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The PIR protein sequence database.
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The genome data base (GDB)--a human gene mapping repository.
The types of gene mapping data and its organization in the Genome Data Base (GDB) recently established at Johns Hopkins Medical School are described. The database provides a continuous online environment for data perusal and editing and is used as the informatics core for running the human gene mapping workshops. Current development is primarily concentrated on extending the types of map object, means of defining map location, map storage and representation. Experimental data structures have been created that permit storage of any type of map information, physical or genetic.
The GDB Human Genome Data Base Anno 1992.
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Compilation of DNA sequences of Escherichia coli (update 1993).
We have compiled the DNA sequence data for E. coli available from the GENBANK and EMBL data libraries and over a period of several years independently from the literature. This is the fifth listing replacing and increasing the former listings substantially. However, in order to save space this printed version contains DNA sequence information only, if they are publically available in electronic form. The complete compilation including a full set of genetic map data and the E. coli protein index can be obtained in machine readable form from the EMBL data library (ECD release 15) as a part of the CD-ROM issue of the EMBL sequence database, released and updated every three months. After deletion of all detected overlaps a total of 2,353,635 individual bp is found to be determined till the end of April 1993. This corresponds to a total of 49.87% of the entire E. coli chromosome consisting of about 4,720 kbp. This number may actually be higher by 9161 bp derived from other strains of E. coli.
A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993.
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Haemophilia B: database of point mutations and short additions and deletions--fourth edition, 1993.
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Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases.
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The glucocorticoid receptor resource.
The glucocorticoid receptor resource focuses on the structure-function relationships of the glucocorticoid receptor. As well as links to sequence and bibliographic databases via the World Wide Web, the database contains sequence comparisons of receptors from different species and source information for glucocorticoid receptor clones, probes, cell lines and antibodies. The resource allows the electronic publication of essays, unpublished data and reviews on steroid receptors. These publications will not be reviewed or edited and should allow the rapid dissemination of information to the scientific community. The resource can be reached at: http://biochem1.basic- sci.georgetown.edu/grr/grr.html.
SGD: Saccharomyces Genome Database.
The Saccharomyces Genome Database (SGD) provides Internet access to the complete Saccharomyces cerevisiae genomic sequence, its genes and their products, the phenotypes of its mutants, and the literature supporting these data. The amount of information and the number of features provided by SGD have increased greatly following the release of the S.cerevisiae genomic sequence, which is currently the only complete sequence of a eukaryotic genome. SGD aids researchers by providing not only basic information, but also tools such as sequence similarity searching that lead to detailed information about features of the genome and relationships between genes. SGD presents information using a variety of user-friendly, dynamically created graphical displays illustrating physical, genetic and sequence feature maps. SGD can be accessed via the World Wide Web at http://genome-www.stanford.edu/Saccharomyces/
The Protein Information Resource.
The Protein Information Resource (PIR) is an integrated public resource of protein informatics that supports genomic and proteomic research and scientific discovery. PIR maintains the Protein Sequence Database (PSD), an annotated protein database containing over 283 000 sequences covering the entire taxonomic range. Family classification is used for sensitive identification, consistent annotation, and detection of annotation errors. The superfamily curation defines signature domain architecture and categorizes memberships to improve automated classification. To increase the amount of experimental annotation, the PIR has developed a bibliography system for literature searching, mapping, and user submission, and has conducted retrospective attribution of citations for experimental features. PIR also maintains NREF, a non-redundant reference database, and iProClass, an integrated database of protein family, function, and structure information. PIR-NREF provides a timely and comprehensive collection of protein sequences, currently consisting of more than 1 000 000 entries from PIR-PSD, SWISS-PROT, TrEMBL, RefSeq, GenPept, and PDB. The PIR web site (http://pir.georgetown.edu) connects data analysis tools to underlying databases for information retrieval and knowledge discovery, with functionalities for interactive queries, combinations of sequence and text searches, and sorting and visual exploration of search results. The FTP site provides free download for PSD and NREF biweekly releases and auxiliary databases and files.
