SEARCH · PubMed Health

Results for “Search Engine”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 433 records · Page 24Linked to original sources

PubMed2005

Characterization of glutathione S-transferases in juvenile white sturgeon.

Glutathione S-transferases (GSTs) are a family of detoxification enzymes that catalyze the conjugation of glutathione (GSH) to electrophiles, thus preventing toxicity. This study characterized the cytosolic GST classes of juvenile white sturgeon (Acipenser transmontanus) liver, using two methods of isolation. The first, which employed affinity chromatography, electrophoresis and immunoblotting against a polyclonal striped bass GST antibody, yielded two cytosolic GSTs. The GSTs were identified by nanospray liquid chromatography-tandem mass spectrometry (LC-MS/MS), peptide mass mapping and MS/MS sequencing, as well as de novo MS/MS sequencing as GST classes pi and mu using the Mascot search engine and the NCBI non-redundant database (nrDB) for both methods. The molecular masses were determined to be 23,548 +/- 23 and 26,027 +/- 23 Da, respectively, using linear matrix assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometry. The second method of isolation, which used affinity chromatography and high-pressure liquid chromatography (HPLC), yielded pi, mu, and possibly two alpha isoforms by MALDI-TOF-TOF, again searching against the NCBI nrDB. The alpha isoforms were determined to have molecular masses of 25,528 +/- 23 and 25,348 +/- 23 Da by electrospray ionization source (ESI)-MS. Overall, it appears that the HPLC method is more sensitive than immunoblotting with the current antibody. Activity of the cytosolic GSTs was evaluated using the substrate 1-chloro-2,4-dinitrobenzene (CDNB) and found to be 2.4 +/- 0.6 U/mg cytosolic protein, and 0.41 +/- 0.05 U/mg cytosolic protein using ethacrynic acid (ETHA).

Amino Acid Sequence↗

PubMedDate not supplied

Genetics and type 1 diabetes: online resources for diabetes educators.

PURPOSE: Genetic education Internet sites and peer-reviewed medical literature were reviewed and critiqued to develop tables summarizing online resources for diabetes health professionals. METHODS: Using Internet search engines, each Web site identified for this project met the following criteria: (1) accurate and valid site content based on widely accepted genetic texts, (2) credibility of the organization that maintained the Web site, (3) ease of navigation, and (4) provision of continuing education credits. PubMed was used to find journal articles using similar criteria. RESULTS: There were 33 Web sites on genetic education for diabetes health professionals that met the inclusion criteria. The literature search identified 36 articles regarding the importance of genetic education for nurses and other health professionals, as well as information regarding genetics and diabetes. CONCLUSIONS: Valid and credible information on genetics and type 1 diabetes is available for diabetes health professionals on the Internet and in the medical literature.

Computer-Assisted Instruction↗

PubMed2005

An algorithm for interpretation of low-energy collision-induced dissociation product ion spectra for de novo sequencing of peptides.

An algorithm for interpretation of product ion spectra of peptides generated from ion trap mass spectrometry is developed for de novo amino acid sequencing of peptides for the purpose of protein identification. It is based on a multi-pass analysis of product ion data using a rigorous data extraction and sequence interpretation protocol in the initial pass. The extraction/interpretation algorithm becomes more relaxed in subsequent passes, considering more of the fragment ions, and potentially more sequence candidates. The possible peptide sequences generated by the algorithm are scored according to those sequences which best explain the fragment ion spectrum. These sequences are searched against a protein database using a BLAST search engine to find likely protein candidates. The method is also suitable for locating and determining protein modifications, and can be applied to de novo interpretation of peptide fragment ions in the tandem mass (MS/MS) spectrum produced from a mixture of two peptides having similar nominal mass, but different sequences. Using a known protein, bovine serum albumin, as an example, it is illustrated that this method is rapid and efficient for MS/MS spectral interpretation. This method combined with BLAST programs is then applied to search homologies and to generate information on post-translational modifications of an unknown protein isolated from shark cartilage that does not have a complete genome or proteome database.

Algorithms↗

PubMed2004

BRENDA, the enzyme database: updates and major new developments.

