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At least 1,477 records · Page 82Linked to original sources
PubMed2001

Automated ribotyping provides rapid phylogenetic subgroup affiliation of clinical extraintestinal pathogenic Escherichia coli strains.

Using the automated Riboprinter system, we have initiated the construction of an electronic Riboprint database composed of 72 ECOR reference strains and 15 archetypal virulent strains in order to provide a new simple molecular characterization method. More than 90% of the ECOR strains clustered in their original phylogenetic group. All but one of the archetypal virulent strains had a profile identical to that of one of the ECOR strains and could be easily affiliated with a phylogenetic group. This method appears to be an accurate and practical tool especially for investigating the genetic relationship between clinical extraintestinal pathogenic strains and B2 subgroup ECOR strains or archetypal pathotype strains.

Bacteremia↗
PubMed1991

TQuery: a context-sensitive temporal query language.

Users of electronic medical databases request pertinent information by recasting their clinical questions into a formal database query language. Because the query language is the user's only access to the data, the query language must be powerful enough to enable users to express their data requirements. However, a competing need is for the query language to be restrictive enough so that queries can have unambiguous semantics and the query processor can generate correct answers. We describe a query language, called TQuery , that was designed specifically to formulate database queries that are dependent on temporal and contextual relationships. TQuery specifications express contextual constraints without the need to explicitly reference calendar dates. TQuery is the database query language used to retrieve patient data from an object-oriented electronic patient medical-record system called the temporal network (TNET). TNET and TQuery were developed to support the real-time temporal reasoning and representation needs of a LISP workstation-based medical expert system.

Databases, Factual↗
PubMed2006

Treatment outcomes in a centralized specialty clinic for hepatitis C virus are comparable with those from clinical trials.

BACKGROUND: Outcomes from industry-sponsored registration trials are often considered to be more favourable than those achieved in clinical practice because patients involved in the former are highly selected and supported, but it is not known if this impression is valid. OBJECTIVE: To determine the outcome of hepatitis C virus (HCV)-infected patients who received therapies for chronic HCV in a single urban centre and compare the results with those derived from contemporary, industry-sponsored trials. DESIGN: Retrospective chart review of HCV-infected patients referred to the Viral Hepatitis Investigative Unit in Winnipeg, Manitoba, between 1998 and 2003. METHODS: The Viral Hepatitis Investigative Unit database was used to identify all referred patients with positive anti-HCV antibodies. Charts were reviewed for the following data: patient demographics; viral genotype; indications and contraindications to treatment; treatment type; and outcome of antiviral therapy. RESULTS: For 1800 anti-HCV positive patients identified, 1078 charts were available for review. Of these patients, the mean age was 47 years (range 11 years to 90 years) and 53% were men. Genotype 1 was the most common (65%). A total of 331 patients (31%) had received antiviral therapy. The sustained viral responses were similar to those described in industry-sponsored registration trials. Specifically, the sustained viral responses for interferon-alpha monotherapy (n=81) was 22.2%, interferon-alpha plus ribavirin (n=180) 44.4%, pegylated interferon monotherapy (n=38) 44.7% and pegylated interferon plus ribavirin (n=24) 54.2%. CONCLUSION: HCV treatment outcomes from a single urban centre were similar to those described in industry-sponsored registration trials despite the high selection and support provided to patients enrolled in the latter studies.

Adolescent↗
PubMed1987

Application of a general database manager in a clinical medical librarian program.

The morning report reference file was automated at the Stollerman Library because the manual system was time-intensive to maintain and cumbersome to search. A general database management system (DBMS) was chosen so that it could be used in the future for other data management functions in the library. DBMS features that should be examined before use with a bibliographic application include size limitations, data entry forms, data types, search options, index files, sort options, report generation, query and programming languages, command and/or menu files, file interaction, interface with other software, and documentation. Desired requirements for this application are discussed. It is noted that a general database manager probably will not meet all of the desired requirements. For some bibliographic applications, software specifically designed for bibliographic information management and retrieval should be used. A database for the purposes of searching the morning report reference file and producing a weekly reference list and a yearly index was developed using CONDOR 3. The structure of the database is described, and examples of the reports are given. The system has been in operation since December 1984 and has been well-received by staff and patrons.

Database Management Systems↗
PubMed2007

Adaptation and evaluation of the National Cancer Institute's Diet History Questionnaire and nutrient database for Canadian populations.

