Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Reference database”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,765 records · Page 98Linked to original sources
PubMed1989

Computerization of academic vascular surgery.

Academic surgical units have a combination of computer needs, including access to the surgical literature, storage and retrieval of patient registry data, laboratory, and research data, generation of reports; statistical analysis of data; and word processing. A system that fulfills these requirements was developed for an academic vascular surgical unit. The system integrates these functions in a multi-user environment and is accessed from menus on multiple terminals in laboratories and offices in three hospitals and in staff members' homes. Databases currently include more than 7000 references to published articles in vascular surgery, a vascular registry consisting of more than 7500 patients, patient data from three integrated noninvasive vascular laboratories, data generated from both clinical and basic research, and a log of resident, fellow, and faculty operative experience. Statistical analysis, using essentially all modern statistical methods including sophisticated log-rank, proportional hazards, and multivariant analyses, can be performed on all databases, either separately or in any combination, without the need to reenter data. An electronic mail and messaging system provides for paperless communication between surgeons, research personnel, and clerical staff.

Academic Medical Centers↗
PubMed2004

Towards a standardized human proteome database: quantitative proteome profiling of living cells.

Comparative proteome profiling, performed by two-dimensional polyacrylamide gel electrophoresis or multidimensional protein identification technology, usually relies on the relative comparison of samples of interest with respect to a reference. Currently, no standardized quantitative protein expression database of human cells, facilitating data comparisons between different laboratories, exists. Recently, we have published two-dimensional polyacrylamide gel electrophoresis-based techniques to assess absolute protein data comprising protein amounts, synthesis rates and biological half-lives (Mol. Cell. Proteomics 2002, 1, 528-537). Determination of protein amounts by fluorography of two-dimensional gels was followed by the exact quantification of the amount of incorporated (35)S radiolabel. Here we demonstrate an application of this highly standardized method to quiescent human T cells, phythaemagglutinin-stimulated T cells and Jurkat cells, a human T lymphoblast cell line. While the protein composition of quiescent T cells differed significantly compared to that of Jurkat cells, it was only slightly different compared to the activated T cells. Synthesis profile analyses demonstrated that activated T cells clearly differed from the quiescent cells, performing apparently almost like lymphoblast cells. The great sensitivity of this approach was further demonstrated with human umbilical vein endothelial cells treated for six hours with vascular endothelial growth factor. While no significant alteration of protein amounts was detected at all upon activation, the synthesis rate of several proteins was found to be more than doubled.

Autoradiography↗
PubMed1996

Use of a food composition database to estimate daily dietary intake of nutrient or trace elements in Japan, with reference to its limitation.

Daily dietary intake of 28 trace elements (Al, As, B, Ba, Be, Bi, Cd, Co, Cr, Cu, Ga, Ge, Li, Mg, Mn, Mo, Ni, Pb, Sb, Sc, Se, Si, Sn, Sr, Ti, Tl, V and Zn) were estimated from the food intake records (collected by the 24-h total food duplicate method), taking advantage of recently published trace element composition tables for foods in Japan. Because the number of food items listed in the tables was not sufficient, the calculation was made with not all foods recorded, and the results should be taken as semi-quantitative. The estimated intake was high (i.e. > 1 mg/day as a median) for Al, Cu, Mg, Mn, Si, Sr and Zn, medium (i.e. 2-985 micrograms/day) for As, B, Ba, Be, Cr, Ge, Mo, Ni, Sb, Sc, Se, Sn and Ti, and low (i.e. < 1 microgram/day) for Cd, Co, Li, Pb and V. Comparison of the present estimates with the reported values in the literature on 15 elements showed that close agreements were observed in the cases of 10 elements (i.e. Al, B, Cr, Cu, Mg, Mn, Mo, Ni, Se and Zn) for which the present estimates are above 1 microgram/day, whereas the discrepancies were significant for four elements (i.e. Cd, Co, Pb and V) with < 1 microgram/day intake. When the expected dietary uptake was compared with that by respiration in the cases of the 16 elements for which the atmospheric concentration data in Japan are available, the uptake was exclusively attributable to the dietary route for all 16 elements with the possible exception of vanadium.

