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At least 145 records · Page 8Linked to original sources
PubMed1997

Factors limiting microbial growth and activity at a proposed high-level nuclear repository, yucca mountain, nevada.

As part of the characterization of Yucca Mountain, Nev., as a potential repository for high-level nuclear waste, volcanic tuff was analyzed for microbial abundance and activity. Tuff was collected aseptically from nine sites along a tunnel in Yucca Mountain. Microbial abundance was generally low: direct microscopic cell counts were near detection limits at all sites (3.2 x 10(sup4) to 2.0 x 10(sup5) cells g(sup-1) [dry weight]); plate counts of aerobic heterotrophs ranged from 1.0 x 10(sup1) to 3.2 x 10(sup3) CFU g(sup-1) (dry weight). Phospholipid fatty acid concentrations (0.1 to 3.7 pmol g(sup-1)) also indicated low microbial biomasses; diglyceride fatty acid concentrations, indicative of dead cells, were in a similar range (0.2 to 2.3 pmol g(sup-1)). Potential microbial activity was quantified as (sup14)CO(inf2) production in microcosms containing radiolabeled substrates (glucose, acetate, and glutamic acid); amendments with water and nutrient solutions (N and P) were used to test factors potentially limiting this activity. Similarly, the potential for microbial growth and the factors limiting growth were determined by performing plate counts before and after incubating volcanic tuff samples for 24 h under various conditions: ambient moisture, water-amended, and amended with various nutrient solutions (N, P, and organic C). A high potential for microbial activity was demonstrated by high rates of substrate mineralization (as much as 70% of added organic C in 3 weeks). Water was the major limiting factor to growth and microbial activity, while amendments with N and P resulted in little further stimulation. Organic C amendments stimulated growth more than water alone.

Journal Article↗
PubMed2005

At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies.

A new method for detecting chimeras and other anomalies within 16S rRNA sequence records is presented. Using this method, we screened 1,399 sequences from 19 phyla, as defined by the Ribosomal Database Project, release 9, update 22, and found 5.0% to harbor substantial errors. Of these, 64.3% were obvious chimeras, 14.3% were unidentified sequencing errors, and 21.4% were highly degenerate. In all, 11 phyla contained obvious chimeras, accounting for 0.8 to 11% of the records for these phyla. Many chimeras (43.1%) were formed from parental sequences belonging to different phyla. While most comprised two fragments, 13.7% were composed of at least three fragments, often from three different sources. A separate analysis of the Bacteroidetes phylum (2,739 sequences) also revealed 5.8% records to be anomalous, of which 65.4% were apparently chimeric. Overall, we conclude that, as a conservative estimate, 1 in every 20 public database records is likely to be corrupt. Our results support concerns recently expressed over the quality of the public repositories. With 16S rRNA sequence data increasingly playing a dominant role in bacterial systematics and environmental biodiversity studies, it is vital that steps be taken to improve screening of sequences prior to submission. To this end, we have implemented our method as a program with a simple-to-use graphic user interface that is capable of running on a range of computer platforms. The program is called Pintail, is released under the terms of the GNU General Public License open source license, and is freely available from our website at http://www.cardiff.ac.uk/biosi/research/biosoft/.

Bacteroides↗
PubMedDate not supplied

Generic data modeling for clinical repositories.

OBJECTIVE: To construct a large-scale clinical repository that accurately captures a detailed understanding of the data vital to the process of health care and that provides highly efficient access to patient information for the users of a clinical information system. DESIGN: Conventional approaches to data modeling encourage the development of a highly specific data schema in order to capture as much information as possible about a given domain. In contrast, current database technology functions most effectively for clinical databases when a generic data schema is used. The technique of "generic data modeling" is presented as a method of reconciling these opposing views of clinical data, using formal operations to transform a detailed schema into a generic one. RESULTS: A complex schema consisting of hundreds of entities and representing a rich set of constraints about the patient care domain is transformed into a generic schema consisting of roughly two dozen tables. The resulting database design is efficient for patient-oriented queries and is highly flexible in adapting to the changing information needs of a health care institution, particularly changes involving the collection of new data elements. CONCLUSION: Conventional approaches to data modeling can be used to develop rich, complex models of clinical data that are useful for understanding and managing the process of patient care. Generic data modeling techniques can successfully transform a detailed design into an efficient generic design that is flexible enough to meet the needs of an operational clinical information system.

