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PubMed1996

Database and knowledge base integration--a data mapping method for Arden Syntax knowledge modules.

One of the most important categories of decision-support systems in medicine are data driven systems where the inference engine is linked to a database. It is, therefore, important to find methods that facilitate the implementation of database queries referred to in the knowledge modules. A method is described for linking clinical databases to a knowledge base with Arden Syntax modules. The method is based on a query meta-database including templates for SQL queries which is maintained by a database administrator. During knowledge module authoring the medical expert refers only to a code in the query meta-database; no knowledge is needed about the database model or the naming of attributes and relations. The method uses standard tools, such as C+2 and ODBC, which makes it possible to implement the method at many platforms and to link to different clinical databases in a standardized way.

Databases, Factual↗
PubMed2004

Definition of the Beijing/W lineage of Mycobacterium tuberculosis on the basis of genetic markers.

Mycobacterium tuberculosis Beijing genotype strains are highly prevalent in Asian countries and in the territory of the former Soviet Union. They are increasingly reported in other areas of the world and are frequently associated with tuberculosis outbreaks and drug resistance. Beijing genotype strains, including W strains, have been characterized by their highly similar multicopy IS6110 restriction fragment length polymorphism (RFLP) patterns, deletion of spacers 1 to 34 in the direct repeat region (Beijing spoligotype), and insertion of IS6110 in the genomic dnaA-dnaN locus. In this study the suitability and comparability of these three genetic markers to identify members of the Beijing lineage were evaluated. In a well-characterized collection of 1,020 M. tuberculosis isolates representative of the IS6110 RFLP genotypes found in The Netherlands, strains of two clades had spoligotypes characteristic of the Beijing lineage. A set of 19 Beijing reference RFLP patterns was selected to retrieve all Beijing strains from the Dutch database. These reference patterns gave a sensitivity of 98.1% and a specificity of 99.7% for identifying Beijing strains (defined by spoligotyping) in an international database of 1,084 strains. The usefulness of the reference patterns was also assessed with large DNA fingerprint databases in two other European countries and for identification strains from the W lineage found in the United States. A standardized definition for the identification of M. tuberculosis strains belonging to the Beijing/W lineage, as described in this work, will facilitate further studies on the spread and characterization of this widespread genotype family of M. tuberculosis strains.

China↗
PubMed2000

Antibiotics for the common cold.

BACKGROUND: The common cold is caused by viruses which cannot be helped by antibiotics. OBJECTIVES: The objective of this review was to assess the effects of antibiotics for the common cold. SEARCH STRATEGY: We searched the Cochrane Controlled Trials Register, MEDLINE, EMBASE, the Family Medicine Database, and reference lists of articles, and we contacted principal investigators. The most recent search was in December 1998. SELECTION CRITERIA: Randomised trials comparing any antibiotic therapy with placebo in acute upper respiratory tract infections. DATA COLLECTION AND ANALYSIS: Both reviewers independently assessed trial quality and extracted data. MAIN RESULTS: Main results: Seven trials involving 2056 people aged between six months and 49 years were included. The overall quality of the included trials was variable. People receiving antibiotics did not do better in terms of cure or improvement than those on placebo (odds ratio 0.95, 95% confidence interval 0.70 to 1.28 fixed effects model). One study found a significant benefit for antibiotics compared with placebo for runny nose (clear or purulent). The only other study to evaluate purulent nasal discharge found no significant benefit for antibiotics. Only one study reported work time lost with 22% of those on antibiotic treatment and 25% of those on placebo but this was not significant. Patients treated with antibiotics had a significant increase in side effects (odds ratio 2.72, 95% confidence interval 1.02 to 7.27, random effects model). REVIEWER'S CONCLUSIONS REVIEWERS' CONCLUSIONS: There is not enough evidence of important benefits from the treatment of upper respiratory tract infections with antibiotics and there is a significant increase in adverse effects associated with antibiotic use.

Anti-Bacterial Agents↗
PubMed2000

Parent-training programmes for improving maternal psychosocial health.

