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PubMed2004

The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols.

The Peptaibol Database is a sequence and structure resource for the unusual class of peptides known as peptaibols. These peptides exhibit antibiotic and membrane channel-forming activities. The database includes sequence, biological source and bibliographical data for the naturally occurring peptaibols. Information is also collated for the growing number of peptaibol 3D structures determined by either crystallography or NMR spectroscopy. The database can be obtained as a whole or can be queried by name, group, sequence motif, biological origin and/or literature reference. The Peptaibol Database can be freely accessed at http://www.cryst.bbk.ac.uk/peptaibol.

Anti-Bacterial Agents↗
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↗
PubMed2006

The Universal Protein Resource (UniProt).

The ability to store and interconnect all available information on proteins is crucial to modern biological research. Accordingly, the Universal Protein Resource (UniProt) plays an increasingly important role by providing a stable, comprehensive, freely accessible central resource on protein sequences and functional annotation. UniProt is produced by the UniProt Consortium, formed in 2002 by the European Bioinformatics Institute (EBI), the Protein Information Resource (PIR) and the Swiss Institute of Bioinformatics (SIB). The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, development of a user-friendly UniProt web site and the provision of additional value-added information through cross-references to other databases. UniProt is comprised of three major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase and the UniProt Reference Clusters. An additional component consisting of metagenomic and environmental sequences has recently been added to UniProt to ensure availability of such sequences in a timely fashion. UniProt is updated and distributed on a bi-weekly basis and can be accessed online for searches or download at http://www.uniprot.org.

Amino Acid Sequence↗
PubMed2005

Maternal posture for cephalic version of breech presentation: a review of the evidence.

BACKGROUND: Maternal posture is commonly recommended to promote cephalic version of breech presentation during pregnancy, but the few studies conducted to examine the efficacy of this obstetric practice are inconclusive. The purpose of this systematic review was to evaluate the research evidence base for postural management of breech presentation. METHODS: This review critically examined the research on maternal posture for breech presentation using guidelines from the third United States Preventive Services Task Force. Database searches were conducted of Ovid Medline, Cumulative Index of Nursing and Allied Health Literature, PubMed, and Cochrane Database of Systematic Reviews, using the keywords "pregnancy," "maternal posture," "maternal position," "postural management," "breech," "presentation." Hand searches were conducted on reference citations from databases, and all research articles, commentaries, and reports of clinical cases were included. RESULTS: Conceptual and methodological issues in the individual studies posed threats to internal validity in each study. Interpretation of the nonsignificant results in the research reports is debatable because the randomized controlled trials were underpowered, and flaws in each study challenged validity of the results. Meta-analysis of previous findings may be inappropriate. CONCLUSIONS: Further research based on explicit theory and improved methods, including sufficient sample size, is needed to determine whether maternal posture promotes cephalic version for pregnant women with breech presentation.

Breech Presentation↗
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↗
PubMed2004

The RESID Database of Protein Modifications as a resource and annotation tool.

The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications and cross-links including pre-, co-, and post-translational modifications. The database provides: systematic and alternate names, atomic formulas and masses, enzymatic activities that generate the modifications, keywords, literature citations, Gene Ontology (GO) cross-references, protein sequence database feature table annotations, structure diagrams, and molecular models. This database is freely accessible on the Internet through resources provided by the European Bioinformatics Institute (http://www.ebi.ac.uk/RESID), and by the National Cancer Institute--Frederick Advanced Biomedical Computing Center (http://www.ncifcrf.gov/RESID). Each RESID Database entry presents a chemically unique modification and shows how that modification is currently annotated in the protein sequence databases, Swiss-Prot and the Protein Information Resource (PIR). The RESID Database provides a table of corresponding equivalent feature annotations that is used in the UniProt project, an international effort to combine the resources of the Swiss-Prot, TrEMBL and PIR. As an annotation tool, the RESID Database is used in standardizing and enhancing modification descriptions in the feature tables of Swiss-Prot entries. As an Internet resource, the RESID Database assists researchers in high-throughput proteomics to search monoisotopic masses and mass differences and identify known and predicted protein modifications.

