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At least 1,693 records · Page 94Linked to original sources
PubMed2000

MitoNuc and MitoAln: two related databases of nuclear genes coding for mitochondrial proteins.

Mitochondria, besides their central role in energy metabolism, have recently been found to be involved in a number of basic processes of cell life and to contribute to the pathogenesis of many degenerative diseases. All functions of mitochondria depend on the interaction of nuclear and organellar genomes. Mitochondrial genomes have been extensively sequenced and analysed and the data collected in several specialised databases. In order to collect information on nuclear coded mitochondrial proteins we developed MitoNuc and MitoAln, two related databases containing, respectively, detailed information on sequenced nuclear genes coding for mitochondrial proteins in Metazoa and yeast, and the multiple alignments of the relevant homologous protein coding regions. MitoNuc and MitoAln retrieval through SRS at http://bio-www.ba.cnr.it:8000/srs6/ can easily allow the extraction of sequence data, subsequences defined by specific features and nucleotide or amino acid multiple alignments.

Databases, Factual↗
PubMed2001

The PACRAT system: an extensible WWW-based system for correlated sequence retrieval, storage and analysis.

With PACRAT (Patterns, Analyses, Correlations. Remote Archive Testbed) we present an online database solution to the problem of accessing high-confidence sequences with specific relationships to classes of genes, such as upstream intergenic regions attached to tRNA genes. In addition the software contains a data warehousing and analysis-facilitating suite to streamline the process of analyzing the collected data. An unexpected additional benefit of the system is that it also provides easy access to sequences of lower confidence, and may be of assistance in such things as resolving ORF-call conflicts in genomic annotation projects.

Computational Biology↗
PubMedDate not supplied

Medical image collection indexing: shape-based retrieval using KD-trees.

The capacity to retrieve images containing objects with shapes similar to a query shape is desirable in medical image databases. We propose a similarity measure and an indexing mechanism for non-rigid comparison of shape which adds this capability to image databases. The (dis-)similarity measure is based on the observations that: (1) the geometry of the same organ in different subjects is not related by a strictly rigid transformation; and (2) the orientation of the organ plays a key role in comparing shape. We propose a similarity measure that computes a non-rigid mapping between curves and uses this mapping to compare oriented shape. We also show how KD-trees can index curves so that retrieval with our similarity measure is efficient. Experiments with real-world data from a database of magnetic resonance images are provided.

Abstracting and Indexing↗
PubMedDate not supplied

The granularity of medical narratives and its effect on the speed and completeness of information retrieval.

OBJECTIVE: Using electronic rather than paper-based record systems improves clinicians' information retrieval from patient narratives. However, few studies address how data should be organized for this purpose. Information retrieval from clinical narratives containing free text involves two steps: searching for a labeled segment and reading its content. The authors hypothesized that physicians can retrieve information better when clinical narratives are divided into many small, labeled segments ("high granularity"). DESIGN: The study tested the ability of 24 internists and 12 residents at a teaching hospital to retrieve information from an electronic medical record--in terms of speed and completeness--when using different granularities of clinical narratives. Participants solved, without time pressure, predefined problems concerning three voluminous, inpatient case records. To mitigate confounding factors, participants were randomly allocated to a sequence that was balanced by patient case and learning effect. RESULTS: Compared with retrieval from undivided notes, information retrieval from problem-partitioned notes was 22 percent faster (statistically significant), whereas retrieval from notes divided into organ systems was only 11 percent faster (not statistically significant). Subdividing segments beyond organ systems was 13 percent slower (statistically significant) than not subdividing. Granularity of medical narratives affected the speed but not the completeness of information retrieval. CONCLUSION: Dividing voluminous free-text clinical narratives into labeled segments makes patient-related information retrieval easier. However, too much subdivision slows retrieval. Study results suggest that a coarser granularity is required for optimal information retrieval than for structured data entry. Validation of these conclusions in real-life clinical practice is recommended.

Cross-Over Studies↗
PubMed2004

Consequences of cold ischemic injury of kidneys in clinical transplantation.

Cold storage allows the effective utilization of organs retrieved for transplantation. However, prolonged cold ischemia contributes to organ damage and increases patients' morbidity and mortality and health care cost. Using recent data from the United Network for Organ Sharing, this paper examines the outcomes of live donor and deceased donor kidney transplants in relation to cold ischemia time.

Cold Temperature↗
PubMed1996

A proposal for improving the acquisition of medical data in forward field hospitals.

