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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↗
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↗
PubMed1993

Managing a personal reference list by computer.

Either of these programs will accomplish the task of storing and organizing a personal bibliography. Reference Manager is more widely used, but more costly. Although it contains more input formats than Papyrus, most of the common formats used in medicine are supported by both programs. Importing is the best way to establish a personal database with many references, since it avoids manually typing the data. The import interface in Reference Manager is simpler to use at first, and faster than Papyrus's, but either program accomplishes the task with relative ease. The authors of Papyrus are receptive to updating import formats and adding new formats to their libraries as requested by users. Why not use MEDLINE alone instead of downloading and maintaining a personal reference list? These programs are more useful than MEDLINE in their output formatting capabilities. The most useful output feature is the generation of bibliographies for manuscripts, and both programs accomplish this task nicely. Papyrus includes fewer specific journal formats than Reference Manager, but both programs permit the user to add detailed output specifications to their personal journal lists.

Databases, Bibliographic↗
PubMed2001

National Cancer Institute initiative: Lung image database resource for imaging research.

Preliminary clinical studies suggest that spiral computed tomography (CT) of the lungs can improve early detection of lung cancer in high-risk individuals. More clinical studies are needed, however, before public health recommendations can be proposed for population-based screening. Spiral CT generates large-volume data sets and thus poses problems in terms of implementation of efficient and cost-effective screening methods. Image processing algorithms such as computer assisted diagnostic (CAD) methods have the potential to assist in lesion (eg, nodule) detection on spiral CT studies. CAD methods may also be used to characterize nodules by either assessing the stability or change in size of lesions based on evaluation of serial CT studies, or quantitatively measuring the temporal parameters related to contrast dynamics when using contrast material-enhanced CT studies. CAD methods therefore have the potential to enhance the sensitivity and specificity of spiral CT lung screening studies. Lung cancer screening studies now under investigation create an opportunity to develop an image database that will allow comparison and optimization of CAD algorithms. This database could serve as an important national resource for the academic and industrial research community that is currently involved in the development of CAD methods. The National Cancer Institute request for applications (RFA) (CA-01-001) has already been announced (April 2000) to establish and support a consortium of academic centers to develop this database, the consortium to be referred to as the Lung Image Database Consortium (LIDC). This RFA is now closed. Five academic sites have been selected to be members of the LIDC, the first meeting of this consortium is planned for spring of 2001, and a public meeting is to be held in 2002. This report is abstracted from the previously published RFA to serve as an example of how an initiative is developed by the National Cancer Institute to support a research resource. For specific details of the RFA, please access the following Internet site: http://www. nci.nih.gov/bip/NCI-DIPinisumm.htm#a11.

Algorithms↗
PubMed1998

Research potentials and pitfalls in the use of an HIV clinical database: Chelsea and Westminster Hospital.

This article summarizes the various problems and pitfalls in using clinical databases for epidemiologic research, with particular reference to an HIV clinical database. The combined population of HIV-infected individuals attending the Chelsea and Westminster Hospital, the Charing Cross Hospital, and the Victoria Clinic in London is the largest cohort of HIV-positive individuals in the U.K. A computerized database was developed in the mid-1980s and was adapted into a clinically oriented observational database for approximately 6,653 HIV-1-positive registered patients from three hospital-based clinics within the Riverside Health Authority in London, U.K.: Chelsea and Westminster Hospital Clinic (n = 5,000); Charing Cross Hospital (n = 500); and the Victoria Clinic (n = 500). The majority (83%) of HIV-infected patients registered at these sites are homosexual or bisexual men. Of 2,078 patients seen within the last 6 months, 22% are asymptomatic and 33% have AIDS; 30% have a CD4 cell count of less than 100 cells/mm3 and 17% have a CD4 cell count of greater than 500 cells/mm3. Dates of seroconversion are known for approximately 285 patients. For each patient, information on demographic characteristics, clinical symptoms, and HIV-related diagnoses, outpatient pharmacy prescriptions, day care treatments and procedures, and enrollment into clinical trials is routinely collected at outpatient clinic visits and entered into the database. Inpatient diagnoses and treatments were integrated into the database in September 1995. Unused serum samples from routine AIDS antibody or antigen testing are stored in a local specimen repository. The main purpose of the HIV database is to provide a multipurpose resource for use by physicians, researchers, and managers for administration, clinical care, and research. The specific functions of the database are the following: to enhance patient management by providing access to a clinical summary sheet detailing up-to-date information; to serve as a research tool for clinical and epidemiologic research; to aid in the identification of patients eligible for planned or ongoing clinical trials; to provide a facility for local and regional AIDS surveillance and reporting; and to provide a facility for administration and resource management of HIV services. The major limitations of this database in the conduct of clinical research have been losses to follow-up and incomplete information about clinical outcomes, because physicians have failed to update the clinical information.