Databases, Factual↗
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↗
PubMed2005

[Estimation of China soil organic carbon storage and density based on 1:1,000,000 soil database].

Based on 1:1,000,000 soil database, and employing the methods of spatial expression, this paper estimated the soil organic carbon storage (SOCS) and density (SOCD) of China. The database consists of 1:1,000,000 digital soil map, soil profile attribution database, and soil reference system. The digital soil map contained 926 soil mapping units, 690 soil families, and 94 000 or more polygons, while the soil profile attribution database collected 7292 soil profiles, including 81 attribution fields. The SOCDs of soil profiles were calculated and linked to the soil polygons in the digital soil map by the method of "GIS linkage based on soil type", resulting in a vector map of 1:1,000,000 China SOCD. The SOCS of the country or of a soil could be estimated by summing up the SOCS of all polygons or the polygons of a soil, and their SOCD were the SOCS of them derived by their areas. The estimated SOCS and SOCD of the country was 89. 14 Pg (1 Pg = 10(15) g) and 9.60 kg m(-2), respectively, covered all the soils with a total area of 928.10 x 10(4) km2, which might be considered closest to the real value.

Carbon↗
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↗
PubMed2003

Assessing gene expression variation in normal human tissues using GeneTag, a novel, global, sensitive profiling method.

GeneTag is a novel expression profiling method that allows the visualization, quantification and identification of expressed genes-whether known or novel-in any species, tissue or cell type, independent of knowledge of the underlying sequence. Here we describe the application of this method to determine variation of gene expression in individual human liver samples and the identification of tissue-specific genes by comparing expression patterns across several human organs. Expression data are stored in a database for future reference and data analysis relies on proprietary software, which allows complex comparisons to be performed. Differentially expressed genes are quickly identified through a link to a sequence database. The results from our study underscore the importance of knowledge of individual variation of gene expression for the design and interpretation of transcript profiling experiments in the context of any biological question.

Brain↗
PubMed2003

PRECIS: protein reports engineered from concise information in SWISS-PROT.

MOTIVATION: There have been several endeavours to address the problem of annotating sequence data computationally, but the task is non-trivial and few tools have emerged that gather useful information on a given sequence, or set of sequences, in a simple and convenient manner. As more genome projects bear fruit, the mass of uncharacterized sequence data accumulating in public repositories grows ever larger. There is thus a pressing need for tools to support the process of automatic analysis and annotation of newly determined sequences. With this in mind, we have developed PRECIS, which automatically creates protein reports from sets of SWISS-PROT entries, collating results into structured reports, detailing known biological and medical information, literature and database cross-references, and relevant keywords.

Abstracting and Indexing↗
PubMed2004

Bone mineral density measurement in the calcaneus with DXL: comparison with hip and spine measurements in a cross-sectional study of an elderly female population.

We investigated the relationship between calcaneal and axial bone mineral density in an elderly female population. We also investigated the influence of changing the reference populations on T-score values. Bone mineral density (BMD) was determined in 388 women (mean age 73 years) participating in a cross-sectional study. BMD values were determined at the left hip and the lumbar spine, L1-L4, using Hologic QDR 4500 equipment for dual X-ray absorptiometry (DXA). The calcaneal measurements were made with DEXA-T, a device using a dual X-ray and laser (DXL) technique that combines DXA measurement with measurement of the heel thickness using a laser reflection technique. DEXA-T is an older version of the Calscan DXL device now commercially available. T-score values were calculated for hip measurements with both the original reference population of the Hologic device and the NHANES III reference population. T scores for heel measurements were calculated with the original reference population of the peripheral device and the Calscan database, a new calcaneal reference population. Changing the reference populations had a great influence on both the heel and the hip T scores, especially those of the femoral neck where the percentage of subjects identified as osteoporotic decreased from 53% to 23%. We conclude that, with the NHANES III and the larger Calscan database, using the cut-off point of -2.5 SD, the heel measurements had optimal accuracy for detecting osteoporosis at either the combination of the lumbar spine and the femoral neck or the combination of the lumbar spine, the femoral neck, the total hip and the trochanter. BMD measurements of the calcaneus with DXL correlated fairly well with measurements at axial sites at the group level, while in individual subjects large deviations were observed between all the measured sites. We also conclude that the influence of the reference populations on the T scores is substantial when different DXA methods are being compared; the total number of subjects classified as osteoporotic varied from 7% to 53% between the sites and with different reference populations.

