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At least 1,117 records · Page 62Linked to original sources
PubMed2000

Integration of cytogenetic data with genome maps and available probes: present status and future promise.

The National Cancer Institute has established an initiative, called the Cancer Chromosome Aberration Project (Ccap), in order to link and integrate the physical and genetic maps of the human genome with cytogenetic data and the location of chromosomal rearrangements in human diseases. This goal will be achieved by high-resolution fluorescence in situ hybridization (FISH) mapping of colony-purified bacterial artificial chromosome (BAC) clones spaced at 1-to 2-Mb intervals across the entire genome. All BAC clones will be anchored on the physical map by the presence of a mapped sequence tagged site (STS). The generation of a publicly accessible clone repository will allow convenient distribution of these BACs. Ccap data can be correlated with other cancer-associated and genomic databases, such as the catalog of chromosomal aberrations in cancer and the emerging full genomic sequence. We anticipate that the use of Ccap clones will expedite and refine the mapping of chromosomal breakpoints. The eventual set of approximately 3,000 Ccap BACs should facilitate the production of BAC-containing DNA chips for assessing copy number of genomic segments by matrix comparative genomic hybridization. In addition, the repository will provide genome-wide tools for defining chromosomal aberrations in cytological specimens by interphase cytogenetics. The Ccap Web site illustrates goals and progress of this initiative (http://www.ncbi.nlm.nih.gov/CCAP/).

Chromosome Mapping↗
PubMed2004

Integration of gene expression data into genome-scale metabolic models.

A framework for integration of transcriptome data into stoichiometric metabolic models to obtain improved flux predictions is presented. The key idea is to exploit the regulatory information in the expression data to give additional constraints on the metabolic fluxes in the model. Measurements of gene expression from chemostat and batch cultures of Saccharomyces cerevisiae were combined with a recently developed genome-scale model, and the computed metabolic flux distributions were compared to experimental values from carbon labeling experiments and metabolic network analysis. The integration of expression data resulted in improved predictions of metabolic behavior in batch cultures, enabling quantitative predictions of exchange fluxes as well as qualitative estimations of changes in intracellular fluxes. A critical discussion of correlation between gene expression and metabolic fluxes is given.

Databases, Genetic↗
PubMed2006

SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology.

BACKGROUND: The biological information in genomic expression data can be understood, and computationally extracted, in the context of systems of interacting molecules. The automation of this information extraction requires high throughput management and analysis of genomic expression data, and integration of these data with other data types. RESULTS: SBEAMS-Microarray, a module of the open-source Systems Biology Experiment Analysis Management System (SBEAMS), enables MIAME-compliant storage, management, analysis, and integration of high-throughput genomic expression data. It is interoperable with the Cytoscape network integration, visualization, analysis, and modeling software platform. CONCLUSION: SBEAMS-Microarray provides end-to-end support for genomic expression analyses for network-based systems biology research.

Chromosome Mapping↗
PubMedDate not supplied

Design methods and architectural issues of integrated medical image data base systems.

The past 20 years have seen tremendous changes in medical imaging techniques. New modalities and protocols are expanding the available digital image data at a rapid rate. Yet a framework for gathering, managing, and using multimodal image information is an integrated database environment is missing. The purpose of this paper is to present the experience of implementing an integrated medical image database system at UCSF. We discuss the general system architecture, software design methods, and specific database tools and illustrate them with application examples. Two immediate issues conforming the building of medical image database systems are: lack of supporting infrastructure and inability to index images by contest. To circumvent these problems, the evolutionary medical image database system being implemented at UCSF is based on a three-tiered client-server architecture: client medical workstations, database application servers, and a hospital-integrated picture archiving and communication system (HIP-PACS). The approach used to integrate content-based retrieval and knowledge base techniques within the existing HI-PACS to make the whole database system useful in medicine.

Adult↗
PubMed2006

Integrated multimedia medical data agent in E-health.

E-Health is producing a great impact in the field of information distribution of the health services to the intra-hospital and the public. Previous researches have addressed the development of system architectures in the aim of integrating the distributed and heterogeneous medical information systems. The easing of difficulties in the sharing and management of medical data and the timely accessibility to these data is a critical need for health care providers. We have proposed a client-server agent that allows a portal to the every permitted Information System of the Hospital that consists of PACS, RIS and HIS via the Intranet and the Internet. Our proposed agent enables remote access into the usually closed information system of the hospital and a server that indexes all the medical data which allows for in-depth and complex search queries for data retrieval.

Computer Communication Networks↗
PubMed1993

Coincidence detectors and two-pulse visual temporal integration: new theoretical results and comparison with data.