SOAP-based services provided by the European Bioinformatics Institute.
SOAP (Simple Object Access Protocol) (http://www.w3.org/TR/soap) based Web Services technology (http://www.w3.org/ws) has gained much attention as an open standard enabling interoperability among applications across heterogeneous architectures and different networks. The European Bioinformatics Institute (EBI) is using this technology to provide robust data retrieval and data analysis mechanisms to the scientific community and to enhance utilization of the biological resources it already provides [N. Harte, V. Silventoinen, E. Quevillon, S. Robinson, K. Kallio, X. Fustero, P. Patel, P. Jokinen and R. Lopez (2004) Nucleic Acids Res., 32, 3-9]. These services are available free to all users from http://www.ebi.ac.uk/Tools/webservices.
Measured creatinine clearance from timed urine collections substantially overestimates glomerular filtration rate in patients with liver cirrhosis: a systematic review and individual patient meta-analysis.
BACKGROUND: Accurate glomerular filtration rate (GFR) assessment in patients with liver cirrhosis is important for prognostication, chronic kidney disease staging, drug dosing and identifying combined liver-kidney transplantation candidates. The objective of this study was to review the accuracy of measured creatinine clearance (MCrCl) from timed urine collections for estimating true GFR. METHODS: A systematic review and individual patient meta-analysis was performed. MEDLINE, old MEDLINE, Index Medicus and Cochrane library bibliographic databases and conference proceedings were searched up to June 2004. Reference lists of relevant studies were searched and experts were contacted. Comparative diagnostic studies describing stable adult patients with cirrhosis categorized according to the Child-Pugh classification were included if a gold standard GFR measurement was performed within 3 days of MCrCl. Individual patient data were abstracted from graphs of primary articles to allow a pooled analysis of agreement between renal measures. RESULTS: Seven studies of 193 patients from 1974 to 2002 were summarized. MCrCl overestimated inulin clearance (CIn) by a mean of +13 ml/min/1.73 m2 and the limits of agreement (mean of the differences+/-2 SD) were +60 ml/min/1.73 m2 and -34 ml/min/1.73 m2. This overestimation was highest in patients with lower GFR. The mean clearance ratios [95% confidence interval (CI)] between MCrCl and CIn in the high (> or =60 ml/min/1.73 m2) and low (<60 ml/min/1.73 m2) GFR subgroups were 1.18 (1.12-1.23) and 1.49 (1.33-1.66), respectively (P<0.0001). Fourteen percent of patients with a MCrCl > or =60 ml/min/1.73 m2 had a CIn of <30 ml/min/1.73 m2. CONCLUSIONS: For patients with liver cirrhosis, MCrCl from timed urine collections consistently overestimates the true GFR. For patients requiring complete clinical evaluation, GFR assessment by CIn is justified.
Systematic review of studies of productivity loss due to rheumatoid arthritis.
BACKGROUND: Rheumatoid arthritis (RA) is a chronic, debilitating disease with a significant impact on workplace productivity. AIM: To perform a systematic review of studies of the relationship between RA and reduced workplace productivity. METHODS: Screening of 307 titles identified in bibliographic database searches resulted in 38 articles subject to systematic review. Productivity loss was expressed by three different measures: work disability, work loss (synonymous with absenteeism or short-term sick leave) and work limitation (reduction in productivity while present at work). RESULTS: A median of 66% (range 36-84%) of employed RA subjects experienced work loss due to RA in the previous 12 months, for a median duration of 39 days (range 7-84 days). The times from RA diagnosis until a 50% probability of being work disabled varied from 4.5 to 22 years. In inception cohort studies, the baseline variables consistently predictive of subsequent work disability were a physically demanding work type, more severe RA and older age. CONCLUSIONS: RA-related work-disability rates were similar in the USA and European countries. An apparent decrease in the prevalence of RA-related work disability since the 1970s may be related to a decrease in physically demanding work rather than to epidemiologic changes in RA. The majority of the literature addresses permanent disability and temporary work loss; none of the studies reviewed reported the effect of RA on presenteeism, i.e. work limitation from the employer perspective, and there are few published studies of the effectiveness of disease-modifying anti-rheumatic drugs in reducing work-related productivity loss.
