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PubMed2003

RefDB: a database of uniformly referenced protein chemical shifts.

RefDB is a secondary database of reference-corrected protein chemical shifts derived from the BioMagResBank (BMRB). The database was assembled by using a recently developed program (SHIFTX) to predict protein (1)H, (13)C and (15)N chemical shifts from X-ray or NMR coordinate data of previously assigned proteins. The predicted shifts were then compared with the corresponding observed shifts and a variety of statistical evaluations performed. In this way, potential mis-assignments, typographical errors and chemical referencing errors could be identified and, in many cases, corrected. This approach allows for an unbiased, instrument-independent solution to the problem of retrospectively re-referencing published protein chemical shifts. Results from this study indicate that nearly 25% of BMRB entries with (13)C protein assignments and 27% of BMRB entries with (15)N protein assignments required significant chemical shift reference readjustments. Additionally, nearly 40% of protein entries deposited in the BioMagResBank appear to have at least one assignment error. From this study it evident that protein NMR spectroscopists are increasingly adhering to recommended IUPAC (13)C and (15)N chemical shift referencing conventions, however, approximately 20% of newly deposited protein entries in the BMRB are still being incorrectly referenced. This is cause for some concern. However, the utilization of RefDB and its companion programs may help mitigate this ongoing problem. RefDB is updated weekly and the database, along with its associated software, is freely available at http://redpoll.pharmacy.ualberta.ca and the BMRB website.

Animals↗
PubMed1998

[A database for thyroid diseases: evaluation with special reference to potential consequences of a nuclear power plant accident].

The concept of a thyroid disease register based on a relational database system with a structured query language (SQL) is reported. More than 5000 examination findings of benign and malignant thyroid disorders have been recorded so far, covering the period from 1986 to 1996. For epidemiological studies these population-based thyroid diseases data can be allocated to a digital data map by means of the five-digit German postal code. When evaluating the data with regard to the function of the thyroid gland as an indicator of preceding nuclear power plant disasters and fallout, we found neither indicators of an increased incidence of thyroid carcinoma as an aftermath of the Chernobyl disaster nor the occurrence of clusters. The data were supplemented by the results of a survey among all Schleswig-Holstein pathologists involved in the diagnosis of thyroid diseases. Data on childhood carcinoma of the thyroid were also provided by the Childhood Tumor Register of the Institute of Pathology, University of Kiel, and by the Childhood Cancer Register of the University of Mainz.

Databases, Factual↗
PubMed2002

'Human' insulin versus animal insulin in people with diabetes mellitus.

BACKGROUND: Human insulin was introduced for the routine treatment of diabetes mellitus in the early 1980s without adequate comparison of efficacy to animal insulin preparations. First reports of altered hypoglycaemia awareness after transfer to human insulin made physicians and especially patients uncertain about potential adverse effects of human insulin. OBJECTIVES: To assess the effects of different insulin species by evaluating their efficacy (in particular glycaemic control) and adverse effects profile (mainly hypoglycaemia). SEARCH STRATEGY: A highly sensitive search for randomised controlled trials combined with key terms for identifying studies on human versus animal insulin was performed using the Cochrane Library (issue 2, 2002), Medline (1966 to May, 2002) and Embase (1974 to February, 2002). We also searched reference lists and databases of ongoing trials. Date of latest search: May 2002. SELECTION CRITERIA: We included randomised controlled clinical trials with diabetic patients of all ages that compared human to animal (for the most part purified porcine) insulin. Trial duration had to be at least one month in order to achieve reliable results on the main outcome parameter glycated haemoglobin. DATA COLLECTION AND ANALYSIS: Trial selection as well as evaluation of study quality was performed by two independent reviewers. The quality of reporting of each trial was assessed according to a modification of the quality criteria as specified by Schulz and by Jadad. MAIN RESULTS: Altogether 2156 participants took part in the 45 randomised controlled studies that were discovered through extensive search efforts. Though many studies were of a randomised, double-blind design, most studies were of poor methodological quality. Purified porcine and semi-synthetic insulin were most often investigated. No significant differences in metabolic control or hypoglycaemic episodes between various insulin species could be elucidated. Insulin dose and insulin antibodies did not show relevant dissimilarities. REVIEWER'S CONCLUSIONS: A comparison of the effects of human and animal insulin as well as of the adverse reaction profile did not show clinically relevant differences. Many patient-oriented outcomes like health-related quality of life or diabetes complications and mortality were never investigated in high-quality randomised clinical trials. The story of the introduction of human might be repeated by contemporary launching campaigns to introduce pharmaceutical and technological innovations that are not backed up by sufficient proof of their advantages and safety.

Animals↗
PubMed1996

Searching for information on toxicological data of chemical substances in selected bibliographic databases--selection of essential databases for toxicological researches.