Exact predictions for two-pulse visual temporal integration data are derived from the Bouman-van der Velden quantum coincidence model for threshold vision. The predictions of the model start with complete summation for superposed pulses, then pass to a transition zone of partial integration, and finally reach the level of probability summation for pulses presented with large interstimulus intervals. From our results we can clearly reject the assumption of constant integration times with the basic model. We thus generalize the coincidence model to allow for variable integration times, derive the corresponding predictions for two-pulse integration data, and compare these predictions to published data currently available. It is shown that detectors of low order of coincidence generally underestimate the actual reduction of threshold intensity (or equivalently the corresponding increase of the detection probability) for two pulses as compared to the simple-pulse performance.

Cybernetics↗
PubMed1999

PACS workstation respecification: display, data flow, system integration, and environmental issues, derived from analysis of the Conquest Hospital pre-DICOM PACS experience.

This paper is based on 4 years of practical experience with a developmental pre- Digital Imaging and Communications in Medicine (DICOM) picture archiving and communication system (PACS) plus analysis from the respecification study data for a DICOM/HTML PACS replacement. High-performance, but economic, workstations are required within PACS for radiologists to rapidly and accurately report images. For economic reasons such workstations should utilise standard landscape orientation monitors. They must have full Radiology Information System (RIS) integrated reporting functionality to optimise radiologists' work. The workstations must also be capable of displaying request data and both new and associated old images and image reports from multiple modalities. All images should be imported as "folders" according to semi-intelligent "knowledge table" based DICOM 3.0 standard Worklist control exerted by image management servers. This information can be obtained by relevant image lists and decision charts. A description of an optimal standard monitor workstation environment and related issues based on experience and literature review is given.

Data Display↗
PubMed1987

Computerized data bases: an integrated approach to monitoring quality of patient care.

Common information is shared by rehabilitation program evaluation, utilization review, and quality assurance. These administrative functions sometimes operate in isolation, not taking advantage of information sharing. This approach fails to recognize the potential for increased efficiency of integrating pertinent information to produce timely and useful reports. We report on a system design which addresses this concern by encouraging information sharing, reducing data duplication and creating a data base to produce needed statistical and management reports. Our discussion highlights the key elements of program evaluation, utilization review, and quality assurance. These elements are described as an integrated approach to meet the Commission on Accreditation of Rehabilitation Facilities and revised Joint Commission on Accreditation of Hospitals standards.

Database Management Systems↗
PubMed2000

Prototype of a JAVA/DICOM image server with integrated findings and data security.

The transfer of medical data within heterogeneous hard- and software infrastructures requires platform-independent standardized protocols and data formats such as DICOM. To avoid costly vendor-specific solutions a DICOM server was implemented in JAVA thereby enabling the data access via internet browser technology. The most important patient and image acquisition information were extracted from the DICOM images and stored into a relational database. For an integrated view patient information such as radiological findings were transferred from the Radiological Information System (RIS) into the data base. Image data were accessed either by a fast preview tool or using a DICOM viewer. Since DICOM does not include inherent data security mechanisms, a second tool allowed the DICOM-conform encryption of DCIOM data for a secure long term storage on CD-R or across unsecure networks.

Computer Security↗
PubMed2005

Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB).

H-Invitational Database (H-InvDB; ) is a human transcriptome database, containing integrative annotation of 41,118 full-length cDNA clones originated from 21,037 loci. H-InvDB is a product of the H-Invitational project, an international collaboration to systematically and functionally validate human genes by analysis of a unique set of high quality full-length cDNA clones using automatic annotation and human curation under unified criteria. Here, 19,574 proteins encoded by these cDNAs were classified into 11,709 function-known and 7865 function-unknown hypothetical proteins by similarity with protein databases and motif prediction (InterProScan). The proportion of "hypothetical proteins" in H-InvDB was as high as 40.4%. In this study, we thus conducted data-mining in H-InvDB with the aim of assigning advanced functional annotations to those hypothetical proteins. First, by data-mining in the H-InvDB version of GTOP, we identified 337 SCOP domains within 7865 H-Inv hypothetical proteins. Second, by data-mining of predicted subcellular localization by SOSUI and TMHMM in H-InvDB, we found 1032 transmembrane proteins within H-Inv hypothetical proteins. These results clearly demonstrate that structural prediction is effective for functional annotation of proteins with unknown functions. All the data in H-InvDB are shown in two main views, the cDNA view and the Locus view, and five auxiliary databases with web-based viewers; DiseaseInfo Viewer, H-ANGEL, Clustering Viewer, G-integra and TOPO Viewer; the data also are provided as flat files and XML files. The data consists of descriptions of their gene structures, novel alternative splicing isoforms, functional RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs in relation with orphan diseases, gene expression profiling, and comparisons with mouse full-length cDNAs in the context of molecular evolution. This unique integrative platform for conducting in silico data-mining represents a substantial contribution to resources required for the exploration of human biology and pathology.

Amino Acid Sequence↗
PubMed2002

Wired and wireless network solution for the integrated management of data and images.

