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PubMed2002

Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders.

Online Mendelian Inheritance in Man (OMIM) is a comprehensive, authoritative and timely knowledgebase of human genes and genetic disorders compiled to support research and education in human genomics and the practice of clinical genetics. Started by Dr Victor A. McKusick as the definitive reference Mendelian Inheritance in Man, OMIM (www.ncbi.nlm.nih.gov/omim) is now distributed electronically by the National Center for Biotechnology Information (NCBI), where it is integrated with the Entrez suite of databases. Derived from the biomedical literature, OMIM is written and edited at Johns Hopkins University with input from scientists and physicians around the world. Each OMIM entry has a full-text summary of a genetically determined phenotype and/or gene and has numerous links to other genetic databases such as DNA and protein sequence, PubMed references, general and locus-specific mutation databases, approved gene nomenclature, and the highly detailed mapviewer, as well as patient support groups and many others. OMIM is an easy and straightforward portal to the burgeoning information in human genetics.

Chromosome Mapping↗
PubMed2001

iProClass: an integrated, comprehensive and annotated protein classification database.

The iProClass database is an integrated resource that provides comprehensive family relationships and structural and functional features of proteins, with rich links to various databases. It is extended from ProClass, a protein family database that integrates PIR superfamilies and PROSITE motifs. The iProClass currently consists of more than 200,000 non-redundant PIR and SWISS-PROT proteins organized with more than 28,000 superfamilies, 2600 domains, 1300 motifs, 280 post-translational modification sites and links to more than 30 databases of protein families, structures, functions, genes, genomes, literature and taxonomy. Protein and family summary reports provide rich annotations, including membership information with length, taxonomy and keyword statistics, full family relationships, comprehensive enzyme and PDB cross-references and graphical feature display. The database facilitates classification-driven annotation for protein sequence databases and complete genomes, and supports structural and functional genomic research. The iProClass is implemented in Oracle 8i object-relational system and available for sequence search and report retrieval at http://pir.georgetown.edu/iproclass/.

Databases, Factual↗
PubMed2004

The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.

The Gene Ontology Annotation (GOA) database (http://www.ebi.ac.uk/GOA) aims to provide high-quality electronic and manual annotations to the UniProt Knowledgebase (Swiss-Prot, TrEMBL and PIR-PSD) using the standardized vocabulary of the Gene Ontology (GO). As a supplementary archive of GO annotation, GOA promotes a high level of integration of the knowledge represented in UniProt with other databases. This is achieved by converting UniProt annotation into a recognized computational format. GOA provides annotated entries for nearly 60,000 species (GOA-SPTr) and is the largest and most comprehensive open-source contributor of annotations to the GO Consortium annotation effort. By integrating GO annotations from other model organism groups, GOA consolidates specialized knowledge and expertise to ensure the data remain a key reference for up-to-date biological information. Furthermore, the GOA database fully endorses the Human Proteomics Initiative by prioritizing the annotation of proteins likely to benefit human health and disease. In addition to a non-redundant set of annotations to the human proteome (GOA-Human) and monthly releases of its GO annotation for all species (GOA-SPTr), a series of GO mapping files and specific cross-references in other databases are also regularly distributed. GOA can be queried through a simple user-friendly web interface or downloaded in a parsable format via the EBI and GO FTP websites. The GOA data set can be used to enhance the annotation of particular model organism or gene expression data sets, although increasingly it has been used to evaluate GO predictions generated from text mining or protein interaction experiments. In 2004, the GOA team will build on its success and will continue to supplement the functional annotation of UniProt and work towards enhancing the ability of scientists to access all available biological information. Researchers wishing to query or contribute to the GOA project are encouraged to email: goa@ebi.ac.uk.

Animals↗
PubMed2005

A two-dimensional electrophoresis reference map of human ovary.

The ovary plays a central role in oogenesis and gonadal hormone secretion. Proteomic analysis is a valuable approach for gaining an increased understanding of the molecular nature of the ovary. In this work, two-dimensional electrophoresis for protein separation followed by matrix-assisted laser desorption/ionization mass spectrometry and database searches, identified 231 protein spots corresponding to 138 individual proteins that were found in gels representing both the follicular and luteal phases. The data were used to construct a database online (http://reprod.njmu.edu.cn/2d). The identified proteins were functionally classified into seven groups: (1) cell signaling/communication, (2) cell division, (3) gene/protein expression, (4) metabolism, (5) cell structure and motility, (6) cell/organism defense, and (7) unclassified. Among the proteins identified, 47% had not been previously reported in the human ovary. In addition, a number of disease-related proteins were identified in this protein map, including some cancer- and polycystic ovarian syndrome-related proteins. Two proteins with phosphorylation were verified by Western blot analysis. Comparison of protein abundance between follicular and luteal stages produced seven protein spots that had been identified in our database. This study provides a preliminary reference map of normal human ovary that will form a basis for comparative studies on normal and pathological conditions of the human ovary and may serve as a potential tool for clinical diagnosis, therapeutics, and prognosis.