BACKGROUND: The prevalence of mental health problems in women is 1:3 and such problems tend to be persistent. There is evidence from a range of studies to suggest that a number of factors relating to maternal psychosocial health can have a significant effect on the mother-infant relationship, and that this can have consequences for the psychological health of the child. It is now thought that parenting programmes may have an important role to play in the improvement of maternal psychosocial health. OBJECTIVES: The objective of this review is to address whether group-based parenting programmes are effective in improving maternal psychosocial health including anxiety, depression and self-esteem. SEARCH STRATEGY: A range of biomedical, social science, educational and general reference electronic databases were searched including MEDLINE, EMBASE CINAHL, PsychLIT, ERIC, ASSIA, Sociofile and the Social Science Citation Index. Other sources of information included the Cochrane Library (SPECTR, CENTRAL), and the National Research Register (NRR). SELECTION CRITERIA: Only randomised controlled trials were included in which participants had been randomly allocated to an experimental and a control group, the latter being either a waiting-list, no-treatment or a placebo control group. Studies had to include at least one group-based parenting programme, and one standardised instrument measuring maternal psychosocial health. DATA COLLECTION AND ANALYSIS: A systematic critical appraisal of all included studies was undertaken using the Journal of the American Medical Association (JAMA) published criteria. The data were summarised using effect sizes but were not combined in a meta-analysis due to the small number of studies within each group and the presence of significant heterogeneity. MAIN RESULTS: A total of 22 studies were included in the review but only 17 provided sufficient data to calculate effect sizes. These 17 studies reported on a total of 59 outcomes including depression, anxiety, stress, self-esteem, social competence, social support, guilt, mood, automatic thoughts, dyadic adjustment, psychiatric morbidity, irrationality, anger and aggression, mood, attitude, personality, and beliefs. Approximately 22% of the outcomes measured suggested significant differences favouring the intervention group. A further 40% showed differences favouring the intervention group but which failed to achieve conventional levels of statistical significance, in some cases due to the small numbers that were used. Approximately 38% of outcomes suggested no evidence of effectiveness. REVIEWER'S CONCLUSIONS: It is suggested that parenting programmes can make a significant contribution to the improvement of psychosocial health in mothers. While the critical appraisal suggests some variability in the quality of the included studies, it is concluded that there is sufficient evidence to support their use with diverse groups of parents. However, it is also suggested that some caution should be exercised before the results are generalised to parents irrespective of the level of pathology present, and that further research is still required.

Anxiety↗
PubMed2005

The European Radiobiology Archives (ERA)--content, structure and use illustrated by an example.

The European Radiobiology Archives (ERA), supported by the European Commission and the European Late Effect Project Group (EULEP), together with the US National Radiobiology Archives (NRA) and the Japanese Radiobiology Archives (JRA) have collected all information still available on long-term animal experiments, including some selected human studies. The archives consist of a database in Microsoft Access, a website, databases of references and information on the use of the database. At present, the archives contain a description of the exposure conditions, animal strains, etc. from approximately 350,000 individuals; data on survival and pathology are available from approximately 200,000 individuals. Care has been taken to render pathological diagnoses compatible among different studies and to allow the lumping of pathological diagnoses into more general classes. 'Forms' in Access with an underlying computer code facilitate the use of the database. This paper describes the structure and content of the archives and illustrates an example for a possible analysis of such data.

Animals↗
PubMed1995

Bibliographic databases: help in preparing reference lists.

Typing bibliography references is time consuming. It is also frustrating to have to retype references when you submit a manuscript to journals using different reference styles. Now you don't need to retype them. Computer programs have been developed which help you reorganize your references to many different styles. This experienced nurse author compares several of these programs for you.

Bibliographies as Topic↗
PubMed2006

[Characteristics of references between GSCC and CST for Semi-Luvisols].

In this paper, the references between Genetic Soil Classification of China (GSCC) and the Chinese Soil Taxonomy (CST) for GSCC-Semi-Luvisols were conducted, and their quantitative and spatial distribution characteristics within CST were studied, based on the 1 : 1 M Soil Database of China, which consists of 1 : 1 M digital soil map, soils profiles attribution database and soil reference system of China. Being a reference system for converting soil names in GSCC into those in CST, ST and WRB, respectively, Chinese Soil Reference System was a computerized retrieving system jointly developed by the experienced scientists of pedology and computer science. The comparison fields and laboratory investigation data of their soil profiles with diagnostic horizons and characteristics related in the target soil classification systems, and 2,540 typical soil species names corresponding in CST, ST and WRB systems were determined, respectively, which were selected from Soil Attributes Database because of their complete sets of attribute data. Finally, the system and reference database were established. "GIS linkage based soil type" method linked the records in the Soil Reference Database to the Soil Spatial Database. In this method, all records of soil profiles in Soil Reference Database as well as their soil reference name in other classification systems were allocated one by one onto corresponding soil type polygons in Soil Spatial Database on the GIS platform, according to the principles of soil type identity and similarity, parent material identity and likeness, and the location of soil profiles relative to linked target polygons. Area statistcs of all soils were conducted based on the polygons. The results showed that GSCC-Semi-Luvisols was a type of GSCC soil with a total area of 427,843.1 km2,which could be sorted to 4 CST Orders, i. e., Luvisols (51.3%), Cambosols (35.2%), Isohumosols (10.7%) and Anthrosols (2.8%), and further into CST 22 Groups and 38 Subgroups. All dark grey forest soil, superficial gleyed black soil, and leached dry red soil of GSCC subgroups could be sorted to Calcaric Hapli-Gelic Cambosols, Pachic Argi-Udic Cambosols and Typic Ferri-Ustic Luvisols of CST subgroups, respectively, and all grey cinnamon-like soil, calcareous grey cinnamonic soil and dry cinnamon soil could be sorted to Typic Ustic Cambosols. Making the reference was so complicated that there was no one to one reference relationship among other soils. The analysis of the area ratios and standard deviations of a certain GSCC soil classified by CST showed that the lower the unit for reference, the easier the reference would be. The results of this study were of high reference value to proper reference GSCC and CST, and to the application and development of CST.

