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Results for “data repository”

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At least 217 records · Page 12Linked to original sources

PubMed2003

Health care quality management by means of an incident report system and an electronic patient record system.

BACKGROUND: Quality management in health care services has not been as successful as in other industries. OBJECTIVE: To assess the potential contribution of an on-line incident reporting system (OIRS) and of an electronic patient record (EPR) system to quality management in hospitals. METHODS: The two approaches are being implemented in Osaka University Hospital. RESULTS: Analysis of the early use of the on-line reporting system indicates that this qualitative approach has been effective to avoid adverse medical events. The quantitative methodology with the EPR is still in the phase of developing. CONCLUSION: Direct data entry by medical staff and an EPR based on dynamic templates and a dynamic problem oriented approach could be useful for building clinical data repositories that can support clinical quality management.

Humans↗

PubMed1999

PCASSO: a design for secure communication of personal health information via the internet.

The Internet holds both promise and peril for the communications of person-identifiable health information. Because of technical features designed to promote accessibility and interoperability rather than security, Internet addressing conventions and transport protocols are vulnerable to compromise by malicious persons and programs. In addition, most commonly used personal computer (PC) operating systems currently lack the hardware-based system software protection and process isolation that are essential for ensuring the integrity of trusted applications. Security approaches designed for electronic commerce, that trade known security weaknesses for limited financial liability, are not sufficient for personal health data, where the personal damage caused by unintentional disclosure may be far more serious. To overcome these obstacles, we are developing and evaluating an Internet-based communications system called PCASSO (Patient-centered access to secure systems online) that applies state of the art security to health information. PCASSO includes role-based access control, multi-level security, strong device and user authentication, session-specific encryption and audit trails. Unlike Internet-based electronic commerce 'solutions,' PCASSO secures data end-to-end: in the server; in the data repository; across the network; and on the client. PCASSO is designed to give patients as well as providers access to personal health records via the Internet.

Computer Security↗

PubMed2001

Application of industrial scale genomics to discovery of therapeutic targets in heart failure.

In recent years intense activity in both academic and industrial sectors has provided a wealth of information on the human genome with an associated impressive increase in the number of novel gene sequences deposited in sequence data repositories and patent applications. This genomic industrial revolution has transformed the way in which drug target discovery is now approached. In this article we discuss how various differential gene expression (DGE) technologies are being utilized for cardiovascular disease (CVD) drug target discovery. Other approaches such as sequencing cDNA from cardiovascular derived tissues and cells coupled with bioinformatic sequence analysis are used with the aim of identifying novel gene sequences that may be exploited towards target discovery. Additional leverage from gene sequence information is obtained through identification of polymorphisms that may confer disease susceptibility and/or affect drug responsiveness. Pharmacogenomic studies are described wherein gene expression-based techniques are used to evaluate drug response and/or efficacy. Industrial-scale genomics supports and addresses not only novel target gene discovery but also the burgeoning issues in pharmaceutical and clinical cardiovascular medicine relative to polymorphic gene responses.

Databases, Genetic↗

PubMed2005

Prevalence of polyps greater than 9 mm in a consortium of diverse clinical practice settings in the United States.

BACKGROUND & AIMS: Colonoscopy is often performed with the goal of identification of patients with serious colon neoplasia. We determined the prevalence of colon masses or polyps greater than 9 mm on the basis of age, gender, race, and procedure indication in diverse clinical practice settings and compared occurrence in patients receiving colonoscopy for screening, surveillance, or evaluation of symptoms. METHODS: We obtained patient demographics, procedure indication, and endoscopic findings from colonoscopy reports in the Clinical Outcomes Research Initiative data repository, which receives endoscopy reports from 73 diverse practice sites in the United States. A multivariate model was developed to measure risk variables for a mass or polyps >9 mm. Absolute risk was calculated in the model on the basis of the number needed to endoscope (NNE) to identify 1 patient with a mass or polyp >9 mm. RESULTS: From 2000-2002, colonoscopies in 141,413 unique patients were analyzed. Sixty-nine percent of the reports came from private practice (nonacademic) settings. Increasing age, male gender, and black race were associated with increased risk of mass or polyps >9 mm. In the 50- to 59-year-old average-risk group, 28 women and 18 men would need to have screening colonoscopy to identify 1 patient with a mass/polyp >9 mm. Patients with positive fecal occult blood test results, hematochezia, and anemia had lower NNE, whereas men older than 60 years receiving adenoma surveillance and patients with irritable bowel symptoms had similar NNE compared with average-risk subjects. CONCLUSIONS: The prevalence of a colon lesion >9 mm varies on the basis of age, gender, race, and procedure indication. Understanding utilization and outcomes can lead to more optimal use of colonoscopy.