PURPOSE: This paper reports on the authors' experience with the implementation of an internal network with open structure model (extranet) inside a private healthcare institution. MATERIALS AND METHODS: An integrated clinical-administrative internal network was set up within a private orthopaedic hospital with about 90 beds. The system consists of a DICOM-based HIS-RIS network connected to the radiological department PACS, and is implemented through an internal web-server over a mixed wired-wireless network. The strengths of the system are: the use of an open-structure model allowing external access; the inclusion of a wireless component of the network, which extends access to mobile workstations; the possibility of conducting the quality assurance procedures directly from outside the hospital. RESULTS: The system allows the diagnostic images generated by the various equipment (Rx, CT, NMR, etc.) to be filed in compliance with the AIPA (Italian Authority for Information Technology in Public Administration) regulations; the images and electronic clinical records are made available to the departments by means of an internal web server. The use of the wireless component of the network has several additional advantages: for example, it enables healthcare personnel to view clinical records and diagnostic images on their laptop monitors from any department or hospital room, and it makes every change or addition readily available to the healthcare personnel. In this way the laptops represent an evolution of the traditional paper-based clinical record. Moreover, a direct connection was set up with the University Department of Image Processing with a view to increasing the hospital's efficiency and productivity. This connection allows adequate quality assurance procedures to be carried out on the radiological department equipment without requiring the physical presence of specialised staff, and therefore reducing costs and machine idle time. A second phase of the project is currently being tested. This consists in the collaboration of a pilot group of twenty family doctors to test system functionality during telebooking, teleconsulting and information exchange with specialists, as well as the possibility of keeping track of the patients' diagnostic work-up and clinical therapy. DISCUSSION AND CONCLUSIONS: In the context of the Italian healthcare system, the creation of adequate hospital information systems (HIS) and their integration with PACS was at first a prerogative of a few large hospitals. Recently, however, more and more patients have started to approach the healthcare world directly through the Internet, at first to request only information (leading to the diffusion of specialised web sites, or portals) and later also e-services. This new demand led us to create a Hospital Information System able to organise the internal activity of the hospital and offer several external services such as telebooking and teleconsulting, and therefore increase the hospital's efficiency and productivity. a method of choice for following patients after interventional procedures or as a mass-screening tool to select patients to be referred for coronary angiography.

Hospital Information Systems↗
PubMed2006

Lectindb: a plant lectin database.

Lectins, a class of carbohydrate-binding proteins, are now widely recognized to play a range of crucial roles in many cell-cell recognition events triggering several important cellular processes. They encompass different members that are diverse in their sequences, structures, binding site architectures, quaternary structures, carbohydrate affinities, and specificities as well as their larger biological roles and potential applications. It is not surprising, therefore, that the vast amount of experimental data on lectins available in the literature is so diverse, that it becomes difficult and time consuming, if not impossible to comprehend the advances in various areas and obtain the maximum benefit. To achieve an effective use of all the data toward understanding the function and their possible applications, an organization of these seemingly independent data into a common framework is essential. An integrated knowledge base ( Lectindb, http://nscdb.bic.physics.iisc.ernet.in ) together with appropriate analytical tools has therefore been developed initially for plant lectins by collating and integrating diverse data. The database has been implemented using MySQL on a Linux platform and web-enabled using PERL-CGI and Java tools. Data for each lectin pertain to taxonomic, biochemical, domain architecture, molecular sequence, and structural details as well as carbohydrate and hence blood group specificities. Extensive links have also been provided for relevant bioinformatics resources and analytical tools. Availability of diverse data integrated into a common framework is expected to be of high value not only for basic studies in lectin biology but also for basic studies in pursuing several applications in biotechnology, immunology, and clinical practice, using these molecules.

Algorithms↗
PubMed2002

Integration of mechanistic data in the toxicological evaluation of endocrine modulators.

Controversy has arisen concerning the likelihood of adverse health effects due to exposure to hormonally active agents or endocrine modulators such as environmental estrogens. With the aim to improve the basis for their toxicological evaluation, several chemicals of anthropogenic (bisphenol A, octylphenol, o,p'-DDT) and of natural origin (daidzein, genistein) were investigated with regard to their mode of hormonal action and potency as well as toxicokinetics. Experimental toxicodynamic and toxicokinetic data illustrate important points in a comparative assessment of environmental estrogens. A novel concept, the Hygiene-Based Margine of Safety (HBMOS), has been suggested to characterize the relative impact of these potential endocrine modulators on human health: It integrates exposure scenarios (i.a. those generated within the European Existing Chemicals Programme) and in vivo rodent potency data for xenoestrogens and for dietary phytoestrogens. On the basis of these informations, HBMOS values calculated for the alkylphenol and bisphenol A appear sufficiently high to ensure the absence of a practical risk to human health under the present exposure conditions. For slowly accumulating compounds (e.g. DDT) with much longer half-lifes than isoflavones, such comparison should be based on comparative blood levels rather than on scenarios of daily exposures.

Animals↗