Adult↗
PubMed2001

Necessity of quality-controlled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species.

The use of the 16S rRNA gene for identification of nontuberculous mycobacteria (NTM) provides a faster and better ability to accurately identify them in addition to contributing significantly in the discovery of new species. Despite their associated problems, many rely on the use of public sequence databases for sequence comparisons. To best evaluate the taxonomic status of NTM species submitted to our reference laboratory, we have created a 16S rRNA sequence database by sequencing 121 American Type Culture Collection strains encompassing 92 species of mycobacteria, and have also included chosen unique mycobacterial sequences from public sequence repositories. In addition, the Ribosomal Differentiation of Medical Microorganisms (RIDOM) service has made freely available on the Internet mycobacterial identification by 16S rRNA analysis. We have evaluated 122 clinical NTM species using our database, comparing >1,400 bp of the 16S gene, and the RIDOM database, comparing approximately 440 bp. The breakdown of analysis was as follows: 61 strains had a sequence with 100% similarity to the type strain of an established species, 19 strains showed a 1- to 5-bp divergence from an established species, 11 strains had sequences corresponding to uncharacterized strain sequences in public databases, and 31 strains represented unique sequences. Our experience with analysis of the 16S rRNA gene of patient strains has shown that clear-cut results are not the rule. As many clinical, research, and environmental laboratories currently employ 16S-based identification of bacteria, including mycobacteria, a freely available quality-controlled database such as that provided by RIDOM is essential to accurately identify species or detect true sequence variations leading to the discovery of new species.

Databases, Nucleic Acid↗
PubMed2000

CyanoBase, the genome database for Synechocystis sp. strain PCC6803: status for the year 2000.

CyanoBase provides an online resource for access to data on genomic information about the cyanobacterium Synechocystis sp. strain PCC6803. The database contains annotations for each protein-coding gene deduced from the entire nucleotide sequence of the genome, gene classification lists, and keyword and similarity search engines. Core portions of CyanoBase consist of annotations for each of the 3168 protein genes deduced from the entire nucleotide sequence of this genome. The contents of each gene were improved by updating with the results of similarity searches and by introducing references for analysis in bioinformatics. The database now contains repository facilities that store and provide experimental information, in addition to providing proposals for the function of each gene. This information should help to avoid unnecessary, overlapping experiments and should assist communication between scientists who wish to elucidate the function of putative genes on the cyanobacteria genome. The current URL of CyanoBase is http://www.kazusa.or.jp:8080/cyano/

Cyanobacteria↗
PubMed2006

Development of the method and U.S. normalization database for Life Cycle Impact Assessment and sustainability metrics.

Normalization is an optional step within Life Cycle Impact Assessment (LCIA) that may be used to assist in the interpretation of life cycle inventory data as well as life cycle impact assessment results. Normalization transforms the magnitude of LCI and LCIA results into relative contribution by substance and life cycle impact category. Normalization thus can significantly influence LCA-based decisions when tradeoffs exist. The U. S. Environmental Protection Agency (EPA) has developed a normalization database based on the spatial scale of the 48 continental U.S. states, Hawaii, Alaska, the District of Columbia, and Puerto Rico with a one-year reference time frame. Data within the normalization database were compiled based on the impact methodologies and lists of stressors used in TRACI-the EPA's Tool for the Reduction and Assessment of Chemical and other environmental Impacts. The new normalization database published within this article may be used for LCIA case studies within the United States, and can be used to assist in the further development of a global normalization database. The underlying data analyzed for the development of this database are included to allow the development of normalization data consistent with other impact assessment methodologies as well.

Air Pollutants↗
PubMed2002

Practical experience with databases for congenital heart disease: a registry versus an academic database.