By using information from printed and online database guides, 18 online bibliographic databases (BD), which cover literature on toxicology were selected from 5 hosts. A search for literature containing information on three selected chemicals was carried out with each of the databases, and the number of documents relevant to toxicology found in them was compared by computer-assisted analysis. Some databases yielded very little information pertinent to toxicology, while others provided a considerable amount. In addition, the databases contained numerous duplicates (references common to more than one database). Most of the relevant documents could be obtained using only 8 of the 18 BDs selected. These databases are: Biosis Previews (BIOSIS), Chemical Abstracts (CA), Chemical Safety Newsbase (CSNB), Excerpta Medica (EMBASE), National Institute for Occupational Safety and Health (NIOSH), Scisearch, Toxicology Information Online (TOXLINE) and the former Toxicology Literature (TOXLIT).

Databases, Bibliographic↗
PubMed2000

The RESID database of protein structure modifications: 2000 update.

The RESID Database contains supplemental information on post-translational modifications for the standardized annotations appearing in the PIR-International Protein Sequence Database. The RESID Database includes: systematic and frequently observed alternate names, Chemical s Service registry numbers, atomic formulas and weights, enzyme activities, indicators for N-terminal, C-terminal or peptide chain cross-link modifications, keywords, literature citations with database cross-references, structural diagrams and molecular models. Since 1995 updates of the RESID Database have appeared as often as weekly, and full releases appear quarterly. The database is freely accessible through the PIR Web site http://pir.georgetown.edu/pirwww/dbinfo/resid.html and by FTP.

Databases, Factual↗
PubMed2001

The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database.

The RESID Database is a comprehensive collection of annotations and structures for protein post-translational modifications including N-terminal, C-terminal and peptide chain cross-link modifications. The RESID Database includes systematic and frequently observed alternate names, Chemical Abstracts Service registry numbers, atomic formulas and weights, enzyme activities, taxonomic range, keywords, literature citations with database cross-references, structural diagrams and molecular models. The NRL-3D Sequence-Structure Database is derived from the three-dimensional structure of proteins deposited with the Research Collaboratory for Structural Bioinformatics Protein Data Bank. The NRL-3D Database includes standardized and frequently observed alternate names, sources, keywords, literature citations, experimental conditions and searchable sequences from model coordinates. These databases are freely accessible through the National Cancer Institute-Frederick Advanced Biomedical Computing Center at these web sites: http://www. ncifcrf.gov/RESID, http://www.ncifcrf.gov/NRL-3D; or at these National Biomedical Research Foundation Protein Information Resource web sites: http://pir.georgetown.edu/pirwww/dbinfo/resid .html, http://pir.georgetown.edu/pirwww/dbinfo/nrl3d .html

Amino Acids↗
PubMed1996

Selecting a database for literature searches in nursing: MEDLINE or CINAHL?

This study compares the usefulness of the MEDLINE and CINAHL databases for students on post-registration nursing courses. We searched for nine topics, using title words only. Identical searches of the two databases retrieved 1162 references, of which 88% were in MEDLINE, 33% in CINAHL and 20% in both sources. The relevance of the references was assessed by student reviewers. The positive predictive value of CINAHL (70%) was higher than that of MEDLINE (54%), but MEDLINE produced more than twice as many relevant references as CINAHL. The sensitivity of MEDLINE was 85% (95% CI 82-88%), and that of CINAHL was 41% (95% CI 37-45%). To assess the ease of obtaining the references, we developed an index of accessibility, based on the holdings of a number of Irish and British libraries. Overall, 47% of relevant references were available in the students' own library, and 64% could be obtained within 48 hours. There was no difference between the two databases overall, but when two topics relating specifically to the organization of nursing were excluded, references found in MEDLINE were significantly more accessible. We recommend that MEDLINE should be regarded as the first choice of bibliographic database for any subject other than one related strictly to the organization of nursing.

Choice Behavior↗
PubMed1995

Conditional reference charts to assess weight gain in British infants.

Growth monitoring in infancy is a useful tool for detecting growth disorders and failure to thrive. However, current weight charts do not monitor growth as such, they only identify infants whose weight centile is low and/or falling. A reference of conditional weight gain is described which compares an infant's current weight with that predicted from their previous weight, allowing for the fact that on average, light infants tend to grow faster than heavier infants. The reference, which expresses conditional weight gain as an SD score of centile, is based on the UK 1990 weight reference supplemented with correlation data on 223 infants from the Cambridge Infant Growth Study measured regularly between 4 weeks and 2 years of age. The reference is validated with data on 727 infants from the Newcastle Regional Health Authority database. The conditional reference provides a valid assessment of the weight gain of British infants, over time periods of four or more weeks, throughout the first two years of life.

