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At least 397 records · Page 22Linked to original sources

PubMed2006

Trusted and relevant medical knowledge: the promise of information retrieval in biomedicine.

As the world of medicine becomes increasingly digitized, the Web has become a de facto resource for physicians to quickly glean pertinent clinical information to carry out diagnostic and therapeutic decisions. At present, physicians face the dual challenge of judging the relevance of the information and trusting its Web source. This paper proposes a trust-relevance framework for conceptualizing computer-accessed medical information resources, a set of criteria for evaluating these information resources, and descriptions of a sample of available online resources. It also presents a usable framework for evaluating information retrieval innovations and explains the different capabilities of representative information retrieval tools and applications. By demystifying the concepts associated with information resources, search engines, and retrieval tools, and presenting a reasonable view of current opportunities as well as future possibilities, the authors hope to provide guidance so physicians can more rapidly adopt innovative computer-assisted search tools for acquiring information that facilitate patient care decision-making.

Humans↗

PubMed2001

Probing the surface of eukaryotic cells using combinatorial toxin libraries.

The success of proteomics hinges in part on the development of approaches able to map receptors on the surface of cells. One strategy to probe a cell surface for the presence of internalized markers is to make use of Shiga-like toxin 1 (SLT-1), a ribosome-inactivating protein that kills eukaryotic cells [1, 2]. SLT-1 binds to the glycolipid globotriaosylceramide [3, 4], which acts as a shuttle, allowing the toxin to be imported and routed near ribosomes. We investigated the use of SLT-1 as a structural template to create combinatorial libraries of toxin variants with altered receptor specificity. Since all SLT-1 variants retain their toxic function, this property served as a search engine enabling us to identify mutants from these libraries able to kill target cells expressing internalizable receptors. Random mutations were introduced in two discontinuous loop regions of the SLT-1 receptor binding subunit. Minimal searches from screening 600 bacterial colonies randomly picked from an SLT-1 library identified toxin mutants able to kill cell lines resistant to the wild-type toxin. One such mutant toxin was shown to bind to a new receptor on these cell lines by flow cytometry. Toxin libraries provide a strategy to delineate the spectrum of receptors on eukaryotic cells.

Amino Acid Sequence↗

PubMed2004

Using a terminology server and consumer search phrases to help patients find physicians with particular expertise.

OBJECTIVES: To design and implement a real world application using a terminology server to assist patients and physicians who use common language search terms to find specialist physicians with a particular clinical expertise. METHOD: Terminology servers have been developed to help users encoding of information using complicated structured vocabulary during data entry tasks, such as recording clinical information. We describe a methodology using Personal Health Terminology trade mark and a SNOMED CT-based hierarchical concept server. RESULTS: Construction of a pilot mediated-search engine to assist users who use vernacular speech in querying data which is more technical than vernacular. CONCLUSION: This approach, which combines theoretical and practical requirements, provides a useful example of concept-based searching for physician referrals.

Abstracting and Indexing↗

PubMed2006

Separation and identification of soybean leaf proteins by two-dimensional gel electrophoresis and mass spectrometry.

To establish a proteomic reference map for soybean leaves, we separated and identified leaf proteins using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Tryptic digests of 260 spots were subjected to peptide mass fingerprinting (PMF) by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) MS. Fifty-three of these protein spots were identified by searching NCBInr and SwissProt databases using the Mascot search engine. Sixty-seven spots that were not identified by MALDI-TOF-MS analysis were analyzed with liquid chromatography tandem mass spectrometry (LC-MS/MS), and 66 of these spots were identified by searching against the NCBInr, SwissProt and expressed sequence tag (EST) databases. We have identified a total of 71 unique proteins. The majority of the identified leaf proteins are involved in energy metabolism. The results indicate that 2D-PAGE, combined with MALDI-TOF-MS and LC-MS/MS, is a sensitive and powerful technique for separation and identification of soybean leaf proteins. A summary of the identified proteins and their putative functions is discussed.

Amino Acid Sequence↗

PubMed2002

MMDB: Entrez's 3D-structure database.

Three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. The goal of Entrez's 3D-structure database is to make this information, and the functional annotation it can provide, easily accessible to molecular biologists. To this end Entrez's search engine provides three powerful features. (i) Sequence and structure neighbors; one may select all sequences similar to one of interest, for example, and link to any known 3D structures. (ii) Links between databases; one may search by term matching in MEDLINE, for example, and link to 3D structures reported in these articles. (iii) Sequence and structure visualization; identifying a homolog with known structure, one may view molecular-graphic and alignment displays, to infer approximate 3D structure. In this article we focus on two features of Entrez's Molecular Modeling Database (MMDB) not described previously: links from individual biopolymer chains within 3D structures to a systematic taxonomy of organisms represented in molecular databases, and links from individual chains (and compact 3D domains within them) to structure neighbors, other chains (and 3D domains) with similar 3D structure. MMDB may be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure.