Increasingly, pooled data from multiple institutions are the source of published clinical results. A computerized database program is essential to compile and analyze clinical experience. The scope of data collection defines a database. Two types of databases, the registry and academic, are compared. In a registry database, some of the data are collected on all patients. The resources dedicated to data collection and entry are the practical limit to the extent of information in the database. The agreement on nomenclature for surgical diagnosis and procedure codes of congenital heart disease has paved the way for the development of a multi-institutional registry database. The registry database could provide a standard of care reference for early results after congenital heart surgery. The practical difficulty of data collection is obviated by limiting information to a basic minimum dataset. The academic database, in which all of the data are collected for a defined subset of patients, is designed to investigate a specific population of patients to generate new knowledge. It contains sufficient data to allow sophisticated statistical analysis to clarify the determinants of good and poor outcome, including early, mid- and long-term follow-up information. Multi-institutional pooling of detailed information derived from academic databases will be of increasing importance in generating new knowledge to foster improved therapy for patients with congenital heart disease.

Cardiac Surgical Procedures↗
PubMed2005

Implementation of DRLs in the UK.

This article describes the system of regulation and practical guidance that has been developed in the UK for implementing the requirement in the EC Medical Exposure Directive that all Member States shall promote the establishment and use of diagnostic reference levels (DRLs) for medical X-ray examinations. In particular, it describes the role of two national patient dose databases maintained by NRPB, which provide important sources of information on which formally adopted numerical values for 'national DRLs' will be based. One database deals with radiographic and fluoroscopic examinations and the recommended 'national reference doses' from the latest review of this database are discussed. The other database deals specifically with computed tomography (CT) examinations, which now account for 50% of the collective dose to the UK population from all medical X rays and are consequently of particular radiation protection concern. The first analysis of this CT database is still underway, but some encouraging indications of a reduction in patient dose for some CT examinations are reported. Progress in formally adopting numerical values for 'national DRLs', as required by the UK regulations, and the provision of authoritative guidance on the implementation of DRLs at the local level, are also discussed.

Adult↗
PubMed2000

Prophylactic antibiotics for cystic fibrosis.

BACKGROUND: Patients with cystic fibrosis are sometimes prescribed antibiotics to take continuously on a prophylactic (preventative) basis. This approach is most commonly used in infants where the objective is to reduce pulmonary infection with Staphylococcus aureus and prevent lung damage. This approach may also be used in older patients. This review evaluates the evidence for the effectiveness of this approach and considers potential adverse effects. OBJECTIVES: To compare continuous oral antibiotic prophylaxis with no prophylaxis (short courses of oral antibiotics given as clinically indicated) in patients with cystic fibrosis. This review considers both the effectiveness of prophylaxis (bacteria isolated from the respiratory tract, requirement for additional antibiotic treatment, lung function, survival) and the adverse effects. SEARCH STRATEGY: The Cochrane Cystic Fibrosis and Genetic Disorders Group clinical trials register was used. This comprises references identified from a comprehensive search of electronic databases, as well as hand searching relevant journals and conference abstracts. Companies manufacturing anti-staphylococcal antibiotics were also approached for unpublished data. Date of the most recent search of the Group's specialised register: November 1999. SELECTION CRITERIA: All randomised or pseudo-randomised trials where continuous oral prophylactic antibiotics, given for a period of at least one year, were compared to intermittent antibiotic therapy given "as required." Cystic fibrosis patients of any disease severity were considered. DATA COLLECTION AND ANALYSIS: Trials were assessed for eligibility, methodological quality and data extraction by two reviewers (AS & SW). The following outcomes were assessed: lung function; nutrition (weight standard deviation score); survival; requirement for additional antibiotic treatment; isolates of pathogens from the respiratory tract; occurrence of adverse reactions to prophylactic antibiotics. MAIN RESULTS: Only two studies, totalling 66 patients (over half of whom were infants), were suitable for inclusion in the review. A reduced prevalence of Staphylococcus aureus in the respiratory secretions was seen in children receiving anti-staphylococcal antibiotic prophylaxis, although no effect was seen on other common pathogens. This is associated with a reduced requirement for additional courses of oral antibiotics and fewer hospital admissions in the first two years of life in patients receiving prophylaxis. No effect on infant lung function has been shown after one year of prophylactic treatment. Data are not available on adverse effects of the interventions. As the duration of the studies reviewed has been of two years or less, conclusions cannot be drawn about the long term effects of prophylaxis on acquisition of Pseudomonas aeruginosa and survival. REVIEWER'S CONCLUSIONS: Anti-staphylococcal antibiotic prophylaxis may be of benefit when commenced early in infancy and continued up to two years of age. There is insufficient evidence from this review to say whether use in older children, or adults, or for periods of over two year is beneficial.