Hospital Information Systems↗
PubMedDate not supplied

Exploring the degree of concordance of coded and textual data in answering clinical queries from a clinical data repository.

OBJECTIVE: To query a clinical data repository (CDR) for answers to clinical questions to determine whether different types of fields (coded and free text) would yield confirmatory, complementary, or conflicting information and to discuss the issues involved in producing the discrepancies between the fields. METHODS: The appropriate data fields in a subset of a CDR (5,135 patient records) were searched for the answers to three questions related to surgical procedures. Each search included at least one coded data field and at least one free-text field. The identified free-text records were then searched manually to ensure correct interpretation. The fields were then compared to determine whether they agreed with each other, were supportive of each other, contained no entry (absence of data), or were contradictory. RESULTS: The degree of concordance varied greatly according to the field and the question asked. Some fields were not granular enough to answer the question. The free-text fields often gave an answer that was not definitive. Absence of data was most logically interpreted in some cases as lack of completion of data and in others as a negative answer. Even with a question as specific as which side a hernia was on, contradictory data were found in 5 to 8 percent of the records. CONCLUSIONS: Using the data in the CDR to answer clinical questions can yield significantly disparate results depending on the question and which data fields are searched. A database cannot just be queried in automated fashion and the results reported. Both coded and textual fields must be searched to obtain the fullest assessment. This can be expected to result in information that may be confirmatory, complementary, or conflicting. To yield the most accurate information possible, final answers to questions require human judgment and may require the gathering of additional information.

Hernia, Ventral↗
PubMed1978

In vitro and in vivo evaluation of benzamidomethyl-benzylpenicillinate (FI7303). A new 'repository' form.

A new type of hydrolyzable ester of penicillin G, benzamidomethyl benzylpenicillinate (FI 7303), was studied for the antibacterial activity and kinetics of absorption in comparison with DBED-penicillin G. FI 7303 resulted to be a good repository form of penicillin G, slowly eliminated in mouse, dog and man. It exerted a remarkable therapeutic activity in mice infected with Staphylococcus aureus even when administered 26 h before infection. The protective effect in mice was more prolonged than that of DBED-penicillin G, in agreement with the longer persistence of significant blood levels.

Absorption↗
PubMed2003

Studies on repository compound stability in DMSO under various conditions.

The chemical stability of repository compounds is affected by various environmental conditions during long-term storage. Studies were carried out to evaluate the effects of the following potential causes of instability of compounds in DMSO at a 10-mM concentration: water, oxygen, freeze/thaw cycles, and storage container material. A set of compounds was selected for the study based on structural diversity and functional group representation. Compound concentration was determined with liquid chromatography/ultraviolet spectroscopy/mass spectrometry (LC/UV/MS) analysis relative to an internal standard added to each sample. An accelerated study was conducted, and results demonstrate that most compounds are stable for 15 weeks at 40 degrees C. Water is more important in causing compound loss than oxygen. The freeze/thaw cycle study was done with freezing at -15 degrees C and thawing under nitrogen atmosphere at 25 degrees C. Two methods were used to redissolve compounds after thawing: agitation and repeated aspiration/dispense. The results indicate no significant compound loss after 11 freeze/thaw cycles. Compound recovery was also measured from glass and polypropylene containers for 5 months at room temperature, and no significant difference was found for these 2 types of containers.

Chromatography, Liquid↗
PubMed2005

TmaDB: a repository for tissue microarray data.