BRENDA (BRaunschweig ENzyme DAtabase) represents a comprehensive collection of enzyme and metabolic information, based on primary literature. The database contains data from at least 83,000 different enzymes from 9800 different organisms, classified in approximately 4200 EC numbers. BRENDA includes biochemical and molecular information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure, application, engineering, stability, disease, isolation and preparation, links and literature references. The data are extracted and evaluated from approximately 46,000 references, which are linked to PubMed as long as the reference is cited in PubMed. In the past year BRENDA has undergone major changes including a large increase in updating speed with >50% of all data updated in 2002 or in the first half of 2003, the development of a new EC-tree browser, a taxonomy-tree browser, a chemical substructure search engine for ligand structure, the development of controlled vocabulary, an ontology for some information fields and a thesaurus for ligand names. The database is accessible free of charge to the academic community at http://www.brenda. uni-koeln.de.

Animals↗

PubMed2003

Self-referred whole-body CT imaging: current implications for health care consumers.

PURPOSE: To conduct an empirical analysis of self-referred whole-body computed tomography (CT) and develop a profile of the geographic and demographic distribution of centers, types of services and modalities, costs, and procedures for reporting results. MATERIALS AND METHODS: An analysis was conducted of Web sites for imaging centers accepting self-referred patients identified by two widely used Internet search engines with large indexes. These Web sites were analyzed for geographic location, type of screening center, services, costs, and procedures for managing imaging results. Demographic data were extrapolated for analysis on the basis of center location. Descriptive statistics, such as frequencies, means, SDs, ranges, and CIs, were generated to describe the characteristics of the samples. Data were compared with national norms by using a distribution-free method for calculating a 95% CI (P <.05) for the median. RESULTS: Eighty-eight centers identified with the search methods were widely distributed across the United States, with a concentration on both coasts. Demographic analysis further situated them in areas of the country characterized by a population that consisted largely of European Americans (P <.05) and individuals of higher education (P <.05) and socioeconomic status (P <.05). Forty-seven centers offered whole-body screening; heart and lung examinations were most frequently offered. Procedures for reporting results were highly variable. CONCLUSION: The geographic distribution of the centers suggests target populations of educated health-conscious consumers who can assume high out-of-pocket costs. Guidelines developed from within the profession and further research are needed to ensure that benefits of these services outweigh risks to individuals and the health care system.

Humans↗

PubMed2004

Inaccurate information about lyme disease on the internet.

OBJECTIVE: Patients and families searching the Internet about Lyme disease may find conflicting information. Our purpose was to review the accuracy of information on Lyme disease easily available on the Internet. METHODS: We used 15 search engines to find general information about Lyme disease. We found 251 Lyme disease websites, which we reviewed. Of these 251 websites, 19 gave general Lyme disease information and were analyzed. We evaluated the accuracy of information concerning 8 Lyme disease topics. RESULTS: Ten of the 19 websites gave accurate information and 9 of the 19 websites provided inaccurate information. There were 8 websites with the word "Lyme" in the domain name, and 7 of the 8 sites gave inaccurate information. There were 2 ".gov" websites, and both gave accurate information. CONCLUSIONS: Patients and families searching the Internet for medical information about Lyme disease may encounter inaccurate information.

Humans↗

PubMed2005

New and automated MSn approaches for top-down identification of modified proteins.

An automated top-down approach including data-dependent MS(3) experiment for protein identification/characterization is described. A mixture of wild-type yeast proteins has been separated on-line using reverse-phase liquid chromatography and introduced into a hybrid linear ion trap (LTQ) Fourier transform ion cylclotron resonance (FTICR) mass spectrometer, where the most abundant molecular ions were automatically isolated and fragmented. The MS(2) spectra were interpreted by an automated algorithm and the resulting fragment mass values were uploaded to the ProSight PTM search engine to identify three yeast proteins, two of which were found to be modified. Subsequent MS(3) analyses pinpointed the location of these modifications. In addition, data-dependent MS(3) experiments were performed on standard proteins and wild-type yeast proteins using the stand alone linear trap mass spectrometer. Initially, the most abundant molecular ions underwent collisionally activated dissociation, followed by data-dependent dissociation of only those MS(2) fragment ions for which a charge state could be automatically determined. The resulting spectra were processed to identify amino acid sequence tags in a robust fashion. New hybrid search modes utilized the MS(3) sequence tag and the absolute mass values of the MS(2) fragment ions to collectively provide unambiguous identification of the standard and wild-type yeast proteins from custom databases harboring a large number of post-translational modifications populated in a combinatorial fashion.

Amino Acid Sequence↗

PubMed2003

Towards a medical question-answering system: a feasibility study.