Animals↗
PubMed2000

The effects of emotion-oriented approaches in the care for persons suffering from dementia: a review of the literature.

OBJECTIVE: This article presents an overview of the results of intervention studies in various emotion-oriented approaches in the care for people suffering from dementia. Recommendations are made with regard to clinical practice and future research. DATA SOURCES: We searched for references (1990-99) in several bibliographical databases, i.e. Medline, PsycLit, Embase, Sociofile and Current Contents. The terms 'dementia' and 'Alzheimer's disease' were linked separately to the search terms: emotion-oriented, validation (therapy), sensory integration/sensory stimulation/snoezelen, simulated presence therapy and reminiscence (therapy)/life-review. Based on references in the articles found, other publications were traced. STUDY SELECTION: We started from the 'emotion-oriented' approaches used in 24-hour care distinguished by the American Psychiatric Association (1997) i.e. validation, sensory stimulation/integration, simulated presence therapy and reminiscence. We selected research articles that describe intervention, design, measuring instruments and results. DATA EXTRACTION: The articles were analyzed with regard to research group, setting, design, effect variables, intervention, measuring instruments, statistical analyses and results. DATA SYNTHESIS: It is shown that mainly positive results (including increased social interaction and decrease of behavior problems) are achieved with these emotion-oriented approaches. Unfortunately many studies have methodological limitations and are done independently, which makes comparison difficult. CONCLUSIONS: Despite the limited cogency of the studies we traced, the results are promising. Emotion-oriented care approaches offer the opportunity to tailor the care to the individual needs of dementing elderly and can be complemented with other psychosocial approaches (e.g. psychomotor therapy and music therapy) when necessary. The challenge for the care sector is to develop guidelines to determine which approach should be applied to whom and when. Scientific research can contribute by examining which emotion-oriented approaches, possibly in combination with each other or with psychosocial therapies, effect an increase in the well-being and improve functioning in which patients.

Aged↗
PubMed1996

Development of an animal genome database and its search system.

An animal genome database has been developed on a Unix workstation and maintained by a relational database management system. This database has focused on the comparative gene mapping between species to assist the mapping of the genes related to phenotypic traits in livestock. The linkage maps, cytogenetic maps, polymerase chain reaction primers of pig, cattle, mouse and human, and their references have been included in the database, and the correspondence among species have been stipulated in the database. In order to search the database effectively, the World Wide Web server (http://ws4.niai.affrc.go.jp/) and the electronic mail server system (e-mail: jgbase-mail@ niai.affrc.go.jp) have been developed on different Unix workstations. These servers are connected to the Internet.

Animals↗
PubMed2005

Suregene, a scalable system for automated term disambiguation of gene and protein names.

Researchers, hindered by a lack of standard gene and protein-naming conventions, endure long, sometimes fruitless, literature searches. A system that is able to automatically assign gene names to their LocusLink ID (LLID) in previously unseen MEDLINE abstracts is described. The system is based on supervised learning and builds a model for each LLID. The training sets for all LLIDs are extracted automatically from MEDLINE references in the LocusLink and SwissProt databases. A validation was done of the performance for all 20,546 human genes with LLIDs. Of these, 7344 produced good quality models (F-measure >0.7, nearly 60% of which were >0.9) and 13,202 did not, mainly due to insufficient numbers of known document references. A hand validation of MEDLINE documents for a set of 66 genes agreed well with the system's internal accuracy assessment. It is concluded that it is possible to achieve high quality gene disambiguation using scaleable automated techniques.

Algorithms↗
PubMed2000

A study of the references used in Cochrane protocols and reviews. Three bibles, three dictionaries, and nearly 25,000 other things.