BACKGROUND AND OBJECTIVE: Despite assumed similarities in Canadian and US dietary habits, some differences in food availability and nutrient fortification exist. Food-frequency questionnaires designed for the USA may therefore not provide the most accurate estimates of dietary intake in Canadian populations. Hence, we undertook to evaluate and modify the National Cancer Institute's Diet History Questionnaire (DHQ) and nutrient database. METHODS: Of the foods queried on the DHQ, those most likely to differ in nutrient composition were identified. Where possible these foods were matched to comparable foods in the Canadian Nutrient File. Nutrient values were examined and modified to reflect the Canadian content of minerals (calcium, iron, zinc) and vitamins (A, C, D, thiamin, riboflavin, niacin, B6, folate and B12). DHQs completed by 13 181 Alberta Cohort Study participants aged 35-69 years were analysed to estimate nutrient intakes using the original US and modified versions of the DHQ databases. Misclassification of intake for meeting the Dietary Reference Intake (DRI) was determined following analysis with the US nutrient database. RESULTS: Twenty-five per cent of 2411 foods deemed most likely to differ in nutrient profile were subsequently modified for folate, 11% for vitamin D, 10% for calcium and riboflavin, and between 7 and 10% for the remaining nutrients of interest. Misclassification with respect to meeting the DRI varied but was highest for folate (7%) and vitamin A (7%) among men, and for vitamin D (7%) among women over 50 years of age. CONCLUSION: Errors in nutrient intake estimates owing to differences in food fortification between the USA and Canada can be reduced in Canadian populations by using nutrient databases that reflect Canadian fortification practices.

Adult↗
PubMed2001

The InterPro database, an integrated documentation resource for protein families, domains and functional sites.

Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Each InterPro entry includes a functional description, annotation, literature references and links back to the relevant member database(s). Release 2.0 of InterPro (October 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification encoded by a total of 6804 different regular expressions, profiles, fingerprints and Hidden Markov Models. Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1,000,000 hits from 462,500 proteins in SWISS-PROT and TrEMBL). The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. Questions can be emailed to interhelp@ebi.ac.uk.

Databases, Factual↗
PubMed1997

[Value of automated medical indexing of an image database and a digital radiological library].

We indexed the contents of a radiology server on the web to facilitate access to research documents and to link reference texts to images contained in radiology databases. Indexation also allows case reports to be transformed with no supplementary work into formats compatible with computer-assisted training. Indexation was performed automatically by ADM-Index, the aim being to identify the medical concepts expressed within each medical text. Two types of texts were indexed: medical imaging reference books (Edicerf) and case reports with illustrations and captions (Iconocerf). These documents are now available on a web server with HTML format for Edicerf and on an Oracle database for Iconocerf. When the user consults a chapter of a book or a case report, the indexed terms are displayed in the heading; all reference texts and case reports containing the indexed terms can then be called up instantaneously. The user can express his search in natural language. Indexation follows the same process allowing instantaneous recall of all reference texts and case reports where the same concept appears in the diagnosis or clinical context. By using the context of the case reports as the search index, all case reports involving a common medical concept can be found. The context is interpreted as a question. When the user responds to this question, ADM-Index compares this response with the answer furnished by the reference texts and case reports. Correct or erroneous responses can thus be identified, converting the system into a computer-assisted training tool.

Abstracting and Indexing↗
PubMed2003

OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy.

BACKGROUND: The alignment of two or more protein sequences provides a powerful guide in the prediction of the protein structure and in identifying key functional residues, however, the utility of any prediction is completely dependent on the accuracy of the alignment. In this paper we describe a suite of reference alignments derived from the comparison of protein three-dimensional structures together with evaluation measures and software that allow automatically generated alignments to be benchmarked. We test the OXBench benchmark suite on alignments generated by the AMPS multiple alignment method, then apply the suite to compare eight different multiple alignment algorithms. The benchmark shows the current state-of-the art for alignment accuracy and provides a baseline against which new alignment algorithms may be judged. RESULTS: The simple hierarchical multiple alignment algorithm, AMPS, performed as well as or better than more modern methods such as CLUSTALW once the PAM250 pair-score matrix was replaced by a BLOSUM series matrix. AMPS gave an accuracy in Structurally Conserved Regions (SCRs) of 89.9% over a set of 672 alignments. The T-COFFEE method on a data set of families with <8 sequences gave 91.4% accuracy, significantly better than CLUSTALW (88.9%) and all other methods considered here. The complete suite is available from http://www.compbio.dundee.ac.uk. CONCLUSIONS: The OXBench suite of reference alignments, evaluation software and results database provide a convenient method to assess progress in sequence alignment techniques. Evaluation measures that were dependent on comparison to a reference alignment were found to give good discrimination between methods. The STAMP Sc Score which is independent of a reference alignment also gave good discrimination. Application of OXBench in this paper shows that with the exception of T-COFFEE, the majority of the improvement in alignment accuracy seen since 1985 stems from improved pair-score matrices rather than algorithmic refinements. The maximum theoretical alignment accuracy obtained by pooling results over all methods was 94.5% with 52.5% accuracy for alignments in the 0-10 percentage identity range. This suggests that further improvements in accuracy will be possible in the future.