Age Factors↗

PubMedDate not supplied

Characterizing bitterness: identification of key structural features and development of a classification model.

This work describes the first approach in the development of a comprehensive classification method for bitterness of small molecules. The data set comprises 649 bitter and 13 530 randomly selected molecules from the MDL Drug Data Repository (MDDR) which are analyzed by circular fingerprints (MOLPRINT 2D) and information-gain feature selection. The feature selection proposes substructural features which are statistically correlated to bitterness. Classification is performed on the selected features via a naïve Bayes classifier. The substructural features upon which the classification is based are able to discriminate between bitter and random compounds, and thus we propose they are also functionally responsible for causing the bitter taste. Such substructures include various sugar moieties as well as highly branched carbon scaffolds. Cynaropicrine contains a number of the substructural features found to be statistically associated with bitterness and thus was correctly predicted to be bitter by our model. Alternatively, both promethazine and saccharin contain fewer of these substructural features, and thus the bitterness in these compounds was not identified. Two different classes of bitter compounds were identified, namely those which are larger and contain mainly oxygen and carbon and often sugar moieties, and those which are rather smaller and contain additional nitrogen and/or sulfur fragments. The classifier is able to predict 72.1% of the bitter compounds. Feature selection reduces the number of false-positives while also increasing the number of false negatives to 69.5% of bitter compounds correctly predicted. Overall, the method presented here presents both one of the largest databases of bitter compounds presently available as well as a relatively reliable classification method.

Algorithms↗

PubMed2006

Our favourite alternative splice site.

Alternative splicing is a widespread mechanism in mammals that generates several mRNAs from one gene, thereby creating genetic diversity of the genome. Variant splice patterns are often specific to different stages of development or particular tissues, and alternative splicing defects are being more frequently detected in genetic diseases and cancers. The increasingly important role of alternative splicing in the function and the regulation of cellular process makes it critical to have an easy-to-use data repository for the biological and medical research communities. We have compared web resources that give access to information on alternatively spliced genes, and the FAST DB (Friendly Alternative Splicing and Transcripts DataBase) site came out as our favourite.

Alternative Splicing↗

PubMed2005

Software agents in molecular computational biology.

Progress made in applying agent systems to molecular computational biology is reviewed and strategies by which to exploit agent technology to greater advantage are investigated. Communities of software agents could play an important role in helping genome scientists design reagents for future research. The advent of genome sequencing in cattle and swine increases the complexity of data analysis required to conduct research in livestock genomics. Databases are always expanding and semantic differences among data are common. Agent platforms have been developed to deal with generic issues such as agent communication, life cycle management and advertisement of services (white and yellow pages). This frees computational biologists from the drudgery of having to re-invent the wheel on these common chores, giving them more time to focus on biology and bioinformatics. Agent platforms that comply with the Foundation for Intelligent Physical Agents (FIPA) standards are able to interoperate. In other words, agents developed on different platforms can communicate and cooperate with one another if domain-specific higher-level communication protocol details are agreed upon between different agent developers. Many software agent platforms are peer-to-peer, which means that even if some of the agents and data repositories are temporarily unavailable, a subset of the goals of the system can still be met. Past use of software agents in bioinformatics indicates that an agent approach should prove fruitful. Examination of current problems in bioinformatics indicates that existing agent platforms should be adaptable to novel situations.

Algorithms↗

PubMed2003

The MUSC DNA Microarray Database.