OBJECTIVES: To describe the types of report that are cited by protocols and reviews included in the Cochrane Database of Systematic Reviews. METHODS: The citation for each reference included in the Cochrane protocols and reviews published in the Cochrane Database of Systematic Reviews in issue 1, 1999 of The Cochrane Library were categorized by reference type (e.g., journal article, conference proceeding, book chapter, personal communication, Cochrane review). RESULTS: Of a total of 24,913 citations, 21,694 (87.1%) were references to journal articles. There was a significant difference between the proportion of references to studies that were journal articles (12,348 of 13,472; 91.7%) and the proportion of other references in this category (9,346 of 11,441; 81.7%). CONCLUSION: The great majority of studies included in Cochrane reviews at the beginning of 1999 had been published as journal articles.

Clinical Protocols↗
PubMed2004

AZuRE, a scalable system for automated term disambiguation of gene and protein names.

Researchers, hindered by a lack of standard gene and protein-naming conventions, endure long, sometimes fruitless, literature searches. A system is described which is able to automatically assign gene names to their LocusLink ID (LLID) in previously unseen MEDLINE abstracts. The system is based on supervised learning and builds a model for each LLID. The training sets for all LLIDs are extracted automatically from MEDLINE references in the LocusLink and SwissProt databases. A validation was done of the performance for all 20,546 human genes with LLIDs. Of these, 7,344 produced good quality models (F-measure > 0.7, nearly 60% of which were > 0.9) and 13,202 did not, mainly due to insufficient numbers of known document references. A hand validation of MEDLINE documents for a set of 66 genes agreed well with the system's internal accuracy assessment. It is concluded that it is possible to achieve high quality gene disambiguation using scaleable automated techniques.

Databases, Protein↗
PubMed2005

Hypospadias: a transgenerational effect of diethylstilbestrol?

BACKGROUND: In 2002, an increased risk of hypospadias was reported for sons of women exposed to diethylstilbestrol (DES) in utero, suggesting transgenerational effects of DES. The aim of this study was to further assess the association between parental DES exposure and hypospadias in a case-referent study. METHODS: Cases with hypospadias were retrieved from the hospital information system. Referents were recruited via the parents of cases. Both parents completed postal questionnaires. Associations were estimated by odds ratios (OR) with 95% confidence intervals (CI). Additionally, conditional logistic regression analyses were performed for a matched subset of parents. RESULTS: The final database included 583 cases and 251 referents. In the initial analyses, an indication was found for an increased risk of hypospadias when mothers were exposed to DES in utero: OR=2.3 (95% CI 0.7-7.9). Conditional logistic regression resulted in a stronger risk estimate: OR=4.9 (95% CI 1.1-22.3). Paternal exposure to DES did not increase the risk. CONCLUSIONS: The results confirm an increased risk of hypospadias when mothers were exposed to DES in utero. However, the excess risk appears to be of much smaller magnitude than in the 2002 study. Further research on the potential health risks for the third generation is of great importance.

Diethylstilbestrol↗
PubMed2005

Characterization of a likelihood based method and effects of markers informativeness in evaluation of admixture and population group assignment.

BACKGROUND: Detection and evaluation of population stratification are crucial issues in the conduct of genetic association studies. Statistical approaches useful for understanding these issues have been proposed; these methods rely on information gained from genotyping sets of markers that reflect population ancestry. Before using these methods, a set of markers informative for differentiating population genetic substructure (PGS) is necessary. We have previously evaluated the performance of a Bayesian clustering method implemented in the software STRUCTURE in detecting PGS with a particular informative marker set. In this study, we implemented a likelihood based method (LBM) in evaluating the informativeness of the same selected marker panel, with respect to assessing potential for stratification in samples of European Americans (EAs) and African Americans (AAs), that are known to be admixed. LBM calculates the probability of a set of genotypes based on observations in a reference population with known specific allele frequencies for each marker, assuming Hardy Weinberg equilibrium (HWE) for each marker and linkage equilibrium among markers. RESULTS: In EAs, the assignment accuracy by LBM exceeded 99% using the most efficient marker FY, and reached perfect assignment accuracy using the 10 most efficient markers excluding FY. In AAs, the assignment accuracy reached 96.4% using FY, and >95% when using at least the 9 most efficient markers. The comparison of the observed and reference allele frequencies (which were derived from previous publications and public databases) shows that allele frequencies observed in EAs matched the reference group more accurately than allele frequencies observed in AAs. As a result, the LBM performed better in EAs than AAs, as might be expected given the dependence of LBMs on prior knowledge of allele frequencies. Performance was not dependent on sample size. CONCLUSION: The performance of the LBM depends on the efficiency and number of markers, and depends greatly on how representative the available reference allele frequencies are for those of the population being assigned. This method is of value when the parental population is known and relevant allele frequencies are available.

Black or African American↗
PubMed1994

Common variable immunodeficiency: diagnosis and management.