Question-answering (QA) systems, as have been presented and evaluated in several TREC conferences, are the next generation of search engines. They combine 'traditional' Information Retrieval (IR) with Natural Language Processing (NLP) and Knowledge Engineering techniques to provide shorter, more precise answers to natural language questions. We study here the feasibility of such a system for French in the health care domain. In this purpose, we collected a corpus of student questions in oral surgery. We examined two enabling conditions: on the IR side, how to select the right keywords in a question to identify relevant material on the Web for answering this question, a prerequisite for success; and on the NLP side, whether the contents of the questions fit the conceptual model of an existing QA prototype, a favorable condition for rapid implementation. A manual Web search enabled us to devise automatable principles for building IR queries for these questions. Besides, we could design a semantic model, using UMLS Semantic Network relations, which is consistent with our prototype and covers 90% of the questions. However, the high specialization of the domain and the clinical orientation of the questions, joined with the more limited resources online in the French language, may restrain the quantity of Web material available for answering these questions.

Expert Systems↗

PubMed2003

Framingham-based tools to calculate the global risk of coronary heart disease: a systematic review of tools for clinicians.

PURPOSE: To examine the features of available Framingham-based risk calculation tools and review their accuracy and feasibility in clinical practice. DATA SOURCES: medline, 1966-April 2003, and the google search engine on the Internet. TOOL AND STUDY SELECTION: We included risk calculation tools that used the Framingham risk equations to generate a global coronary heart disease (CHD) risk. To determine tool accuracy, we reviewed all articles that compared the performance of various Framingham-based risk tools to that of the continuous Framingham risk equations. To determine the feasibility of tool use in clinical practice, we reviewed articles on the availability of the risk factor information required for risk calculation, subjective preference for 1 risk calculator over another, or subjective ease of use. DATA EXTRACTION: Two reviewers independently reviewed the results of the literature search, all websites, and abstracted all articles for relevant information. DATA SYNTHESIS: Multiple CHD risk calculation tools are available, including risk charts and computerized calculators for personal digital assistants, personal computers, and web-based use. Most are easy to use and available without cost. They require information on age, smoking status, blood pressure, total and HDL cholesterol, and the presence or absence of diabetes. Compared to the full Framingham equations, accuracy for identifying patients at increased risk was generally quite high. Data on the feasibility of tool use was limited. CONCLUSIONS: Several easy-to-use tools are available for estimating patients' CHD risk. Use of such tools could facilitate better decision making about interventions for primary prevention of CHD, but further research about their actual effect on clinical practice and patient outcomes is required.

Coronary Disease↗

PubMed2004

Validation of a discharge summary term search method to detect adverse events.

OBJECTIVE: Adverse events are poor health outcomes caused by medical care. Measuring them is necessary for quality improvements, but current detection methods are inadequate. We performed this study to validate a previously derived method of adverse event detection using term searching in physician-dictated discharge summaries. DESIGN: This was a retrospective, chart review study of a random sample of 245 adult medicine and surgery patients admitted to a multicampus academic medical center in 2002. MEASUREMENTS: The authors used a commercially available search engine to scan discharge summaries for the presence of 104 terms that potentially indicate an adverse event. Summaries with any of these terms were reviewed by a physician to determine the term's context. Screen-positive summaries had a term that was contextually indicative of an adverse event. We used a two-stage chart review as the gold standard to determine the true presence or absence of an adverse event. RESULTS: The average patient age was 62 years (standard deviation 18.6) and 55% were admitted to a medical service. By gold standard criteria, 48 of 245 patients had an adverse event. Term searching classified 27 cases with an adverse event, with 11 true positives; 218 cases were classified as not having an adverse event, with 181 true negatives. The sensitivity, specificity, and positive and negative predictive values were 0.23 (95% confidence interval [CI]=0.11-0.35), 0.92 (95% CI=0.88-0.96), 0.41 (95% CI=0.25-0.59), and 0.83 (95% CI=95% 0.77-0.97), respectively. CONCLUSION: Although the sensitivity of the method is low, its high specificity means that the method could be used to replace expensive manual chart reviews by nurses.

Academic Medical Centers↗

PubMed2006

TuBaFrost 5: multifunctional central database application for a European tumor bank.