BACKGROUND: Tissue microarray (TMA) technology has been developed to facilitate large, genome-scale molecular pathology studies. This technique provides a high-throughput method for analyzing a large cohort of clinical specimens in a single experiment thereby permitting the parallel analysis of molecular alterations (at the DNA, RNA, or protein level) in thousands of tissue specimens. As a vast quantity of data can be generated in a single TMA experiment a systematic approach is required for the storage and analysis of such data. DESCRIPTION: To analyse TMA output a relational database (known as TmaDB) has been developed to collate all aspects of information relating to TMAs. These data include the TMA construction protocol, experimental protocol and results from the various immunocytological and histochemical staining experiments including the scanned images for each of the TMA cores. Furthermore the database contains pathological information associated with each of the specimens on the TMA slide, the location of the various TMAs and the individual specimen blocks (from which cores were taken) in the laboratory and their current status i.e. if they can be sectioned into further slides or if they are exhausted. TmaDB has been designed to incorporate and extend many of the published common data elements and the XML format for TMA experiments and is therefore compatible with the TMA data exchange specifications developed by the Association for Pathology Informatics community. Finally the design of the database is made flexible such that TMA experiments from several types of cancer can be stored in a single database, which incorporates the national minimum data set required for pathology reports supported by the Royal College of Pathologists (UK). CONCLUSION: TmaDB will provide a comprehensive repository for TMA data such that a large number of results from the numerous immunostaining experiments can be efficiently compared for each of the TMA cores. This will allow a systematic, large-scale comparison of tumour samples to facilitate the identification of gene products of clinical importance such as therapeutic or prognostic markers. In addition this work will contribute to the establishment of a standard for reporting TMA data analogous to MIAME in the description of microarray data.

Data Interpretation, Statistical↗
PubMed2003

The GRID: the General Repository for Interaction Datasets.

We have developed a relational database, called the General Repository for Interaction Datasets (The GRID) to archive and display physical, genetic and functional interactions. The GRID displays data-rich interaction tables for any protein of interest, combines literature-derived and high-throughput interaction datasets, and is readily accessible via the web. Interactions parsed in The GRID can be viewed in graphical form with a versatile visualization tool called Osprey.

DNA, Fungal↗
PubMed1985

Morphological subclassification of follicular lymphoma: variability of diagnoses among hematopathologists, a collaborative study between the Repository Center and Pathology Panel for Lymphoma Clinical Studies.

A collaborative study between the Repository Center for Lymphoma Clinical Studies and the members of the lymphoma pathology subcommittee of the major cooperative oncology groups was undertaken in an effort to ascertain the reproducibility and the interobserver agreement for the cytologic diagnosis of follicular lymphomas. A group of 105 patients with follicular lymphomas were subclassified by seven hematopathologists according to two methods. In the first method, cases were subclassified according to the Rappaport, Lukes, and Collins, and Working Formulation systems. In these systems, follicular lymphomas are subclassified by estimation of the different cell populations without the actual counting of cells. With this method, great variability in diagnosis was noted. For example: (1) The consensus diagnosis was that of poorly differentiated lymphocytic lymphoma (PDL) in 39 cases, but among the individual pathologists the number of cases thus diagnosed ranged from 24 to 65; (2) In 40 cases, the consensus diagnosis was follicular lymphoma, mixed-cell type; however, all seven pathologists independently agreed on this subtype in only one case; (3) A major disagreement was noted in 39 cases (37%), in which both diagnostic extremes (small cleaved and large noncleaved) were expressed. In the second method, only precise counts of different cells were made, according to a modification of the method recommended by Berard. With this counting method, diagnoses were independently derived based on the counts provided by the seven pathologists for large cleaved, small noncleaved, and large noncleaved cells. The variability in the results was wide also with this second method. For example, the average number of large cells found by each pathologist was ascertained, and the ranges were determined. The average range was 28 cells, which was considered high. The same determinations were performed only for large noncleaved cells, and the range was found to be 15 cells, which was also considered high. When the diagnoses derived from counts of only large noncleaved cells were compared with the traditional, more subjective diagnoses, fairly close agreement was obtained. In summary, the great variability in diagnoses of follicular lymphomas among pathologists may be attributed to the difficulties inherent in accurate determination of cell size and of the precise percentages of different cells. Until solutions to these problems are developed, one can subclassify follicular lymphomas according to the Berard method or the estimation method.