Absorptiometry, Photon↗
PubMed2001

The core region of the coat protein gene is highly useful for establishing the provisional identification and classification of begomoviruses.

Polymerase chain reaction (PCR) was applied to detect and establish provisional identity of begomoviruses through amplification of a approximately 575 bp fragment of the begomoviral coat protein gene (CP), referred to as the 'core' region of the CP gene (core CP). The core CP fragment contains conserved and unique regions, and was hypothesized to constitute a sequence useful for begomovirus classification. Virus relationships were predicted by distance and parsimony analyses using the A component (bipartite viruses) or full genome (monopartite viruses), CP gene, core CP, or the 200 5'-nucleotides (nt) of the CP. Reconstructed trees and sequence divergence estimates yielded very similar conclusions for all sequence sets, while the CP 5'-200 nt was the best strain discriminator. Alignment of the core CP region for 52 field isolates with reference begomovirus sequences permitted provisional virus identification based on tree position and extent of sequence divergence. Geographic origin of field isolates was predictable based on phylogenetic separation of field isolates examined here. A 'closest match' or genus-level identification could be obtained for previously undescribed begomoviruses using the BLAST program to search a reference core CP database located at our website and/or in GenBank. Here, we describe an informative molecular marker that permits provisional begomovirus identification and classification using a begomoviral sequence that is smaller than the presently accepted, but less accessible CP sequence.

Capsid↗
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↗
PubMed2005

Locating the evidence base for musculoskeletal nursing: an overview of the rheumatology nursing literature.

The main aim of this study was to locate and classify publications, particularly research publications, produced by nurses working and/or researching in the area of rheumatology in order to develop a research strategy for a newly established academic and clinical nursing unit. Database searches were undertaken to identify journal articles. Theses, dissertations, research reports, conference abstracts and books were also included in the study. The publications once located were entered into a Reference Manager electronic database and the facilities of this package were used to analyse and classify the data. The findings of the study demonstrated that over the past 40 years nurses have been steadily increasing the publication output in this area and in the last 10 years there has been a substantial increase in all publications, but particularly research and investigative articles. However there is a lack of clinical research in this area and this needs to be addressed in future as nurses develop more advanced roles in this speciality. The main limitations was the difficulty in accurately identifying nursing publications because of inadequate details of authorship.

Academic Dissertations as Topic↗
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↗
PubMed2005

A systematic review of the literature associating breastfeeding with type 2 diabetes and gestational diabetes.

As diabetes becomes more prevalent in younger women, diabetes and maternal-child health issues such as breastfeeding co-exist with increasing frequency. We sought to determine the relationship between breastfeeding and both type 2 diabetes and gestational diabetes (GDM) in a variety of clinical contexts, with a focus on prevention. The Medline database from 1966-2003, relevant references of selected articles, the Cochrane database, and the NIH Clinical Trials website were searched. Search terms included breastfeeding, infant nutrition, and diabetes. The search was restricted to the English language and human subjects. Each study was reviewed by at least two of the authors and included if it pertained to the relationship between type 2 diabetes or GDM and breastfeeding. Twelve of 15 identified studies (80%) met selection criteria. All studies were observational. Specific maternal-child health populations varied by study. Two of the authors abstracted information from each article on 1) study design, 2) target population, 3) sample size/power, 4) definition of breastfeeding, 5) definition of diabetes, and 6) confounders. Higher rates of pregnancy and neonatal complications among women with type 2 or gestational diabetes can pose significant challenges to breastfeeding. Low estrogen levels in breastfeeding women may have a protective effect on glucose metabolism and subsequent risk of diabetes. Having been breastfed for at least 2 months may lower the risk of diabetes in children. Initial research has begun on the long-term effects of diabetes during pregnancy on children. Breastfeeding may lower both maternal and pediatric rates of diabetes. Women with diabetes should be strongly encouraged to breastfeed because of maternal and childhood benefits specific to diabetes that are above and beyond other known benefits of breastfeeding.

Breast Feeding↗