Developing a tissue bank database has become more than just logically arranging data in tables combined with a search engine. Current demand for high quality samples and data, and the ever-changing legal and ethical regulations mean that the application must reflect TuBaFrost rules and protocols for the collection, exchange and use of tissue. To ensure continuation and extension of the TuBaFrost European tissue bank, the custodianship of the samples, and hence the decision over whether to issue samples to requestors, remains with the local collecting centre. The database application described in this article has been developed to facilitate this open structure virtual tissue bank model serving a large group. It encompasses many key tasks, without the requirement for personnel, hence minimising operational costs. The Internet-accessible database application enables search, selection and request submission for requestors, whereas collectors can upload and edit their collection. Communication between requestor and involved collectors is started with automatically generated e-mails.

Computer Simulation↗

PubMedDate not supplied

Willow: a uniform search interface.

The objective of the Willow Project is to develop a uniform search interface that allows a diverse community of users to retrieve information from heterogeneous network-based information resources. Willow separates the user interface from the database management or information retrieval system. It provides a graphic user interface to a variety of information resources residing on diverse hosts, and using different search engines and idiomatic query languages through networked-based client-server and Transmission Control Protocol/Internet Protocol (TCP/IP) protocols. It is based on a "database driver'' model, which allows new database hosts to be added without altering Willow itself. Willow employs a multimedia extension mechanism to launch external viewers to handle data in almost any form. Drivers are currently available for a local BRS/SEARCH system and the Z39.50 protocol. Students, faculty, clinicians, and researchers at the University of Washington are currently offered 30 local and remote databases via Willow. They conduct more than 250,000 sessions a month in libraries, medical centers and clinics, laboratories, and offices, and from home. The Massachusetts Institute of Technology is implementing Willow as its uniform search interface to Z39.50 hosts.

Computer Communication Networks↗

PubMed2003

Modelisation of consumer health information in a quality-controlled gateway.

The amount of health data accessible on the Web is increasing and Internet has become a major source of health information. Many tools and search engines are available but medical information retrieval remains difficult for both the health professional and the patients. In this paper we describe CISMeF-patients. It is a sub-part of CISMeF, a structured quality-controlled subject gateway. CISMeF-patients has been designed for the patients, their families and the general public who are often unfamiliar with the medical domain and the medical vocabulary. The resources included in CISMeF-patients are described using the Dublin Core metadata format. To index them, CISMeF-patients and CISMeF share the same terminology, which 'encapsulates' the MeSH thesaurus with a layer of synonyms. Unlike Medline-plus and Medline, sharing the same terminology allows to a CISMeF-patients end-user the possibility to extend his query to the CISMeF catalogue (e.g. for searching teaching resources or clinical guidelines).

Abstracting and Indexing↗

PubMed1997

Endoscopy information online: can endoscopists close the gap between what is known and what they do?

When do you go to the Internet and when do you go to online hosts for information about gastrointestinal endoscopy? This paper describes key concepts such as hosts, online databases such as MEDLINE and EMBASE, search engines, retrieval and query languages, and thesauri. The focus is on two specific thesaurus issues: the use (or absence of) complex hierarchical thesauri such as MEDLINE's Medical Subject Headings (MeSH) and EMBASE's EMTREE. This allows us to review briefly the great advantages of "term explosion" and automatic mapping of synonyms (and the absence of these facilities on the Internet). The introductory section ends with questions on what your information needs are - clinical information? Product information? Patient information? Research information? The main part of the article is concerned with what is available on the Internet and the host services that are available today and in the future. A light glance (perhaps more of a provocative preview) is cast at future developments relevant to information retrieval in the field of endoscopy. Conclusions include the following: - The Internet should be searched for: guidelines, training, and product information. - There is little published research available for free on the Internet. - For published research, search MEDLINE and EMBASE together, or DIMDI, STN or DataStar (in that order of preference). - Search EMBASE if you need the most recent endoscopy research. - Search EMBASE if you need the most recent drug information relevant in endoscopy - Search MEDLINE if you have no budget. - Search PubMed as the preferred (free) form of access to MEDLINE. - Distrust all Internet information.

Anti-Ulcer Agents↗

PubMedDate not supplied

Cyberchondriacs.

Over 110 million Americans have accessed the internet for healthcare information. This information is often used in medical consultations and possibly contributing to increasing health care burdens. Although well informed patients are an advantage in disease management, the quality and reliability of information online is variable. Adolescents today have grown up with the Internet as a primary knowledge source, but still lack the skills to effectively filter credible information. Voluntary standards on health information have been attempted by Health on the Net Foundation; however their success has been limited, mainly due to the fact that most people searching for health information on line use a search engine rather than a specific site. This makes regulations almost impossible. Cyberchondriacs, a term used to describe anyone who seeks health-related information on the Internet, are not only at risk of acquiring unreliable information on line and therefore potential unnecessary anxiety, but they could also be financially exploited, for example, by e-health organisations and pharmaceutical companies. Moreover, the vulnerable e-health seeker, such as the inexperienced adolescent, is able to buy any quantity of nearly any medication on-line. Reasons for patients seeking information on line are varied, but include not having enough time at consultations. To try to address these issues, organisations such as NHS direct have been set up but their success is difficult to measure due to a lack of data. However, potential exploitation of a vulnerable population and the motivations behind their search for information on the internet merit further study.