China↗
PubMed2001

Human immunodeficiency virus type 1 drug resistance testing: a comparison of three sequence-based methods.

The use of genotypic assays for determining drug resistance in human immunodeficiency virus (HIV) type 1 (HIV-1)-infected patients is increasing. These tests lack standardization and validation. The aim of this study was to evaluate several tests used for the determination of HIV-1 drug resistance. Two genotypic tests, the Visible Genetics TruGene HIV-1 Genotyping Kit and the Applied Biosystems HIV Genotyping System, were compared using 22 clinical samples. Genotyping results were also obtained from an independent reference laboratory. The Visible Genetics and Applied Biosystems genotyping tests identified similar mutations when differences in the drug databases and reference strains were taken into account, and 19 of 21 samples were equivalent. The concordance between the two assays was 99% (249 of 252 mutation sites). Mutations identified by the reference laboratory varied the most among those identified by the three genotypic tests, possibly because of differences in the databases. The concordance of the reference laboratory results with the results of the other two assays was 80% (201 of 252). Samples with 500 to 750 HIV RNA copies/ml could be sequenced by the Visible Genetics and Applied Biosystems assays using 1 ml of input. The Visible Genetics and Applied Biosystems assays both generated an accurate sequence. However, the throughput of the Visible Genetics assay is more limited and may require additional instruments. The two assays differ technically but are similar in overall complexity. Data analysis in the two assays is straightforward, but only the reports provided by Visible Genetics contain information relating mutations to drug resistance. HIV drug resistance genotyping by sequencing is a complex technology which presents a challenge for analysis, interpretation, and reporting.

Anti-HIV Agents↗
PubMed2004

A database for G proteins and their interaction with GPCRs.

BACKGROUND: G protein-coupled receptors (GPCRs) transduce signals from extracellular space into the cell, through their interaction with G proteins, which act as switches forming hetero-trimers composed of different subunits (alpha,beta,gamma). The alpha subunit of the G protein is responsible for the recognition of a given GPCR. Whereas specialised resources for GPCRs, and other groups of receptors, are already available, currently, there is no publicly available database focusing on G Proteins and containing information about their coupling specificity with their respective receptors. DESCRIPTION: gpDB is a publicly accessible G proteins/GPCRs relational database. Including species homologs, the database contains detailed information for 418 G protein monomers (272 Galpha, 87 Gbeta and 59 Ggamma) and 2782 GPCRs sequences belonging to families with known coupling to G proteins. The GPCRs and the G proteins are classified according to a hierarchy of different classes, families and sub-families, based on extensive literature searchs. The main innovation besides the classification of both G proteins and GPCRs is the relational model of the database, describing the known coupling specificity of the GPCRs to their respective alpha subunit of G proteins, a unique feature not available in any other database. There is full sequence information with cross-references to publicly available databases, references to the literature concerning the coupling specificity and the dimerization of GPCRs and the user may submit advanced queries for text search. Furthermore, we provide a pattern search tool, an interface for running BLAST against the database and interconnectivity with PRED-TMR, PRED-GPCR and TMRPres2D. CONCLUSIONS: The database will be very useful, for both experimentalists and bioinformaticians, for the study of G protein/GPCR interactions and for future development of predictive algorithms. It is available for academics, via a web browser at the URL: http://bioinformatics.biol.uoa.gr/gpDB.

Databases, Protein↗
PubMed2001

Efficient DNA database laboratory strategy for high through-put STR typing of reference samples.