Female↗
PubMed1999

O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins.

O-GLYCBASE is a database of glycoproteins with O-linked glycosylation sites. Entries with at least one experimentally verified O-glycosylation site have been compiled from protein sequence databases and literature. Each entry contains information about the glycan involved, the species, sequence, a literature reference and http-linked cross-references to other databases. Version 4.0 contains 179 protein entries, an approximate 15% increase over the last version. Sequence logos representing the acceptor specificity patterns for GalNAc, GlcNAc, mannosyl and xylosyl transferases are shown. The O-GLYCBASE database is available through the WWW at http://www.cbs.dtu.dk/databases/OGLYCBASE/

Acetylgalactosamine↗
PubMed1999

Mapping the literature of perfusion.

Perfusionists select and operate the equipment necessary for monitoring, supporting, or temporarily replacing the patient's circulatory or respiratory function. There are over 3,000 perfusionists working in U.S. hospitals, medical and perfusionist groups, and as independent contractors. The purpose of this study was to identify the core literature of perfusion and to determine which major databases provide the most thorough access to this literature. This paper is part of the Medical Library Association Nursing and Allied Health Resource Section's project to map the literature of the allied health professions. It uses a bibliometric methodology to identify core journals. A group of forty-three journals was determined to make up the core journal literature of perfusion. MEDLINE provided the best overall indexing coverage for these journals, but librarians and perfusionists will wish to supplement its use with the Cumulative Index to Nursing and Allied Health Literature in order to access the journals written primarily for perfusionists. The study results can guide purchasing and database searching decisions of collection development and reference librarians, encourage the database producer to increase coverage of titles that are unindexed or underindexed, and advise perfusionists of the best access to their core literature.

Abstracting and Indexing↗
PubMed1982

A personal reference retrieval system for medium sized computers allowing automatic data entry from ONLINE databases.

A series of programs has been developed for the storage and retrieval of bibliographic references, which allow automatic cross-referencing of the stored entries. Reference retrieval becomes successively faster as more searches are performed and references are automatically sub-grouped under indexed terms allow complete sub-sets to be scanned independently. The indexing allows complete sub-collections of references to be printed, e.g. for a review, with no further searching requirements. This style of retrieval is conceptually similar to card systems in use by many scientists and should enable a rapid familiarization with the retrieval system. The editing features of the programs provide for the direct collection of references from large ONLINE databases (e.g. MEDLINE) and the automatic entering of the references into the personal data collection. The programs provide reliable storage of references for individual scientists, so that their collections from library databases, or from manual input may be updated and searched quickly.

Abstracting and Indexing↗
PubMed2003

Predicting ADME properties and side effects: the BioPrint approach.

Computational methods are increasingly used to streamline and enhance the lead discovery and optimization process. However, accurate prediction of absorption, distribution, metabolism and excretion (ADME) and adverse drug reactions (ADR) is often difficult, due to the complexity of underlying physiological mechanisms. Modeling approaches have been hampered by the lack of large, robust and standardized training datasets. In an extensive effort to build such a dataset, the BioPrint database was constructed by systematic profiling of nearly all drugs available on the market, as well as numerous reference compounds. The database is composed of several large datasets: compound structures and molecular descriptors, in vitro ADME and pharmacology profiles, and complementary clinical data including therapeutic use information, pharmacokinetics profiles and ADR profiles. These data have allowed the development of computational tools designed to integrate a program of computational chemistry into library design and lead development. Models based on chemical structure are strengthened by in vitro results that can be used as additional compound descriptors to predict complex in vivo endpoints. The BioPrint pharmacoinformatics platform represents a systematic effort to accelerate the process of drug discovery, improve quantitative structure-activity relationships and develop in vitro/in vivo associations. In this review, we will discuss the importance of training set size and diversity in model development, the implementation of linear and neighborhood modeling approaches, and the use of in silico methods to predict potential clinical liabilities.

Animals↗
PubMed1998

A researcher's guide to population information Web sites.

"Thanks to the Internet, researchers now have instant and easy access to reference sources and databases and in many cases, no longer have to pay search fees. Highlighted here are some of the most useful reference sources for population research on the Internet."

Data Collection↗
PubMed2001

The TRANSPATH signal transduction database: a knowledge base on signal transduction networks.