Current medical recording policy in forward field hospitals adequately delineates battle and non-battle injuries and incapacitation from sickness or disease. Although useful for planning, such data do not often provide insights that could improve medical care. The author has gathered combat medical data in Vietnam and Desert Storm and concludes that by providing and storing carbon copies of admission and operating room logs plus operative notes, discharge summaries, and the clinical record cover sheet, the Army Medical Corps would have a permanent, analyzable account of field hospital medical activities. Digital copying and disk storage of these specific documents would greatly increase their usefulness, especially if coupled with standard data formats for admission and operating logs and a simple diagnosis coding scheme to aid data retrieval either by hand or computer. Medical data should be made available to concerned forward medical personnel because in past wars some of the most insightful medical observations of immediate help to the sick and wounded have been made by individual physicians analyzing medical data at the front.

Automation↗
PubMed1999

Scaling a data retrieval and mining application to the enterprise-wide level.

Most medical institutions have had difficulty in adopting practices that use stored clinical and administrative data effectively. This stems in part from the lack of available tools to easily and accurately retrieve datasets of interest. In this work, we describe the development of a data retrieval and mining application, Goldminer, which allows authorized personnel at our institution to query clinical and demographic data stores through a graphical, non-programmer interface. It builds upon DXtractor, our previously described tool that retrieves data from a smaller, more specialized dataset. We discuss the difficulties encountered in scaling this application to the enterprise-wide level, and our solutions.

Databases as Topic↗
PubMedDate not supplied

Time needed for data collection in clinical studies on fixed prosthodontics.

PURPOSE: Realistic appraisals of time and costs are crucial for research grants and financing of clinical studies by sponsors, but little is known about the time actually needed for clinical data collection in dental studies. This survey evaluated the net time of patient contact necessary for collection and documentation of clinical data to establish an empirical base for more efficient study management and budgeting. MATERIALS AND METHODS: The time needed for the clinical examination of 41 prosthodontic patients in systematic follow-up was recorded. Examination covered dental status, oral hygiene status, and quality assessment of restorations by modified CDA criteria. Completion of the case report forms, data check, and provisions for data retrieval were also included. The recorded times were analyzed to obtain empirical estimates of the time actually needed for specific examination blocks and to detect potential variables of influence. RESULTS: Predominant time records were 5 to 10 minutes for dental status (according to status complexity) or hygiene. The time needed for CDA ranking showed a linear correlation to the number of units, approximately 1 minute each. Documentation times were similar to the total contact times of all examination blocks, between 15 and 30 minutes per patient. CONCLUSION: The overall time for collection and documentation of retrievable data is considerable (about 30 minutes, up to 1 hour). The data provide an empirical base for sound managing and budgeting of follow-up periods in clinical investigations, which is of major importance for the quality of clinical data, and thus for the success and value of clinical investigations.

Crowns↗
PubMed1998

Molecular Probe Data Base (MPDB).

In this paper, the current status of the Molecular Probe Data Base (http://www.biotech.ist.unige.it/interlab/ mpdb.html ) is briefly presented together with a short analysis of its activity during 1997. This has been performed by statistically evaluating the 'logs' of the Internet servers that are used for its distribution with reference to the geographical origin of the requests, the words that were utilized to carry out of the searches and the oligonucleotides that were retrieved. Planned enhancements of this database are also described. They include a revision of its data structure and, even more relevant, of its data management procedures.

Computer Communication Networks↗
PubMed2003

Implementation of a WAP-based telemedicine system for patient monitoring.

Many parties have already demonstrated telemedicine applications that use cellular phones and the Internet. A current trend in telecommunication is the convergence of wireless communication and computer network technologies, and the emergence of wireless application protocol (WAP) devices is an example. Since WAP will also be a common feature found in future mobile communication devices, it is worthwhile to investigate its use in telemedicine. This paper describes the implementation and experiences with a WAP-based telemedicine system for patient-monitoring that has been developed in our laboratory. It utilizes WAP devices as mobile access terminals for general inquiry and patient-monitoring services. Authorized users can browse the patients' general data, monitored blood pressure (BP), and electrocardiogram (ECG) on WAP devices in store-and-forward mode. The applications, written in wireless markup language (WML), WMLScript, and Perl, resided in a content server. A MySQL relational database system was set up to store the BP readings, ECG data, patient records, clinic and hospital information, and doctors' appointments with patients. A wireless ECG subsystem was built for recording ambulatory ECG in an indoor environment and for storing ECG data into the database. For testing, a WAP phone compliant with WAP 1.1 was used at GSM 1800 MHz by circuit-switched data (CSD) to connect to the content server through a WAP gateway, which was provided by a mobile phone service provider in Hong Kong. Data were successfully retrieved from the database and displayed on the WAP phone. The system shows how WAP can be feasible in remote patient-monitoring and patient data retrieval.