Acquired Immunodeficiency Syndrome↗
PubMed1995

"Hyperstat": an educational and working tool in epidemiology.

The work of a researcher in epidemiology is based on studying literature, planning studies, gathering data, analyzing data and writing results. Therefore he has need for performing, more or less, simple calculations, the need for consulting or quoting literature, the need for consulting textbooks about certain issues or procedures, and the need for looking at a specific formula. There are no programs conceived as a workstation to assist the different aspects of researcher work in an integrated fashion. A hypertextual system was developed which supports different stages of the epidemiologist's work. It combines database management, statistical analysis or planning, and literature searches. The software was developed on Apple Macintosh by using Hypercard 2.1 as a database and HyperTalk as a programming language. The program is structured in 7 "stacks" or files: Procedures; Statistical Tables; Graphs; References; Text; Formulas; Help. Each stack has its own management system with an automated Table of Contents. Stacks contain "cards" which make up the databases and carry executable programs. The programs are of four kinds: association; statistical procedure; formatting (input/output); database management. The system performs general statistical procedures, procedures applicable to epidemiological studies only (follow-up and case-control), and procedures for clinical trials. All commands are given by clicking the mouse on self-explanatory "buttons". In order to perform calculations, the user only needs to enter the data into the appropriate cells and then click on the selected procedure's button. The system has a hypertextual structure. The user can go from a procedure to other cards following the preferred order of succession and according to built-in associations. The user can access different levels of knowledge or information from any stack he is consulting or operating. From every card, the user can go to a selected procedure to perform statistical calculations, to the reference database management system, to the textbook in which all procedures and issues are discussed in detail, to the database of statistical formulas with automated table of contents, to statistical tables with automated table of contents, or to the help module. he program has a very user-friendly interface and leaves the user free to use the same format he would use on paper. The interface does not require special skills. It reflects the Macintosh philosophy of using windows, buttons and mouse. This allows the user to perform complicated calculations without losing the "feel" of data, weight alternatives, and simulations. This program shares many features in common with hypertexts. It has an underlying network database where the nodes consist of text, graphics, executable procedures, and combinations of these; the nodes in the database correspond to windows on the screen; the links between the nodes in the database are visible as "active" text or icons in the windows; the text is read by following links and opening new windows. The program is especially useful as an educational tool, directed to medical and epidemiology students. The combination of computing capabilities with a textbook and databases of formulas and literature references, makes the program versatile and attractive as a learning tool. The program is also helpful in the work done at the desk, where the researcher examines results, consults literature, explores different analytic approaches, plans new studies, or writes grant proposals or scientific articles.

Computer-Assisted Instruction↗
PubMed1999

PhosphoBase, a database of phosphorylation sites: release 2.0.

PhosphoBase contains information about phosphorylated residues in proteins and data about peptide phosphorylation by a variety of protein kinases. The data are collected from literature and compiled into a common format. The current release of PhosphoBase (October 1998, version 2.0) comprises 414 phosphoprotein entries covering 1052 phosphorylatable serine, threonine and tyrosine residues. The kinetic data from peptide phosphorylation assays for approximately 330 oligopeptides is also included. The database entries are cross-referenced to the corresponding records in the Swiss-Prot protein database and literature references are linked to MedLine records. PhosphoBase is available via the WWW at http://www.cbs.dtu. dk/databases/PhosphoBase/

Animals↗
PubMed2000

Acute reference doses: theory and practical approaches.

The approach of the Joint Meeting on Pesticide Residues to the establishment of the acute reference dose for pesticides is presented and related issues are discussed. Three main points seem relevant when discussing the acute reference dose: (1) what compounds should have an acute reference dose, (2) what toxicological database is required for the establishment of an acute reference dose; (3) what safety factors are to be used. It is concluded that (1) groups of compounds that need an acute reference dose can be identified, whereas general rules for identifying groups not requiring an acute reference dose cannot be easily given; (2) studies from the standard toxicological database can often be used to allocate an acute reference dose and the usefulness of refinements (by requesting specific studies) should be evaluated after intake assessment; general rules on study requirements cannot be easily given; (3) more thought should be given to what safety factors apply in certain circumstances.

Animals↗