SUMMARY: The Medical University of South Carolina (MUSC) DNA Microarray Database is a web-accessible archive of DNA microarray data. The database was developed using the DNA microarray project/data management system, micro ArrayDB. Annotations for each DNA microarray project and associated cRNA target information are stored in a MySQL relational database and linked to array hybridization data (raw and normalized). At the discretion of investigators, data are placed into the public domain where they can be interrogated and downloaded through a web browser. In addition to serving as an online resource of gene expression data, the MUSC DNA Microarray Database is a model for other academic DNA microarray data repositories. AVAILABILITY: Browsing and downloading of MUSC DNA Microarray Database information can be done after registration at http://proteogenomics.musc.edu/pss/home.php.

Academic Medical Centers↗

PubMed2026

circASbase: A Comprehensive Database of Alternative Splicing Events in circRNAs.

Although extensive evidence has underscored the critical role of alternative splicing (AS) in generating mature circular RNA (circRNA) isoforms and augmenting their functional diversity, a significant gap remains in the availability of specialized databases housing circRNA AS events. To bridge this gap, we develop circASbase, a pioneering and comprehensive database that catalogs 452,129 AS events in 884,047 full-length circRNAs from 581 samples across 13 species, and provides rich annotations to facilitate understanding the splicing regulation of circRNA. Our findings reveal substantial differences between circRNAs and linear transcripts regarding the distribution and occurrence of AS events, highlighting the unique regulatory landscape of circRNAs. These special splicing events result in functional differences of circRNAs by affecting internal ribosome entry sites, N6-methyladenosine sites, open reading frames, protein features, microRNA targets, and more. In summary, circASbase not only meets the urgent need of the research community for data repositories, but also represents a significant advancement in our understanding of circRNA biology. With its user-friendly interfaces and web-based visualization tools, circASbase is poised to become an indispensable resource for researchers exploring the regulatory mechanisms and functional roles of AS events in circRNAs. This database will continuously drive new insights and discoveries in the field, setting the stage for further advancements in circRNA research. circASbase is freely available at http://reprod.njmu.edu.cn/cgi-bin/circASbase/.

Alternative Splicing↗

PubMed2005

Farm animal genomics and informatics: an update.

Farm animal genomics is of interest to a wide audience of researchers because of the utility derived from understanding how genomics and proteomics function in various organisms. Applications such as xenotransplantation, increased livestock productivity, bioengineering new materials, products and even fabrics are several reasons for thriving farm animal genome activity. Currently mined in rapidly growing data warehouses, completed genomes of chicken, fish and cows are available but are largely stored in decentralized data repositories. In this paper, we provide an informatics primer on farm animal bioinformatics and genome project resources which drive attention to the most recent advances in the field. We hope to provide individuals in biotechnology and in the farming industry with information on resources and updates concerning farm animal genome projects.

Animals↗

PubMed2006

VectorBase: a home for invertebrate vectors of human pathogens.

VectorBase (http://www.vectorbase.org/) is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing an integrated resource for the research community. Currently, VectorBase contains genome information for two organisms: Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever.

Aedes↗

PubMed2005

Managing knowledge and technology to foster innovation at the Ohio State University Medical Center.

Biomedical knowledge is expanding at an unprecedented rate-one that is unlikely to slow anytime in the future. While the volume and scope of this new knowledge poses significant organizational challenges, it creates tremendous opportunities to release and direct its power to the service of significant goals. The authors explain how the Center for Knowledge Management at The Ohio State University Medical Center, created during the academic year 2003-04, is doing just that by integrating numerous resource-intensive, technology-based initiatives-including personnel, services and infrastructure, digital repositories, data sets, mobile computing devices, high-tech patient simulators, computerized testing, and interactive multimedia-in a way that enables the center to provide information tailored to the needs of students, faculty and staff on the medical center campus and its surrounding health sciences colleges. The authors discuss how discovering, applying, and sharing new knowledge, information assets, and technologies in this way is a collaborative process. This process creates open-ended opportunities for innovation and a roadmap for working toward seamless integration, synergy, and substantial enhancement of the academic medical center's research, educational, and clinical mission areas.