Adult↗
PubMed2005

GrainGenes 2.0. an improved resource for the small-grains community.

GrainGenes (http://wheat.pw.usda.gov) is an international database for genetic and genomic information about Triticeae species (wheat [Triticum aestivum], barley [Hordeum vulgare], rye [Secale cereale], and their wild relatives) and oat (Avena sativa) and its wild relatives. A major strength of the GrainGenes project is the interaction of the curators with database users in the research community, placing GrainGenes as both a data repository and information hub. The primary intensively curated data classes are genetic and physical maps, probes used for mapping, classical genes, quantitative trait loci, and contact information for Triticeae and oat scientists. Curation of these classes involves important contributions from the GrainGenes community, both as primary data sources and reviewers of published data. Other partially automated data classes include literature references, sequences, and links to other databases. Beyond the GrainGenes database per se, the Web site incorporates other more specific databases, informational topics, and downloadable files. For example, unique BLAST datasets of sequences applicable to Triticeae research include mapped wheat expressed sequence tags, expressed sequence tag-derived simple sequence repeats, and repetitive sequences. In 2004, the GrainGenes project migrated from the AceDB database and separate Web site to an integrated relational database and Internet resource, a major step forward in database delivery. The process of this migration and its impacts on database curation and maintenance are described, and a perspective on how a genomic database can expedite research and crop improvement is provided.

Breeding↗
PubMed2006

A new way for multidimensional medical data management: volume of interest (VOI)-based retrieval of medical images with visual and functional features.

The advances in digital medical imaging and storage in integrated databases are resulting in growing demands for efficient image retrieval and management. Content-based image retrieval (CBIR) refers to the retrieval of images from a database, using the visual features derived from the information in the image, and has become an attractive approach to managing large medical image archives. In conventional CBIR systems for medical images, images are often segmented into regions which are used to derive two-dimensional visual features for region-based queries. Although such approach has the advantage of including only relevant regions in the formulation of a query, medical images that are inherently multidimensional can potentially benefit from the multidimensional feature extraction which could open up new opportunities in visual feature extraction and retrieval. In this study, we present a volume of interest (VOI) based content-based retrieval of four-dimensional (three spatial and one temporal) dynamic PET images. By segmenting the images into VOIs consisting of functionally similar voxels (e.g., a tumor structure), multidimensional visual and functional features were extracted and used as region-based query features. A prototype VOI-based functional image retrieval system (VOI-FIRS) has been designed to demonstrate the proposed multidimensional feature extraction and retrieval. Experimental results show that the proposed system allows for the retrieval of related images that constitute similar visual and functional VOI features, and can find potential applications in medical data management, such as to aid in education, diagnosis, and statistical analysis.

Algorithms↗
PubMedDate not supplied

MRA calibration and measurement capabilities--radioactivity.

The practical realisation of the Mutual Recognition Arrangement relies on its two main Appendices, B and C. Appendix B relates to the equivalence of national measurement standards. The dissemination of these standards is achieved by the provision of physical standards and measurement services, where the associated measurement values are traceable to the SI. Appendix C specifies the quantities and ranges for which participating institutes recognise the validity of calibration and measurement certificates issued by other participating institutes and these are detailed in the database devoted to these standards and services, commonly referred to as calibration and measurement capabilities. Each participating institute has the opportunity to submit entries, via its Regional Metrology Organisation (RMO), to the database but, in order for users to be able to make informed choices, it is important that the data are entered to a common standard. The Joint Committee of the RMOs and the Bureau International des Poids et Mesures is responsible for the coordination of data provided by the RMOs. It is for individual RMOs to ensure the correctness of their own entries and to review and comment on those from others. This paper details that process and describes the various entries in the tables. It also addresses some of the remaining issues that still need to be resolved, in particular, the magnitudes of uncertainties and the need for supporting comparisons, both of which still present some significant problems.

