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At least 1,621 records · Page 90Linked to original sources
PubMed2004

Genome information resources - developments at Ensembl.

Genome information resources such as Ensembl manage and present DNA sequence and annotation arising from genome projects. Recent developments in the Ensembl system include access to inter-species comparisons at both the genomic and protein sequence levels and improvements to the display of polymorphism data. Users can now display their own data in the context of other annotation. In addition, a fast and flexible data retrieval system, EnsMart, has been developed.

Animals↗
PubMedDate not supplied

Case based reasoning in criminal intelligence using forensic case data.

A model that is based on the knowledge of experienced investigators in the analysis of serial crime is suggested to bridge a gap between technology and methodology. Its purpose is to provide a solid methodology for the analysis of serial crimes that supports decision making in the deployment of resources, either by guiding proactive policing operations or helping the investigative process. Formalisation has helped to derive a computerised system that efficiently supports the reasoning processes in the analysis of serial crime. This novel approach fully integrates forensic science data.

Crime↗
PubMed2003

GenoMap, a circular genome data viewer.

A Tcl/Tk-based application called GenoMap is described, a viewer for genome-wide map of microarray expression data within a circular bacterial genome. An interactive interface facilitates easy identification of the expressed region. This software is also used for drawing genome-wide quantitative data.

Computer Graphics↗
PubMed2003

The World Health Organization Global Database on Child Growth and Malnutrition: methodology and applications.

BACKGROUND: For decades nutritional surveys have been conducted using various definitions, indicators and reference populations to classify child malnutrition. The World Health Organization (WHO) Global Database on Child Growth and Malnutrition was initiated in 1986 with the objective to collect, standardize, and disseminate child anthropometric data using a standard format. METHODS: The database includes population-based surveys that fulfil a set of criteria. Data are checked for validity and consistency and raw data sets are analysed following a standard procedure to obtain comparable results. Prevalences of wasting, stunting, under- and overweight in preschool children are presented using z-scores based on the National Center for Health Statistics (NCHS)/WHO international reference population. New surveys are included on a continuous basis and updates are published bimonthly on the database's web site. RESULTS: To date, the database contains child anthropometric information derived from 846 surveys. With 412 national surveys from 138 countries and 434 sub-national surveys from 155 countries, the database covers 99% and 64% of the under 5 year olds in developing and developed countries, respectively. This wealth of information enables international comparison of nutritional data, helps identifying populations in need, evaluating nutritional and other public health interventions, monitoring trends in child growth, and raising political awareness of nutritional problems. CONCLUSIONS: The 15 years experience of the database can be regarded as a success story of international collaboration in standardizing child growth data. We recommend this model for monitoring other nutritional health conditions that as yet lack comparable data.

Child↗
PubMed2006

High-resolution ultrasonic imaging using fast two-dimensional homomorphic filtering.

A new method for two-dimensional deconvolution of medical ultrasonic images is presented. The spatial resolution of the deconvolved images is much higher compared to the common images of the fundamental and second harmonic. The deconvolution also results in a more distinct speckle pattern. Unlike the most published deconvolution algorithms for ultrasonic images, the presented technique can be implemented using currently available hardware in real-time imaging, with a rate up to 50 frames per second. This makes it attractive for application in the current ultrasound scanners. The algorithm is based on two-dimensional homomorphic deconvolution with simplified assumptions about the point spread function. Broadband radio frequency image data are deconvolved instead of common fundamental harmonic data. Thus, information of both the first and second harmonics is used. The method was validated on image data recorded from a tissue-mimicking phantom and on clinical image data.

Algorithms↗
PubMed2006

cPath: open source software for collecting, storing, and querying biological pathways.

BACKGROUND: Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. RESULTS: We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. CONCLUSION: cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling.

Computational Biology↗
PubMed2002

MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002.