Academic Medical Centers↗

PubMed2003

Impact of intensive care unit (ICU) drug use on hospital costs: a descriptive analysis, with recommendations for optimizing ICU pharmacotherapy.

OBJECTIVE: To determine the cost impact of intensive care unit (ICU) drug use on a hospital's total drug expense and to compare ICU pharmacy resource utilization with resource utilization of other hospital departments that provided services to the ICU. Additionally, to suggest strategies, based on these methods and results, to optimize ICU drug use. METHODS: Financial transactions for all ICU patients (n = 23,107) treated during fiscal years 1999-2002 were retrieved from the hospital's data repository. ICU drug costs were calculated both as the percentage of total drug costs for each fiscal year and adjusted for hospital volume (ICU patient days). ICU department charges were calculated as a percentage of total ICU charges and analyzed by simple descriptive statistics (mean +/- sd). Drug utilization was retrieved for those patients accounting for the highest percentage of ICU pharmacy charges. MAIN RESULTS: ICU drug costs accounted for 38.4% (+/-4.1% sd) of the total drug costs and have increased at a rate greater than non-ICU drug costs (12% vs. 6%). ICU pharmacy charges accounted for an average of 11.1% (+/-9.2% sd) of the total ICU charges, ranking as the fourth most costly of ICU charges. Both costly and highly used ICU therapies were identified for focus on cost-effectiveness analyses or application of an evidence-based drug use and disease state management program model to ICU pharmacotherapy. CONCLUSIONS: ICU drug therapies have a significant impact on hospital costs, and effective clinical informatics services and multidisciplinary collaboration programs are necessary to optimize ICU pharmacotherapy.

Academic Medical Centers↗

PubMed2005

The future of microarray technology: networking the genome search.

In recent years microarray technology has been increasingly used in both basic and clinical research, providing substantial information for a better understanding of genome-environment interactions responsible for diseases, as well as for their diagnosis and treatment. However, in genomic research using microarray technology there are several unresolved issues, including scientific, ethical and legal issues. Networks of excellence like GA(2)LEN may represent the best approach for teaching, cost reduction, data repositories, and functional studies implementation.

Allergy and Immunology↗

PubMed2006

Characterization and comparison of health-related utility in people with diabetes with various single and multiple vascular complications.

AIMS: To characterize and compare health-related utility in a large cohort of patients treated in hospital with diabetes and with single and multiple comorbidities. METHODS: The study was conducted in Cardiff and the Vale of Glamorgan, UK. Health-related utility was measured using the EQ5D(index), a standardized instrument for measuring health outcome. Patients from the Health Outcomes Data Repository (HODaR) were surveyed by postal questionnaire 6 weeks post discharge for in-patients and during clinics for patients attending as out-patients between January 2002 and July 2005. Patients with diabetes were identified by a previous history of in-patient admission with diabetes or as an out-patient with diabetes recorded as a coexisting diagnosis. RESULTS: We identified 4502 patients with diabetes. Mean ages were 65.4 and 64.2 years for males and females, respectively. Of these, 2003 (45%) had no recorded vascular complication. Overall, the EQ5D(index) was 0.584 (sd 0.325) for males and 0.533 (sd 0.351) for females. For those without any vascular complications the mean EQ5D(index) was 0.735 (sd 0.288). In a general linear model, the presence of single and multiple complications had a detrimental impact on the EQ5D(index). CONCLUSION: The results of this study provide an indication of the true impact of diabetes in terms of health-related utility. There was a decrease in the mean EQ5D(index) for those with vascular complications. Economic models of diabetes that have used additive or multiplicative methods to assess utility in individuals with several complications may be unreliable, and direct measurements, such as this, are recommended.

Aged↗

PubMed2005

Barriers to the treatment of hepatitis C. Patient, provider, and system factors.