Cell Count↗
PubMed2006

Will we see data repositories for telehealth activity in the near future?

Policy-makers and researchers lament the absence of telehealth registries to enhance knowledge regarding outcomes and efficacy of telehealth interventions. A number of different organizations operate registries, but there do not appear to be any true telehealth registries. One reason is that federal requirements through such policies as the Health Insurance Portability and Accountability Act (HIPAA) have led to heightened fear of inadvertently releasing confidential or unauthorized information. Also, it would be more efficient if patient data were captured electronically at the local level, ideally through electronic medical records (EMRs), and then transferred electronically to registries. However, the diffusion of EMRs at the local level is in its infancy. As a result, it is unlikely that we will see a comprehensive telehealth data repository within the next decade.

Forecasting↗
PubMed2007

Proteomic data exchange and storage: the need for common standards and public repositories.

The ever increasing volumes of proteomic data now being produced by laboratories across the world have resulted in major issues in data storage and accessibility. The further demands of multilaboratory initiatives has highlighted issues when collaborators cannot import data generated within the same project but generated by different hardware types and processed by laboratory-specific work flows and analyses packages. There is an increasing need for common data standards that will allow the interchange of data between different instrumentation, search engines, and between laboratory databases. This could then lead to the establishment of data repositories from where benchmark datasets could be accessed and reanalyzed. The Human Proteome Organization is currently supporting efforts to establish such standards. The work of the Proteomics Standards Initiative has lead to the development of the mzData XML interchange standard and is now broadening its scope to produce a spectral analysis output format, mzIdent. Accompanying controlled vocabularies allow the accurate, while systematic, representation of metadata throughout both schema.

Benchmarking↗
PubMed2003

Regional repositories, reintermediation and the new GMS contract: cardiovascular disease in Tayside.

BACKGROUND: The new contract for general medical practitioners will make increasing demands on the primary care informatics community. There are a number of potential ways to provide reports which meet the requirements for data on the quality of care being provided by practices. In Scotland there are four components of the national information technology strategy which make meaningful comparisons of data possible. OBJECTIVE: Using cardiovascular data as an example, to describe how the community health index number, managed clinical networks (MCNs), increasing consistency of Read codes, and regional repositories of data make the acquisition, processing and use of data more straightforward. METHOD: The cardiovascular MCN collects the majority of its data electronically and four properties are crucial to its success: automatic collection of electronic data from many sources, prioritisation of data derived from multiple sources, record linkage processes, and manual validation of electronic data. RESULTS: Clinicians in primary and secondary care enter data during consultations and see the results of consultations recorded elsewhere. Because all data from the region are able to be Read coded according to prespecified templates, we are able to indicate to practices where they are in relation to the new contract targets and indicate which patients need to be seen, or excluded from, calculations. CONCLUSION: Effectively integrated management is facilitated by provision of regular prompted recall and review of people with chronic disease by multidisciplinary teams collaborating across the health service and into the community. In Scotland, use of newer informatics tools are proving to be useful contributions from primary care computing to equitable, evidence-based care.

Cardiovascular Diseases↗
PubMed2005

CSF proteome: a protein repository for potential biomarker identification.