Acupuncture for the alleviation of lateral epicondyle pain: a systematic review.
OBJECTIVES: Lateral epicondyle pain is a common complaint in North America. In the past 10 yr acupuncture has become increasingly recognized as an alternative treatment for pain, including epicondyle pain. This review evaluates the effectiveness of acupuncture as a treatment for lateral epicondylitis using the appropriate analysis. METHODS: Online bibliographic database searches in any language from Medline, PsychINFO, CINAHL, Healthstar, PMID, CAM, EMBASE, Cochrane Database of Systematic Review (3rd quarter 2003), articles listed in reference lists of key articles and the author's personal files were performed. Randomized and quasi-randomized controlled trials examining the effects of acupuncture on lateral epicondyle pain were selected. From the six studies that met inclusion criteria, the first author, year of publication, population studied, dropout rate, treatment plan, assessment scale and outcome measures were extracted. Study quality was determined by using the Jadad scale, in which all studies were rated as high quality. A best evidence synthesis approach was used to analyse the data presented in the six studies. RESULTS: All the studies suggested that acupuncture was effective in the short-term relief of lateral epicondyle pain. Five of six studies indicated that acupuncture treatment was more effective compared to a control treatment. CONCLUSIONS: There is strong evidence suggesting that acupuncture is effective in the short-term relief of lateral epicondyle pain.
The Human Genome Project: a paradigm for information management in the life sciences.
The major product of the Human Genome Project will be a series of linked data sets containing the genetic and physical location of all genes on each chromosome, plus the complete nucleotide sequence of the genome for humans and several model organisms. Here we summarize the current status of attempts to collect, analyze, and distribute this information in an electronically accessible form. Although formidable problems remain to be solved in the acquisition and adequate representation of the genetic, physical, and biological data, this project is a model for the rapid dissemination of genome and related information in biology and medicine.
Unavailability of online supplementary scientific information from articles published in major journals.
Printed articles increasingly rely on online supplements to store critical scientific information, but such data may eventually become unavailable. We checked the current availability of online supplementary scientific information published in six top-cited scientific journals (Science, Nature, Cell, New England Journal of Medicine, Lancet, Proceedings of the National Academy of Sciences USA). Here we show that in 4.7% and 9.6% of articles with online supplementary material, some of the supplements became unavailable within 2 and 5 years of their publication, respectively.
Examining the evidence in anesthesia literature: a critical appraisal of systematic reviews.
UNLABELLED: Systematic reviews are structured reviews that use scientific strategies to reduce bias in the collection, appraisal, and interpretation of relevant studies. We undertook a systematic review of published systematic reviews in perioperative medicine to summarize the areas currently covered by this type of literature, to evaluate the quality of systematic reviews in this field, and to assess some of the methodologic and reporting issues that are unique to systematic reviews. Computerized bibliographic databases, citation review, and hand searches were performed to identify eligible articles. Quality was assessed using the Overview Quality Assessment Questionnaire. Eight-two systematic reviews were found. Reviews in perioperative medicine tended to evaluate prophylactic or therapeutic interventions. No differences were seen in quality between reviews published in anesthesia and nonanesthesia journals. Nearly half of all systematic reviews had only minor or minimal flaws; however, methods can be improved with expanded search strategies, use of least two reviewers to assess each study, use of validated methods to evaluate quality, and assessment of potential sources of bias. IMPLICATIONS: The quality of systematic reviews relating to perioperative medicine was examined systematically and found to be similar in quality to those in other specialties. Adoption of recently published criteria on writing and methods could further improve this type of literature.