Calibration↗
PubMed2004

Gene expression analysis in the hippocampal formation of tree shrews chronically treated with cortisol.

Adrenal corticosteroids influence the function of the hippocampus, the brain structure in which the highest expression of glucocorticoid receptors is found. Chronic high levels of cortisol elicited by stress or through exogenous administration can cause irreversible damage and cognitive deficits. In this study, we searched for genes expressed in the hippocampal formation after chronic cortisol treatment in male tree shrews. Animals were treated orally with cortisol for 28 days. At the end of the experiments, we generated two subtractive hippocampal hybridization libraries from which we sequenced 2,246 expressed sequenced tags (ESTs) potentially regulated by cortisol. To validate this approach further, we selected some of the candidate clones to measure mRNA expression levels in hippocampus using real-time PCR. We found that 66% of the sequences tested (10 of 15) were differentially represented between cortisol-treated and control animals. The complete set of clones was subjected to a bioinformatic analysis, which allowed classification of the ESTs into four different main categories: 1) known proteins or genes (approximately 28%), 2) ESTs previously published in the database (approximately 16%), 3) novel ESTs matching only the reference human or mouse genome (approximately 5%), and 4) sequences that do not match any public database (50%). Interestingly, the last category was the most abundant. Hybridization assays revealed that several of these clones are indeed expressed in hippocampal tissue from tree shrew, human, and/or rat. Therefore, we discovered an extensive inventory of new molecular targets in the hippocampus that serves as a reference for hippocampal transcriptional responses under various conditions. Finally, a detailed analysis of the genomic localization in human and mouse genomes revealed a survey of putative novel splicing variants for several genes of the nervous system.

Animals↗
PubMed2006

The PROSITE database.

The PROSITE database consists of a large collection of biologically meaningful signatures that are described as patterns or profiles. Each signature is linked to a documentation that provides useful biological information on the protein family, domain or functional site identified by the signature. The PROSITE database is now complemented by a series of rules that can give more precise information about specific residues. During the last 2 years, the documentation and the ScanProsite web pages were redesigned to add more functionalities. The latest version of PROSITE (release 19.11 of September 27, 2005) contains 1329 patterns and 552 profile entries. Over the past 2 years more than 200 domains have been added, and now 52% of UniProtKB/Swiss-Prot entries (release 48.1 of September 27, 2005) have a cross-reference to a PROSITE entry. The database is accessible at http://www.expasy.org/prosite/.

Amino Acids↗
PubMed2026

Metagenomics indicates new taxa in Candidatus Saccharimonadia and proposal of Parviradicicola hetaonensis gen. nov. sp. nov. and Parviputeicola dengkouensis gen. nov. sp. nov. following the rules of the SeqCode.

Candidatus Saccharimonadia is a core lineage within the phylum Patescibacteriota (formerly the bacterial candidate phyla radiation, CPR), yet the class has long lacked a standardized, complete taxonomic framework. This nomenclatural gap severely hinders consistent academic exchange and global research into its diversity, evolutionary history, and ecological roles. Here, we recovered 29 medium- to high-quality Ca. Saccharimonadia metagenome-assembled genomes (MAGs) from groundwater, rhizosphere soil, and saline-alkali soil in the Hetao Irrigation District, Inner Mongolia, China, and performed integrated phylogenomic, genome size evolution, and metabolic analyses alongside reference genomes from the GTDB r220 database. Based on robust polyphasic taxonomic evidence (multi-dimensional phylogenetic analyses, widely accepted genome-wide ANI/AAI thresholds) and SeqCode rules, we formally propose two novel taxa: Parviradicicola hetaonensis gen. nov., sp. nov. (type material: txb011_bin.8.strictTS) and Parviputeicola dengkouensis gen. nov., sp. nov. (type material: sgl022_bin.19.origTS), plus two novel families and one novel order. We further identified potential drivers and important associations related to Ca. Saccharimonadia genome size evolution and adaptive metabolic traits. This work refines the Ca. Saccharimonadia taxonomic framework, providing critical genomic references for follow-up research.

