Structured data management--the design and implementation of a web-based video archive prototype.
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In response to the lack of readily available multimedia rich medical knowledge sources to support medical education and patient care, we designed and implemented a web-based video publishing platform. In order to promote the development of high-quality, up-to-date educational content, we have devised a scalable structure that allows online submissions and continuous updating of video and accompanying textual descriptions. Our goal is to enable experts in varied medical domains to collaborate in the construction of a video library using an intuitive web-based interface. Neurologists at Stanford built a well-annotated neurology video collection that initially emphasized childhood and adult movement disorders. The collection may be accessed either as a stand-alone resource or as part of the Stanford Skolar MD, an integrated online medical knowledge provider. This manuscript discusses the design framework and implementation details of structured media content development. We present examples illustrating media data collection, content indexing using UMLS concepts, media storage, and web presentation. (+info)
GENOTRACE: cDNA-based local GENOme assembly from TRACE archives.
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GENOTRACE identifies the genomic organization for a cDNA using raw data from genome sequencing projects in progress (trace archives). Local genomic contigs are generated, allowing for example the design of PCR primers in intronic sequences to amplify coding regions of a gene, needed for example for mutation or SNP detection. AVAILABILITY: The package and examples of output files can be downloaded from http://rat.niob.knaw.nl/GENOTRACE (+info)
Determination of cyclin D1 and CD20 mRNA levels by real-time quantitative RT-PCR from archival tissue sections of mantle cell lymphoma and other non-Hodgkin's lymphomas.
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Cyclin D1 overexpression is a valuable marker for the diagnosis of mantle cell lymphoma (MCL). We used a real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) method to quantify levels of cyclin D1, CD20, and cyclophilin A mRNA in manually microdissected, paraffin-embedded tissue sections using an ABI 7700 qRT-PCR system. The study group included 21 cases of MCL and 37 cases of other types of B-cell non-Hodgkin's lymphoma. Cyclin D1 mRNA copy number was normalized to CD20 and cyclophilin A mRNA and evaluated statistically by analysis of variance. The relative cyclin D1 levels were similar whether normalized to CD20 or cyclophilin A, indicating that CD20 levels are stable and can be used as a B-cell-specific normalizer. Statistically significant differences were found in the median levels of cyclin D1 mRNA (expressed as % CD20 mRNA) among cases of MCL (87.6), small lymphocytic lymphoma (9.9), follicular lymphoma (2.4), diffuse large B-cell lymphoma (5.9), marginal zone B-cell lymphoma (39.8), and Burkitt lymphoma (7.1) (P < 0.05). We conclude that qRT-PCR can be used to quantify cyclin D1 mRNA levels in archival tissue sections. Normalization of cyclin D1 to a B-cell-specific marker more accurately reflects overexpression by MCL than other methods that normalize using constitutively expressed mRNA species. (+info)
Cost of managing digital diagnostic images for a 614-bed hospital.
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The cost of recording and archiving digital diagnostic imaging data is presented for a Radiology Department serving a 614 bed University-Hospital with a large outpatient population. Digital diagnostic imaging modalities include computed tomography, nuclear medicine, ultrasound, and digital radiography. The archiving media include multiformat video film recordings, magnetic tapes, and disc storage. The estimated cost per patient for the archiving of digital diagnostic imaging data is presented. (+info)
The EMBL sequence version archive.
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SUMMARY: The EMBL Nucleotide Sequence Database, maintained at the European Bioinformatics institute, is Europe's primary nucleotide sequences database. Its entries are subject to changes, but only the most recent versions are preserved in the database. The EMBL Sequence Version Archive is a new publicly available database retaining also the earlier versions of these entries. AVAILABILITY: http://www.ebi.ac.uk/embl/sva/ (+info)
Assessment of the accuracy of a three-dimensional imaging system for archiving dental study models.
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OBJECTIVE: The use of stone and plaster study models is an integral part of any dental practice and is required for research. Storage of study models is problematic in terms of space and cost. Ayoub et al.(1) introduced a new technique based on the recent advances in stereophotogrammetry for archiving dental study models in a digital format. However, assessment of the accuracy of the generated three-dimensional (3D) models has not been carried out yet. It was the aim of this study to evaluate the accuracy of this technique. DESIGN: A comparative assessment between direct measurements of dental study models and measurements of computer generated 3D images of the same study models was performed. MATERIALS AND METHODS: Twenty-two dental study models stored at Glasgow Dental Hospital and School for the purposes of research were used in the study. The models were captured in three dimensions using a photostereometric technique and stored in digital format. MAIN OUTCOME MEASURES: Measurements were conducted directly on dental study models and on the computer generated 3D images using Euclidean Distance Matrix Analysis.(2) The difference between the two sets of measurements was statistically analysed using a two-sample t-test. RESULTS: The average difference between measurements of dental casts and 3D images was 0.27 mm. This difference was within the range of operator errors (0.10-0.48 mm) and was not statistically significant (P < 0.05). CONCLUSION: This study shows that it is possible to use 3D imaging to store dental study models for treatment monitoring and research with a satisfactory degree of accuracy. (+info)
Detection and identification of Variola virus in fixed human tissue after prolonged archival storage.
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Smallpox disease has been eradicated from the human population since 1979, but is again a concern because of its potential use as an agent of bioterrorism or biowarfare. World Health Organization-sanctioned repositories of infectious Variola virus are known to occur in both Russia and the United States, but many believe other undeclared and unregulated sources of the virus could exist. Thus, validation of improved methods for definitive identification of smallpox virus in diagnostic specimens is urgently needed. In this paper, we describe the discovery of suspected Variola infected human tissue, fixed and preserved for decades in largely unknown solutions, and the use of routine histology, electron microscopy, and ultimately DNA extraction and fluorogenic 5' nuclease (TaqMan) assays for its identification and confirmation. (+info)
Androgen and vitamin D receptor expression in archival human breast tumors.
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BACKGROUND: The present study was undertaken for quantitation of androgen (AR) and vitamin D (VDR) receptor expression in human male and female breast tumors by flow cytometry. METHODS: Nuclei isolated from sections of paraffin-embedded tumors by pepsin digestion were treated for antigen unmasking and incubated with antibodies to AR and VDR. Flow cytometric analysis was used to determine the percentage of receptor-positive nuclei with fluorescence greater than 95% of the isotype nuclei. Mean log fluorescence channel values were used for comparing antigen density of the isotype and the antibody-treated nuclei. RESULTS: Six of 23 female breast tumors had aneuploid DNA content. Nineteen of 20 estrogen receptor-positive female tumors by immunohistochemical analysis (IHC) were also AR positive by flow analysis. Aneuploid subpopulations had higher percentages of AR-positive nuclei than did diploid populations. Eight of 33 male breast tumors had aneuploid DNA content. Twenty-three of 33 male breast tumors were AR positive by flow analysis compared with six that were AR positive by IHC. Six AR-positive (IHC) male tumors were also AR positive by flow analysis. VDR expression was higher in diploid female tumors than in aneuploid tumors. CONCLUSIONS: Lack of a strong correlation between IHC and flow analysis may be due to differences in criteria used for identification of receptor-positive and -negative tumors by the two methods. (+info)