BACKGROUND: Hepatitis C virus (HCV) infection is both prevalent and undertreated. OBJECTIVE: To identify barriers to HCV treatment in primary care practice. DESIGN: Cross-sectional study. SETTING AND PARTICIPANTS: A cohort of 208 HCV-infected patients under the care of a primary care physician (PCP) between December 2001 and April 2004 at a single academically affiliated community health center. MEASUREMENTS: Data were collected from the electronic medical record (EMR), the hospital clinical data repository, and interviews with PCPs. MAIN RESULTS: Our cohort consisted of 208 viremic patients with HCV infection. The mean age was 47.6 (+/-9.7) years, 56% were male, and 79% were white. Fifty-seven patients (27.4% of the cohort) had undergone HCV treatment. Independent predictors of not being treated included: unmarried status (adjusted odds ratio [aOR] for treatment 0.36, P=.02), female gender (aOR 0.31, P=.01), current alcohol abuse (aOR 0.08, P=.0008), and a higher ratio of no-shows to total visits (aOR 0.005 per change of 1.0 in the ratio of no-shows to total visits, P=.002). The major PCP-identified reasons not to treat included: substance abuse (22.5%), patient preference (16%), psychiatric comorbidity (15%), and a delay in specialist input (12%). For 13% of the untreated patients, no reason was identified. CONCLUSIONS: HCV treatment was infrequent in our cohort of outpatients. Barriers to treatment included patient factors (patient preference, alcohol use, missed appointments), provider factors (reluctance to treat past substance abusers), and system factors (referral-associated delays). Multimodal interventions may be required to increase HCV treatment rates.

Adult↗

PubMed2002

Changes in human immunodeficiency virus type 1 Gag at positions L449 and P453 are linked to I50V protease mutants in vivo and cause reduction of sensitivity to amprenavir and improved viral fitness in vitro.

Human immunodeficiency virus type 1 (HIV-1) Gag protease cleavage sites (CS) undergo sequence changes during the development of resistance to several protease inhibitors (PIs). We have analyzed the association of sequence variation at the p7/p1 and p1/p6 CS in conjunction with amprenavir (APV)-specific protease mutations following PI combination therapy with APV. Querying a central resistance data repository resulted in the detection of significant associations (P < 0.001) between the presence of APV protease signature mutations and Gag L449F (p1/p6 LP1'F) and P453L (p1/p6 PP5'L) CS changes. In population-based sequence analyses the I50V mutant was invariably linked to either L449F or P453L. Clonal analysis revealed that both CS mutations were never present in the same genome. Sequential plasma samples from one patient revealed a transition from I50V M46L P453L viruses at early time points to I50V M46I L449F viruses in later samples. Various combinations of the protease and Gag mutations were introduced into the HXB2 laboratory strain of HIV-1. In both single- and multiple-cycle assay systems and in the context of I50V, the L449F and P453L changes consistently increased the 50% inhibitory concentration of APV, while the CS changes alone had no measurable effect on inhibitor sensitivity. The decreased in vitro fitness of the I50V mutant was only partially improved by addition of either CS change (I50V M46I L449F mutant replicative capacity approximately 16% of that of wild-type virus). Western blot analysis of Pr55 Gag precursor cleavage products from infected-cell cultures indicated accumulation of uncleaved Gag p1-p6 in all I50V viruses without coexisting CS changes. Purified I50V protease catalyzed cleavage of decapeptides incorporating the L449F or P453L change 10-fold and 22-fold more efficiently than cleavage of the wild-type substrate, respectively. HIV-1 protease CS changes are selected during PI therapy and can have effects on both viral fitness and phenotypic resistance to PIs.

Binding Sites↗

PubMed2005

Computational, integrative, and comparative methods for the elucidation of genetic coexpression networks.

Gene expression microarray data can be used for the assembly of genetic coexpression network graphs. Using mRNA samples obtained from recombinant inbred Mus musculus strains, it is possible to integrate allelic variation with molecular and higher-order phenotypes. The depth of quantitative genetic analysis of microarray data can be vastly enhanced utilizing this mouse resource in combination with powerful computational algorithms, platforms, and data repositories. The resulting network graphs transect many levels of biological scale. This approach is illustrated with the extraction of cliques of putatively co-regulated genes and their annotation using gene ontology analysis and cis-regulatory element discovery. The causal basis for co-regulation is detected through the use of quantitative trait locus mapping.

Journal Article↗