Phylogeny↗
PubMed1997

Chronic debilitating fatigue in Irish general practice: a survey of general practitioners' experience.

BACKGROUND: Doctors are called upon to treat chronic debilitating fatigue without the help of a protocol of care. AIMS: To estimate the incidence of chronic debilitating fatigue in Irish general practice, to obtain information on management strategy and outcome, to explore the attitudes of practitioners (GPs) towards the concept of a chronic fatigue syndrome (CFS), and to recruit practitioners to a prospective study of chronic fatigue in primary care. METHOD: A total of 200 names were selected from the database of the Irish College of General Practitioners (ICGP); 164 of these were eligible for the study. RESULTS: Altogether, 118 questionnaires were returned (72%). Ninety-two (78%) responders identified cases of chronic fatigue, giving an estimated 2.1 cases per practice and an incidence of 1 per 1000 population. All social classes were represented, with a male to female ratio of 1:2. Eleven disparate approaches to treatment were advocated. Many (38%) were dissatisfied with the quality of care delivered, and 45% seldom or hardly ever referred cases for specialist opinion. The majority (58%) accepted CFS as a distinct entity, 34% were undecided, and 8% rejected it. Forty-two (35%) GPs volunteered for a prospective study. CONCLUSION: Chronic fatigue is found in Irish general practice among patients of both sexes and all social classes. Doctors differ considerably in their management of patients and are dissatisfied with the quality of care they deliver. Many cases are not referred for specialist opinion. A prospective database is required to accurately assess the scale of this public health problem and to develop a protocol of care.

Adult↗
PubMed2005

Virtual screening for anti-HIV-1 RT and anti-HIV-1 PR inhibitors from the Thai medicinal plants database: a combined docking with neural networks approach.

The virtual screening approach for docking small molecules into a known protein structure is a powerful tool for drug design. In this work, a combined docking and neural network approach, using a self-organizing map, has been developed and applied to screen anti-HIV-1 inhibitors for two targets, HIV-1 RT and HIV-1 PR, from active compounds available in the Thai Medicinal Plants Database. Based on nevirapine and calanolide A as reference structures in the HIV-1 RT binding site and XK-263 in the HIV-1 PR binding site, 2,684 compounds in the database were docked into the target enzymes. Self-organizing maps were then generated with respect to three types of pharmacophoric groups. The map of the reference structures were then superimposed on the feature maps of all screened compounds. Only the structures having similar features to the reference compounds were accepted. By using the SOMs, the number of candidates for HIV-1 RT was reduced to six and nine compounds consistent with nevirapine and calanolide A, respectively, as references. For the HIV-1 PR target, there are 135 screened compounds showed good agreement with the XK-263 feature map. These screened compounds will be further tested for their HIV-1 inhibitory affinities. The obtained results indicate that this combined method is clearly helpful to perform the successive screening and to reduce the analyzing step from AutoDock and scoring procedure.

Anti-HIV Agents↗
PubMed1999

The SWISS-2DPAGE database: what has changed during the last year.

SWISS-2DPAGE (http://www.expasy.ch/ch2d/) is an annotated two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) database established in 1993. The current release contains 21 reference maps from human and mouse biological samples, as well as from Saccharomyces cerevisiae, Escherichia coli and Dictyostelium discoideum origin. These reference maps now have 2480 identified spots, corresponding to 528 separate protein entries in the database, in addition to virtual entries for each SWISS-PROT sequence. During the last year, the SWISS-2DPAGE has undergone major changes. Six new maps have been added, and new functions to access the data have been provided through the ExPASy server. Finally, an important change concerns the database funding source.

Animals↗