OBJECTIVE: Common variable immunodeficiency is a heterogeneous syndrome characterized by humoral immunodeficiency, recurrent bacterial infections, and a variety of immunologic abnormalities. The goal of this article is to review the pathogenesis, clinical manifestations, diagnosis, and management of common variable immunodeficiency. DATA SOURCES: References are limited to the English language literature. Sources include computerized databases and bibliographies of recent articles and books. STUDY SELECTION: References that made important contributions to our understanding of the pathogenesis, clinical manifestations, diagnosis, and treatment of this disease were selected for inclusion in this review. RESULTS AND CONCLUSION: Common variable immunodeficiency is an idiopathic state of immune dysregulation that results in impaired antibody synthesis and the development of recurrent bacterial infections. This syndrome is also associated with a variety of autoimmune and neoplastic disorders. Effective management of these patients includes intravenous immunoglobulin replacement, vigorous treatment of infections, and readiness to promptly evaluate and treat unusual autoimmune and neoplastic complications should they appear.

Common Variable Immunodeficiency↗
PubMed1993

Diversity of ribosomal DNA fingerprints of Leptospira serovars provides a database for subtyping and species assignation.

Ribosomal DNA fingerprints from 103 pathogenic Leptospira strains were examined using EcoRI restriction and fragment length polymorphisms of rRNA genes. Sixty-nine new leptospiral ribotypes were described, in addition to 49 previously observed. Except for 5 strains, a good correlation between DNA homology data and ribotyping was observed. The genospecies of 31 reference strains could be presumed, since they shared 13 ribotypes with strain(s) previously studied by DNA homology. Furthermore, the definition of common rRNA hybridization fragments in each recognized DNA hybridization group provides information about the status of Leptospira reference strains yet to be classified. With 118 ribotypes now defined among the validated serovar reference strains, rRNA fingerprints constitute a database for subtyping Leptospira species.

DNA Fingerprinting↗
PubMed2000

[The ZEBET database on alternative methods to animal experiments in the Internet--a concrete contribution to the protection of animals].

Up from February of the year 2000 ZEBET (German Centre for the Documentation and Validation of Alternative Methods) at the Federal Institute for Consumer Health Protection and Veterinary Medicine (BgVV) put the ZEBET-database on alternative methods to animal experiments on the Internet in English via DIMDI, the German Institute for Medical Documentation and Information (http://gripsdb.dimdi.de/engl/guieng.html). The access is free, moreover DIMDI's complete service is available to visitors of the ZEBET-database. The ZEBET database contains documents on alternatives to testing in animals, which have been carefully evaluated by ZEBET's staff according to the "3Rs"-concept established by Russel and Burch in 1959. Therefore, methods documented in the ZEBET database must meet at least one of the following criteria: "replacement" of an animal experiment by a non-animal method, "reduction" of the number of animals used, "refinement" of an experiment by minimising pain and suffering of animals. In addition, the ZEBET-database provides information on the current stage of development and validation of a method and on the acceptance for either scientific or regulatory purposes. Each document is characterised by the following criteria: the title of a method, keywords, assessment, summary and bibliographic references. To search DIMDI<<s-database and host-system the grips software has to be used. Examples are given for searching in the ZEBET-database. Currently 125 alternative methods are meeting the criteria of the ZEBET database. 50 of them are available online on the internet via DIMDI, the remaining 75 documents will be available by the end of the year 2000. International fellow organisations, e.g. FRAME (Fund for the Replacement of Animals in Medical Experiments) in the UK and CAAT (Johns Hopkins Center for Alternatives to Animal Testing) in the USA, have established links on their web sites to provide visitors free access to the ZEBET-database.

Animal Testing Alternatives↗
PubMed1993

Spine and total body bone mineral density in amenorrheic endurance athletes.

Lumbar spine, total body, and regional bone mineral densities (BMDs) were measured in eumenorrheic and amenorrheic runners and triathletes by using dual-energy X-ray absorptiometry (Lunar DPX). Values were also compared with age- and weight-matched reference data from the Lunar British database. The amenorrheic group had significantly lower lumbar spine (P = 0.003), arm (P = 0.018), trunk (P = 0.014), and total spine (P < 0.0001) BMDs compared with the eumenorrheic group and significantly lower lumbar (P = 0.002) and total spine (P < 0.001) values compared with the reference controls. Leg (P = 0.009) and arm (P < 0.001) densities were significantly higher than controls. All regions, apart from the lumbar spine, were significantly higher in the eumenorrheic group compared with the reference group. There were no within-group differences for the runners and triathletes. Compared with the eumenorrheic athletes, the amenorrheic women had significantly later age of menarche (P = 0.0032). The type of physical activity undertaken by these athletes can compensate for the loss of menses at the majority of skeletal sites with the exception of the spine.