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 organelle genomes. Mitochondrial genomes have been extensively sequenced and analysed and data have been collected in several specialised databases. In order to collect information on nuclear coded mitochondrial proteins we developed MitoNuc, a database containing detailed information on sequenced nuclear genes coding for mitochondrial proteins in Metazoa. The MitoNuc database can be retrieved through SRS and is available via the web site http://bighost.area.ba.cnr.it/mitochondriome where other mitochondrial databases developed by our group, the complete list of the sequenced mitochondrial genomes, links to other mitochondrial sites and related information, are available. The MitoAln database, related to MitoNuc in the previous release, reporting the multiple alignments of the relevant homologous protein coding regions, is no longer supported in the present release. In order to keep the links among entries in MitoNuc from homologous proteins, a new field in the database has been defined: the cluster identifier, an alpha numeric code used to identify each cluster of homologous proteins. A comment field derived from the corresponding SWISS-PROT entry has been introduced; this reports clinical data related to dysfunction of the protein. The logic scheme of MitoNuc database has been implemented in the ORACLE DBMS. This will allow the end-users to retrieve data through a friendly interface that will be soon implemented.

Animals↗
PubMed1977

MEDINFO--a medical information system.

The MEDINFO (MEDical INFOrmation) system is a general purpose computer-based information storage, retrieval, and analysis system. It is designed for a time sharing, on-line computer system for the rapid and easy creation, maintenance, and analysis of general data files. A wide variety of types of information may be used. These include numeric, categoric, text, date, and multiple-response. The file structure allows several sets of data, including date-orientated data, to be used. MEDINFO permits a study to be created, a description of the data made, data to be entered and updated into records, and for the data to be displayed or analyzed by the investigator without programmer intervention.

Computers↗
PubMed1992

Alzheimer's dementia produces a loss of discrimination but no increase in rate of memory decay in delayed matching to sample.

Patients diagnosed with senile dementia of the Alzheimer type (SDAT) were compared with control subjects on a computerized delayed matching to sample task. Performance was assessed with a measure of discriminability at zero delay and a measure of rate of forgetting--these are the two parameters of an exponential function derived from extensive animal testing. The SDAT group showed significantly poorer discriminability at zero delay than controls but equivalent rates of forgetting over a 32-sec delay. These data suggest that SDAT may have little effect on the decay rate of the short term (or 'primary') memory trace and may instead affect encoding, initial storage or retrieval mechanisms. The effects of SDAT on this task are consistent with previous results with anticholinergic agents in rats.

Aged↗
PubMed2005

Combining different standards and different approaches for health information retrieval in a quality-controlled gateway.

Internet as source of information is increasing in preeminence in numerous fields, including health. We describe in this paper the CISMeF project (acronym of Catalogue and Index of French-speaking Medical Sites) which has been designed to help the health information consumers and health professionals to find what they are looking for among the numerous health documents available online. The catalogue is founded on two standards: a set of metadata and a terminology based on the MeSH thesaurus which has the same structure and use as an ontology of the medical domain. The structure of the catalogue allows us to place the project at an overlap between the present Web, which is informal, and the forthcoming Semantic Web. Many features of information retrieval and navigation through the catalogue were developed. These features take into account the kind of the end-user (health professional, medical student, patient). The CISMeF-patients catalogue is a sub-catalogue of CISMeF and is dedicated to the patients and the general public. It shares the same model as CISMeF whereas MEDLINE and MedlinePlus do not. We also propose to couple two approaches (morphological processing and data mining) to help the users by correcting and refining their queries.

France↗
PubMed2003

Comprehensive graphic-based display of clinical pathology laboratory data.

In this age of ever-increasing demands for and uses of patient data, technologic advancements in the form of electronic patient records permit improved data access and prompt retrieval of higher quality patient care data, with more versatility in display, facilitating the integration of information concerning patients over time and between settings of care, which is in turn more accessible for use by practitioners and provides more efficient and effective decision support in areas of patient care. The graphic display of laboratory data is central to the evolving computerized patient record and needs to be taken into careful consideration along with clinician perception and ease of data interpretation in redesigning the graphic reporting of numeric clinical pathology laboratory data. An ideal system should generate user-friendly, graphic-based comprehensive reports highlighting abnormalities with trends for diagnosis, clinical management, and risk-factor detection.