Animals↗

PubMed2005

Bioinformatic analysis of peptide precursor proteins.

Neuropeptides are among the most important signal molecules in animals. Traditional identification of peptide hormones through peptide purification is a tedious and time-consuming process. With the advent of the genome sequencing projects, putative peptide precursor can be mined from the genome. However, because bioactive peptides are usually quite short in length and because the active core of a peptide is often limited to only a few amino acids, using the BLAST search engine to identify neuropeptide precursors in the genome is difficult and sometimes impossible. To overcome these shortcomings, we subject the entire set of all known Drosophila melanogaster peptide precursor sequences to motif-finding algorithms in search of a motif that is common for all prepropeptides and that could be used in the search for new peptide precursors.

Amino Acid Sequence↗

PubMed2007

Sentinel lymph node mapping in colon cancer: current status.

BACKGROUND: The primary role of sentinel lymph node (SLN) mapping in colon cancer is to increase the accuracy of nodal staging by identifying those lymph nodes with the greatest potential for harbouring metastatic disease. Ultrastaging techniques aim to identify the otherwise undetected metastases. Until now, no consensus exists as to the most optimal procedure in patients with colon cancer. METHODS: A systematic literature search on the value of different SLN mapping techniques in patients with colon cancer was performed using the electronic search engine PubMed. Prospective studies published before 1 December 2005 were included and further articles were selected by cross-referencing. The results of different techniques using either blue dye or radiocolloid, were investigated. RESULTS: The literature search yielded 17 relevant articles. SLN mapping using blue dye was described in 15 studies. Two studies reported the results of SLN mapping using a combination of blue dye and radiocolloid. The reported results on identification rate varied between 71 and 100%. Accuracy rates were between 78 and 100%, sensitivity rates between 25 and 100% and true upstaging rates between 0 and 26%. The results were not affected by the addition of radiocolloid to blue dye. CONCLUSIONS: Sentinel lymph node mapping in patients with colon cancer remains an experimental procedure with varying results. Further evaluation may lead to a standardized technique that offers the potential for significant upstaging of stage II patients. This may have important implications as to tailor adjuvant chemotherapeutic regimens in these patients.

Colonic Neoplasms↗

PubMed2000

CyanoBase, the genome database for Synechocystis sp. strain PCC6803: status for the year 2000.

CyanoBase provides an online resource for access to data on genomic information about the cyanobacterium Synechocystis sp. strain PCC6803. The database contains annotations for each protein-coding gene deduced from the entire nucleotide sequence of the genome, gene classification lists, and keyword and similarity search engines. Core portions of CyanoBase consist of annotations for each of the 3168 protein genes deduced from the entire nucleotide sequence of this genome. The contents of each gene were improved by updating with the results of similarity searches and by introducing references for analysis in bioinformatics. The database now contains repository facilities that store and provide experimental information, in addition to providing proposals for the function of each gene. This information should help to avoid unnecessary, overlapping experiments and should assist communication between scientists who wish to elucidate the function of putative genes on the cyanobacteria genome. The current URL of CyanoBase is http://www.kazusa.or.jp:8080/cyano/

Cyanobacteria↗

PubMed1992

The MEDLINE Button.

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

Diagnosis, Computer-Assisted↗

PubMed2006

MASCOT HTML and XML parser: an implementation of a novel object model for protein identification data.

Protein identification using MS is an important technique in proteomics as well as a major generator of proteomics data. We have designed the protein identification data object model (PDOM) and developed a parser based on this model to facilitate the analysis and storage of these data. The parser works with HTML or XML files saved or exported from MASCOT MS/MS ions search in peptide summary report or MASCOT PMF search in protein summary report. The program creates PDOM objects, eliminates redundancy in the input file, and has the capability to output any PDOM object to a relational database. This program facilitates additional analysis of MASCOT search results and aids the storage of protein identification information. The implementation is extensible and can serve as a template to develop parsers for other search engines. The parser can be used as a stand-alone application or can be driven by other Java programs. It is currently being used as the front end for a system that loads HTML and XML result files of MASCOT searches into a relational database. The source code is freely available at http://www.ccbm.jhu.edu and the program uses only free and open-source Java libraries.

Databases, Protein↗

PubMed2005

Personalized online information search and visualization.