Proteomic analysis is not limited to the analysis of serum or tissues. Synovial, peritoneal, pericardial and cerebrospinal fluid represent unique proteomes for disease diagnosis and prognosis. In particular, cerebrospinal fluid serves as a rich source of putative biomarkers that are not solely limited to neurologic disorders. Peptides, proteolytic fragments and antibodies are capable of crossing the blood-brain barrier, thus providing a repository of pathologic information. Proteomic technologies such as immunoblotting, isoelectric focusing, 2D gel electrophoresis and mass spectrometry have proven useful for deciphering this unique proteome. Cerebrospinal fluid proteins are generally less abundant than their corresponding serum counterparts, necessitating the development and use of sensitive analytical techniques. This review highlights some of the promising areas of cerebrospinal fluid proteomic research and their clinical applications.

Alzheimer Disease↗
PubMed1992

Information architecture: the repository alternative.

The skillful design of an information architecture that suits a healthcare organization is a top priority for information managers. But they have been hampered both in their conceptual approach to managing information flow and their technological capabilities for designing that flow. Information--both clinical and administrative--must be fluid and accessible. These key success factors lie in the increasingly prevalent database repository approach. And the technology is here to make it happen.

Computer Systems↗
PubMedDate not supplied

Clinical database repository--a solution for outcomes assessment.

This paper describes how implementation of a Clinical Database Repository (CDR) presents health care organizations with a tool to respond actively to quality and cost demands of the current delivery setting. The CDR is an innovative technological solution to integrate unlimited laboratory data with data from other systems, thereby expanding the contribution of routinely collected laboratory data to broader outcomes assessment goals of an organization. The technical components of a CDR, implementation methods, and deployment benefits to an organization are discussed. The resulting outcomes assessment from this tool will enable an organization to positively and cost-effectively influence how care is provided through system rules validation, measuring benefits of new technology, reducing unwarranted practice pattern variation, and validating practice guidelines. Although the value of systems such as CDR has been documented, their full potential for outcomes assessment has yet to be explored.

Clinical Laboratory Information Systems↗
PubMed1999

Internet-based physician's workbench as user interface for a central medical case repository.

Two World Health Organization Radiation Medical Emergency Preparedness and Assistance Network centers have constructed a standardized central repository of acute radiation syndrome case histories. The case histories are stored on a database server. Radiation protection centers can remotely access the database by user-friendly client software over the Internet. Physicians can use the medical information system to retrieve similar case histories for decision support, to improve their medical knowledge by inspecting real case histories, and for research on the acute radiation syndrome. The system architecture is presented and it is shown in detail how the information system can be employed to deliver medical decision support. Dialogue-response times over narrow-bandwidth Internet connections are better than when using conventional World-Wide-Web technology. However, the latter does not require the installation of client software other than a browser. A Java applet as client could combine the advantages of the two approaches.

Acute Disease↗
PubMed2000

Secure remote access to a clinical data repository using a wireless personal digital assistant (PDA).

TCP/IP and World-Wide-Web (WWW) technology have become the universal standards for networking and delivery of information. Personal digital assistants (PDAs), cellular telephones, and alphanumeric pagers are rapidly converging on a single pocket device that will leverage wireless TCP/IP networks and WWW protocols and can be used to deliver clinical information and alerts anytime, anywhere. We describe a wireless interface to clinical information for physicians based on Palm Corp.'s Palm VII pocket computer, a wireless digital network, encrypted data transmission, secure web servers, and a clinical data repository (CDR).

Computer Security↗
PubMed2001

Integrated web-based viewing and secure remote access to a clinical data repository and diverse clinical systems.

The advent of the World-Wide-Web protocols and client-server technology has made it easy to build low-cost, user-friendly, platform-independent graphical user interfaces to health information systems and to integrate the presentation of data from multiple systems. The authors describe a Web interface for a clinical data repository (CDR) that was moved from concept to production status in less than six months using a rapid prototyping approach, multi-disciplinary development team, and off-the-shelf hardware and software. The system has since been expanded to provide an integrated display of clinical data from nearly 20 disparate information systems.

Computer Graphics↗