Adolescent↗

PubMed2004

Pharmacist computer skills and needs assessment survey.

BACKGROUND: To use technology effectively for the advancement of patient care, pharmacists must possess a variety of computer skills. We recently introduced a novel applied informatics program in this Canadian hospital clinical service unit to enhance the informatics skills of our members. OBJECTIVE: This study was conducted to gain a better understanding of the baseline computer skills and needs of our hospital pharmacists immediately prior to the implementation of an applied informatics program. METHODS: In May 2001, an 84-question written survey was distributed by mail to 106 practicing hospital pharmacists in our multi-site, 1500-bed, acute-adult-tertiary care Canadian teaching hospital in Vancouver, British Columbia. RESULTS: Fifty-eight surveys (55% of total) were returned within the two-week study period. The survey responses reflected the opinions of licensed BSc and PharmD hospital pharmacists with a broad range of pharmacy practice experience. Most respondents had home access to personal computers, and regularly used computers in the work environment for drug distribution, information management, and communication purposes. Few respondents reported experience with handheld computers. Software use experience varied according to application. Although patient-care information software and e-mail were commonly used, experience with spreadsheet, statistical, and presentation software was negligible. The respondents were familiar with Internet search engines, and these were reported to be the most common method of seeking clinical information online. Although many respondents rated themselves as being generally computer literate and not particularly anxious about using computers, the majority believed they required more training to reach their desired level of computer literacy. Lack of familiarity with computer-related terms was prevalent. Self-reported basic computer skill was typically at a moderate level, and varied depending on the task. Specifically, respondents rated their ability to manipulate files, use software help features, and install software as low, but rated their ability to access and navigate the Internet as high. Respondents were generally aware of what online resources were available to them and Clinical Pharmacology was the most commonly employed reference. In terms of anticipated needs, most pharmacists believed they needed to upgrade their computer skills. Medical database and Internet searching skills were identified as those in greatest need of improvement. CONCLUSIONS: Most pharmacists believed they needed to upgrade their computer skills. Medical database and Internet searching skills were identified as those in greatest need of improvement for the purposes of improving practice effectiveness.

Adult↗

PubMed2005

Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database.

HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anti-coagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics.med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay-based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false-positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.

Algorithms↗

PubMed2005

Improving protein identification using complementary fragmentation techniques in fourier transform mass spectrometry.

Identification of proteins by MS/MS is performed by matching experimental mass spectra against calculated spectra of all possible peptides in a protein data base. The search engine assigns each spectrum a score indicating how well the experimental data complies with the expected one; a higher score means increased confidence in the identification. One problem is the false-positive identifications, which arise from incomplete data as well as from the presence of misleading ions in experimental mass spectra due to gas-phase reactions, stray ions, contaminants, and electronic noise. We employed a novel technique of reduction of false positives that is based on a combined use of orthogonal fragmentation techniques electron capture dissociation (ECD) and collisionally activated dissociation (CAD). Since ECD and CAD exhibit many complementary properties, their combined use greatly increased the analysis specificity, which was further strengthened by the high mass accuracy (approximately 1 ppm) afforded by Fourier transform mass spectrometry. The utility of this approach is demonstrated on a whole cell lysate from Escherichia coli. Analysis was made using the data-dependent acquisition mode. Extraction of complementary sequence information was performed prior to data base search using in-house written software. Only masses involved in complementary pairs in the MS/MS spectrum from the same or orthogonal fragmentation techniques were submitted to the data base search. ECD/CAD identified twice as many proteins at a fixed statistically significant confidence level with on average a 64% higher Mascot score. The confidence in protein identification was hereby increased by more than 1 order of magnitude. The combined ECD/CAD searches were on average 20% faster than CAD-only searches. A specially developed test with scrambled MS/MS data revealed that the amount of false-positive identifications was dramatically reduced by the combined use of CAD and ECD.

Cyclotrons↗