Amino Acid Sequence↗
PubMed2002

Animal models for assessing the consequences of intrauterine growth restriction on subsequent glucose metabolism of the offspring: a review.

OBJECTIVE: The aim of this article was to review the most current animal models for intrauterine growth restriction. METHODS: The databases of MEDLINE and Pubmed were searched for articles published between 1969 and 2001. Additional sources included abstract proceedings and relevant reference lists of articles identified by database review. Key words included intrauterine growth retardation, small for gestational age, animal models and glucose metabolism. The inclusion criteria used to select studies included animal models of intrauterine growth retardation in which glucose metabolism was assessed after birth. RESULTS: A variety of physiological and metabolic variables regulate fetal growth, and alteration of these variables can result in fetal growth restriction. Fetal growth restriction is secondary to initiation of fetal adaptation measures in response to inadequate supply of oxygen and nutrients. Several animal models have led to a greater understanding of the pathophysiology and consequences of intrauterine growth restriction. These observations are comparable to those observed in humans born small for gestational age, and are of interest because of the known association between poor fetal growth and development of glucose intolerance and type 2 diabetes mellitus later in life. CONCLUSION: Experimental manipulations have apparently altered a number of metabolic and physiological variables, but the pattern of alterations seems to vary with the procedure employed. This allows only a preliminary conclusion to be drawn at best. Either the laboratory procedures vitiate the natural process under study, or the process itself is variable with respect to the triggering mechanism. As yet, we cannot tell which.

Animals↗
PubMed1995

Comparison of eight microcomputer dietary analysis programs with the USDA Nutrient Data Base for Standard Reference.

OBJECTIVE: To compare the general operating features and nutrient databases of eight microcomputer dietary analysis programs. DESIGN: A 3-day food record with 73 food items was entered into each program by the authors. The general operating features of the program were summarized and evaluated. The nutrient database was evaluated by comparing the nutrient analysis output with the 1993 US Department of Agriculture (USDA) Nutrient Data Base for Standard Reference (NDB), full version, release 10, for microcomputers. RESULTS: The programs varied in cost, number of foods and nutrients in the database, use of non-USDA data, and inputting of data for missing values. We also found differences in the quality of user manuals and help screens, ease of food entry and averaging of 3-day nutrient intake, speed of analyzing and printing results, quality and number of print/export options, and overall ease of learning and using the program. All but one of the programs were within 15% of the USDA NDB for energy, protein, total fat, and total carbohydrates. However, there was some difference in the number of other nutrients and food components varying more than 15% from the USDA NDB. These differences occurred because of variations in the number of food items included in each programs' database and the number of missing nutrient values in the database. APPLICATIONS: Our results demonstrate the importance of carefully choosing a microcomputer dietary analysis program that is suitable to the user's specific and predetermined needs.

Databases, Factual↗
PubMed2003

Randomized controlled trials in pediatric complementary and alternative medicine: where can they be found?

BACKGROUND: The safety and effectiveness of CAM interventions are of great relevance to pediatric health care providers. The objective of this study is to identify sources of reported randomized controlled trials (RCTs) in the field of pediatric complementary and alternative medicine (CAM). METHODS: Reports of RCTs were identified by searching Medline and 12 additional bibliographic databases and by reviewing the reference lists of previously identified pediatric CAM systematic reviews. RESULTS: We identified 908 reports of RCTs that included children under 18 and investigated a CAM therapy. Since 1965, there has been a steady growth in the number of these trials that are being published. The four journals that published the most reported RCTs are The American Journal of Clinical Nutrition, Pediatrics, Journal of Pediatrics, and Lancet. Medline, CAB Health, and Embase were the best database sources for identifying these studies; they indexed 93.2%, 58.4% and 42.2 % respectively of the journals publishing reports of pediatric CAM RCTs. CONCLUSIONS: Those working or interested in the field of pediatric CAM should routinely search Medline, CAB Health and Embase for literature in the field. The four core journals identified above should be included in their collection.