Clinical Chemistry Tests↗
PubMed1999

Memory card: A tool to assess patient compliance with peritoneal dialysis.

Lack of compliance with prescribed peritoneal dialysis (PD) therapy is a common cause of inadequate dialysis and poor outcomes. Because measurements of delivered doses are performed infrequently, the values obtained may not reflect actual delivered therapy. To evaluate compliance with therapy and to record accurate and complete treatment history for each patient undergoing automated PD, a memory card with the capability to track and store 2 months of treatment data was developed and incorporated into a commercial PD cycler. The memory card is brought to the clinic during the monthly visit. The data is downloaded into a personal computer (PC) with specific software. The following parameters can be retrieved and displayed as a graph or chart: the time of the exchange, length of the exchange, solution transit time, drain time, automated exchanges and last fill, inflow and drain volume, net ultrafiltration, and times of drain alarms. The data can be displayed as daily therapy, mean of therapy values, or total therapy. With the information available, the renal team can incorporate changes into the prescription and provide feedback to the patient based on his/her compliance record. The data can be transferred to a central data pool via modem. This data collection system can also be used for quality improvement, to model delivered therapy, and to compare compliance scores among centers and by cohorts of patients according to demographic or comorbid conditions.

Data Display↗
PubMed1993

GenBank.

The GenBank sequence database has undergone an expansion in data coverage, annotation content and the development of new services for the scientific community. In addition to nucleotide sequences, data from the major protein sequence and structural databases, and from U.S. and European patents is now included in an integrated system. MEDLINE abstracts from published articles describing the sequences provide an important new source of biological annotation for sequence entries. In addition to the continued support of existing services, new CD-ROM and network-based systems have been implemented for literature retrieval and sequence similarity searching. Major releases of GenBank are now more frequent and the data are distributed in several new forms for both end users and software developers.

Amino Acid Sequence↗
PubMed2006

The caCORE Software Development Kit: streamlining construction of interoperable biomedical information services.

BACKGROUND: Robust, programmatically accessible biomedical information services that syntactically and semantically interoperate with other resources are challenging to construct. Such systems require the adoption of common information models, data representations and terminology standards as well as documented application programming interfaces (APIs). The National Cancer Institute (NCI) developed the cancer common ontologic representation environment (caCORE) to provide the infrastructure necessary to achieve interoperability across the systems it develops or sponsors. The caCORE Software Development Kit (SDK) was designed to provide developers both within and outside the NCI with the tools needed to construct such interoperable software systems. RESULTS: The caCORE SDK requires a Unified Modeling Language (UML) tool to begin the development workflow with the construction of a domain information model in the form of a UML Class Diagram. Models are annotated with concepts and definitions from a description logic terminology source using the Semantic Connector component. The annotated model is registered in the Cancer Data Standards Repository (caDSR) using the UML Loader component. System software is automatically generated using the Codegen component, which produces middleware that runs on an application server. The caCORE SDK was initially tested and validated using a seven-class UML model, and has been used to generate the caCORE production system, which includes models with dozens of classes. The deployed system supports access through object-oriented APIs with consistent syntax for retrieval of any type of data object across all classes in the original UML model. The caCORE SDK is currently being used by several development teams, including by participants in the cancer biomedical informatics grid (caBIG) program, to create compatible data services. caBIG compatibility standards are based upon caCORE resources, and thus the caCORE SDK has emerged as a key enabling technology for caBIG. CONCLUSION: The caCORE SDK substantially lowers the barrier to implementing systems that are syntactically and semantically interoperable by providing workflow and automation tools that standardize and expedite modeling, development, and deployment. It has gained acceptance among developers in the caBIG program, and is expected to provide a common mechanism for creating data service nodes on the data grid that is under development.