UNLABELLED: TRANSPATH is an information system on gene-regulatory pathways, and an extension module to the TRANSFAC database system (Wingender et al., Nucleic Acids Res., 28, 316-319, 2000). It focuses on pathways involved in the regulation of transcription factors in different species, mainly human, mouse and rat. Elements of the relevant signal transduction pathways like complexes, signaling molecules, and their states are stored together with information about their interaction in an object-oriented database. The database interface provides clickable maps and automatically generated pathway cascades as additional ways to explore the data. All information is validated with references to the original publications. Also, references to other databases are provided (TRANSFAC, SWISS-PROT, EMBL, PubMed and others). AVAILABILITY: The database is available over (http://transpath.gbf.de) for interactive perusal. As an exchange format for the data, eXtensible Markup Language (XML) flatfiles and a Document Type Definition (DTD) are provided.

Algorithms↗
PubMed2000

Systematic review processes and the management of opioid withdrawal.

OBJECTIVE: To assess the diversity of research on the management of opioid withdrawal, identify sources of heterogeneity and provide a context for subsequent systematic reviews to establish evidence-based best practice. METHODS: References were identified through searches of multiple electronic databases and handsearching the reference lists of retrieved articles. The principal criterion for inclusion in the literature mapping process was that it be a study of an intervention intended to manage the process of opioid withdrawal. RESULTS: Of 218 references assessed, all participants were dependent on heroin in 41% and on methadone or l-alpha acetyl methadol (LAAM) in 24%. More than 17 different types of treatment approach were identified. Only 42% of references used a rating instrument to assess withdrawal severity and reported sufficient results to indicate the timing and magnitude of the peak and/or duration of withdrawal. The type of rating instrument used and the way in which results were reported varied enormously. A clear parameter for completion of detoxification was used for 37% of references. CONCLUSIONS: The capacity for rigorous systematic reviews of the management of opioid withdrawal is currently limited. There are multiple sources of heterogeneity that will need to be taken into account. IMPLICATIONS: The use of narrative reviews and observational studies are important complements to formal systematic reviews in the establishment of evidence-based practice in any area that combines aspects of psychology, behaviour, social context and medical treatment.

Humans↗
PubMed1999

Hormone replacement therapy and colon cancer among members of a health maintenance organization.

We investigated the association between hormone replacement therapy (HRT), primarily conjugated estrogens with or without medroxyprogesterone acetate, and colon cancer risk in a nested case-control study among women ages 55-79 years enrolled in Group Health Cooperative, a health maintenance organization in Washington state. Cases were diagnosed between 1984 and 1993. We selected controls randomly from enrollment files. HRT use was ascertained from a computerized database containing virtually all prescriptions dispensed since 1977. Among subjects with at least 5 years of pharmacy database information before reference date (1 year before diagnosis date), there were 341 cases of incident colon cancer and 1,679 controls. Estrogen use during the 5 years before reference date was not associated with risk of colon cancer [odds ratio (OR) = 0.85 and 95% confidence interval (CI) = 0.57-1.27 for 1-749 estrogen tablets; OR = 0.97 and 95% CI = 0.68-1.40 for > or =750 estrogen tablets]. An analysis including only women with at least 10 years of pharmacy database coverage found no association with use during the 10 years before reference date [OR = 1.07 (95% CI = 0.61-1.86) for 1-749 estrogen tablets; OR = 1.11 (95% CI = 0.69-1.80) for 750 or more estrogen tablets]. These results do not support the hypothesis that recent HRT use substantially reduces risk of colon cancer.

Adenocarcinoma↗
PubMedDate not supplied

A comprehensive review of the effects of worksite health promotion on health-related outcomes.

PURPOSE: This article provides the foundation for a series of literature reviews that critically examine the effectiveness of worksite health promotion programs. This issue reviews the exercise, health risk appraisal, nutrition and cholesterol, and weight control literatures; a future issue will review the alcohol, HIV/AIDS, multicomponent program, seat belt, smoking, and stress management literatures. METHODS: The literature search used a four-step process that included a computerized database search, a reference search, a manual search of relevant health promotion journals, and the writing of the review by a recognized expert in the area being searched. The databases were searched from 1968 through 1994 and included Medline, Aidsline, Psychological Abstracts, Combined Health Information Database, Employee Benefits Infosource, National Prevention Evaluation Research Collection, National Resource Center on Worksite Health Promotion, National Technical Information Service, and the Substance Abuse Information database. A total of 288 articles were identified by the search, not including the 37 articles in the hypertension literature. Authors of each review were requested to incorporate additional studies not identified by the search, provide a research rating for each individual article, and a rating for the overall literature for their respective area. The authors reviewed 316 studies. FINDINGS: The overall ratings for the reviews reported in this issue were suggestive for exercise, weak for health risk appraisals, suggestive/indicative for both nutrition and cholesterol, and indicative for weight control. The ratings for the other reviews will be reported in the subsequent issue. CONCLUSIONS: Research reported in these reviews suggests the effectiveness of worksite health promotion programs, however, additional research is required to provide conclusive evidence of their impact.

Health Knowledge, Attitudes, Practice↗