Authorship↗
PubMed1995

Reference materials and reference measurement systems in laboratory medicine. Harmonization of nomenclature and definitions in reference measurement systems.

Reliability of clinical laboratory results is obtained through quality assurance in both their production and transmission. The former involves a reference measurement system of reference materials and reference measurement procedures with metrological and statistical verification of results. The latter requires that sender and receiver have access to a common terminology. Thus, two data banks are required. A plurilingual systematic vocabulary related to the reference measurement system, giving concepts with terms and definitions concerning measurement standards, reference measurement procedures, internal quality control, external quality assessment, probability and statistics-mainly based on existing authoritative publications. The material should be processed by standard scientific terminological procedure and offered to pertinent organizations and specialists for comment before finalization and authorization. A multilingual collection of systematic names for properties examined by the branches of Laboratory Medicine, such as clinical chemistry, clinical immunology, clinical microbiology, clinical pharmacology, haematology and blood banking, and histochemistry and cytology. The database should function as a reference to consultation and as a link in the transmission of data between local laboratory "dialects". This should be based on the ongoing comprehensive IUPAC/IFCC project for forming names in collaboration with relevant scientific organisations and area specialists. The relational data base including "run-time" software would be accessed by e-mail (gopher or other storage medium).

Chemistry, Clinical↗
PubMed1999

Transcription Regulatory Regions Database (TRRD):its status in 1999.

The Transcription Regulatory Regions Database (TRRD) is a curated database designed for accumulation of experimental data on extended regulatory regions of eukaryotic genes, the regulatory elements they contain, i.e., transcription factor binding sites, promoters, enhancers, silencers, etc., and expression patterns of the genes. Release 4.1 of TRRD offers a number of significant improvements, in particular, a more detailed description of transcription factor binding sites, transcription factors per se, and gene expression patterns in a computer-readable format. In addition, the new TRRD release provides considerably more references to other molecular biological databases. TRRD 4.1 is installed under SRS and is available through the WWW at http://www.bionet.nsc.ru/trrd/

Animals↗
PubMed2003

Evaluation of Health Interview Surveys and Health Examination Surveys in the European Union.

BACKGROUND: The project 'Health surveys in the EU: HIS and HIS/HES evaluations and models' aims to assess the coverage of specific health and health-related areas in national and international surveys by reviewing and evaluating surveys, their methods and comparability, and by recommending appropriate survey designs and methods. METHODS: As basis for the evaluation, the project developed a health survey database. At present, Health Interview Surveys (HIS) and Health Examination Surveys (HES) from 18 Western European countries as well as from Canada, Australia and the USA are included. RESULTS: National HISs have been carried out regularly in almost all Western European countries. The HIS may consist of short health sections or modules within multi-purpose surveys or lengthy health interviews with several questionnaires. National HESs with a comprehensive focus have been conducted at regular or irregular intervals in five countries. The HES may comprise an interview and a few measurements or a comprehensive health examination. Sampling frames, fieldwork, quality control procedures and response rates vary greatly. Differences between measurement instruments used, in the wording of questions and in examination protocols reduce the comparability of many findings. CONCLUSION: The Internet based HIS/HES database allows for a quick reference and comparison of methods and instruments used in national health surveys. It illustrates the need for improving comparability. Collaboration and co-ordination is needed to promote comprehensive health monitoring supporting the development of national and European-level health policy.

Databases, Factual↗
PubMed2005

Insulin and oral agents for managing cystic fibrosis-related diabetes.

