yeasts and cell lines that indicates which collections carry the strain of interest. The search agent is named Agent to Help Microbial Information Integration (AHMII) and the URL address is http://www.wdcm.org/AHMII/ahmii.html.

Bacteria↗

BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases.

SRS (Sequence Retrieval System) is a widely used keyword search engine for querying biological databases. BLAST2 is the most widely used tool to query databases by sequence similarity search. These tools allow users to retrieve sequences by shared keyword or by shared similarity, with many public web servers available. However, with the increasingly large datasets available it is now quite common that a user is interested in some subset of homologous sequences but has no efficient way to restrict retrieval to that set. By allowing the user to control SRS from the BLAST output, BLAST2SRS (http://blast2srs.embl.de/) aims to meet this need. This server therefore combines the two ways to search sequence databases: similarity and keyword.

Animals↗

An introduction to information retrieval: applications in genomics.

Information retrieval (IR) is the field of computer science that deals with the processing of documents containing free text, so that they can be rapidly retrieved based on keywords specified in a user's query. IR technology is the basis of Web-based search engines, and plays a vital role in biomedical research, because it is the foundation of software that supports literature search. Documents can be indexed by both the words they contain, as well as the concepts that can be matched to domain-specific thesauri; concept matching, however, poses several practical difficulties that make it unsuitable for use by itself. This article provides an introduction to IR and summarizes various applications of IR and related technologies to genomics.

Animals↗

Googling for a diagnosis--use of Google as a diagnostic aid: internet based study.

OBJECTIVE: To determine how often searching with Google (the most popular search engine on the world wide web) leads doctors to the correct diagnosis. DESIGN: Internet based study using Google to search for diagnoses; researchers were blind to the correct diagnoses. SETTING: One year's (2005) diagnostic cases published in the case records of the New England Journal of Medicine. CASES: 26 cases from the New England Journal of Medicine; management cases were excluded. MAIN OUTCOME MEASURE: Percentage of correct diagnoses from Google searches (compared with the diagnoses as published in the New England Journal of Medicine). RESULTS: Google searches revealed the correct diagnosis in 15 (58%, 95% confidence interval 38% to 77%) cases. CONCLUSION: As internet access becomes more readily available in outpatient clinics and hospital wards, the web is rapidly becoming an important clinical tool for doctors. The use of web based searching may help doctors to diagnose difficult cases.

Decision Support Techniques↗

A general procedure for locating and analyzing protein-binding sequence motifs in nucleic acids.

In the last decade, two tools, one drawn from information theory and the other from artificial neural networks, have proven particularly useful in many different areas of sequence analysis. The work presented herein indicates that these two approaches can be joined in a general fashion to produce a very powerful search engine that is capable of locating members of a given nucleic acid sequence family in either local or global sequence searches. This program can, in turn, be queried for its definition of the motif under investigation, ranking each base in context for its contribution to membership in the motif family. In principle, the method used can be applied to any binding motif, including both DNA and RNA sequence families, given sufficient family size.

Base Sequence↗