BACKGROUND: The rapid growth of online publications such as the Medline and other sources raises the questions how to get the relevant information efficiently. It is important, for a bench scientist, e.g., to monitor related publications constantly. It is also important, for a clinician, e.g., to access the patient records anywhere and anytime. Although time-consuming, this kind of searching procedure is usually similar and simple. Likely, it involves a search engine and a visualization interface. Different words or combination reflects different research topics. The objective of this study is to automate this tedious procedure by recording those words/terms in a database and online sources, and use the information for an automated search and retrieval. The retrieved information will be available anytime and anywhere through a secure web server. RESULTS: We developed such a database that stored searching terms, journals and et al., and implement a piece of software for searching the medical subject heading-indexed sources such as the Medline and other online sources automatically. The returned information were stored locally, as is, on a server and visible through a Web-based interface. The search was performed daily or otherwise scheduled and the users logon to the website anytime without typing any words. The system has potentials to retrieve similarly from non-medical subject heading-indexed literature or a privileged information source such as a clinical information system. The issues such as security, presentation and visualization of the retrieved information were thus addressed. One of the presentation issues such as wireless access was also experimented. A user survey showed that the personalized online searches saved time and increased and relevancy. Handheld devices could also be used to access the stored information but less satisfactory. CONCLUSION: The Web-searching software or similar system has potential to be an efficient tool for both bench scientists and clinicians for their daily information needs.

Databases, Bibliographic↗

PubMedDate not supplied

[International bibliographic databases--Current Contents on disk and in FTP format (Internet): presentation and guide].

This paper aims to provide technical and practical advice about finding references using Current Contents on disk (Macintosh or PC) or via the Internet (FTP). Seven editions are published each week. They are all organized in the same way and have the same search engine. The Life Sciences edition, extensively used in medical research, is presented here in detail, as an example. This methodological note explains, in French, how to use this reference database. It is designed to be a practical guide for browsing and searching the database, and particularly for creating search profiles adapted to the needs of researchers.

CD-ROM↗

PubMedDate not supplied

The age one dental visit: information on the web.

As consumers increasingly turn to the Internet as a health resource it is likely that parents may seek information on the recommended age for a first dental visit. A meta-search engine was used to determine whether a parent would find available, accessible, and authoritative information when seeking this recommendation. Of 47 "hits" on the phrase "first dental visit", only 2 were associated with major national health professional associations. Information obtained through this search technique was readily available and accessible but not authoritative. Individual searches on sites of leading dental and pediatric organizations revealed that all major dental organizations that provide consumer information and the Bright Futures consortium of child healthcare providers site all advocate the age 1 visit. The American Academy of Pediatrics, however suggests age 3 for the first visit. Information obtained from selected sites is available and authoritative but not particularly accessible unless the names of leading organizations are known.

Age Factors↗

PubMedDate not supplied

Integrated approach for manual evaluation of peptides identified by searching protein sequence databases with tandem mass spectra.

Quantitative proteomics relies on accurate protein identification, which often is carried out by automated searching of a sequence database with tandem mass spectra of peptides. When these spectra contain limited information, automated searches may lead to incorrect peptide identifications. It is therefore necessary to validate the identifications by careful manual inspection of the mass spectra. Not only is this task time-consuming, but the reliability of the validation varies with the experience of the analyst. Here, we report a systematic approach to evaluating peptide identifications made by automated search algorithms. The method is based on the principle that the candidate peptide sequence should adequately explain the observed fragment ions. Also, the mass errors of neighboring fragments should be similar. To evaluate our method, we studied tandem mass spectra obtained from tryptic digests of E. coli and HeLa cells. Candidate peptides were identified with the automated search engine Mascot and subjected to the manual validation method. The method found correct peptide identifications that were given low Mascot scores (e.g., 20-25) and incorrect peptide identifications that were given high Mascot scores (e.g., 40-50). The method comprehensively detected false results from searches designed to produce incorrect identifications. Comparison of the tandem mass spectra of synthetic candidate peptides to the spectra obtained from the complex peptide mixtures confirmed the accuracy of the evaluation method. Thus, the evaluation approach described here could help boost the accuracy of protein identification, increase number of peptides identified, and provide a step toward developing a more accurate next-generation algorithm for protein identification.

Algorithms↗

PubMed2005

Cancer pain assessment in clinical trials. A review of the literature (1999-2002).

The aim of this review was to evaluate the methods of pain measurement in controlled clinical trials in oncology published between 1999 and 2002. An electronic literature search strategy was used according to established criteria applied to the Medline database and PubMed search engine. Articles were selected to include only studies that had chronic cancer pain as the primary or secondary objective of a controlled clinical trial. A specific evaluation scheme was used to examine how pain measurement methods were chosen and implemented in the study procedures. The search strategy identified 613 articles, and 68 were selected for evaluation. Most articles (69%) chose unidimensional pain measurement tools, such as visual analogue scales, numerical rating scales and verbal rating scales, whereas others used questionnaires. The implementation of the pain assessment method was problematic in many studies, especially as far as time frame of pain assessment (70%), administration modalities (46%), and use of non-validated measurement methods (10%). Design of study and data analysis were often unclear about the definition of pain outcome measure (40%), patient compliance with pain assessment (98%), and impact of missing data (56%). Statistical techniques were seldom appropriate to the type of data collected and often inadequate to describe the pain variable under study. It is clear from this review that most authors were aware of the need of valid pain measurement tools to be used in clinical trials. However, too often these tools were not appropriately used in the trial, or at least their use was not described with sufficient accuracy in the trial methods.