Blood Pressure↗
PubMed2001

The life sciences Global Image Database (GID).

Although a vast amount of life sciences data is generated in the form of images, most scientists still store images on extremely diverse and often incompatible storage media, without any type of metadata structure, and thus with no standard facility with which to conduct searches or analyses. Here we present a solution to unlock the value of scientific images. The Global Image Database (GID) is a web-based (http://www.gwer.ch/qv/gid/gid.ht m ) structured central repository for scientific annotated images. The GID was designed to manage images from a wide spectrum of imaging domains ranging from microscopy to automated screening. The annotations in the GID define the source experiment of the images by describing who the authors of the experiment are, when the images were created, the biological origin of the experimental sample and how the sample was processed for visualization. A collection of experimental imaging protocols provides details of the sample preparation, and labeling, or visualization procedures. In addition, the entries in the GID reference these imaging protocols with the probe sequences or antibody names used in labeling experiments. The GID annotations are searchable by field or globally. The query results are first shown as image thumbnail previews, enabling quick browsing prior to original-sized annotated image retrieval. The development of the GID continues, aiming at facilitating the management and exchange of image data in the scientific community, and at creating new query tools for mining image data.

Biological Science Disciplines↗
PubMed1995

Evaluation of an object-based data model implemented over a proprietary, legacy data model.

Most computerized medical information today is contained in legacy systems. As vendors slowly move to open systems, legacy systems remain in use and contain valuable information. This paper evaluates the use of an object model imposed on an existing database to improve the ease with which data can be accessed. This study demonstrates that data elements can be retrieved without specific programming knowledge of the underlying data structure. It also suggests that underlying data structures can be changed without updating application code. Programs written using the object model were easier to program but ran greater than one order of magnitude slower than traditionally coded programs. In this paper, the legacy information system is introduced, the methods used to implement and evaluate the object-based data model are explained, and the results and conclusions are presented.

Computer Systems↗
PubMed2005

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.

biomaRt is a new Bioconductor package that integrates BioMart data resources with data analysis software in Bioconductor. It can annotate a wide range of gene or gene product identifiers (e.g. Entrez-Gene and Affymetrix probe identifiers) with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Furthermore biomaRt enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. Fast and up-to-date data retrieval is possible as the package executes direct SQL queries to the BioMart databases (e.g. Ensembl). The biomaRt package provides a tight integration of large, public or locally installed BioMart databases with data analysis in Bioconductor creating a powerful environment for biological data mining.

Algorithms↗
PubMed2006

Presentation of 3D isotropic imaging data for optimal viewing.

Three-dimensional (3D) isotropically sampled data facilitates retrospective viewing of arbitrarily aligned image planes and simplifies automated computer analysis of 3D structures. However, compared to acquisitions that employ thick slices, MRI acquisitions with isotropic sampling have a lower signal-to-noise ratio (SNR). A rater study was performed to examine viewer preference for the trade-off between SNR and the partial-volume effect of through-plane averaging. A robust preference for a 5:1 ratio in through-plane to in-plane was found for a typical SNR of 11.

Algorithms↗
PubMed2004

[Use of the internet for health care information: results from a national telephone survey].

OBJECTIVES: The Internet has attracted considerable attention as a means to improve health and health care delivery, but it is not clear how prevalent internet use for health care really is. Available estimates for Germany don't exist. Without accurate estimates of use, it is difficult to focus policy discussions or design appropriate policy activities. METHODS: 2026 individuals aged 16 years or older were interviewed in Germany using computer-assisted telephone interview (CATI) in 2001. The sampling frame based on a modified RLD-Design. RESULTS: Approximately 50% of respondents with Internet access reported using the internet to look for advice or information about health or health care. The internet is differently used by the population for the health care information. There is a higher use rate of men, of younger people, of people with high socio-economic status and of the healthy ones. After controlling in multivariate analysis for the user, merely an significant age effect exists. CONCLUSIONS: The use of the internet for health care information in Germany is quite different. Questions about consequences remain unanswered. Do the differences increase or do they decrease? And which role does play the health politics? This and other questions could be answered by further studies.

Adolescent↗