Adult↗
PubMed2000

Gradual versus abrupt discontinuation of oxygen in preterm or low birth weight infants.

BACKGROUND: This section is under preparation and will be included in the next issue. OBJECTIVES: In preterm or low birth weight infants, does gradual versus abrupt discontinuation of supplemental oxygen influence mortality, retinopathy of prematurity, lung function, growth or development? SEARCH STRATEGY: The standard search strategy of the Cochrane Neonatal Review Group was used. This included searches of the Oxford Database of Perinatal trials, MEDLINE, previous reviews including cross references, abstracts, conferences and symposia proceedings, expert informants, journal handsearching mainly in the English language. An additional literature search of the MEDLINE, EMBASE, and CINAHL databases was conducted in order to locate any trials in addition to those provided by the Cochrane Controlled Trials Register (CENTRAL/CCTR). SELECTION CRITERIA: All trials utilising random or quasi-random patient allocation, in which gradual weaning was compared with abrupt discontinuation of supplemental oxygen in preterm or low birth weight infants, were eligible for inclusion. DATA COLLECTION AND ANALYSIS: The methodological quality of the eligible trial was assessed independently by each author for the degree selection, performance, attrition and detection bias. Data were extracted and reviewed independently by the each author. Results were compared and differences resolved as required. Data analysis was conducted according to the standards of the Cochrane Neonatal Review Group. MAIN RESULTS: The results of the one small trial of 51 infants included in this systematic review indicate a significant reduction in vascular retrolental fibroplasia (i.e. severe ROP) for infants weaned gradually from high oxygen concentrations compared with abrupt discontinuation (RR 0.22, 95% CI 0.07-0.68). This finding was independent of the duration of oxygen therapy. REVIEWER'S CONCLUSIONS: The results of this systematic review provide additional evidence linking routine exposure to high ambient oxygen in the early neonatal period to the development of ROP in preterm/LBW infants. However, due to small numbers and historical oxygen monitoring techniques, they provide little assistance to clinicians with regard to the most appropriate method of oxygen weaning, gradual or abrupt, in modern neonatal care settings.

Humans↗
PubMed2000

Early versus late discontinuation of oxygen in preterm or low birth weight infants.

BACKGROUND: This section is under preparation and will be included in the next issue. OBJECTIVES: In preterm or low birth weight infants, does early versus late weaning from supplementary oxygen influence mortality, retinopathy of prematurity, lung function, growth or development? SEARCH STRATEGY: The standard search strategy of the Neonatal Review Group was used. This included searches of the Oxford Database of Perinatal Trials, MEDLINE, previous reviews including cross references, abstracts, conferences and symposia proceedings, expert informants, journal handsearching mainly in the English language. An additional literature search of the MEDLINE, EMBASE, and CINAHL databases was conducted in order to locate any trials in addition to those provided by the Cochrane Controlled Trials Register (CENTRAL/CCTR). SELECTION CRITERIA: All trials utilising random or quasi-random patient allocation, in which early weaning was compared with late discontinuation of supplemental oxygen in preterm or low birth weight infants, were eligible for inclusion. DATA COLLECTION AND ANALYSIS: The methodological quality of the one eligible trial was assessed independently by each author for the degree of selection, performance, attrition and detection bias. Data regarding clinical outcomes including mortality, retinopathy of prematurity, and long term growth and development were extracted and reviewed independently by each author. Results were compared and differences resolved as required. Data analysis was conducted according to the standards of the Cochrane Neonatal Review Group. MAIN RESULTS: In the single eligible trial of 99 infants with birthweights less than 1650g, there were no significant differences in neonatal death rates or retrolental fibroplasia (any grade or severe) for all infants, or among infants with birth weights of less than 1000g. No other outcome measures specified a priori as clinically meaningful were reported in enough detail or with satisfactory follow-up rates to include in the analysis (early death; chronic lung disease; and long term growth, development, lung or visual function). REVIEWER'S CONCLUSIONS: The results of this systematic review do not provide strong evidence for either the benefits or harms of early oxygen weaning in preterm/LBW infants. Future research should be directed toward addressing the question of what are the most appropriate target levels of oxygenation, in both the early and late neonatal periods, rather than whether oxygen should be weaned early or late.

Humans↗