BACKGROUND: Insulin therapy is recommended by the Cystic Fibrosis Foundation when cystic fibrosis-related diabetes has been diagnosed. Diagnosis is based on an elevated fasting blood glucose level greater than 6.94 mmol/liter (125 mg/deciliter) or symptomatic diabetes for random glucose levels greater than 11.11 mmol/liter (200 mg/deciliter). OBJECTIVES: To examine the evidence that, when treated with agents for managing diabetes, people with cystic fibrosis improve their sugar metabolic control resulting in beneficial impact on lung function and the ability to maintain optimal weight. SEARCH STRATEGY: We searched the Cochrane Cystic Fibrosis and Genetic Disorders Group Trials Register comprising references identified from comprehensive electronic database searches and handsearches of relevant journals and abstract books of conference proceedings. We also handsearched abstracts from pulmonary and North American Cystic Fibrosis Conference symposia. Date of the most recent search of the Group's Trials Register: December 2004. SELECTION CRITERIA: Randomized controlled trials comparing all methods of diabetes therapy for one month or longer in people with cystic fibrosis. DATA COLLECTION AND ANALYSIS: No studies were found which were eligible for inclusion in this review. MAIN RESULTS: Six references to four studies were identified by the searches, but none were eligible for inclusion in the review as they were not randomized controlled trials. AUTHORS' CONCLUSIONS: While some cystic fibrosis centers use oral medications to help control diabetes, a condition which complicates the course of cystic fibrosis, insulin therapy is the recommended and most widely used treatment method. Lung function has been reported to improve with the use of insulin, but this has not been correlated to the degree in which sugar metabolism has been affected. While the Cystic Fibrosis Foundation recommends insulin therapy be used in managing diabetes, this systematic review identifies the need for a multicentre randomized controlled trial assessing both the efficacy of insulin or other insulin-releasing or insulin-sensitizing medications and their possible adverse effects in managing cystic fibrosis-related diabetes.

Administration, Oral↗
PubMed2006

Improving sensitivity in shotgun proteomics using a peptide-centric database with reduced complexity: protease cleavage and SCX elution rules from data mining of MS/MS spectra.

Correct identification of a peptide sequence from MS/MS data is still a challenging research problem, particularly in proteomic analyses of higher eukaryotes where protein databases are large. The scoring methods of search programs often generate cases where incorrect peptide sequences score higher than correct peptide sequences (referred to as distraction). Because smaller databases yield less distraction and better discrimination between correct and incorrect assignments, we developed a method for editing a peptide-centric database (PC-DB) to remove unlikely sequences and strategies for enabling search programs to utilize this peptide database. Rules for unlikely missed cleavage and nontryptic proteolysis products were identified by data mining 11 849 high-confidence peptide assignments. We also evaluated ion exchange chromatographic behavior as an editing criterion to generate subset databases. When used to search a well-annotated test data set of MS/MS spectra, we found no loss of critical information using PC-DBs, validating the methods for generating and searching against the databases. On the other hand, improved confidence in peptide assignments was achieved for tryptic peptides, measured by changes in DeltaCN and RSP. Decreased distraction was also achieved, consistent with the 3-9-fold decrease in database size. Data mining identified a major class of common nonspecific proteolytic products corresponding to leucine aminopeptidase (LAP) cleavages. Large improvements in identifying LAP products were achieved using the PC-DB approach when compared with conventional searches against protein databases. These results demonstrate that peptide properties can be used to reduce database size, yielding improved accuracy and information capture due to reduced distraction, but with little loss of information compared to conventional protein database searches.

Amino Acid Sequence↗
PubMed1988

A two-dimensional electrophoresis study of phosphorylation and dephosphorylation of chromaffin cell proteins in response to a secretory stimulus.

Phosphorylated proteins of bovine chromaffin cells, radioactively labeled with [32P]orthophosphate, have been analyzed by two-dimensional polyacrylamide gel electrophoresis and autoradiography. Complex two-dimensional electrophoretograms were studied with the aid of computer-assisted image analysis (CAIA). A database map of 32P-labeled proteins was constructed; approximately 500 polypeptides have been detected, numbered, and characterized according to the intensity of labeling, molecular weight, and isoelectric point. The database was constructed from cells kept in resting conditions or stimulated with 59 mM K+ in 2.5 mM Ca2+ or in 0 Ca2+ solution. These manipulations caused statistically significant changes in the degree of phosphorylation of 20 proteins; they were classified as Ca2+-dependent substrates for the phosphorylation or dephosphorylation processes. These changes were also shown in cells stimulated in the presence of the Ca2+ channel activator Bay K 8644. New proteins that show as much as a fivefold increase in their phosphorylation state during cell stimulation have been located with this methodology, as well as many others that had not previously been detected with conventional methods. These experiments provide the first CAIA database of chromaffin cell phosphoproteins; the map constructed with these data will allow the location of specific phosphoproteins and serve as a reference for future ongoing studies. The database will continue to grow to identify more proteins and to facilitate the comparison of complex patterns obtained in different laboratories for normal and transformed pheochromocytoma PC12 cells.

Adrenal Medulla↗