DNA intelligence databases were installed successfully in various countries during the past few years. It is a general trend that laboratories performing STR analysis for DNA databases have to adjust to increased sample through-put, especially when dealing with a high number of reference samples. In contrast to routine forensic casework analysis, where samples of suspects and unknown samples are interpreted with regard to the specific circumstances of the case and are kept distinctly apart from other cases, DNA databases consist of single, primarily unlinked DNA profiles. Problems areas associated with the high number of anonymous DNA profiles are the risk of logistic errors, such as sample mix-up during the laboratory procedure, and the risk of typing errors during manual transcription of data and/or results. Thus, DNA databases clearly require new laboratory strategies to rise to the challenge. This paper presents an efficient automated laboratory strategy on the platform of a laboratory management information system (LIMS) with the Austrian DNA Intelligence Database as example. Two goals were tackled in particular: first, data safety by avoiding both manual interaction during critical laboratory steps (i.e. when DNA is transferred form one tube into another), and errors due to manual transcription of sample information and results. Secondly, efficient sample processing by automizing the laboratory procedure with the help of robotic instruments, thus, giving the DNA staff more time to analyze data.

Austria↗
PubMed2026

MetaFX: feature extraction from whole-genome metagenomic sequencing data.

MOTIVATION: Microbial communities consist of thousands of microorganisms and viruses and have a tight connection with an environment, such as gut microbiota modulation of host body metabolism. However, the direct relationship between the presence of certain microorganism and the host state often remains unknown. Toolkits using reference-based approaches are limited to microbes present in databases. Reference-free methods often require enormous resources for metagenomic assembly or results in many poorly interpretable features based on k-mers. RESULTS: Here we present MetaFX-an open-source library for feature extraction from whole-genome metagenomic sequencing data and classification of groups of samples. Using a large volume of metagenomic samples deposited in databases, MetaFX compares samples grouped by metadata criteria (e.g. disease, treatment, etc.) and constructs genomic features distinct for certain types of communities. Features constructed based on statistical k-mer analysis and de Bruijn graphs partition. Those features are used in machine learning models for classification of novel samples. Extracted features can be visualized on de Bruijn graphs and annotated for providing biological insights. We demonstrate the utility of MetaFX by building classification models for 590 human gut samples with inflammatory bowel disease. Our results outperform the previous research disease prediction accuracy up to 17%, and improves classification results compared to taxonomic analysis by 9±10% on average. AVAILABILITY AND IMPLEMENTATION: MetaFX is a feature extraction toolkit applicable for metagenomic datasets analysis and samples classification. The source code, test data, and relevant information for MetaFX are freely accessible at https://github.com/ctlab/metafx under the MIT License. Alternatively, MetaFX can be obtained via http://doi.org/10.5281/zenodo.16949369.

Metagenomics↗
PubMed1992

Genome-related datasets within the E. coli Genetic Stock Center database.

The contents of the E. coli Genetic Stock Center database and the availability in electronic form of the subset of information most relevant to sequence databases are described. The database uses the long-standing Stock Center records (developed and curated by Dr B.J.Bachmann) in describing genotypes of mutant derivatives of E.coli K-12 in terms of alleles, structural mutations, mating type, and plasmids as well as the derivation, names and originators of the strain, and references. The database includes descriptions of mutations, mutation properties, genes, gene properties, and gene products, with EC number identifiers for enzymes. Sequence information is not included, but entries refer to sequence database accession numbers for sequenced regions. A gene is described as a subtype of a more general category of chromosome interval called Site. Since sites are used to describe any chromosomal interval, mapping information is associated with sites. Alleles are described as mutations of those sites and they are not primary map objects, but inherit map position information from the corresponding site description. The database design is intended to preserve richness of detail where it is known and uncertainty of measurements or information as it occurs in order to represent the stock center records as accurately as possible.

Bacterial Proteins↗
PubMed2005

CysMap and CysJoin: database and tools for protein disulphides localisation.

We have developed a computer program able to make user-customised databases derived from the public PIR non-redundant reference protein database. When the database of interest has been created, the user will generate the map of all the possible linear peptides containing one and two cysteines for each protein and combine them to calculate the mass of all the possible clusters of linear peptides linked by a disulphide bridge with a cysteine pair. It is also possible to create selected maps corresponding to peptides formed by the action of specific proteases. In this way, mass spectrometric data obtained from the hydrolysis of proteins of unknown sequence can be related to that contained in the database for quick disulphide assignment and protein identification. To confirm signal attribution, the program will also furnish the expected mass of cluster peptides after performing a cycle of Edman degradation. The utility of the program is discussed and examples of application are given.