Chronic Disease↗

PubMedDate not supplied

[INTERNET AIDS FOR THE GASTROENTEROLOGIST]

The medical Internet is growing in paralell with the online information explotion. The aim of this study is to identify the online resources available to gastroenterologists, both in English and Spanish on the Internet.We searched the internet using the following resources: general and medical search engines, biomedical databases, books and listservs.We included for analisis the websites that fulfilled the following criteria: content, autorship, attribution, currency and disclosure.We identified 46 websites in Spanish and 104 in English that met the inclussion criteria. We further categorized these sites into six categories: digestive diseases search resources, professionals organizations, academic department sites, sites with focused areas of interest to gastroenterologists, on line journals and discussion groups (listservs).A variety of very useful web sites related to digestive diseases exist on the Internet, and their numbers are growing. Many of these sites have valuable information that can be used to improve patient care, promote medical education, and facilitate research. The Internet represents a useful source of information of increasing utility for daily gastroenterologic practice.

Journal Article↗

PubMed2003

Internet marketing of herbal products.

CONTEXT: Passage of the Dietary Supplement Health and Education Act in 1994 restricted the Food and Drug Administration's control over dietary supplements, leading to enormous growth in their promotion. The Internet is often used by consumers as a source of information on such therapies. OBJECTIVE: To assess the information presented and indications claimed on the Internet for the 8 best-selling herbal products. DATA SOURCES: We searched the Internet using the 5 most commonly used search engines. For each, we entered the names of the 8 most widely used herbal supplements (ginkgo biloba, St John's wort, echinacea, ginseng, garlic, saw palmetto, kava kava, and valerian root). We analyzed the health content of all Web sites listed on the first page of the search results. STUDY SELECTION: We analyzed all accessible, English-language Web sites that pertained to oral herbal supplements. A total of 522 Web sites were identified; of these, 443 sites met inclusion criteria for the analysis. DATA EXTRACTION: The nature of the Web site (retail or nonretail), whether it was a sponsored link, and all references, indications, claims, and disclaimers were recorded. Two reviewers independently categorized medical claims as disease or nondisease according to Food and Drug Administration criteria. DATA SYNTHESIS: Among 443 Web sites, 338 (76%) were retail sites either selling product or directly linked to a vendor. A total of 273 (81%) of the 338 retail Web sites made 1 or more health claims; of these, 149 (55%) claimed to treat, prevent, diagnose, or cure specific diseases. More than half (153/292; 52%) of sites with a health claim omitted the standard federal disclaimer. Nonretail sites were more likely than retail sites to include literature references, although only 52 (12%) of the 443 Web sites provided referenced information without a link to a distributor or vendor. CONCLUSIONS: Consumers may be misled by vendors' claims that herbal products can treat, prevent, diagnose, or cure specific diseases, despite regulations prohibiting such statements. Physicians should be aware of this widespread and easily accessible information. More effective regulation is required to put this class of therapeutics on the same evidence-based footing as other medicinal products.

Advertising↗

PubMed2006

Towards pathogenomics: a web-based resource for pathogenicity islands.

Pathogenicity islands (PAIs) are genetic elements whose products are essential to the process of disease development. They have been horizontally (laterally) transferred from other microbes and are important in evolution of pathogenesis. In this study, a comprehensive database and search engines specialized for PAIs were established. The pathogenicity island database (PAIDB) is a comprehensive relational database of all the reported PAIs and potential PAI regions which were predicted by a method that combines feature-based analysis and similarity-based analysis. Also, using the PAI Finder search application, a multi-sequence query can be analyzed onsite for the presence of potential PAIs. As of April 2006, PAIDB contains 112 types of PAIs and 889 GenBank accessions containing either partial or all PAI loci previously reported in the literature, which are present in 497 strains of pathogenic bacteria. The database also offers 310 candidate PAIs predicted from 118 sequenced prokaryotic genomes. With the increasing number of prokaryotic genomes without functional inference and sequenced genetic regions of suspected involvement in diseases, this web-based, user-friendly resource has the potential to be of significant use in pathogenomics. PAIDB is freely accessible at http://www.gem.re.kr/paidb.

Bacteria↗