Humans↗
PubMed2004

A process for systematically reviewing the literature: providing the research evidence for public health nursing interventions.

BACKGROUND: Several groups have outlined methodologies for systematic literature reviews of the effectiveness of interventions. The Effective Public Health Practice Project (EPHPP) began in 1998. Its mandate is to provide research evidence to guide and support the Ontario Ministry of Health in outlining minimum requirements for public health services in the province. Also, the project is expected to disseminate the results provincially, nationally, and internationally. Most of the reviews are relevant to public health nursing practice. AIMS: This article describes four issues related to the systematic literature reviews of the effectiveness of public health nursing interventions: (1) the process of systematically reviewing the literature, (2) the development of a quality assessment instrument, (3) the results of the EPHPP to date, and (4) some results of the dissemination strategies used. METHODS: The eight steps of the systematic review process including question formulation, searching and retrieving the literature, establishing relevance criteria, assessing studies for relevance, assessing relevant studies for methodological quality, data extraction and synthesis, writing the report, and dissemination are outlined. Also, the development and assessment of content and construct validity and intrarater reliability of the quality assessment questionnaire used in the process are described. RESULTS: More than 20 systematic reviews have been completed. Content validity was ascertained by the use of a number of experts to review the questionnaire during its development. Construct validity was demonstrated through comparisons with another highly rated instrument. Intrarater reliability was established using Cohen's Kappa. Dissemination strategies used appear to be effective in that professionals report being aware of the reviews and using them in program planning/policymaking decisions. CONCLUSIONS: The EPHPP has demonstrated the ability to adapt the most current methods of systematic literature reviews of effectiveness to questions related to public health nursing. Other positive outcomes from the process include the development of a critical mass of public health researchers and practitioners who can actively participate in the process, and the work on dissemination has been successful in attracting external funds. A program of research in this area is being developed.

Confounding Factors, Epidemiologic↗
PubMedDate not supplied

Taking it to the streets: recording medical outreach data on personal digital assistants.

Carrying hundreds of patient files in a suitcase makes medical street outreach to the homeless clumsy and difficult. Healthcare for the Homeless--Houston (HHH) began a case study under the assumption that tracking patient information with a personal digital assistant (PDA) would greatly simplify the process. Equipping clinicians with custom-designed software loaded onto Palm V Handheld Computers (palmOne, Inc, Milpitas, CA), Healthcare for the Homeless--Houston assessed how this type of technology augmented medical care during street outreach to the homeless in a major metropolitan area. Preliminary evidence suggests that personal digital assistants free clinicians to focus on building relationships instead of recreating documentation during patient encounters. However, the limits of the PDA for storing and retrieving data made it impractical long-term. This outcome precipitated a new study to test the feasibility of tablet personal computers loaded with a custom-designed software application specific to the needs of homeless street patients.

Community-Institutional Relations↗
PubMed1992

Picture archiving and communication systems: an overview.

Organizational techniques that enable small departments to function efficiently often fail as departments become larger. With the recent growth in imaging technology, the capacity of film-based systems to meet the increasing needs of radiology departments has decreased. Electronic picture archiving and communication systems (PACS) have been developed in an attempt to provide economical storage, rapid retrieval of images, access to images acquired with multiple modalities, and simultaneous access at multiple sites. Input to a PACS may come from digital or analog sources (when the latter have been digitized). A PACS consists primarily of an image acquisition device (an electronic gateway to the system), data management system (a specialized computer system that controls the flow of information on the network), image storage devices (both short- and long-term archives), transmission network (which serves local or wide areas), display stations (which include a computer, text monitor, image monitors, and a user interface), and devices to produce hard-copy images (currently, a multiformat or laser camera). The goals of PACS are to improve operational efficiency while maintaining or improving diagnostic ability.

Radiology Information Systems↗