Amino Acid Sequence↗
PubMed1991

Comparison and evaluation of nine bibliographic databases concerning adverse drug reactions.

Few evaluations and statistical comparisons of bibliographic databases have been published. As a drug information center, we were particularly interested in databases providing references on adverse drug reactions (ADRs). Ten drugs were randomly chosen from the 2000 files at our center. Nine databases were selected according to the high frequency of references concerning ADRs: eight online systems (MEDLINE, BIOSIS, TOXLINE, Iowa Drug Information System, PASCAL, EMBASE, PHARMLINE, and International Pharmaceutical Abstracts [IPA]), and one Compact Disk Read Only Memory (CD-ROM) system (Core MEDLINE). The total number of references, the number of references from 1987 to 1989, and the number of relevant references from 1987 to 1989 were analyzed using the Friedman two-way ANOVA by ranks. The overlap between databases for only one drug, carboplatin, and the quality:cost ratio were also studied. Considering the total number of references, TOXLINE and EMBASE were significantly superior to IPA, PHARMLINE, PASCAL, and Core MEDLINE. For the period 1987-1989, EMBASE was significantly superior to PASCAL, IPA, PHARMLINE, and Core MEDLINE with regard to total number of references, and significantly superior to PASCAL, Core MEDLINE, and IPA with regard to relevance. MEDLINE, TOXLINE, and EMBASE had the best quality:cost ratio. EMBASE had the slightest overlap of references, with 53 percent of the unique references on carboplatin. This comparative evaluation showed that the ability of bibliographic databases to provide information on ADRs is dependent on both the size and the quality of each database.

Databases, Bibliographic↗
PubMed1991

Algorithm for point-to-point correlation of geometrically nearly similar microscopic objects.

An algorithm is presented that compares two quasi similar images by correlating selected points on them--assuming their coordinates are available. The procedure involves translational, magnificational and rotational operations to find corresponding point pairs on the pictures. The algorithm automatically compensates for slight dissimilarities between images and constructs a reference point database for correlation during the evaluation process. Establishment of the reference point networks on the images prior to the examination is avoided.

Algorithms↗
PubMed2005

Hyperbaric oxygen therapy for stroke: a systematic review of the evidence.

OBJECTIVE: To identify the benefits and harms of using hyperbaric oxygen therapy to treat acute or subacute stroke or the chronic effects of a stroke. We aimed to identify any gaps in the evidence to provide guidance for future research. DESIGN: A systematic review of the evidence. SEARCH STRATEGY: We searched MEDLINE, EMBASE, the Cochrane Library, HealthSTAR, CINAHL, MANTIS, bibliographic databases from professional societies and hyperbaric oxygen therapy practitioners, and reference lists. Databases were searched from inception to December 2003. INCLUSION CRITERIA STUDIES: Controlled clinical trials and observational studies published in English. PARTICIPANTS: Patients with ischaemic stroke in any inpatient or outpatient setting. OUTCOMES: Mortality, functional health outcomes and adverse events. DATA COLLECTION AND ANALYSIS: Using predetermined criteria, two reviewers assessed each study for inclusion, and abstracted data about study design, population, interventions, and outcomes. We assigned an overall quality rating (good, fair, or poor) based on internal validity. RESULTS: We identified only four randomized controlled trials and one controlled clinical trial. The best evidence shows no benefit to hyperbaric oxygen therapy in patients with stroke, but because the stage of patients enrolled (acute, subacute, or chronic), the documentation of type and severity of stroke, and the dosage of hyperbaric oxygen therapy given varied considerably, the generalizability of these results is limited. We identified 17 observational studies; all were poor quality. CONCLUSIONS: The overall evidence is insufficient to determine the effectiveness of hyperbaric oxygen therapy in any subgroup of stroke patients. To determine if hyperbaric oxygen therapy for stroke provides any benefit and that these outweigh potential harms, good quality studies are needed.

Brain Ischemia↗
PubMed2006

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.

NCBI's reference sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. The database includes 3774 organisms spanning prokaryotes, eukaryotes and viruses, and has records for 2,879,860 proteins (RefSeq release 19). RefSeq records integrate information from multiple sources, when additional data are available from those sources and therefore represent a current description of the sequence and its features. Annotations include coding regions, conserved domains, tRNAs, sequence tagged sites (STS), variation, references, gene and protein product names, and database cross-references. Sequence is reviewed and features are added using a combined approach of collaboration and other input from the scientific community, prediction, propagation from GenBank and curation by NCBI staff. The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence.

Amino Acid Sequence↗